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•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•2026•DOI: 10.3724/abbs.2025135
Despite the high efficacy of all-trans retinoic acid (ATRA) and arsenic trioxide (ATO) in treating acute promyelocytic leukemia (APL), approximately 10%–20% of patients develop drug resistance due to mutations in PML-RARα and other factors. Here, we find that inhibition of USP2 with ML364 or USP2 silencing reduces PML-RARα protein levels in both ATRA-sensitive and ATRA-resistant APL cells, and this effect is reversed by proteasome inhibition. Conversely, USP2 overexpression enhances PML-RARα stability. Mechanistically, USP2 interacts with and deubiquitinates PML-RARα, including its drug-resistant mutants. Consistent with PML-RARα degradation, ML364 treatment significantly induces apoptosis in APL cell lines and primary leukemia cells. In conclusion, this study identifies USP2 as a novel deubiquitinating enzyme for PML-RARα and highlights USP2 inhibition as a potential therapeutic strategy for APL with PML-RARα mutations.
Acta Biochimica et Biophysica Sinica•2026•DOI: 10.3724/abbs.2026043
Pentatrichomonas hominis is a zoonotic protozoan belonging to the family Trichomonadidae that primarily inhabits the cecum and colon. Although traditionally regarded as an opportunistic pathogen, P. hominis is increasingly recognized for its pathogenic potential, including roles in animal diarrheal disease and the induction of intestinal epithelial damage and chronic inflammation in mice. A previous study further identified a significant correlation between P. hominis infection and colorectal cancer, underscoring its growing clinical and public health significance. This parasite infects a wide range of hosts, among which dogs, displaying infection rates as high as 47.4%, are regarded as a potential zoonotic reservoir because of their close contact with humans. Consequently, establishing reliable detection methods for P. hominis in dogs is essential for veterinary practice and public health surveillance. Current methods for detecting P. hominis infections in dogs mainly include direct smear microscopy and polymerase chain reaction (PCR)-based techniques. Although direct smear microscopy is straightforward, it frequently exhibits low sensitivity. In comparison, PCR demonstrates high sensitivity and specificity, yet it relies on specialized equipment, trained operators, and extended processing time. Recently, reported nucleic acid detection approaches, such as recombinase polymerase amplification coupled with lateral flow dipstick (RPA-LFD) and RPA-CRISPR/Cas12a assays, have enhanced the efficiency and accessibility of molecular detection for P. hominis. However, these methods still necessitate nucleic acid extraction, controlled temperature conditions, and operational complexity. In addition, some emerging detection technologies, such as microfluidic chips and nanozyme-based detection systems, offer advantages of high throughput and sensitivity but have not yet been widely applied in the field of detection of parasitic infection. Although immunoassays, including enzyme-linked immunosorbent assay (ELISA) and colloidal gold immunochromatographic strips, have been successfully used for the detection of infections of some intestinal protozoans, such as Giardia, there have been no reports on their application for detecting P. hominis infections, primarily due to the lack of specific detection antigens. To address the detection need, liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used as the primary discovery tool to identify specific detected antigens. Using this targeted proteomics approach, we precisely identified immunoreactive proteins and selected glyceraldehyde 3 phosphate dehydrogenase (GAPDH), an immunogenic and species-specific antigen in related parasites, as the candidate antigen. Based on this identified antigen, we subsequently developed and evaluated the detection performance in both indirect ELISA and colloidal gold immunochromatographic strips using recombinant GAPDH. This study aimed to identify novel antigens for immunodetection of P. hominis and to establish a practical, on-site method for detecting dog infections, thereby facilitating further epidemiological and clinical research.
Acta Biochimica et Biophysica Sinica•2025•DOI: 10.3724/abbs.2025065
Stem cell fate is profoundly influenced by a complex interplay of biochemical and biophysical cues, with the latter increasingly recognized for its roles in cellular processes, yet the mechanisms are unclear. Since chromatin accessibility is a critical determinant in the processes of osteogenesis and bone repair, investigating the contributions of open chromatin regions (OCRs) to the intracellular signaling pathways triggered by topographical cues, which lead to osteogenic differentiation is highly valuable. This study explores the impact of the nanotopography of biomaterials on the osteogenic differentiation of human bone marrow stem cells (hBMSCs). By utilizing electrospun poly-L-lactide (PLLA) membranes with random fiber arrangements, we mimic the natural extracellular matrix (ECM) topography to study its effects on hBMSCs, contrasting them with flat PLLA controls. Through high-throughput Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) and RNA sequencing (RNA-seq), we reveal that the nanotopography of electrospun surfaces promotes osteogenic differentiation by modulating the chromatin accessibility of the YBX1 gene promoter, leading to its upregulation. Lentiviral knockdown experiments further confirm the crucial role of YBX1, revealing a reversal of the osteogenic effects induced by nanotopography. This study emphasizes the importance of YBX1 in the osteogenic response to the surface topography of biomaterials and suggests that nanotopographical cues could be harnessed to direct stem cell fate. These findings are important for developing biomaterials that promote specific stem cell outcomes in regenerative medicine. Our results further contribute to a deeper understanding of the mechanisms underlying stem cell differentiation in response to environmental cues and pave the way for the rational design of biomaterials with enhanced osteogenic potential. By elucidating the role of chromatin accessibility and specific transcription factors such as YBX1, this study highlights the intricate interplay between cell-material interactions and the intracellular signaling pathways that govern stem cell fate.
Acta Biochimica et Biophysica Sinica•2025•DOI: 10.3724/abbs.2025069
Inflammation, while essential for host defense, can contribute to diseases like inflammatory bowel disease (IBD) when dysregulated. IBD involves chronic intestinal inflammation linked to bacterial infection and disruption of the intestinal epithelial barrier (IEB). The IEB maintains intestinal homeostasis, preventing the entry of harmful substances like lipopolysaccharide (LPS) while allowing nutrient absorption. Preserving IEB function is crucial in managing various diseases. Current IBD treatments often have adverse effects, including facial swelling and acne from corticosteroids, and allergic reactions, nausea, elevated liver tests, and pancreatitis from immunomodulators, increasing interest in natural products. Flavonoids, a diverse class of plant metabolites, have shown promising anti-inflammatory properties. Lutonarin (LU), a flavonoid abundant in barley seedlings, has exhibited various biological activities, including anti-inflammatory effects in LPS-stimulated macrophages. However, its specific impacts on IEB function remain unclear. This study aims to investigate the protective effects of LU against LPS-induced IEB dysfunction using an in vitro Caco-2 cell monolayer model. To assess the possible cytotoxicity of LU and optimize the suitable concentration, the viability of Caco-2 cells was assessed by CCK-8 assay. LU concentrations up to 96 μM did not significantly affect cell viability after 24 and 48 h of exposure. To evaluate the protective effect of LU against LPS-induced cytotoxicity, Caco-2 cells were pretreated with LU (3‒96 μM) for 48 h prior to exposure to 15 μg/mL LPS for 24 h. LPS significantly reduced cell viability, while LU pretreatment attenuated this reduction in a concentration-dependent manner. Concentrations of 12 μM LU were selected for subsequent experiments to minimize potential off-target effects. The Caco-2 cell monolayer model, a well-established in vitro system for investigating IEB function, was employed to study the effects of LU on IEB integrity. Barrier integrity was evaluated using transepithelial electrical resistance (TEER) measurements. LPS treatment significantly reduced TEER, indicating impaired barrier function. Pretreatment with 12 μM LU preserved TEER values, suggesting a protective effect against LPS-induced barrier disruption. Furthermore, paracellular permeability was evaluated using fluorescein isothiocyanate-dextran 4 (FITC-dextran, 4 kDa). LPS significantly increased FITC-dextran (FD4) flux, indicating increased permeability. LU pretreatment markedly attenuated this effect, confirming its ability to prevent LPS-induced permeability changes. To detect if LPS and LU pretreatment changes the expressions of tight junction (TJ) proteins Zonula occludens-1 (ZO-1) and Occludin, real-time qPCR and immunofluorescence staining assays were applied. LPS treatment significantly reduced mRNA expression levels of TJ proteins ZO-1 and Occludin. LU pretreatment effectively mitigated this downregulation, restoring their expression to levels comparable to the CON group.
Acta Biochimica et Biophysica Sinica•2025•DOI: 10.3724/abbs.2024211
RNA splicing and 3′-cleavage and polyadenylation (CPA) are essential processes for the maturation of RNA. There have been extensive independent studies of these regulated processing events, including alternative splicing (AS) and alternative polyadenylation (APA). However, growing evidence suggests potential crosstalk between splicing and 3′-end processing in regulating AS or APA. Here, we first provide a brief overview of the molecular machines involved in splicing and 3′-end processing events, and then review recent studies on the functions and mechanisms of the crosstalk between the two processes. On the one hand, 3′-end processing can affect splicing, as 3′-end processing factors and CPA-generated polyA tail promote the splicing of the last intron. Beyond that, 3′-end processing factors can also influence the splicing of internal and terminal exons. Those 3′-end processing factors can also interact with different RNA-binding proteins (RBPs) to exert their effects on AS. The length of 3′ untranslated region (3′ UTR) can affect the splicing of upstream exons. On the other hand, splicing and CPA may compete within introns in generating different products. Furthermore, splicing within the 3′ UTR is a significant factor contributing to 3′ UTR diversity. Splicing also influences 3′-end processing through the actions of certain splicing factors. Interestingly, some classical RBPs play dual roles in both splicing and 3′-end processing. Finally, we discuss how long-read sequencing technologies aid in understanding the coordination of AS-APA events and envision that these findings may potentially promote the development of new strategies for disease diagnosis and treatment.
Chinese Traditional and Herbal Drugs•2026•DOI: 10.7501/j.issn.0253-2670.2026.16.20261616
This study interrogates the therapeutic efficacy and molecular mechanism of aconitine combined with paeoniflorin in a rat model of knee osteoarthritis (KOA), focusing on the Indian hedgehog (Ihh)-glioma-associated oncogene homolog (Gli) signaling axis. Anterior cruciate ligament transection (ACLT) was performed on male rats, which were then allocated to sham, model, celecoxib (24 mg/kg), and three aconitine-paeoniflorin dose groups (5+50, 10+100, 20+200 μg/kg; n=10 per group). Behavioral tests, hematoxylin-eosin staining, micro-computed tomography, ELISA for matrix metalloproteinase 13 (MMP13) and type II collagen (Col II), immunofluorescence, and qRT-PCR for Ihh, Gli, patched 1 (Ptch1), and MMP13 were conducted. Molecular docking assessed binding affinities. Safety was evaluated via serum aspartate aminotransferase, creatinine, blood urea nitrogen, urinary protein, and histopathology of heart, liver, and kidney. Results demonstrated that the combination significantly elevated mechanical and thermal pain thresholds (P<0.05, 0.01, 0.001), restored cartilage matrix integrity, improved bone microarchitecture, decreased serum MMP13, and increased Col II (P<0.05, 0.01, 0.001). Ihh, Gli, Ptch1, and MMP13 protein and gene expressions were markedly downregulated (P<0.05, 0.01, 0.001). Docking confirmed binding energies ≤−5 kcal/mol for aconitine and paeoniflorin with Ihh, Gli, ADAMTS5, and MMP13. No significant hepatic, renal, or cardiac toxicity was observed. The combination inhibits aberrant Ihh-Gli pathway activation, suppresses cartilage matrix degradation, and offers a safer, multi-target alternative to celecoxib for KOA management.
Acta Biochimica et Biophysica Sinica•2026•DOI: 10.3724/abbs.2026043
Pentatrichomonas hominis is a zoonotic protozoan that primarily inhabits the cecum and colon of dogs, with infection rates as high as 47.4%, posing a significant public health risk due to close human contact. Current detection methods, including direct smear microscopy and PCR, have limitations in sensitivity, equipment requirements, and operational complexity. To address the need for a practical on-site detection method, we employed liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify specific antigens from P. hominis excretory-secretory (ES) proteins. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was selected as a candidate antigen due to its high immunogenicity and species specificity. The GAPDH gene was cloned and expressed in E. coli, and the recombinant protein was purified. Mouse anti-GAPDH serum was generated, and its reactivity was confirmed by Western blot and indirect ELISA (titer 1:102,400). Immunofluorescence localization showed GAPDH in the cytoplasm of P. hominis trophozoites. Based on this antigen, we developed a colloidal gold immunochromatographic strip for rapid detection of P. hominis in dogs. The strip demonstrated high sensitivity and specificity, providing a practical tool for veterinary diagnosis and epidemiological surveillance. This study is the first to report an immunochromatographic strip for P. hominis detection, offering a rapid, user-friendly alternative to existing methods.
Chinese Journal of Tissue Engineering Research•2026•DOI: 10.12307/2026.21293
BACKGROUND: As the primary organ for arsenic metabolism in the body, the liver has become a focal point for research on the mechanisms of arsenic toxicity. OBJECTIVE: To investigate the role of pregnane X receptor in sodium arsenite-induced oxidative stress and inflammatory injury in human normal hepatocytes. METHODS: Human normal hepatocyte MIHA cells were exposed to 0 (control), 10, 20, 30 μmol/L sodium arsenite for 48 hours. Changes in cell morphology were observed. Cell viability was measured via the cell counting kit-8 assay. Intracellular reactive oxygen species levels were detected using fluorescence probe staining combined with a microplate reader. Malondialdehyde levels were measured by thiobarbituric acid method. Glutathione reductase activity was detected by NADPH method. Total superoxide dismutase activity was measured by WST-8 method. Levels of interleukin-6, interleukin-1β, and tumor necrosis factor-α in cell supernatant were detected by ELISA. mRNA expression of pregnane X receptor and cytochrome P450 3A4 enzyme was detected by qRT-PCR. Protein expression of pregnane X receptor, cytochrome P450 3A4, nuclear factor-κB p65, nuclear factor-κB p-p65, proliferating cell nuclear antigen, interleukin-6, interleukin-1β, tumor necrosis factor-α, nuclear factor-κB inhibitor protein α, cyclooxygenase-2, p-nuclear factor-κB inhibitor protein α, nuclear factor erythroid 2-related factor 2, Keap1, and p-nuclear factor erythroid 2-related factor 2 was detected by western blot. RESULTS AND CONCLUSION: Compared with the control group, cells in all sodium arsenite groups showed unclear cell membrane boundaries, reduced cytoplasm, decreased cell fusion rate, and widened intercellular spaces. Compared with the control group, intracellular reactive oxygen species and malondialdehyde levels were increased (P < 0.05), levels of interleukin-6, interleukin-1β, and tumor necrosis factor-α in cell supernatant were increased (P < 0.05), protein expression of p-nuclear factor-κB inhibitor protein α, nuclear factor-κB p-p65, nuclear factor-κB p65, tumor necrosis factor-α, and interleukin-1β were increased (P < 0.05), cell viability was decreased (P < 0.05), protein expression of proliferating cell nuclear antigen, nuclear factor erythroid 2-related factor 2, p-nuclear factor erythroid 2-related factor 2 and total superoxide dismutase activity were decreased (P < 0.05), and mRNA and protein expression of pregnane X receptor and cytochrome P450 3A4 enzyme were decreased (P < 0.05). Compared with the control group, glutathione reductase activity was decreased in 20 and 30 μmol/L sodium arsenite groups (P < 0.05), and protein expression of Keap1, interleukin-6, and cyclooxygenase-2 was increased (P < 0.05). These results indicate that sodium arsenite may induce oxidative stress and inflammatory injury in hepatocytes by downregulating pregnane X receptor expression, inhibiting the nuclear factor erythroid 2-related factor 2 antioxidant pathway, and activating the nuclear factor-κB inflammatory pathway, while also inhibiting the expression of the drug-metabolizing enzyme cytochrome P450 3A4.
Chinese Journal of Tissue Engineering Research•2026•DOI: 10.12307/2026.21288
BACKGROUND: As crucial stabilizers of the knee joint, the medial collateral ligament and lateral collateral ligament play essential roles in restricting valgus and varus movements, respectively. However, the mechanical differences between the medial collateral ligament and lateral collateral ligament, the microstructure characteristics, and the effect of elastin degradation on their mechanical properties remain poorly understood. OBJECTIVE: To compare the mechanical differences between the medial collateral ligament and lateral collateral ligament, quantify the structural characteristics of the collagen fiber alignment, and investigate the effect of elastin degradation on the mechanical properties of both ligaments. METHODS: Left medial collateral ligaments and lateral collateral ligaments were harvested from adult pigs, frozen, and thawed. Quasi-static uniaxial tensile tests were performed to measure the mechanical properties of the medial collateral ligament and lateral collateral ligament, and the effects of repeated stretching on their mechanical properties were compared. Second harmonic generation imaging using a two-photon microscope was used to quantify the collagen fiber structure of the medial collateral ligament and lateral collateral ligament. After repeated stretching, the medial collateral ligament and lateral collateral ligament were incubated in elastase solution for 12 hours, followed by uniaxial tensile tests to determine the effect of elastin treatment on ligament mechanical properties. RESULTS AND CONCLUSION: (1) Quasi-static uniaxial tensile tests showed that the high-tension elastic modulus of the medial collateral ligament was higher than that of the lateral collateral ligament (P < 0.05), while there was no significant difference in the low-tension elastic modulus between the two groups (P > 0.05). Repeated stretching significantly reduced the low-tension elastic modulus of both the medial collateral ligament and lateral collateral ligament. (2) Elastase treatment significantly reduced the low-tension and high-tension elastic moduli of both the medial collateral ligament and lateral collateral ligament, and the decrease in the high-tension elastic modulus of the lateral collateral ligament was greater than that of the medial collateral ligament. After elastase treatment, both the low-tension and high-tension elastic moduli of the medial collateral ligament were higher than those of the lateral collateral ligament (P < 0.05). (3) Two-photon imaging showed that the collagen fibers of the medial collateral ligament maintained a crimped structure, and its fiber waviness was significantly higher than that of the lateral collateral ligament. (4) These results indicate that the medial collateral ligament has stronger elastic properties than the lateral collateral ligament, and elastase treatment has a greater effect on the mechanical properties of the lateral collateral ligament. These mechanical results may be related to the more crimped collagen fiber arrangement in the medial collateral ligament.
Chinese Journal of Tissue Engineering Research•2026•DOI: 10.12307/2026.21415
BACKGROUND: Our group developed a rat lumbar spine model inducing L6-S1 segmental degeneration by prolonged fixation in an abnormal forward-bending posture through a specific device. However, biomechanical evaluation of this model remains lacking. OBJECTIVE: To evaluate the biomechanical properties of L6-S1 motion segment in rats with abnormal forward bending posture through X-ray verification and finite element analysis. METHODS: This study utilized a previously established SD rat model of abnormal forward-flexed posture. Lateral X-ray images of three healthy female SD rats were taken in both restrained (unanesthetized) and relaxed (anesthetized) states to measure the L6-S1 disc angle and analyze its changes under different postures. Micro-CT data from one healthy female SD rat were used to reconstruct a 3D L6-S1 model with Mimics, Geomagic Wrap, and SolidWorks. The model was then meshed, assigned material properties, and subjected to forward flexion loading simulation in ANSYS Workbench to calculate stress distribution in L6-S1 disc structures. RESULTS AND CONCLUSION: (1) The mean L6-S1 intervertebral disc angle was (12.16±0.57)° in relaxed posture and (1.26±0.26)° in restrained posture. (2) Under 10° forward flexion, the maximum von Mises stresses in the upper endplate, lower endplate, annulus fibrosus, and nucleus pulposus were 10.398, 19.928, 6.819, and 0.104 MPa, respectively, with endplates showing significantly higher stresses. (3) The forward-flexed posture reduced the L6-S1 disc angle, altering disc morphology and load distribution. The finite element model simulated the biomechanical environment under abnormal posture, indicating that endplates may be the earliest structures to undergo degenerative changes.
Chinese Journal of Tissue Engineering Research•2026•DOI: 10.12307/2026.21313
BACKGROUND: Peri-implant bone defects may affect implant stability. Platelet-rich fibrin, a second-generation autologous platelet concentrate, contains abundant growth factors and fibrin scaffolds and can facilitate bone regeneration. Nevertheless, its mechanism of action in the context of peri-implant bone defects remains to be fully investigated. OBJECTIVE: To investigate the effects of platelet-rich fibrin on osteogenic genes, bone microstructure, and IκB kinase/inhibitor of nuclear factor-κB/nuclear factor-κB signaling pathway in rats with peri-implant bone defect using a rat tibia model to simulate peri-implant bone defects, combined with ligature-induced inflammation. METHODS: Thirty male Sprague-Dawley rats were selected, and 20 of them were selected to establish peri-implant bone defect model. After modeling, they were randomly divided into model group and platelet-rich fibrin group, with an average of 10 rats per group, and the remaining 10 rats were assigned to the control group. The control group and the model group were not treated with any intervention, and the platelet-rich fibrin group was treated with platelet-rich fibrin implantation at the bone defect site. After 8 weeks, Image-Pro-Plus software was used to detect implant-bone contact rate and new bone formation rate; Micro-CT was used to detect bone microstructure changes; hematoxylin-eosin staining was used to observe histopathological changes; western blot was used to detect the protein expression of nuclear factor-κB, inhibitor of nuclear factor-κB, and IκB kinase in tibial tissue; RT-PCR was used to detect the expression of osteogenic-related genes osteopontin, osteocalcin, and Runt-related transcription factor 2. RESULTS AND CONCLUSION: (1) At 4 and 8 weeks after surgery, the new bone formation rate and implant-bone contact rate in the model group and platelet-rich fibrin group were increased (P < 0.05); the new bone formation rate and implant-bone contact rate in the platelet-rich fibrin group were significantly higher than those in the model group (P < 0.05). (2) Compared with the control group, the model group showed decreased trabecular bone number, bone volume fraction, Lane-Sandhu histological score, and mRNA expression of Runt-related transcription factor 2, osteocalcin, and osteopontin (P < 0.05), while trabecular separation, and protein expression of IκB kinase, inhibitor of nuclear factor-κB, and nuclear factor-κB were increased (P < 0.05). Compared with the model group, the platelet-rich fibrin group showed increased trabecular bone number, bone volume fraction, Lane-Sandhu histological score, and mRNA expression of Runt-related transcription factor 2, osteocalcin, and osteopontin (P < 0.05), while trabecular separation, and protein expression of IκB kinase, inhibitor of nuclear factor-κB, and nuclear factor-κB were decreased (P < 0.05). (3) Micro-CT showed no new bone tissue formation in the model group, while a large amount of new bone formation and connection with bone ends were observed in the platelet-rich fibrin group. (4) Hematoxylin-eosin staining showed that the platelet-rich fibrin group had good bone repair status and a large number of new bone cells around the defect. These results suggest that platelet-rich fibrin can accelerate the process of bone cell repair, has a significant promoting effect on bone healing in rats with peri-implant bone defects, can increase the expression level of osteogenic-related genes, improve bone microstructure, and enhance the activity of the IκB kinase/inhibitor of nuclear factor-κB/nuclear factor-κB signaling pathway.
Chinese Journal of Tissue Engineering Research•2026•DOI: 10.12307/2026.21341
BACKGROUND: Collagen triple helix repeat-containing protein 1 (CTHRC1) is a positive regulator of bone formation. However, its role and underlying mechanisms in periodontal ligament stem cells (PDLSCs) remain unclear. OBJECTIVE: To investigate the effects of CTHRC1 on the proliferation and osteogenic differentiation of PDLSCs and its mechanism of action. METHODS: Human PDLSCs were isolated and cultured in vitro, and cells were transfected with a lentiviral vector overexpressing CTHRC1. The effect of CTHRC1 overexpression on the proliferation activity of PDLSCs was determined by CCK-8 assay and flow cytometry. The effect of CTHRC1 overexpression on the osteogenic differentiation of PDLSCs was determined by alkaline phosphatase (ALP) activity and Alizarin Red staining. Western blot was used to detect the expression of extracellular signal-regulated kinase 1/2 (ERK1/2) and phosphorylated ERK1/2 (p-ERK1/2) after CTHRC1 overexpression. After blocking the ERK1/2 signaling pathway, the expression of osteogenic differentiation-related factors Runt-related transcription factor 2 (Runx2), osteocalcin (OCN), and Osterix was detected by Western blot and qRT-PCR. RESULTS AND CONCLUSION: CCK-8 and flow cytometry results showed that CTHRC1 overexpression promoted the proliferation of PDLSCs. ALP activity and Alizarin Red staining showed that CTHRC1 overexpression promoted the osteogenic differentiation of PDLSCs. Western blot results showed that CTHRC1 overexpression activated the ERK1/2 signaling pathway. Western blot and qRT-PCR results showed that CTHRC1 overexpression promoted the expression of Runx2, OCN, and Osterix at both protein and mRNA levels. When the ERK signaling pathway was inhibited by the specific inhibitor PD98059, the upregulation of osteogenic-related factors was partially suppressed. These results suggest that overexpression of CTHRC1 can promote the proliferation and osteogenic differentiation of PDLSCs, and its osteogenic differentiation effect may be related to the activation of the ERK1/2 signaling pathway.
Chinese Journal of Tissue Engineering Research•2026•DOI: 10.12307/2026.21544
BACKGROUND: The biomimetic design and functional gradient regulation of bone scaffolds are key to improving the efficacy of bone defect repair. Currently, homogeneous scaffolds struggle to balance mechanical load-bearing and material transport, often leading to stress concentration or inadequate nutrient supply after implantation, thus limiting bone regeneration outcomes. OBJECTIVE: To investigate the differences in mechanical performance, mass transport capacity, and cellular microenvironment construction among Primitive (P-type), Gyroid (G-type), and GP composite scaffold structures. METHODS: Based on digital light processing and triply periodic minimal surface theory, a Sigmoid function-driven topological gradient algorithm was proposed to fabricate β-calcium silicate/bioglass radially graded scaffolds with single G-type structure, single P-type structure, and GP type composite structure. The performance of the three types of scaffolds was systematically compared through mechanical simulation, fluid dynamics simulation, and wall shear stress analysis. RESULTS AND CONCLUSION: Finite element analysis showed that the G-type scaffold had uniform stress distribution and the highest maximum Mises stress, while the GP composite scaffold had the lowest maximum Mises stress and more uniform stress distribution than single-structure scaffolds. The P-type scaffold had the largest maximum displacement, while the GP composite scaffold had the smallest. Static compression tests showed elastic moduli of 2.90, 3.39, and 3.38 GPa for G, P, and GP scaffolds, respectively. Fluid dynamics simulation and permeability tests showed that the GP composite scaffold had a permeability of 3.4×10⁻⁹ m², significantly higher than single-structure scaffolds, and within the optimal range for cancellous bone. The average wall shear stress was 0.86 Pa (max 1.13 Pa) for G, 1.40 Pa (max 2.65 Pa) for P, and 1.01 Pa (max 1.68 Pa) for GP, all within the optimal stimulation range for bone regeneration. These results indicate that the GP composite scaffold, designed with a Haversian-like gradient, effectively balances mechanical support and biological function.
Chinese Journal of Tissue Engineering Research•2026•DOI: 10.12307/2026.21593
BACKGROUND: Intervertebral disc degeneration is a core pathological mechanism of discogenic diseases, characterized by an imbalance in extracellular matrix metabolism. Tissue inhibitors of metalloproteinases, as endogenous antagonists of matrix metalloproteinases, play a crucial role in regulating extracellular matrix homeostasis, but the specific functions of subtypes, signaling pathway interactions, and epigenetic regulatory mechanisms have not been systematically clarified. OBJECTIVE: To review the expression changes, functional heterogeneity, and regulatory networks of tissue inhibitors of metalloproteinases in intervertebral disc degeneration, focusing on the molecular mechanisms and signaling pathways in oxidative stress, mechanical load, and inflammatory microenvironment, and to evaluate the translational potential of gene therapy strategies based on tissue inhibitors of metalloproteinases. METHODS: The first author searched PubMed, Web of Science, Embase, CNKI, Wanfang and other databases from inception to March 2025. Chinese search terms included '椎间盘退变，椎间盘退行性变，椎间盘退化，金属蛋白酶类组织抑制剂，信号通路', and English search terms included 'Tissue Inhibitor of Metalloproteinases, Tissue Inhibitor of Metalloproteinase, TIMPs, Intervertebral disc degeneration, Disc degeneration, Degenerative Disc Disease, Degenerative Intervertebral Discs'. Finally, 76 eligible articles were included for review. RESULTS AND CONCLUSION: (1) Subtype functions of tissue inhibitors of metalloproteinases: TIMP1 exhibits dual regulation (early protection/late depletion); TIMP2 maintains extracellular matrix homeostasis by inhibiting matrix metalloproteinase activity, and its abnormal expression can activate pro-apoptotic signaling pathways (e.g., miR-185-5p/MMP2 axis and inflammatory factor-mediated MMP/TIMP imbalance); TIMP3 exerts multi-dimensional protective effects by inhibiting matrix metalloproteinase activity, tumor necrosis factor-alpha converting enzyme/tumor necrosis factor-alpha axis, and angiogenesis; TIMP4 is regulated by miR-155-5p/fibroblast growth factor 2 and participates in extracellular matrix homeostasis. (2) Epigenetic reprogramming mechanisms: Abnormal mechanical stress degrades TIMP3 mRNA through the WTAP/YTHDF2-m6A axis, while miR-222 targets TIMP3 to synergistically accelerate extracellular matrix degradation. (3) Multi-modal therapeutic strategies: Photobiomodulation (wavelength-specific regulation of TIMP/MMP), stem cell exosomes (miR-199a/GREM1 axis), and irisin intervention can remodel matrix metabolic balance. This review summarizes the theoretical framework of 'functional network imbalance of tissue inhibitors of metalloproteinases', revealing its multi-level regulatory characteristics as a core driver of intervertebral disc degeneration, and providing a theoretical basis for developing precise therapies targeting epigenetic modifications and mechano-biological coupling interventions.
Acta Biochimica et Biophysica Sinica•2025•DOI: 10.3724/abbs.2025065
Stem cell fate is profoundly influenced by a complex interplay of biochemical and biophysical cues, with the latter increasingly recognized for its roles in cellular processes, yet the mechanisms are unclear. Since chromatin accessibility is a critical determinant in the processes of osteogenesis and bone repair, investigating the contributions of open chromatin regions (OCRs) to the intracellular signaling pathways triggered by topographical cues, which lead to osteogenic differentiation is highly valuable. This study explores the impact of the nanotopography of biomaterials on the osteogenic differentiation of human bone marrow stem cells (hBMSCs). By utilizing electrospun poly-L-lactide (PLLA) membranes with random fiber arrangements, we mimic the natural extracellular matrix (ECM) topography to study its effects on hBMSCs, contrasting them with flat PLLA controls. Through high-throughput Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) and RNA sequencing (RNA-seq), we reveal that the nanotopography of electrospun surfaces promotes osteogenic differentiation by modulating the chromatin accessibility of the YBX1 gene promoter, leading to its upregulation. Lentiviral knockdown experiments further confirm the crucial role of YBX1, revealing a reversal of the osteogenic effects induced by nanotopography. This study emphasizes the importance of YBX1 in the osteogenic response to the surface topography of biomaterials and suggests that nanotopographical cues could be harnessed to direct stem cell fate. These findings are important for developing biomaterials that promote specific stem cell outcomes in regenerative medicine. Our results further contribute to a deeper understanding of the mechanisms underlying stem cell differentiation in response to environmental cues and pave the way for the rational design of biomaterials with enhanced osteogenic potential. By elucidating the role of chromatin accessibility and specific transcription factors such as YBX1, this study highlights the intricate interplay between cell-material interactions and the intracellular signaling pathways that govern stem cell fate.