A Transcriptome Sequencing Study on Genome-Wide Gene Expression Differences of Lung Cancer Cells Modulated by Fucoidan

Revealing the mechanism of 755-nm long-pulsed alexandrite laser in inhibiting infantile hemangioma endothelial cells through transcriptome sequencing

Laser therapy has shown promising outcomes in treating infantile hemangiomas. However, the molecular mechanisms underlying laser treatment for IH remain incompletely elucidated. This study aimed to unravel the molecular mechanisms of laser therapy in IH treatment. We evaluated the inhibitory effects of laser treatment on the proliferation and promotion of apoptosis in human hemangioma endothelial cells (HemECs) through cell counting kit-8 (CCK-8) assay, Hoechst 33342 staining, and flow cytometric analysis. Transcriptome sequencing analysis of HemECs following laser treatment revealed a significant decrease in the expression level of the GSTM5 gene. The qRT-PCR and western blot analysis also showed that GSTM5 expression in HemECs was downregulated compared to human umbilical vein endothelial cells (HUVECs), and concomitantly, the p62-Nrf2 pathway was suppressed. Using siRNA to downregulate GSTM5 expression, we observed that inhibiting GSTM5 expression could restrain cell proliferation, elevate intracellular ROS levels, and induce apoptosis in HemECs. Furthermore, upon inhibition of the p62-Nrf2 pathway using p62-specific siRNA, a significant decrease in GSTM5 expression and an elevation in intracellular ROS levels were noted in laser-treated HemECs. These findings suggested that laser treatment may operate by inhibiting the p62-Nrf2 pathway, thereby downregulating GSTM5 expression, elevating ROS levels, and consequently inducing apoptosis in HemECs.

Exosome and lipid metabolism-related genes in pancreatic adenocarcinoma: a prognosis analysis

OBJECTIVE

The purpose of the study was to investigate the role of exosome and lipid metabolism-related genes (EALMRGs) mRNA levels in the diagnosis and prognosis of Pancreatic Adenocarcinoma (PAAD).

METHODS

The mRNA expression pattern of PAAD and pan-cancers with prognostic data were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. EALMRGs were acquired from GeneCards and MSigDB database after merging and deduplication. Prognostic EALMRGs were screened through univariate COX regression analysis, and a prognostic model was constructed based on these genes by least absolute shrinkage and selection operator (LASSO) regression. The prognostic value of EALMRGs was then validated in pan-cancer data. The time characteristics ROC curve analysis was performed to evaluate the effectiveness of the prognostic genes.

RESULTS

We identified 5 hub genes (ABCB1, CAP1, EGFR, PPARG, SNCA) according to high and low-risk groups of prognoses. The risk formula was verified in three other cohort of pancreatic cancer patients and was explored in pan-cancer data. Additionally, T cell and dendritic cell infiltration was significantly increased in low-risk group. The expression of the 5 hub genes was also identified in single-cell sequencing data of pancreatic cancer with pivotal pathways. Additionally, functional enrichment analysis based on pancreatic cancer data in pancreatic cancer showed that protein serine/threonine kinase activity, focal adhesion, actin binding, cell-substrate junction, organic acid transport, and regulation of transporter activity were significant related to the expression of genes in EALMRGs.

CONCLUSIONS

Our risk formula shows potential prognostic value in multiple cancers and manifest pivotal alterations in immune infiltration and biological pathway in pancreatic cancer.

Identification of Autophagy-Related Targets of Berberine against Non-Small Cell Lung Cancer and Their Correlation with Immune Cell Infiltration By Combining Network Pharmacology, Molecular Docking, and Experimental Verification

OBJECTIVE

Non-small cell lung cancer (NSCLC) is the most common lung cancer type with high incidence. This study aimed to reveal the anti-NSCLC mechanisms of berberine and identify novel therapeutic targets.

METHODS

Berberine-related targets were acquired from SuperPred, SwissTargetPrediction, and GeneCards. NSCLC-re-lated targets were collected from GeneCards and DisGeNET. Differentially expressed genes (DEGs) were identified GEO database, UCSC Xena, and limma. GO and KEGG analyses were performed using clusterProfiler. Autophagy-related genes and transcriptional factors were collected from HADb and KnockTF, respectively. STRING and Cytoscape were used for PPI network analysis. Immune cell infiltration in NSCLC was assessed using CIBERSORT, and its correlation with autophagy-related targets was evaluated. Molecular docking was conducted using PyMOL and AutoDock. qRT-PCR and CCK-8 assay was used for in vitro verification.

RESULTS

Thirty intersecting targets of berberine-related targets, NSCLC-related targets, and DEGs were obtained. GO and KEGG analyses revealed that the intersecting targets were mainly implicated in oxidative stress, focal adhesion, and cell-substrate junction, as well as AGE-RAGE, relaxin, FoxO, and estrogen signaling pathways. Significantly, CAPN1, IKBKB, and SIRT2 were identified as the foremost autophagy-related targets, and 21 corresponding transcriptional factors were obtained. PPI network analysis showed that CAPN1, IKBKB, and SIRT2 interacted with 50 other genes. Fifty immune cell types, such as B cells naive, T cells CD8, T cells CD4 naive, T cells follicular helper, and monocytes, were implicated in NSCLC pathogenesis, and CAPN1, IKBKB, and SIRT2 were related to immune cells. Molecular docking revealed the favorable binding activity of berberine with CAPN1, IKBKB, and SIRT2. In vitro assays showed lower CAPN1, IKBKB, and SIRT2 expression in NSCLC cells than that in normal cells. Notably, berberine inhibited the viability and elevated CAPN1, IKBKB, and SIRT2 expression in NSCLC cells.

CONCLUSIONS

Berberine might treat NSCLC mainly by targeting CAPN1, IKBKB, and SIRT2.

Upregulation of nuclear division cycle 80 contributes to therapeutic resistance via the promotion of autophagy-related protein-7-dependent autophagy in lung cancer

Lung cancer remains the leading cause of malignant mortality worldwide. Hence, the discovery of novel targets that can improve therapeutic effects in lung cancer patients is an urgent need. In this study, we screened differentially expressed genes using isobaric tags for relative and absolute quantitation (iTRAQ) analysis and datasets from the cancer genome atlas database, and found that nuclear division cycle 80 (NDC80) might act as a novel prognostic indicator of lung cancer. The expression of NDC80 was significantly increased in lung cancer tissues, as compared to normal tissues, and high expression levels of NDC80 were correlated with unfavorable survival rates. Furthermore, an in vitro analysis showed that the stable knockdown of NDC80 decreased the cell viability and increased therapeutic sensitivity in two lung cancer cell lines, A549-IRR and H1246-IRR. Moreover, gene set enrichment analysis results showed that NDC80 was enriched in autophagy-related pathways. The downregulation of NDC80 inhibited the formation of autophagosomes, and reduced the expression of autophagy-related proteins such as LC3II, Beclin-1, and p62 in lung cancer cells. To further clarify the role of NDC80 as a downstream regulator of autophagy, we validated autophagic mediators through iTRAQ analysis and real-time polymerase chain reaction arrays. Autophagy-related protein7 (ATG7) was observed to be downregulated after the knockdown of NDC80 in lung cancer cells. Immunohistochemistry assay results revealed that both NDC80 and ATG7 were upregulated in an array of lung adenocarcinoma samples, compared to normal tissues, and the expression of NDC80 was identified to be positively associated with the levels of ATG7. Our findings suggest that NDC80 promotes the development of lung cancer by regulating autophagy, and might serve as a potential target for increasing the therapeutic sensitivity of lung cancer.

Fucoidan-derived carbon dots against Enterococcus faecalis biofilm and infected dentinal tubules for the treatment of persistent endodontic infections

Enterococcus faecalis (E. faecalis) biofilm-associated persistent endodontic infections (PEIs) are one of the most common tooth lesions, causing chronic periapical periodontitis, root resorption, and even tooth loss. Clinical root canal disinfectants have the risk of damaging soft tissues (e.g., mucosa and tongue) and teeth in the oral cavity, unsatisfactory to the therapy of PEIs. Nanomaterials with remarkable antibacterial properties and good biocompatibility have been developed as a promising strategy for removing pathogenic bacteria and related biofilm. Herein, carbon dots (CDs) derived from fucoidan (FD) are prepared through a one-pot hydrothermal method for the treatment of PEIs. The prepared FDCDs (7.15 nm) with sulfate groups and fluorescence property are well dispersed and stable in water. Further, it is found that in vitro FDCDs display excellent inhibiting effects on E. faecalis and its biofilm by inducing the formation of intracellular and extracellular reactive oxygen species and altering bacterial permeability. Importantly, the FDCDs penetrated the root canals and dentinal tubules, removing located E. faecalis biofilm. Moreover, the cellular assays show that the developed FDCDs have satisfactory cytocompatibility and promote macrophage recruitment. Thus, the developed FDCDs hold great potential for the management of PEIs.

Cell membrane-camouflaged inorganic nanoparticles for cancer therapy

Inorganic nanoparticles (INPs) have been paid great attention in the field of oncology in recent past years since they have enormous potential in drug delivery, gene delivery, photodynamic therapy (PDT), photothermal therapy (PTT), bio-imaging, driven motion, etc. To overcome the innate limitations of the conventional INPs, such as fast elimination by the immune system, low accumulation in tumor sites, and severe toxicity to the organism, great efforts have recently been made to modify naked INPs, facilitating their clinical application. Taking inspiration from nature, considerable researchers have exploited cell membrane-camouflaged INPs (CMCINPs) by coating various cell membranes onto INPs. CMCINPs naturally inherit the surface adhesive molecules, receptors, and functional proteins from the original cell membrane, making them versatile as the natural cells. In order to give a timely and representative review on this rapidly developing research subject, we highlighted recent advances in CMCINPs with superior unique merits of various INPs and natural cell membranes for cancer therapy applications. The opportunity and obstacles of CMCINPs for clinical translation were also discussed. The review is expected to assist researchers in better eliciting the effect of CMCINPs for the management of tumors and may catalyze breakthroughs in this area.