Tumor microenvironment RNA test to predict immunotherapy outcomes in advanced gastric cancer: The TIMES001 trial.

BACKGROUND: Clinical trials support the efficacy of immune checkpoint blockades (ICBs) plus chemotherapy in a subset of patients with metastatic gastric cancer (mGC). To identify the determinants of response, we developed a TMEscore model to assess tumor microenvironment (TME), which was previously proven to be a biomarker for ICBs. METHODS: A reference database of TMEscore assays was established using PCR assay kits containing 30 TME genes. This multi-center prospective clinical trial (NCT#04850716) included patients with mGC who were administered ICB combined with chemotherapy as a first-line regimen. Eighty-six tumor samples extracted from five medical centers before treatment were used to estimate the TMEscore, PD-L1 (CPS), and mismatch repair deficiency. FINDINGS: The objective response rate (ORR) and median PFS of the cohort were 31.4% and six months. Enhanced ORR was observed in TMEscore-high mGC patients (ORR = 59%). The survival analysis demonstrated that high TMEscore was significantly associated with a more favorable PFS and OS. Moreover, TMEscore was found to be a predictive biomarker that surpassed MSI and CPS (AUC = 0.873, 0.511, and 0.524, respectively). By integrating the TMEscore and clinical variables, the fused model further enhances the predictive efficiency and translational application in a clinical setting. CONCLUSIONS: This prospective clinical study indicates that the TMEscore assay is a robust biomarker for screening patients with mGC who may derive survival benefits from ICB plus chemotherapy. FUNDING: Guangdong Basic and Applied Basic Research Foundation (2023A1515011214), Science and Technology Program of Guangzhou (202206080011), and Guangzhou Science and Technology Project (2023A03J0722 and 2023A04J2357).

Nicotinamide metabolism face-off between macrophages and fibroblasts manipulates the microenvironment in gastric cancer.

Immune checkpoint blockade has led to breakthroughs in the treatment of advanced gastric cancer. However, the prominent heterogeneity in gastric cancer, notably the heterogeneity of the tumor microenvironment, highlights the idea that the antitumor response is a reflection of multifactorial interactions. Through transcriptomic analysis and dynamic plasma sample analysis, we identified a metabolic "face-off" mechanism within the tumor microenvironment, as shown by the dual prognostic significance of nicotinamide metabolism. Specifically, macrophages and fibroblasts expressing the rate-limiting enzymes nicotinamide phosphoribosyltransferase and nicotinamide N-methyltransferase, respectively, regulate the nicotinamide/1-methylnicotinamide ratio and CD8+ T cell function. Mechanistically, nicotinamide N-methyltransferase is transcriptionally activated by the NOTCH pathway transcription factor RBP-J and is further inhibited by macrophage-derived extracellular vesicles containing nicotinamide phosphoribosyltransferase via the SIRT1/NICD axis. Manipulating nicotinamide metabolism through autologous injection of extracellular vesicles restored CD8+ T cell cytotoxicity and the anti-PD-1 response in gastric cancer.

Synovial fluid exosome-derived miR-182-5p alleviates osteoarthritis by downregulating TNFAIP8 and promoting autophagy through LC3 signaling.

OBJECTIVE: To investigate the role of exosomal miRNAs from synovial fluid (SF) in osteoarthritis (OA) patients and investigate the underlying molecular mechanism. METHODS: Degenerated knee tissues were collected from male and female OA patients. Enzyme-linked immunosorbent assay (ELISA) was used to detect the differences in the expression of inflammatory indicators, including TNF-α, IL-6, and IL-10, between the degenerative and injury groups. Exosomes were isolated from SF using the Exoquick kit, and a microarray was used to identify differentially expressed miRNAs (DEmiRNAs), which were analyzed using bioinformatics. The predicted relationship between DEmiRNAs and target genes was verified using a luciferase reporter gene assay. CCK-8 and transwell assays were used to assess cell viability and migration. Immunofluorescence and TUNEL assay were used to detect cell autophagy and apoptosis. The interaction between proteins was detected by immunoprecipitation and verified by Mab rescue assay. RESULTS: The relative expression of TNF-α/IL6 was significantly higher in the degeneration group than in the injury group. The OA degeneration group released significantly more and smaller exosomes than the injury group. The expression of miR-182-5p was markedly reduced in OA patients and had a higher correlation with inflammatory indicators. Tumor necrosis factor α-induced protein 8 (TNFAIP8) was a target of miR-182-5p, and its overexpression promoted chondrocyte proliferation, migration, and invasion and enhanced the wound healing efficiency. We also found a direct interaction of TNFAIP8 with autophagy-related gene 3 (ATG3). TNFAIP8 triggered ATG3 LC3-mediated autophagy. CONCLUSION: The downregulation of exosomal miR-182-5p inhibits OA degeneration by targeting TNFAIP8 via the ATG/LC3 pathway.

Role of the cAMP-PKA-NF-κB pathway in Mucin1 over-expression in A549 cells during Respiratory syncytial virus infection.

Respiratory syncytial virus (RSV) is the most common pathogen associated with acute lower respiratory tract infections in infants and young children worldwide. RSV commonly presents as bronchiolitis in young children; however, it can sometimes progress to pneumonia, respiratory failure, apnoea and even death. Although mucin1 (MUC1), a type of transmembrane glycoprotein present on airway epithelial surfaces, plays a crucial anti-inflammatory role in airway infections; however, its roles in RSV-associated acute lower respiratory tract infections have rarely been explored. In this study, we first revealed very high MUC1 protein levels in the exacerbation phase in sputum samples from children with RSV bronchiolitis. Because MUC1 is the downstream target of tumour necrosis factor-alpha (TNF-α) in RSV-infected A549 cells, we observed the inhibition of NF-κB activity, main downstream signalling of TNF-α and remarkably reduced levels of MUC1 in RSV-infected and TNF-α treated A549 cells. Furthermore, the cyclic adenosine monophosphate (cAMP) analogue (dbcAMP) downregulated the protein levels of p-IκBα and MUC1 in TNF-α-treated A549 cells. By contrast, a protein kinase A inhibitor (KT5720) up-regulated the levels of those proteins. dbcAMP and KT5720 had the same effects on MUC1 protein levels in RSV-infected A549 cells. In conclusion, we found that the cAMP-PKA-NF-κB pathway may play a role in the regulation of MUC-1 over-expression during RSV infection.

Single-cell analysis of a tumor-derived exosome signature correlates with prognosis and immunotherapy response.

BACKGROUND: Tumor-derived exosomes (TEXs) are involved in tumor progression and the immune modulation process and mediate intercellular communication in the tumor microenvironment. Although exosomes are considered promising liquid biomarkers for disease diagnosis, it is difficult to discriminate TEXs and to develop TEX-based predictive biomarkers. METHODS: In this study, the gene expression profiles and clinical information were collected from The Cancer Genome Atlas (TCGA) database, IMvigor210 cohorts, and six independent Gene Expression Omnibus datasets. A TEXs-associated signature named TEXscore was established to predict overall survival in multiple cancer types and in patients undergoing immune checkpoint blockade therapies. RESULTS: Based on exosome-associated genes, we first constructed a tumor-derived exosome signature named TEXscore using a principal component analysis algorithm. In single-cell RNA-sequencing data analysis, ascending TEXscore was associated with disease progression and poor clinical outcomes. In the TCGA Pan-Cancer cohort, TEXscore was elevated in tumor samples rather than in normal tissues, thereby serving as a reliable biomarker to distinguish cancer from non-cancer sources. Moreover, high TEXscore was associated with shorter overall survival across 12 cancer types. TEXscore showed great potential in predicting immunotherapy response in melanoma, urothelial cancer, and renal cancer. The immunosuppressive microenvironment characterized by macrophages, cancer-associated fibroblasts, and myeloid-derived suppressor cells was associated with high TEXscore in the TCGA and immunotherapy cohorts. Besides, TEXscore-associated miRNAs and gene mutations were also identified. Further experimental research will facilitate the extending of TEXscore in tumor-associated exosomes. CONCLUSIONS: TEXscore capturing tumor-derived exosome features might be a robust biomarker for prognosis and treatment responses in independent cohorts.

Tumor microenvironment evaluation promotes precise checkpoint immunotherapy of advanced gastric cancer.

BACKGROUND: Durable efficacy of immune checkpoint blockade (ICB) occurred in a small number of patients with metastatic gastric cancer (mGC) and the determinant biomarker of response to ICB remains unclear. METHODS: We developed an open-source TMEscore R package, to quantify the tumor microenvironment (TME) to aid in addressing this dilemma. Two advanced gastric cancer cohorts (RNAseq, N=45 and NanoString, N=48) and other advanced cancer (N=534) treated with ICB were leveraged to investigate the predictive value of TMEscore. Simultaneously, multi-omics data from The Cancer Genome Atlas of Stomach Adenocarcinoma (TCGA-STAD) and Asian Cancer Research Group (ACRG) were interrogated for underlying mechanisms. RESULTS: The predictive capacity of TMEscore was corroborated in patient with mGC cohorts treated with pembrolizumab in a prospective phase 2 clinical trial (NCT02589496, N=45, area under the curve (AUC)=0.891). Notably, TMEscore, which has a larger AUC than programmed death-ligand 1 combined positive score, tumor mutation burden, microsatellite instability, and Epstein-Barr virus, was also validated in the multicenter advanced gastric cancer cohort using NanoString technology (N=48, AUC=0.877). Exploration of the intrinsic mechanisms of TMEscore with TCGA and ACRG multi-omics data identified TME pertinent mechanisms including mutations, metabolism pathways, and epigenetic features. CONCLUSIONS: Current study highlighted the promising predictive value of TMEscore for patients with mGC. Exploration of TME in multi-omics gastric cancer data may provide the impetus for precision immunotherapy.

IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures.

Recent advances in next-generation sequencing (NGS) technologies have triggered the rapid accumulation of publicly available multi-omics datasets. The application of integrated omics to explore robust signatures for clinical translation is increasingly emphasized, and this is attributed to the clinical success of immune checkpoint blockades in diverse malignancies. However, effective tools for comprehensively interpreting multi-omics data are still warranted to provide increased granularity into the intrinsic mechanism of oncogenesis and immunotherapeutic sensitivity. Therefore, we developed a computational tool for effective Immuno-Oncology Biological Research (IOBR), providing a comprehensive investigation of the estimation of reported or user-built signatures, TME deconvolution, and signature construction based on multi-omics data. Notably, IOBR offers batch analyses of these signatures and their correlations with clinical phenotypes, long non-coding RNA (lncRNA) profiling, genomic characteristics, and signatures generated from single-cell RNA sequencing (scRNA-seq) data in different cancer settings. Additionally, IOBR integrates multiple existing microenvironmental deconvolution methodologies and signature construction tools for convenient comparison and selection. Collectively, IOBR is a user-friendly tool for leveraging multi-omics data to facilitate immuno-oncology exploration and to unveil tumor-immune interactions and accelerating precision immunotherapy.

Transfers of the Ipsilateral C7 Plus the Spinal Accessory Nerve Versus Triple Nerve Transfers for Treatment of C5-C6 Avulsion of the Brachial Plexus.

PURPOSE: To compare the long-term results of transfers of the ipsilateral C7 (IC7) plus spinal accessory nerve (SAN) with those of triple nerve transfers (TNT) using one fascicle of the ulnar nerve to the biceps motor branch (Oberlin's procedure), SAN transferred to the suprascapular nerve, and transfer of the long head of triceps nerve branch to the anterior branch of axillary nerve to treat C5-C6 avulsion of the brachial plexus. METHODS: The IC7 group included 9 patients undergoing transfers of IC7 to the upper trunk and SAN to the suprascapular nerve. Median age at surgery was 26 years and interval between injury and surgery was 2.8 months. Patients were observed for a median of 118 months. The TNT group contained 13 patients, median age 33 years; interval between injury and surgery was 3.1 months. Patients were observed for a median of 103 months. RESULTS: In the IC7 group, median shoulder abduction was 105° and median external rotation of the shoulder was 64°, which was similar to that of the TNT group (89° abduction and 58° external rotation). Eight of nine patients recovered at least M3 (Modified Narakas scale) strength of deltoid in the IC7 group, which was similar to that in the TNT group (11 of 13 patients). Six of nine patients achieved at least Medical Research Council grade 3 (MRC3) strength of biceps in the IC7 group, which was similar to that in the TNT group (11 of 13 patients). Of 4 patients in the IC7 group with a preoperative latissimus dorsi strength of MRC3 or less, 3 gained a deltoid strength of M3 or less, and 3 a biceps strength of MRC2 or less. CONCLUSIONS: Transfers of IC7 plus SAN provide results comparable to those of TNT for treatment of C5-C6 avulsion. TYPE OF STUDY/LEVEL OF EVIDENCE: Therapeutic IV.

The characterization of lung microbiome in lung cancer patients with different clinicopathology.

There were few knowledge concerned correlation between lung microbiome and different clinicopathology of lung cancer. Bronchial washing fluid (BWF) and sputum are commonly used sample types but there was no study comparing difference of microbiome between these two in lung cancer. In this study, we aimed to compare difference of microbiome between these two sample types and characterize lung microbiome in squamous cell lung carcinoma with (SCC_M1) or without distant metastasis (SCC_M0) and lung adenocarcinoma with (AD_M1) or without distant metastasis (AD_M0). We collected 40 BWF samples and 52 sputum samples from newly diagnosed lung cancer patients. Bacterial species were sequenced via 16S rRNA sequencing. Phylum Proteobacteria in BWF samples were significantly higher than sputum samples (Wilcoxon test, P = 0.003). At phylum level, microbiome of BWF samples was more similar to that of lung cancer tissues reported in the previous literature. LEFse analysis showed that in BWF group, genera Veillonell, Megasphaera, Actinomyces and Arthrobacter in AD_M0 were significantly higher than those in SCC_M0, and genera Capnocytophaga and Rothia in AD_M1 were significantly lower than that in SCC_M1. Compared with AD_M0, genus Streptococcus of AD_M1 was significantly lower, and genera Veillonella and Rothia in SCC_M1 were significantly higher than that in SCC_M1. Our study suggested that BWF samples might better reflect the microbiome of lung cancer tissues. In different metastatic states of lung cancer, differential genera between squamous cell carcinoma and adenocarcinoma were different. And in different histologic types of lung cancer, distant metastasis-related genera were not the same.

MicroRNA-27a alleviates IL-1ß-induced inflammatory response and articular cartilage degradation via TLR4/NF-κB signaling pathway in articular chondrocytes.

Osteoarthritis (OA) is a common disease of the articular cartilage, and inflammatory response and articular cartilage degradation have been implicated in the pathogenesis of OA. In recent years, microRNAs (miRNAs) have been potentially involved in the pathogenesis of OA. However, little is known about the role of miRNAs in the inflammatory response and articular cartilage degradation in OA and the underlying molecular mechanism. In the present study, we analyze miRNA profiles in the articular tissues from OA patients using microarray. miR-27a has attracted considerable interest for its suppressive effects on inflammation. Subsequently, the expression levels of miR-27a were validated in the articular tissues of OA patients and IL-1ß-stimulated chondrocytes. Using this IL-1ß-induced chondrocyte injury model, we found that upregulation of miR-27a suppressed articular cartilage degradation, the reactive oxygen species (ROS) production and inflammatory response as reflected by reductions in pro-inflammatory cytokines, including interleukin (IL)-6 and IL-8 and tumor necrosis factor (TNF)-α. Moreover, toll-like receptor 4 (TLR4), one upstream molecule of NF-κB signaling pathway, was identified as a direct target of miR-27a in chondrocytes. Furthermore, it was demonstrated that overexpression of TLR4 by pcDNA-TLR4 markedly abrogated the inhibitory effects of miR-27a on the inflammatory response and the degeneration of articular cartilage induced by IL-1ß. Our findings suggest that miR-27a may be considered as a potential therapeutic target in the treatment of OA.

Involvement of Notch1/Hes signaling pathway in ankylosing spondylitis.

We aimed to investigate the role of Notch1/Hes signaling pathway in the pathogenesis of abnormal ossification of hip ligament in patients with ankylosing spondylitis (AS). 22 AS patients scheduled for artificial hip arthroplasty were randomly chosen as AS group. As controls, we used 4 patients diagnosed with transcervical fracture who underwent hip replacement surgery. Notch1 and Hes mRNA expressions were detected by real-time fluorescent quantitative polymerase chain reaction (RFQ-PCR). Immunohistochemistry (IHC) was used to detect Notch1 and Hes protein expression. Correlation analyses of Notch-l and Hes with AS-related clinical factors were conducted with spearman's correlation analysis and partial correlation analysis. RFQ-PCR results showed significant differences in Notch1 and Hes mRNA expressions between AS group and the control group (all P<0.05). IHC analysis further indicated positive nuclear signals of Notch1 and Hes protein, indicating functional activation of the Notch1 and Hes pathways. Semi-quantitative IHC showed a higher Notch1 and Hes expression levels in AS group compared to the control group (all P<0.05). Correlation analysis suggested that Hes protein expression was positively associated with the clinical course of the disease in AS patients. In conclusion, Notch1 and Hes overexpression was clearly detected in hip joint ligaments of AS patients, Hes protein expression was associated with the clinical course of AS. Taken together, we suggest that signaling pathways mediated by Notch1-Hes may contribute to ligament ossification of hip joints in AS patients.