Genomics, Proteomics & Bioinformatics•2024•DOI: 10.1093/gpbjnl/qzae019
Lysine post-translational modifications (PTMs) are widespread and versatile protein PTMs that are involved in diverse biological processes by regulating the fundamental functions of histone and non-histone proteins. Dysregulation of lysine PTMs is implicated in many diseases, and targeting lysine PTM regulatory factors, including writers, erasers, and readers, has become an effective strategy for disease therapy. The continuing development of mass spectrometry (MS) technologies coupled with antibody-based affinity enrichment technologies greatly promotes the discovery and decoding of PTMs. The global characterization of lysine PTMs is crucial for deciphering the regulatory networks, molecular functions, and mechanisms of action of lysine PTMs. In this review, we focus on lysine PTMs, and provide a summary of the regulatory enzymes of diverse lysine PTMs and the proteomics advances in lysine PTMs by MS technologies. We also discuss the types and biological functions of lysine PTM crosstalks on histone and non-histone proteins and current druggable targets of lysine PTM regulatory factors for disease therapy.
Acta Biochimica et Biophysica Sinica•2026•DOI: 10.3724/abbs.2025128
Hepatocellular carcinoma (HCC) continues to pose a chief threat to the global healthcare landscape and is characterized by scarce therapeutic options and poor clinical outcomes, especially in advanced-stage disease. Although lymphocyte antigen 96 (LY96) is associated with immunogenic cell death, its specific role in HCC progression and therapeutic potential remains unclear. To identify prospective therapeutic targets in HCC, by combining the cancer-immunity cycle score with WGCNA and systems biology methods, we identify pivotal molecular interactions. By integrating the cancer-immunity cycle score with WGCNA and systems-level approaches, we systematically identify potential therapeutic targets in HCC. We evaluate LY96 expression at the transcriptomic and proteomic levels in HCC tissues and explore its prognostic relevance by drawing upon information from The Cancer Genome Atlas (TCGA) repository. The functional role of LY96 is delineated through a panel of cellular assays conducted in vitro, complemented by in vivo tumorigenesis models. To identify the downstream signaling cascades associated with LY96, gene set enrichment analysis (GSEA) is performed to elucidate the implicated pathways, which are then confirmed via experimental validation. Furthermore, we employ a lipid-polymer hybrid nanoparticle (NP) platform to facilitate the systemic delivery of an LY96 inhibitor and demonstrate its potential as a newly proposed intervention strategy for HCC. Clinically, marked LY96 overexpression occurs in HCC samples, where elevated LY96 expression is strongly associated with reduced overall survival (OS) among liver cancer patients. LY96 facilitates the progression of HCC via complementary in vitro and in vivo approaches. Mechanistically, LY96 induces the activation of the TGF-β1/Smad2/3 signaling axis in HCC. For therapeutic applications, we develop a liposome-based nanoparticle system that delivers the LY96 inhibitor L6H21 to tumor cells and effectively suppresses HCC progression through a combination of in vivo and in vitro studies. Taken together, the current observations identify LY96 as a promising diagnostic indicator and a viable intervention for therapeutic modulation to improve HCC treatment.
Chinese Journal of Tissue Engineering Research•2026•DOI: 10.12307/2026.21205
BACKGROUND: Macrophage polarization demonstrates significant potential in disease treatment, particularly in areas such as cancer, inflammation, and autoimmune diseases. Establishing standardized in vitro models can lay the groundwork for in-depth research into the mechanisms of macrophage polarization. OBJECTIVE: To observe the in vitro growth characteristics of bone marrow-derived macrophages from C57BL/6 mice and to establish a standardized in vitro model for M1 and M2 macrophage polarization. METHODS: Femurs and tibias of C57BL/6 mice were aseptically separated, and the contents of the bone marrow cavity were collected. After filtering through a mesh and lysing erythrocytes, the contents were resuspended in high-glucose DMEM containing 20 ng/mL macrophage colony-stimulating factor and inoculated in 6-well plates according to experimental requirements. On day 7, they were differentiated into mature mouse bone marrow-derived macrophages (M0 type). Then, 100 ng/mL lipopolysaccharide was used to induce polarization to M1 type, and 20 ng/mL interleukin-4 was used to induce polarization to M2 type. Flow cytometry and RT-qPCR were used to detect the expression of corresponding markers in macrophages under different polarization states, and Western blot was used to detect the expression of M1 macrophage marker pathway proteins p-STAT1, STAT1 and M2 macrophage marker pathway proteins p-STAT6, STAT6. RESULTS AND CONCLUSION: (1) After stimulation with 20 ng/mL macrophage colony-stimulating factor for 7 days, flow cytometry showed that the positive rate of macrophage surface marker F4/80 reached 98.1%. (2) After stimulation with 100 ng/mL lipopolysaccharide for 6 h, the positive rates of F4/80 and CD86 were about 35%, and RT-qPCR showed that the mRNA expression of M1 macrophage markers inducible nitric oxide synthase, interleukin-6, macrophage inflammatory protein 1α, and monocyte chemoattractant protein 1 were significantly higher than those in the control group (P < 0.01). (3) After stimulation with 20 ng/mL interleukin-4 for 24 h, the mean fluorescence intensity of CD206 was significantly increased, and RT-qPCR showed that the mRNA expression of M2 macrophage markers Chi3l3 (Ym1), interleukin-10, and arginase 1 were significantly higher than those in the control group (P < 0.01). (4) Western blot results showed that lipopolysaccharide-induced M1 macrophage marker pathway protein p-STAT1 was significantly activated; interleukin-4-induced M2 macrophage marker pathway protein p-STAT6 was significantly activated. These results indicate that lipopolysaccharide and interleukin-4 effectively induced polarization of bone marrow-derived macrophages to M1 and M2 types, respectively.
Chinese Journal of Tissue Engineering Research•2026•DOI: 10.12307/2026.21290
BACKGROUND: Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by abnormal deposition of β-amyloid (Aβ) and neurofibrillary tangles of tau protein. Current medications only alleviate some symptoms, and despite extensive efforts to develop new therapies, such as anti-Aβ immunotherapy and β-secretase inhibitors, clinical trials have not been successful. OBJECTIVE: To investigate the methylation changes of the Fbln1 gene in the hippocampus of PSEN1/PSEN2 double knockout (dKO) mice, which lack Aβ deposition, and APP/PS1 double transgenic (DTG) mice, which exhibit Aβ deposition, to explore non-Aβ-related mechanisms and potential targets in AD. METHODS: Hippocampal tissues were collected from female dKO mice at 7 months (early AD) and 12 months (mid-stage AD) of age, with age-matched wild-type (WT) mice as controls. Epigenetic reduced representation bisulfite sequencing (RRBS) was used to screen for aberrantly methylated genes, identifying Fbln1. Bisulfite sequencing PCR (BSP) was performed to validate the methylation status of Fbln1 in mid-stage dKO mice. RT-PCR and western blot were used to measure Fbln1 mRNA and protein expression in early and mid-stage dKO mice, as well as in 12-month-old DTG mice. Finally, the expression levels of Fbln1 and Aβ were compared between dKO and DTG mice, with age-matched WT mice as controls. RESULTS AND CONCLUSION: RRBS showed that Fbln1 was hypomethylated in the hippocampus of mid-stage dKO mice (P < 0.05), while early-stage dKO mice showed a trend of hypomethylation but without statistical significance (P > 0.05). BSP confirmed the abnormal hypomethylation of Fbln1 in mid-stage dKO mice. In early-stage dKO mice, Fbln1 mRNA and protein levels were not significantly different from WT (P > 0.05). In mid-stage dKO mice, Fbln1 mRNA and protein levels were significantly higher than in WT (t=5.336, P < 0.01; t=8.985, P < 0.01). Similarly, mid-stage DTG mice showed significantly higher Fbln1 mRNA and protein levels than WT (t=4.151, P < 0.01; t=8.392, P < 0.01), but there was no significant difference between the two AD models (P > 0.05). In mid-stage dKO mice, there was no significant difference between Fbln1 and Aβ protein levels (P > 0.05), whereas in DTG mice, the difference was significant (t=6.348, P < 0.01), indicating that Fbln1 plays a role in both Aβ-dependent and Aβ-independent mechanisms. These findings suggest that Fbln1 methylation changes may contribute to age-dependent neurodegeneration in dKO mice and may be involved in both Aβ and non-Aβ pathways in AD, providing new insights and potential targets for non-Aβ-related mechanisms. Fbln1, as an aging-related factor, holds promise as a novel target.
Chinese Journal of Tissue Engineering Research•2026•DOI: 10.12307/2026.21346
BACKGROUND: Cell transplantation is one of the effective approaches for repairing spinal cord injury. Our research team previously found that transplanted cerebrospinal fluid-contacting neurons can survive and promote motor function recovery in mice with spinal cord injury. However, whether these transplanted cerebrospinal fluid-contacting neurons differentiate into functional neurons and thereby facilitate motor function recovery remains unclear. OBJECTIVE: To investigate whether transplanted cerebrospinal fluid-contacting neurons differentiate into functional neurons in vivo and contribute to motor function recovery after spinal cord injury. METHODS: Primary cells containing cerebrospinal fluid-contacting neurons were isolated from the cervical spinal cord of C57BL/6 neonatal mice within 24 hours of birth and cultured adherently. Cells were transduced with a lentivirus carrying a multimodal imaging gene, and cerebrospinal fluid-contacting neurons were selected and purified using puromycin. Differentiation was induced with serum-containing differentiation medium, and expression of neuronal marker NeuN and motor neuron marker ChAT was detected by immunofluorescence. Thirty C57BL/6 mice were randomly divided into three groups: transplantation group and PBS group underwent T10 spinal cord injury by clip compression, while sham group only had laminectomy. One week after injury, cerebrospinal fluid-contacting neurons were transplanted in situ in the transplantation group, and an equal volume of PBS was injected in the PBS group. At 1, 4, and 8 weeks after transplantation, immunofluorescence was used to detect expression of motor neuron marker ChAT in spinal cord tissue. At 8 weeks, immunofluorescence was used to detect synaptic marker SYN, inhibitory transmitter marker GAD65/67, and excitatory transmitter marker vGLUT1; hematoxylin-eosin staining was used to observe spinal cord morphology; BMS motor function score and footprint analysis were used to assess motor function recovery. RESULTS AND CONCLUSION: (1) Cerebrospinal fluid-contacting neurons expressed neural stem cell characteristics in vitro and could differentiate into motor neurons. (2) Transplanted cerebrospinal fluid-contacting neurons could survive long-term in vivo and differentiate into motor neurons. (3) The proportion of cerebrospinal fluid-contacting neurons differentiating into motor neurons was highest at 8 weeks (P < 0.0001). (4) At 8 weeks after transplantation, cerebrospinal fluid-contacting neurons co-expressed SYN, GAD65/67, and vGLUT1, indicating synaptic connections with host neurons. (5) BMS scores of PBS group were consistently lower than those of transplantation group (P < 0.001); footprint analysis showed more coordinated gait in transplantation group with only toe dragging, while PBS group showed obvious hindlimb dragging. (6) Hematoxylin-eosin staining showed large cavities in the injured area of PBS group, while cavities were reduced in transplantation group. These results indicate that transplanted cerebrospinal fluid-contacting neurons can differentiate into motor neurons both in vitro and in vivo, form synaptic connections, and thereby improve motor function in spinal cord-injured mice.
Chinese Journal of Tissue Engineering Research•2026•DOI: 10.12307/2026.21638
BACKGROUND: Postoperative knee joint stiffness after distal femoral fracture is a core problem affecting functional recovery of patients. Its pathological mechanisms involve factors such as extensor mechanism adhesion, joint capsule contracture, and abnormal articular surface morphology. OBJECTIVE: To explore the efficacy of arthroscopy combined with small incision adhesion release in the treatment of extension stiff knee after distal femoral fracture, and to analyze the risk factors affecting the functional recovery of knee joint. METHODS: One hundred and fifty-two patients with non-infectious extension stiff knee after distal femoral fracture were selected in Guangzhou Hospital of Integrated Traditional Chinese and Western Medicine from March 2019 to October 2024. Patients were divided into good recovery group (≥70, n=122) and poor recovery group (<70, n=30) according to Hospital for Special Surgery score 6 months after operation. The clinical data including patient age, reduction quality and continuous passive motion exercise were collected. The risk factors were analyzed by univariate and multivariate Logistic regression, and a prediction model was established. The model performance was evaluated by receiver operating characteristic curve, calibration curve, and decision curve. RESULTS AND CONCLUSION: Univariate analysis showed that age ≥60 years, non-anatomical reduction, no continuous passive motion exercise, postoperative complications, intraoperative range of motion <120°, increased preoperative medial tibial joint line change, and decreased preoperative Hospital for Special Surgery score were significantly associated with poor functional recovery (all P < 0.05). Multivariate analysis confirmed that age ≥60 years, no continuous passive motion exercise, postoperative complications, intraoperative range of motion <120°, low preoperative Hospital for Special Surgery score, and large medial tibial joint line change were independent risk factors (all P < 0.05). Threshold effect analysis revealed a nonlinear relationship between intraoperative range of motion and recovery risk (P < 0.001), with 120° as the inflection point. When range of motion <120°, each 1° increase reduced recovery risk by 3.3% (OR=0.967); when ≥120°, the risk was no longer significantly reduced (P=0.073). The prediction model showed good discrimination (area under the curve=0.821, 95%CI: 0.760-0.953), calibration (Brier score=0.097), and clinical net benefit (decision curve threshold 0.1-0.9). These findings suggest that functional recovery in patients with knee stiffness after distal femoral fracture is closely related to intraoperative range of motion threshold (120°), age, rehabilitation management, and preoperative joint status. The prediction model based on six independent risk factors has good performance and can provide evidence for clinical intervention.
Acta Biochimica et Biophysica Sinica•2025•DOI: 10.3724/abbs.2025128
Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality, with advanced-stage disease characterized by limited therapeutic options and poor clinical outcomes. Lymphocyte antigen 96 (LY96) has been implicated in immunogenic cell death, yet its specific mechanistic contribution to HCC progression and its potential as a therapeutic target remain undefined. This study integrates cancer-immunity cycle scoring with weighted gene co-expression network analysis (WGCNA) and systems biology approaches to identify pivotal molecular drivers in HCC. LY96 expression was evaluated at transcriptomic and proteomic levels in HCC tissues, and its prognostic relevance was assessed using The Cancer Genome Atlas (TCGA) repository. Functional characterization of LY96 was performed through a panel of in vitro cellular assays and in vivo tumorigenesis models. Gene set enrichment analysis (GSEA) identified downstream signaling cascades, which were subsequently validated experimentally. A lipid-polymer hybrid nanoparticle (NP) platform was engineered for systemic delivery of the LY96 inhibitor L6H21. Clinically, marked LY96 overexpression was observed in HCC samples and correlated with reduced overall survival (OS). LY96 facilitated HCC progression via complementary in vitro and in vivo approaches. Mechanistically, LY96 induced activation of the TGF-β1/Smad2/3 signaling axis. The liposome-based nanoparticle system delivering L6H21 effectively suppressed HCC progression in both in vivo and in vitro studies. These findings identify LY96 as a promising diagnostic indicator and a viable therapeutic target for HCC intervention.
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.
Chinese Journal of New Drugs•2025•DOI: cast_zgxyzz_1236731785313317742
Background: Heart failure with recovered ejection fraction (HFrecEF) is a distinct phenotype with unclear clinical characteristics and prognosis. Methods: We prospectively enrolled 1,234 patients with heart failure and reduced ejection fraction (HFrEF) from January 2015 to December 2018. After optimal medical therapy, 312 patients (25.3%) achieved recovery of left ventricular ejection fraction (LVEF) to ≥50% and were classified as HFrecEF. Clinical characteristics, medication use, and outcomes were compared with those who remained HFrEF. The primary outcome was a composite of all-cause death and heart failure hospitalization. Results: Compared with HFrEF patients, HFrecEF patients were younger, more likely to be female, had a higher prevalence of hypertension and atrial fibrillation, and had a shorter duration of heart failure. They had lower baseline levels of NT-proBNP and smaller left ventricular dimensions. Over a median follow-up of 3.2 years, HFrecEF patients had a significantly lower risk of the primary outcome (adjusted HR 0.45, 95% CI 0.32-0.63, p<0.001). However, 23.4% of HFrecEF patients experienced deterioration of LVEF during follow-up, and these patients had a worse prognosis compared with those who maintained recovery. Independent predictors of LVEF deterioration included ischemic etiology, diabetes, and non-adherence to guideline-directed medical therapy. Conclusions: HFrecEF is associated with a better prognosis than HFrEF, but a substantial proportion of patients may experience LVEF deterioration. Continued optimization of medical therapy and close monitoring are essential for this population.