Genomics, Proteomics & Bioinformatics•2024•DOI: 10.1093/gpb/art_1124
Large-scale transcriptomic data are crucial for understanding the molecular features of hepatocellular carcinoma (HCC). Integrated 15 transcriptomic datasets of HCC clinical samples, the first version of HCC database (HCCDB v1.0) was released in 2018. Through the meta-analysis of differentially expressed genes and prognosis-related genes across multiple datasets, it provides a systematic view of the altered biological processes and the inter-patient heterogeneities of HCC with high reproducibility and robustness. With four years having passed, the database now needs integration of recently published datasets. Furthermore, the latest single-cell and spatial transcriptomics have provided a great opportunity to decipher complex gene expression variations at the cellular level with spatial architecture. Here, we present HCCDB v2.0, an updated version that combines bulk, single-cell, and spatial transcriptomic data of HCC clinical samples. It dramatically expands the bulk sample size by adding 1656 new samples from 11 datasets to the existing 3917 samples, thereby enhancing the reliability of transcriptomic meta-analysis. A total of 182,832 cells and 69,352 spatial spots are added to the single-cell and spatial transcriptomics sections, respectively. A novel single-cell level and 2-dimension (sc-2D) metric is proposed as well to summarize cell type-specific and dysregulated gene expression patterns. Results are all graphically visualized in our online portal, allowing users to easily retrieve data through a user-friendly interface and navigate between different views. With extensive clinical phenotypes and transcriptomic data in the database, we show two applications for identifying prognosis-associated cells and tumor microenvironment. HCCDB v2.0 is available at http://lifeome.net/database/hccdb2.
Stem Cell Research & Therapy•2026•DOI: 10.1186/s13287-025-04883-5
Background Pulmonary arterial hypertension (PAH) is a fatal condition characterized by progressive vascular remodeling in the pulmonary arteries, eventually leading to right heart failure and death. Dysregulated extracellular matrix (ECM) remodeling is central to PAH pathogenesis and represents a potential therapeutic target. Mesenchymal stromal cells (MSCs) have shown promise in preclinical studies; however, the optimal therapeutic window, dosing frequency, and mechanistic basis for their regulation of vascular ECM remain unclear. Methods We employed a monocrotaline (MCT)-induced rat model of PAH to evaluate different MSC treatment regimens, including early administration (day 1 post-MCT), delayed administration (days 7 and 14), and repeated dosing (days 1 and 11). Additionally, we combined in vivo and in vitro approaches to investigate how MSCs modulate the activation of pulmonary arterial adventitial fibroblasts (PAAFs) and influence ECM remodeling. Results Biodistribution studies indicated that MSC retention in lung tissue peaked within 24 h and gradually declined by day 21. A single early dose of MSCs (on day 1) significantly ameliorated PAH progression, increasing the 28-day survival rate, reducing right ventricular systolic pressure (RVSP), improving right ventricular function, and attenuating small pulmonary vascular remodeling, including reductions in medial thickening, excessive muscularization, and collagen deposition. Repeated MSC administration did not provide additional therapeutic benefit. Both in animal models and cell cultures, MSCs effectively suppressed PAAF activation and reduced ECM protein production. This anti-fibrotic effect was mediated via the SOCS3/STAT3 signaling pathway. Conclusions Early single-dose MSC therapy effectively alleviates PAH by suppressing PAAF activation and ECM remodeling through the SOCS3/STAT3 pathway, offering a potential therapeutic strategy for PAH.
Stem Cell Research & Therapy•2024•DOI: 10.1186/s13287-024-04112-5
Correction to: Stem Cell Research & Therapy (2024) 15:440. The original article initially erroneously presented co-author, Min Xu's name as Xu Min; this has since been amended.
Acta Biochimica et Biophysica Sinica•2025•DOI: 10.3724/abbs.2025047
Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by a complex pathogenesis that was previously thought to involve primarily adaptive immunity. Emerging evidence underscores the role of neutrophils in shaping immune dysregulation and inducing organ damage in lupus. This study aims to investigate the dynamics of neutrophil senescence and its relationship with lupus, an area that remains poorly understood. Here, we identify a significantly elevated proportion of CXCR4hiCD62Llo senescence-like neutrophils in the peripheral blood of SLE patients compare to that in the healthy donors. Increased numbers of senescence-like neutrophils are positively correlated with SLE disease activity and autoantibody production in SLE patients. In addition, senescence-like neutrophils derived from SLE patients exhibit an impaired ability to suppress the proinflammatory activity of natural killer (NK) cells and CD4+ T cells. Further mechanistic exploration suggests that these senescence-like neutrophils might exert their immunosuppressive effects via reactive oxygen species (ROS) production under physiological conditions. Our results demonstrate that senescence-like neutrophils could serve as biomarkers for assessing the disease activity of SLE. The compromised immunosuppressive function of senescence-like neutrophils provides a new perspective on SLE pathophysiology and may pave the way for the development of novel therapies.
Acta Biochimica et Biophysica Sinica•2025•DOI: 10.3724/abbs.2024221
Ferroptosis is a type of programmed death characterized by iron-dependent lipid peroxidation, and targeting ferroptosis has been shown to efficiently kill highly aggressive cancer cells. Previously, we confirmed that nuclear receptors regulate ferroptosis in pancreatic cancer. However, whether nuclear receptor co-activators regulate ferroptosis is unclear. Here, we show that knocking down the nuclear receptor co-activator, NCOA6, enhances the sensitivity of pancreatic cancer cells to ferroptosis. Mechanistically, NCOA6 knockdown promotes the expression of ACSL4 while inhibiting the expression of SCD1, resulting in changes in lipid metabolism, sensitivity to RSL3-induced ferroptosis, and sensitivity to gemcitabine in pancreatic cancer. The relationships between NCOA6 and ACSL4 or SCD1 are further explored in clinical specimens. This study reveals that targeting NCOA6 might alleviate gemcitabine resistance in pancreatic cancer.
Acta Biochimica et Biophysica Sinica•2025•DOI: 10.3724/abbs.2024186
Pyruvate dehydrogenase kinase 1 (PDK1) is a new therapeutic target that is dysregulated in multiple tumors. This study aims to explore the potential role and regulatory mechanism of PDK1 in epithelial ovarian cancer (EOC). We detect PDK1 expression in EOC tissues and cells using qRT-PCR and western blot analysis, and the effects of PDK1 on EOC cell malignant behaviors are explored. RNA sequencing analyses are performed to explore the differentially expressed genes in PDK1-silenced EOC cells. Furthermore, tumor-bearing mouse models are established to assess the impacts of PDK1 and BGN on EOC tumor growth and metastasis in vivo. The results show that PDK1 is upregulated in EOC tissues and cell lines. Biglycan (BGN) is downregulated in PDK1-silenced EOC cells, and its expression is positively correlated with PDK1 levels in EOC tissues. PDK1 depletion inhibits EOC cell proliferation, migration and invasion. Mechanistically, PDK1 and BGN are colocalized in the cytoplasm of EOC cells and interact with each other. PDK1 positively regulates BGN expression by enhancing BGN mRNA stability. BGN overexpression partially reverses the anti-tumor effects of PDK1 depletion on EOC cell malignant behaviors. PDK1 has also been revealed to upregulate BGN to activate the NF-κB oncogenic pathway in EOC cells. Additionally, PDK1 accelerates tumor growth and metastasis by modulating BGN expression. In conclusion, PDK1 functions as an oncogene, facilitating EOC progression by upregulating BGN and activating the NF-κB pathway. These findings may provide valuable biomarkers for the diagnosis and treatment of EOC.
Acta Biochimica et Biophysica Sinica•2024•DOI: 10.3724/abbs.2024110
Immune checkpoint inhibitors (ICIs) targeting programmed cell death 1/programmed cell death ligand-1 (PD-1/PD-L1) have significantly prolonged the survival of advanced/metastatic patients with lung cancer. However, only a small proportion of patients can benefit from ICIs, and clinical management of the treatment process remains challenging. Glycosylation has added a new dimension to advance our understanding of tumor immunity and immunotherapy. To systematically characterize anti-PD-1/PD-L1 immunotherapy-related changes in serum glycoproteins, a series of serum samples from 12 patients with metastatic lung squamous cell carcinoma (SCC) and lung adenocarcinoma (ADC), collected before and during ICIs treatment, are firstly analyzed with mass-spectrometry-based label-free quantification method. Second, a stratification analysis is performed among anti-PD-1/PD-L1 responders and non-responders, with serum levels of glycopeptides correlated with treatment response. In addition, in an independent validation cohort, a large-scale site-specific profiling strategy based on chemical labeling is employed to confirm the unusual characteristics of IgG N-glycosylation associated with anti-PD-1/PD-L1 treatment. Unbiased label-free quantitative glycoproteomics reveals serum levels’ alterations related to anti-PD-1/PD-L1 treatment in 27 out of 337 quantified glycopeptides. The intact glycopeptide EEQFN177STYR (H3N4) corresponding to IgG4 is significantly increased during anti-PD-1/PD-L1 treatment (FC=2.65, P=0.0083) and has the highest increase in anti-PD-1/PD-L1 responders (FC=5.84, P=0.0190). Quantitative glycoproteomics based on protein purification and chemical labeling confirms this observation. Furthermore, obvious associations between the two intact glycopeptides (EEQFN177STYR (H3N4) of IgG4, EEQYN227STFR (H3N4F1) of IgG3) and response to treatment are observed, which may play a guiding role in cancer immunotherapy. Our findings could benefit future clinical disease management.
Stem Cell Research & Therapy•2026•DOI: 10.1186/s13287-025-04883-5
Pulmonary arterial hypertension (PAH) is a fatal disease characterized by progressive vascular remodeling, leading to right heart failure. Dysregulated extracellular matrix (ECM) remodeling is central to PAH pathogenesis. Mesenchymal stromal cells (MSCs) have shown promise, but optimal dosing and mechanisms remain unclear. In a monocrotaline (MCT)-induced rat model, we evaluated early (day 1), delayed (days 7 and 14), and repeated (days 1 and 11) MSC administration. Biodistribution showed peak lung retention at 24 h, declining by day 21. A single early dose significantly improved 28-day survival, reduced right ventricular systolic pressure (RVSP), improved right ventricular function, and attenuated vascular remodeling, including medial thickening, muscularization, and collagen deposition. Repeated dosing provided no additive benefit. MSCs suppressed pulmonary arterial adventitial fibroblast (PAAF) activation and ECM protein production in vivo and in vitro. Mechanistically, MSCs upregulated SOCS3 and inhibited STAT3 signaling. These findings support early single-dose MSC therapy for PAH.
Chinese Journal of Tissue Engineering Research•2026•DOI: 10.12307/2026.21408
BACKGROUND: Interlocking intramedullary nail fixation is the "gold standard" for the treatment of femoral shaft fractures, and the difficulty of distal locking nail implantation has always been a difficult problem to solve. OBJECTIVE: By comparing the clinical effects of correction leverage technique and free-hand locking nail technique, it is further explained whether the correction leverage technique can be fast and accurate. The distal locking screw of femoral intramedullary nail was placed without direct X-ray radiation exposure, thereby solving the problem of difficult distal locking screw placement. METHODS: A total of 52 patients with femoral shaft fractures who had difficulty in distal locking screw placement during interlocking intramedullary nail fixation were enrolled from the Department of Orthopedics and Traumatology, Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University from July 2022 to September 2024. They were divided into two groups according to the placement protocol: correction leverage group (26 cases) used the correction leverage technique for distal locking screw placement, and free-hand group (26 cases) used the traditional free-hand technique. The distal locking screw placement time, number of X-ray exposures, and first-attempt accuracy were compared between the two groups. RESULTS AND CONCLUSION: (1) The distal locking screw placement time in the correction leverage group was significantly shorter than that in the free-hand group (t=-4.136, P < 0.001). (2) The number of X-ray exposures in the correction leverage group was less than that in the free-hand group (t=-19.696, P < 0.001). (3) The first-attempt accuracy in the correction leverage group (100%) was higher than that in the free-hand group (71%), with a significant difference (χ2=5.253, P < 0.05). (4) These results indicate that compared with simple free-hand screw placement, the correction leverage technique has the advantages of faster locking, higher accuracy, and lower X-ray radiation. This technique does not require auxiliary equipment and has strong operability, and is worthy of further clinical validation and promotion for interlocking intramedullary nail fixation of femoral shaft fractures.
Chinese Journal of Tissue Engineering Research•2026•DOI: 10.12307/2026.21314
BACKGROUND: Preliminary studies have demonstrated that Shaoyang Shenggu Fang can alleviate joint cartilage degeneration and promote cartilage repair, but its specific mechanism for alleviating knee osteoarthritis symptoms remains unclear. The Wnt/β-catenin pathway and oxidative stress play crucial roles in maintaining articular cartilage homeostasis. OBJECTIVE: To investigate the molecular mechanisms by which Shaoyang Shenggu Fang regulates the Wnt/β-catenin pathway to inhibit oxidative stress in cartilage and thereby delay cartilage aging in a rat model of knee osteoarthritis. METHODS: Thirty-two Sprague-Dawley rats were randomly divided into four groups: a blank control group, a model group, a Western medicine group, and a Chinese medicine group. Animal models of knee osteoarthritis were established in all groups except for the blank control group by transecting the anterior cruciate ligament and resecting the anterior horn of the medial meniscus. After 28 days of modeling, the Chinese medicine group was administered concentrated Shaoyang Shenggu Fang at a dose of 16 g/(kg·d) by gavage, the Western medicine group received glucosamine hydrochloride solution at 4 mL/d, and the blank and model groups received the same volume of normal saline. After 4 weeks, hematoxylin-eosin staining and Safranin O-fast green staining were used to observe the degree of cartilage damage and degeneration. ELISA was used to detect serum levels of inflammatory factors and oxidative stress indicators. Western blot was used to detect the expression of p21Cip1, p16INK4a, and Wnt signaling pathway-related proteins in knee cartilage. RESULTS AND CONCLUSION: Compared with the model group, the Western medicine and Chinese medicine groups showed significant improvement in cartilage defects, thinning of the cartilage layer, and decreased density, with significantly lower Mankin scores (P < 0.05). Compared with the model group, serum levels of interleukin-1β, tumor necrosis factor-α, and interleukin-6 were significantly decreased in the Western medicine and Chinese medicine groups (P < 0.05), while superoxide dismutase and glutathione peroxidase levels were increased and malondialdehyde concentration was decreased (all P < 0.05). In the Chinese medicine group, the expression levels of p21Cip1, p16INK4a, and Wnt5a proteins were significantly decreased (P < 0.05 and P < 0.01), β-catenin and C-Myc protein expression levels were decreased (P < 0.05), and glycogen synthase kinase-3β protein expression was significantly increased (P < 0.05). These results suggest that Shaoyang Shenggu Fang can significantly reduce inflammation and alleviate cartilage aging in rats with knee osteoarthritis, and the potential mechanism may be through regulation of the Wnt/β-catenin pathway to inhibit cartilage oxidative stress.
Chinese Journal of Tissue Engineering Research•2026•DOI: 10.12307/2026.21591
BACKGROUND: Pharmacodynamic characteristics and mechanisms of action of icariin in combating osteoporosis gradually gain recognition within the academic community. Related basic research and clinical translation efforts are increasingly becoming the focal point of research. OBJECTIVE: To summarize the research progress of icariin on anti-osteoporosis. METHODS: China National Knowledge Infrastructure (CNKI) and PubMed databases were searched for relevant literature. Chinese and English search terms included “icariin, osteoporosis, Chinese medicine compound, pathogenesis, signal path, BMSCs, osteoblast, osteoclast.” Based on inclusion criteria, 90 articles were ultimately included in the review. RESULTS AND CONCLUSION: Icariin treatment increased alkaline phosphatase activity and induced the expression of core binding factor α1, bone morphogenetic protein 2, and bone morphogenetic protein 4 in bone marrow mesenchymal stem cells in a dose-dependent manner. Icariin promoted fracture healing by increasing serum levels of osteocalcin, bone-specific alkaline phosphatase, N-terminal peptide of type I collagen, C-terminal peptide of type I collagen, and tartrate-resistant acid phosphatase 5b, thereby enhancing osteocalcin secretion at the fracture site. Icariin promoted proliferation and osteogenic differentiation of bone marrow mesenchymal stem cells in ovariectomized osteoporotic rats by upregulating alkaline phosphatase and osteocalcin levels and inhibiting the expression of Notch-1, CBF1, and Jagged-1 proteins in the Notch pathway, thus achieving prevention and treatment of osteoporosis. Icariin regulates bone metabolism through multiple signaling axes including Wnt/β-catenin, mitogen-activated protein kinase, phosphatidylinositol 3-kinase/protein kinase B, osteoprotegerin/receptor activator of nuclear factor-κB ligand/receptor activator of nuclear factor-κB, and Notch. Among these, the Wnt/β-catenin pathway and the osteoprotegerin/receptor activator of nuclear factor-κB ligand/receptor activator of nuclear factor-κB axis constitute the core regulatory mechanism, modulating the osteoblast-osteoclast dynamic balance through synergistic interactions. Icariin can influence the biological behavior of osteoblasts, osteoclasts, and bone marrow mesenchymal stem cells through multidimensional interventions including regulation of mRNA expression modifications, inhibition of oxidative stress, and improvement of the inflammatory microenvironment.
Acta Biochimica et Biophysica Sinica•2026•DOI: 10.3724/abbs.2026021
Macrophages play a pivotal role in bone regeneration, making their polarization a key target for immune regulation and therapeutic intervention. Modulating macrophage polarization represents a promising strategy for enhancing bone repair. Luteolin, a plant-derived flavonoid with well-documented anti-inflammatory properties, has been explored for its role in bone repair. However, its specific effects on macrophage polarization in bone repair remain unclear. This study investigates the role of luteolin in macrophage polarization and its underlying mechanisms. Our findings demonstrate that luteolin promotes M2 polarization while suppressing M1 polarization, as indicated by a reduction in the expression of pro-inflammatory markers, including IL-6 and iNOS, and an increase in the expression of anti-inflammatory factors, such as CD206, IL-10, and TGF-β. Mechanistically, luteolin inhibits STING oligomerization, thereby suppressing the STING-TBK1 pathway and mitigating downstream inflammatory responses. In vivo, in a mouse tibial bone defect model, luteolin effectively alleviates inflammation, facilitates angiogenesis, enhances collagen deposition, and improves bone density. Collectively, these findings highlight the potential of luteolin as a therapeutic agent for bone repair by modulating macrophage polarization and inhibiting STING-TBK1 signaling.
Acta Biochimica et Biophysica Sinica•2026•DOI: 10.3724/abbs.2025181
Colorectal cancer (CRC) is one of the most prevalent and lethal cancers worldwide and is characterized by uncontrolled cell invasion, migration, and proliferation. The progression of CRC is driven by genetic mutations and alterations in key signaling pathways. This study investigates the role of GPSM2 and ZNF263 implicated in CRC progression. The GPSM2 gene, which regulates G protein signaling pathways, plays a vital role in cell movement and growth, contributing to the metastatic potential of cancer cells. The ZNF263 gene, a zinc finger protein involved in gene expression regulation, is also linked to CRC progression, with its dysregulation affecting the cell cycle, apoptosis, and migration. In particular, this study explores how ZNF263 acts as a transcription factor, modulating the expression of GPSM2 to increase CRC cell invasion, migration, and proliferation. This study confirms that ZNF263 activates the cell cycle pathway in a GPSM2-dependent manner, driving the aggressive behavior of CRC cells. Bioinformatics analysis using the GEO database further supports these findings, identifying key genetic alterations in CRC. These insights provide a deeper understanding of the molecular mechanisms underlying CRC progression and highlight the potential of ZNF263 and GPSM2 as therapeutic targets for intervention. This study underscores the importance of early detection and exploration of targeted therapies to improve CRC patient outcomes.
Acta Biochimica et Biophysica Sinica•2025•DOI: 10.3724/abbs.2025047
Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease with complex pathogenesis historically attributed to adaptive immunity. Emerging data implicate neutrophils in immune dysregulation and organ damage. This study investigates neutrophil senescence dynamics in SLE. We identified a significantly elevated proportion of CXCR4hiCD62Llo senescence-like neutrophils in peripheral blood of SLE patients versus healthy donors. Increased senescence-like neutrophil numbers positively correlated with SLE disease activity and autoantibody production. Functionally, senescence-like neutrophils from SLE patients exhibited impaired suppression of proinflammatory activity in natural killer (NK) cells and CD4+ T cells. Mechanistically, these cells may exert immunosuppressive effects via reactive oxygen species (ROS) production under physiological conditions. Our results position senescence-like neutrophils as candidate biomarkers for SLE disease activity. The compromised immunosuppressive function of these cells offers a new perspective on SLE pathophysiology and may inform development of novel therapies. Limitations include small sample size and heterogeneous treatment backgrounds, necessitating further validation. Future studies will address NET release and potential subset markers.
Chinese Journal of New Drugs•2025•DOI: cast_zgxyzz_1236731781232251260
Background: Iron deficiency anemia (IDA) is a global health concern, and intravenous iron preparations are increasingly used. Ferric derisomaltose (FDI) is a newer formulation with potential advantages. This systematic review and meta-analysis aimed to evaluate the efficacy and safety of FDI compared with other iron therapies or placebo in treating IDA. Methods: We searched PubMed, Embase, Cochrane Library, and CNKI up to October 2023 for randomized controlled trials (RCTs) comparing FDI with active comparators or placebo in patients with IDA. The primary outcomes were change in hemoglobin (Hb) from baseline, and safety outcomes included adverse events (AEs), serious adverse events (SAEs), and hypersensitivity reactions. Data were pooled using random-effects models. Results: A total of 15 RCTs involving 3,452 patients were included. FDI significantly increased Hb levels compared with placebo (mean difference [MD] 1.2 g/dL, 95% CI 0.8-1.6) and was non-inferior to other intravenous iron formulations (MD 0.1 g/dL, 95% CI -0.2 to 0.4). FDI was associated with fewer hypersensitivity reactions compared with ferric carboxymaltose (risk ratio [RR] 0.3, 95% CI 0.1-0.9). The incidence of AEs was similar between FDI and other iron preparations. Subgroup analyses showed consistent results across different etiologies of IDA. Conclusion: Ferric derisomaltose is effective and safe for treating IDA, with a lower risk of hypersensitivity reactions compared with some other intravenous iron formulations. These findings support its use in clinical practice.