Advancing cancer driver gene identification through an integrative network and pathway approach.

OBJECTIVE: Cancer is a complex genetic disease characterized by the accumulation of various mutations, with driver genes playing a crucial role in cancer initiation and progression. Distinguishing driver genes from passenger mutations is essential for understanding cancer biology and discovering therapeutic targets. However, the majority of existing methods ignore the mutational heterogeneity and commonalities among patients, which hinders the identification of driver genes more effectively. METHODS: This study introduces MCSdriver, a novel computational model that integrates network and pathway information to prioritize the identification of cancer driver genes. MCSdriver employs a bidirectional random walk algorithm to quantify the mutual exclusivity and functional relationships between mutated genes within patient cohorts. It calculates similarity scores based on a mutual exclusivity-weighted network and pathway coverage patterns, accounting for patient-specific heterogeneity and molecular profile similarity. RESULTS: This approach enhances the accuracy and quality of driver gene identification. MCSdriver demonstrates superior performance in identifying cancer driver genes across four cancer types from The Cancer Genome Atlas, showing a higher F-score, Recall and Precision compared to existing ranking list-based and module-based models. CONCLUSION: The MCSdriver model not only outperforms other models in identifying known cancer driver genes but also effectively identifies novel driver genes involved in cancer-related biological processes. The model's consideration of patient-specific heterogeneity and similarity in molecular profiles significantly enhances the accuracy and quality of driver gene identification. Validation through Gene Ontology enrichment analysis and literature mining further underscores its potential application value in personalized cancer therapy, offering a promising tool for advancing our understanding and treatment of cancer.

Privacy-Preserving Identification of Cancer Subtype-Specific Driver Genes Based on Multigenomics Data with Privatedriver.

Identifying cancer subtype-specific driver genes from a large number of irrelevant passengers is crucial for targeted therapy in cancer treatment. Recently, the rapid accumulation of large-scale cancer genomics data from multiple institutions has presented remarkable opportunities for identification of cancer subtype-specific driver genes. However, the insufficient subtype samples, privacy issues, and heterogenous of aberration events pose great challenges in precisely identifying cancer subtype-specific driver genes. To address this, we introduce privatedriver, the first model for identifying subtype-specific driver genes that integrates genomics data from multiple institutions in a data privacy-preserving collaboration manner. The process of identifying subtype-specific cancer driver genes using privatedriver involves the following two steps: genomics data integration and collaborative training. In the integration process, the aberration events from multiple genomics data sources are combined for each institution using the forward and backward propagation method of NetICS. In the collaborative training process, each institution utilizes the federated learning framework to upload encrypted model parameters instead of raw data of all institutions to train a global model by using the non-negative matrix factorization algorithm. We applied privatedriver on head and neck squamous cell and colon cancer from The Cancer Genome Atlas website and evaluated it with two benchmarks using macro-Fscore. The comparison analysis demonstrates that privatedriver achieves comparable results to centralized learning models and outperforms most other nonprivacy preserving models, all while ensuring the confidentiality of patient information. We also demonstrate that, for varying predicted driver gene distributions in subtype, our model fully considers the heterogeneity of subtype and identifies subtype-specific driver genes corresponding to the given prognosis and therapeutic effect. The success of privatedriver reveals the feasibility and effectiveness of identifying cancer subtype-specific driver genes in a data protection manner, providing new insights for future privacy-preserving driver gene identification studies.

3D Printed Personalized Nerve Guide Conduits for Precision Repair of Peripheral Nerve Defects.

The treatment of peripheral nerve defects has always been one of the most challenging clinical practices in neurosurgery. Currently, nerve autograft is the preferred treatment modality for peripheral nerve defects, while the therapy is constantly plagued by the limited donor, loss of donor function, formation of neuroma, nerve distortion or dislocation, and nerve diameter mismatch. To address these clinical issues, the emerged nerve guide conduits (NGCs) are expected to offer effective platforms to repair peripheral nerve defects, especially those with large or complex topological structures. Up to now, numerous technologies are developed for preparing diverse NGCs, such as solvent casting, gas foaming, phase separation, freeze-drying, melt molding, electrospinning, and three-dimensional (3D) printing. 3D printing shows great potential and advantages because it can quickly and accurately manufacture the required NGCs from various natural and synthetic materials. This review introduces the application of personalized 3D printed NGCs for the precision repair of peripheral nerve defects and predicts their future directions.

Research progress of stimulus-responsive antibacterial materials for bone infection.

Infection is one of the most serious complications harmful to human health, which brings a huge burden to human health. Bone infection is one of the most common and serious complications of fracture and orthopaedic surgery. Antibacterial treatment is the premise of bone defect healing. Among all the antibacterial strategies, irritant antibacterial materials have unique advantages and the ability of targeted therapy. In this review, we focus on the research progress of irritating materials, the development of antibacterial materials and their advantages and disadvantages potential applications in bone infection.

Ginsenoside Rb1 Protects Human Umbilical Vein Endothelial Cells against High Glucose-Induced Mitochondria-Related Apoptosis through Activating SIRT3 Signalling Pathway.

OBJECTIVE: To investigate whether ginsenoside Rb1 (Rb1) can protect human umbilical vein endothelial cells (HUVECs) against high glucose-induced apoptosis and examine the underlying mechanism. METHODS: HUVECs were divided into 5 groups: control group (5.5 mmol/L glucose), high glucose (HG, 40 mmol/L) treatment group, Rb1 (50 µ mol/L) treatment group, Rb1 plus HG treatment group, and Rb1 and 3-(1H-1,2,3-triazol-4-yl) pyridine (3-TYP, 16 µ mol/L) plus HG treatment group. Cell viability was evaluated by cell counting kit-8 assay. Mitochondrial and intracellular reactive oxygen species were detected by MitoSox Red mitochondrial superoxide indicator and dichloro-dihydro-fluorescein diacetate assay, respectively. Annexin V/propidium iodide staining and fluorescent dye staining were used to measure the apoptosis and the mitochondrial membrane potential of HUVECs, respectively. The protein expressions of apoptosis-related proteins [Bcl-2, Bax, cleaved caspase-3 and cytochrome c (Cyt-c)], mitochondrial biogenesis-related proteins [proliferator-activated receptor gamma coactivator 1-alpha, nuclear respiratory factor-1 and mitochondrial transcription factor A)], acetylation levels of forkhead box O3a and SOD2, and sirtuin-3 (SIRT3) signalling pathway were measured by immunoblotting and immunoprecipitation. RESULTS: Rb1 ameliorated survival in cells in which apoptosis was induced by high glucose (P<0.05 or P<0.01). Upon the addition of Rb1, mitochondrial and intracellular reactive oxygen species generation and malondialdehyde levels were decreased (P<0.01), while the activities of antioxidant enzymes were increased (P<0.05 or P<0.01). Rb1 preserved the mitochondrial membrane potential and reduced the release of Cyt-c from the mitochondria into the cytosol (P<0.01). In addition, Rb1 upregulated mitochondrial biogenesis-associated proteins (P<0.01). Notably, the cytoprotective effects of Rb1 were correlated with SIRT3 signalling pathway activation (P<0.01). The effect of Rb1 against high glucose-induced mitochondria-related apoptosis was restrained by 3-TYP (P<0.05 or P<0.01). CONCLUSION: Rb1 could protect HUVECs from high glucose-induced apoptosis by promoting mitochondrial function and suppressing oxidative stress through the SIRT3 signalling pathway.

Shear Speed-Regulated Properties of Long-Acting Docetaxel Control Release Poly (Lactic-Co-Glycolic Acid) Microspheres.

Advanced drug carriers for the controlled release of chemotherapeutics in the treatment of malignant tumors have drawn significant notice in recent years. In the current study, microspheres (MPs) loaded with docetaxel (DTX) were prepared using polylactic-co-glycolic acid copolymer (PLGA). The double emulsion solvent evaporation method is simple to perform, and results in high encapsulation efficiency. Electron micrographs of the MPs showed that controlling the shear rate can effectively control the size of the MPs. At present, most DTX sustained-release carriers cannot maintain stable and long-term local drug release. The 1.68 µm DTX-loaded microspheres (MP/DTX) with elastase was completely degraded in 14 d. This controlled degradation period is similar to a course of treatment for most cancers. The drug release profile of all kinds of MP/DTX demonstrated an initial rapid release, then slower and stable release to the end. The current study demonstrates that it is possible to create drug-loaded MPs with specific degradation times and drug release curves, which may be useful in achieving optimal treatment times and drug release rates for different diseases, and different drug delivery routes. The initial burst release reaches the effective concentration of the drug at the beginning of release, and then the drug concentration is maintained by stable release to reduce the number of injections and improve patient compliance.

Reduction-responsive polypeptide nanomedicines significantly inhibit progression of orthotopic osteosarcoma.

Osteosarcoma (OS) is the most common malignant bone tumor with high metastasis and mortality. Neoadjuvant chemotherapy is an effective therapeutic regimen, but the clinical application is limited by the unsatisfactory efficacies and considerable side effects. In this study, the reduction-responsive polypeptide micelles based on methoxy poly(ethylene glycol)-block-poly(S-tert-butylmercapto-L-cysteine) copolymers (mPEG113-b-PBMLC4, P4M, and mPEG113-b-PBMLC9, P9M) were developed to control the delivery of doxorubicin (DOX) in OS therapy. Compared to free DOX, P4M/DOX and P9M/DOX exhibited 2.6 and 3.5 times increase in the area under the curve of pharmacokinetics, 1.6 and 2.0 times increase in tumor accumulation, and 1.6 and 1.7 times decrease of the distribution in the heart. Moreover, the selective accumulation of micelles, especially P9M/DOX, in tumors induced stronger antitumor effects on both primary and lung metastatic OSs with less systematic toxicity. These micelles with smart responsiveness to intracellular microenvironments are highly promising for the targeted delivery of clinical chemotherapeutic drugs in cancer therapy.

Silencing of GAS5 represses the malignant progression of atherosclerosis through upregulation of miR-135a.

Long non-coding RNA growth arrest-specific 5 (GAS5) has been demonstrated to be involved in the pathogenesis of atherosclerosis (AS). The purpose of the present study was to investigate the underlying mechanisms of GAS5 on the inflammation and lipid metabolic disorders of AS. ApoE-/- mice were fed on a high fat diet (HFD) and THP-1 macrophages were treated with ox-LDL to construct AS model in vivo and in vitro, respectively. The detections of blood lipids and inflammatory cytokines were performed using corresponding assay kits. qRT-PCR was used to assess the expression of GAS5 and miR-135a. Western blot was performed to detect PPARα and CPT1 levels. The targeted interaction between GAS5 and miR-135a was determined by dual-luciferase reporter assay and RNA immunoprecipitation assay. Our data revealed that GAS5 was upregulated in AS mice model and ox-LDL-treated macrophages. GAS5 silencing alleviated lipid metabolic disorders and inflammation in AS mice and ox-LDL-treated macrophages. Moreover, GAS5 directly targeted miR-135a and repressed miR-135a expression. MiR-135a expression restoration abrogated the alleviative effects of GAS5 silencing on inflammation and lipid metabolic disorders in ox-LDL-treated macrophages. In conclusion, our study suggested that GAS5 silencing repressed the malignant progression of AS at least partly through upregulation of miR-135a. Targeting GAS5 might be a promising treatment strategy for AS management.

SRSF1 promotes vascular smooth muscle cell proliferation through a Δ133p53/EGR1/KLF5 pathway.

Though vascular smooth muscle cell (VSMC) proliferation underlies all cardiovascular hyperplastic disorders, our understanding of the molecular mechanisms responsible for this cellular process is still incomplete. Here we report that SRSF1 (serine/arginine-rich splicing factor 1), an essential splicing factor, promotes VSMC proliferation and injury-induced neointima formation. Vascular injury in vivo and proliferative stimuli in vitro stimulate SRSF1 expression. Mice lacking SRSF1 specifically in SMCs develop less intimal thickening after wire injury. Expression of SRSF1 in rat arteries enhances neointima formation. SRSF1 overexpression increases, while SRSF1 knockdown suppresses the proliferation and migration of cultured human aortic and coronary arterial SMCs. Mechanistically, SRSF1 favours the induction of a truncated p53 isoform, Δ133p53, which has an equal proliferative effect and in turn transcriptionally activates Krüppel-like factor 5 (KLF5) via the Δ133p53-EGR1 complex, resulting in an accelerated cell-cycle progression and increased VSMC proliferation. Our study provides a potential therapeutic target for vascular hyperplastic disease.

Downregulated miR-486-5p acts as a tumor suppressor in esophageal squamous cell carcinoma.

microRNAs (miRNAs/miRs) are crucial regulators of gene expression at the post-translational level through promoting mRNA degradation or the repression of translation of target genes. miRs have been confirmed to serve a dominant role in tumor biology. miR-486-5p has been ascertained to be involved in non-small-cell lung cancer, breast cancer and hepatocellular carcinoma; however, the expression and function of miR-486-5p in esophageal squamous cell carcinoma (ESCC) has yet to be elucidated. The present study aimed to analyze the expression levels of miR-486-5p in ESCC tissues and paired normal adjacent tissues, and determine the effects of miR-486-5p on esophageal cancer cells using MTT, wound scratch and apoptosis assays. The current results showed that miR-486-5p was significantly downregulated in ESCC specimens. Ectopic expression of miR-486-5p by synthetic mimics reduced cell proliferation and migration and induced increased cell apoptosis. The results indicated miR-486-5p may function as a tumor suppressor in ESCC. The present study demonstrated that miR-486-5p was downregulated in ESCC and served a anti-oncogene role in ESCC via affecting cellular migration.

lncRNA-UCA1 enhances cell proliferation through functioning as a ceRNA of Sox4 in esophageal cancer.

Esophageal cancer (EC) is one of the most common gastrointestinal cancers, which leads to the sixth ranking of cancer-related death. Long non-coding RNAs (lncRNAs) play pivotal roles in many biological processes. lncRNA human urothelial carcinoma associated 1 (UCA1) is significantly upregulated and functions as an important oncogene in many types of human cancers. However, the role of UCA1 in EC and its underlying mechanism remains unclear. In the present study, we demonstrated that UCA1 was significantly upregulated in EC tissues and associated with poor prognosis. Overexpression of UCA1 promoted the proliferation of EC cells, while silence of UCA1 inhibited EC cells growth. Furthermore, we found that Sox4 was a direct target gene of UCA1. UCA1 regulated Sox4 expression through functioning as a competing endogenous RNA (ceRNA). UCA1 directly interacted with miR-204 and decreased the binding of miR-204 to Sox4 3'UTR, which suppressed the degradation of Sox4 mRNA by miR-204. This study provides the first evidence that UCA1 promotes cell proliferation through Sox4 in EC, suggesting that UCA1 and Sox4 may be potential therapeutic targets for EC.

Minimally invasive direct coronary artery bypass for left anterior descending artery revascularization - analysis of 300 cases.

INTRODUCTION: Minimally invasive direct coronary artery bypass (MIDCAB) grafting is performed via small, left anterolateral thoracotomy. The left internal mammary artery was grafted to the left anterior descending (LAD) artery in 300 consecutive patients. AIM: In-hospital results were evaluated and compared with the conventional, off-pump coronary artery bypass graft procedure. MATERIAL AND METHODS: One hundred and sixty-three (54.33%) of 300 patients underwent staged hybrid coronary revascularization, 93 (31%) were treated for a single LAD lesion, and 44 (14.67%) were treated for multi-vessel disease with reasonably incomplete revascularization. Major in-hospital cardiac adverse events and postoperative data were compared between groups. RESULTS: Preoperative data were similar between groups. However, the difference in left ventricular ejection fraction (p < 0.001) was significant. No conversions to sternotomy occurred during the primary MIDCAB procedures. Shorter operation time (p < 0.001), shorter postoperative mechanical ventilation time (p < 0.001), shorter intensive care unit stay (p < 0.001), and less red blood cell transfusion (p < 0.001) were noted in the MIDCAB group. Postoperative coronary angiography conducted in the MIDCAB group within one week after the operation showed that 2 of 163 patients developed graft occlusion. These patients underwent conventional CABG and recovered well. No significant differences were observed in postoperative MI, delayed wound healing or 30-day in-hospital mortality between the two groups. CONCLUSIONS: The use of a chest wall lifting system and modified stabilizer makes the MIDCAB procedure safer and easier. The MIDCAB procedure is demonstrated to be a feasible and minimally invasive alternative for patients with coronary artery disease involving LAD lesions.

Upregulated miR-193a-3p as an oncogene in esophageal squamous cell carcinoma regulating cellular proliferation, migration and apoptosis.

MicroRNAs (miRs) are small endogenous non-coding RNAs that play a vital role in carcinogenesis. miR-193a-3p has been described in multiple cancers. However, the function of miR-193a-3p in esophageal squamous cell carcinoma (ESCC) is still unclear. To explore the role of miR-193a-3p in ESCC, reverse transcription-quantitative polymerase chain reaction was used to evaluate the expression of miR-193a-3p in 48 paired ESCC and adjacent normal tissues. In addition, the impact of miR-193a-3p on cell proliferation, migration and apoptosis were analyzed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, wound scratch assay and flow cytometry, respectively. The results revealed that miR-193a-3p was upregulated in ESCC, compared with adjacent normal tissues. Downregulation of miR-193a-3p expression using a synthesized inhibitor suppressed cell proliferation and migration, and induced cell apoptosis, indicating that miR-193a-3p could be characterized as an oncogene in ESCC. In summary, the present study demonstrated that miR-193a-3p was upregulated in ESCC, where it plays a significant role by affecting cellular proliferation, migration and apoptosis.

Collecting duct carcinoma of the kidney: A case report.

Collecting duct carcinoma (CDC) is a rare type of renal tumor, arising from the distal collecting ducts. The prognosis of this disease is extremely poor due to its rapid progression with widespread metastases. The present study reported a case of CDC involving the right renal region of a 62-year-old female patient, presented with right-flank pain that had persisted for one month. A computed tomography scan demonstrated multiple hypoattenuating quasicircular lesions, 0.5-4.3 cm in size, in the upper pole of the right kidney. Following the diagnosis of a right renal tumor, laparoscopic radical resection of the right kidney was performed. Pathological examination demonstrated that the tumor cells were arranged in a glandular or papillary pattern, and marked cytological atypia was observed. Immunohistochemical staining revealed that the tumor cells were positive for epithelial membrane antigen and cytokeratin (CK)7, while they reacted focally with vimentin. However, the tumor cells were negative for CK20, CD10, uroplakin III and p63. Based on these findings, the patient was diagnosed with CDC. In conclusion, immunohistochemical analysis is critical in establishing an accurate diagnosis of CDC and distinguishing this tumor from other subtypes of RCC.

Effect of brimonidine on retinal and choroidal neovascularization in a mouse model of retinopathy of prematurity and laser-treated rats.

PURPOSE: To determine whether chronic treatment with brimonidine (BRI) attenuates retinal vascular leakage and neovascularization in neonatal mice after exposure to high oxygen in a mouse model of retinopathy of prematurity (ROP), and choroidal neovascularization (CNV) in rats after laser treatment. METHODS: Experimental CNV was induced by laser treatment in Brown Norway (BN) rats. BRI or vehicle (VEH) was administered by osmotic minipumps, and CNV formation was measured 11 days after laser treatment. Oxygen-induced retinopathy was generated in neonatal mice by exposure to 75% oxygen from postnatal day (P)7 to P12. BRI or VEH was administered by gavage, and vitreoretinal vascular endothelial growth factor (VEGF) concentrations and retinal vascular leakage, neovascularization, and vaso-obliteration were measured on P17. Experimental CNV was induced in rabbits by subretinal lipopolysaccharide/fibroblast growth factor-2 injection. RESULTS: Systemic BRI treatment significantly attenuated laser-induced CNV formation in BN rats when initiated 3 days before or within 1 hour after laser treatment. BRI treatment initiated during exposure to high oxygen significantly attenuated vitreoretinal VEGF concentrations, retinal vascular leakage, and retinal neovascularization in P17 mice subjected to oxygen-induced retinopathy. Intravitreal treatment with BRI had no effect on CNV formation in a rabbit model of nonischemic angiogenesis. CONCLUSIONS: BRI treatment significantly attenuated vitreoretinal VEGF concentrations, retinal vascular leakage, and retinal and choroidal neovascularization in animal models of ROP and CNV. BRI may inhibit underlying event(s) of ischemia responsible for upregulation of vitreoretinal VEGF and thus reduce vascular leakage and retinal-choroidal neovascularization.