Integrative analysis of single-cell and bulk RNA-sequencing data revealed T cell marker genes based molecular sub-types and a prognostic signature in lung adenocarcinoma.

Immunotherapy has emerged as a promising modality for addressing advanced or conventionally drug-resistant malignancies. When it comes to lung adenocarcinoma (LUAD), T cells have demonstrated significant influence on both antitumor activity and the tumor microenvironment. However, their specific contributions remain largely unexplored. This investigation aimed to delineate molecular subtypes and prognostic indicators founded on T cell marker genes, thereby shedding light on the significance of T cells in LUAD prognosis and precision treatment. The cellular phenotypes were identified by scrutinizing the single-cell data obtained from the GEO repository. Subsequently, T cell marker genes derived from single-cell sequencing analyses were integrated with differentially expressed genes from the TCGA repository to pinpoint T cell-associated genes. Utilizing Cox analysis, molecular subtypes and prognostic signatures were established and subsequently verified using the GEO dataset. The ensuing molecular and immunological distinctions, along with therapy sensitivity between the two sub-cohorts, were examined via the ESTIMATE, CIBERSORT, and ssGSEA methodologies. Compartmentalization, somatic mutation, nomogram development, chemotherapy sensitivity prediction, and potential drug prediction analyses were also conducted according to the risk signature. Additionally, real-time qPCR and the HPA database corroborated the mRNA and protein expression patterns of signature genes in LUAD tissues. In summary, this research yielded an innovative T cell marker gene-based signature with remarkable potential to prognosis and anticipate immunotherapeutic outcomes in LUAD patients.

Targeted delivery of organic small-molecule photothermal materials with engineered extracellular vesicles for imaging-guided tumor photothermal therapy.

Imaging-guided photothermal therapy (PTT) for cancers recently gathered increasing focus thanks to its precise diagnosis and potent therapeutic effectiveness. Croconaine (CR) dyes demonstrate potential in expanding utility for near infrared (NIR) dyes in bio-imaging/theranostics. However, reports on CR dyes for PTT are scarce most likely due to the short of the efficacious delivery strategies to achieve specific accumulation in diseased tissues to induce PTT. Extracellular vesicles (EVs) are multifunctional nanoparticle systems that function as safe platform for disease theragnostics, which provide potential benefits in extensive biomedical applications. Here, we developed a novel delivery system for photothermal molecules based on a CR dye that exerts photothermal activity through CDH17 nanobody-engineered EVs. The formed CR@E8-EVs showed strong NIR absorption, excellent photothermal performance, good biological compatibility and superb active tumor-targeting capability. The CR@E8-EVs can not only visualize and feature the tumors through CR intrinsic property as a photoacoustic imaging (PAI) agent, but also effectively retard the tumor growth under laser irradiation to perform PTT. It is expected that the engineered EVs will become a novel delivery vehicle of small organic photothermal agents (SOPTAs) in future clinical PTT applications.

Identification and validation of a m7G-related lncRNA signature for predicting the prognosis and therapy response in hepatocellular carcinoma.

BACKGROUND: N7-methylguanosine (m7G) is one of the most common RNA posttranscriptional modifications; however, its potential role in hepatocellular carcinoma (HCC) remains unknown. We developed a prediction signature based on m7G-related long noncoding RNAs (lncRNAs) to predict HCC prognosis and provide a reference for immunotherapy and chemotherapy. METHODS: RNA-seq data from The Cancer Genome Atlas (TCGA) database and relevant clinical data were used. Univariate and multivariate Cox regression analyses were conducted to identify m7G-related lncRNAs with prognostic value to build a predictive signature. We evaluated the prognostic value and clinical relevance of this signature and explored the correlation between the predictive signature and the chemotherapy treatment response of HCC. Moreover, an in vitro study to validate the function of CASC19 was performed. RESULTS: Six m7G-related lncRNAs were identified to create a signature. This signature was considered an independent risk factor for the prognosis of patients with HCC. TIDE analyses showed that the high-risk group might be more sensitive to immunotherapy. ssGSEA indicated that the predictive signature was strongly related to the immune activities of HCC. HCC in high-risk patients was more sensitive to the common chemotherapy drugs bleomycin, doxorubicin, gemcitabine, and lenalidomide. In vitro knockdown of CASC19 inhibited the proliferation, migration and invasion of HCC cells. CONCLUSION: We established a 6 m7G-related lncRNA signature that may assist in predicting the prognosis and response to chemotherapy and immunotherapy of HCC.

Nicotine promotes renal interstitial fibrosis via upregulation of XIAP in an alpha7-nAChR-dependent manner.

Renal fibrosis, characterized by excessive accumulation of the extracellular matrix in the renal tubulointerstitium, can lead to chronic kidney disease (CKD), resulting in a heavy burden on families and society. Clinical studies have shown that smoking is closely associated with CKD deterioration in patients with diabetes, hypertension, polycystic kidney disease, and kidney transplantation. However, the mechanism of action of nicotine in renal fibrosis pathogenesis remains largely unknown. X-linked inhibitor of apoptosis (XIAP), a member of the inhibitor of apoptosis protein (IAP) family, is involved in apoptosis, necroptosis, autophagy, and immune response. Here, the upregulated expression of XIAP and α7 nicotine acetylcholine receptor (α7-nAChR) was determined in the kidneys of the CKD smoking group in human and animal studies. A significant positive correlation between XIAP and cotinine was observed. In addition, the nuclear translocation and transcriptional activity of SP1 were promoted when nicotine bound to α7-nAChR, resulting in XIAP overexpression and renal interstitial fibrosis progression. This phenotype can be reversed by the nicotine receptor subtype α7-nAChR antagonists methyllycaconitine. Our results revealed the complex underlying mechanism of nicotine in promoting renal fibrosis by altering SP1 nucleocytoplasmic translocation and regulating XIAP expression. These results provide novel insights into the pathogenesis and treatment of CKD.

Integrated Analysis of Single-Cell RNA-Seq and Bulk RNA-Seq Combined with Multiple Machine Learning Identified a Novel Immune Signature in Diabetic Nephropathy.

Background: Increasing evidence suggests that immune modulation contributes to the pathogenesis and progression of diabetic nephropathy (DN). However, the role of immune modulation in DN has not been elucidated. The purpose of this study was to search for potential immune-related therapeutic targets and molecular mechanisms of DN. Methods: Gene expression datasets were obtained from the Gene Expression Omnibus (GEO) database. A total of 1793 immune-related genes were acquired from the Immunology Database and Analysis Portal (ImmPort). Weighted gene co-expression network analysis (WGCNA) was performed for GSE142025, and the red and turquoise co-expression modules were found to be key for DN progression. We utilized four machine learning algorithms, namely, random forest (RF), support vector machine (SVM), adaptive boosting (AdaBoost), and k-nearest neighbor (KNN), to evaluate the diagnostic value of hub genes. Immune infiltration patterns were analyzed using the CIBERSORT algorithm, and the correlation between immune cell type abundance and hub gene expression was also investigated. Results: A total of 77 immune-related genes of advanced DN were selected for subsequent analyzes. Functional enrichment analysis showed that the regulation of cytokine-cytokine receptor interactions and immune cell function play a corresponding role in the progression of DN. The final 10 hub genes were identified through multiple datasets. In addition, the expression levels of the identified hub genes were corroborated through a rat model. The RF model exhibited the highest AUC. CIBERSORT analysis and single-cell sequencing analysis revealed changes in immune infiltration patterns between control subjects and DN patients. Several potential drugs to reverse the altered hub genes were identified through the Drug-Gene Interaction database (DGIdb). Conclusion: This pioneering work provided a novel immunological perspective on the progression of DN, identifying key immune-related genes and potential drug targets, thus stimulating future mechanistic research and therapeutic target identification for DN.

[Roles of Histidine Kinases and Histidine Phosphatases in Cancer].

Phosphorylation is the most common and important post-translational modification of proteins, which plays an important role in the regulation of cell proliferation, differentiation, development and metabolism, and is closely related to the tumorigenesis and metastasis of cancer. Protein kinases and phosphatases generally regulate protein phosphorylation levels as a pair of opposite acting enzymes. Protein phosphorylation in eukaryotes occurs mainly in serine, threonine, and tyrosine residues, and their roles in tumorigenesis and development have been extensively studied. But the roles on histidine phosphorylation is less known due to the immature mass spectrometry and enrichment techniques. In recent years, with the rapid development of related technologies and the discovery of new histidine phosphatases, researchers have paid more attention to the roles of histidine phosphorylation in tumors. Therefore, we aim to review the roles of histidine kinases and phosphatases in tumor.
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Prognostic and immunological significance of metastasis associated lung adenocarcinoma transcript 1 among different kinds of cancers.

LncRNAs belong to the type of noncoding RNA transcripts, which exceed 200 nucleotides in size. MALAT1 as one of the earlier identified lncRNAs in cancer is investigated by more and more scientific researchers. Expression, clinical significance and function of MALAT1 in pan-cancer exist as big difference. To detect the expression and clinical significance of MALAT1 gene precisely and comprehensively among different kinds of cancers, some classical databases such as GEPIA, TIMER, KM Plotter, and PrognoScan were fully applied. An immunological role of MALAT1 among different kinds of cancers was also determined in TIMER database. Our results showed that MALAT1 was differently expressed in different kinds of cancers using GEPIA, Oncomine, and TIMER databases to analyze. Especially, MALAT1 high RNA level was related to the early stage in lung and gastric cancer patients. MALAT1 expression was closely related to prognosis among different cancer patients. Furthermore, expression of MALAT1 was related to tumor immune cell infiltrating. Expression level of MALAT1 was also related to immune makers such as macrophage, T cell, NK cells, and so on. These findings indicate that MALAT1 could be a potential prognostic biomarker of some kinds of cancer and was significantly correlated with tumor-infiltrating immune cells in a wide variety of cancers.

Facile synthesis of tribenzosilepins from terphenyls and dihydrosilanes by electrophilic double silylation.

Tribenzosilepins were synthesized from terphenyls and dihydrosilanes via a facile approach using a double sila-Friedel-Crafts reaction. Several silepin derivatives were obtained in moderate to high yield. The reaction system was found to be suitable for synthesizing a bidirectional silepin. Furthermore, the transformation of the amino groups of tribenzosilepin derivatives to aryl groups and the extension of the backbone π-system in tribenzosilepin were demonstrated.

Synthesis of six-membered silacycles by borane-catalyzed double sila-Friedel-Crafts reaction.

We have developed a catalytic synthetic method to prepare phenoxasilins. A borane-catalyzed double sila-Friedel-Crafts reaction between amino group-containing diaryl ethers and dihydrosilanes can be used to prepare a variety of phenoxasilin derivatives in good to excellent yields. The optimized reaction conditions were also applicable for diaryl thioethers to afford their corresponding six-membered silacyclic products. The gram-scale synthesis of a representative bis(dimethylamino)phenoxasilin and the transformation of its amino groups have also been demonstrated.

Lewis acid-catalyzed synthesis of silafluorene derivatives from biphenyls and dihydrosilanes via a double sila-Friedel-Crafts reaction.

The synthesis of silafluorene derivatives from aminobiphenyl compounds and dihydrosilanes via a double sila-Friedel-Crafts reaction using a borane catalyst has been achieved. This method is applicable to the synthesis of a variety of silafluorene derivatives, such as multisubstituted silafluorenes, spirosilabifluorenes, and silicon-bridged terphenyl compounds, which are not readily obtained using conventional synthetic methods. In addition, we have demonstrated the transformation of the amino groups in these silafluorene derivatives into other substituents.

Enhanced singlet oxygen generation of a soft salt through efficient energy transfer between two ionic metal complexes.

In this study, a soft salt complex based photosensitizer has been developed for photodynamic therapy (PDT) of cancer cells. The iridium(iii) complex [Ir(L)(L')]3+(PF6-)3 (C1) with L and L' being terpyridine ligands (L = 4'-phenyl-2,2':6',2''-terpyridine, L' = 3-([2,2':6',2''-terpyridin]-4'-yl)-9-hexyl-9H-carbazole) was chosen as the cationic component, and the iridium(iii) complex [Ir(dfppy)2CN2]-Bu4N+ (A1) was selected as the anionic component. Complexes C1 and A1 are directly connected through electrostatic interaction to form a soft salt based photosensitizer (S1), which exhibited an enhanced singlet oxygen generation rate because of efficient energy transfer between two ionic metal complexes. Furthermore, this novel photosensitizer was successfully applied in photodynamic therapy (PDT) of cancer cells for the first time.