Immune-related miRNA signature identifies prognosis and immune landscape in head and neck squamous cell carcinomas

A novel ferroptosis-related microRNA signature with prognostic value in osteosarcoma

The induction of ferroptosis is suggested to be a potential therapeutic strategy for cancers. MicroRNAs (miRNAs) are reported to play an important role in cell death processes. This study aims to construct and validate a risk model based on ferroptosis-related miRNAs (FR_miRNAs) to predict prognosis and identify novel therapeutic targets for osteosarcoma. Data from the Therapeutically Applicable Research to Generate Effective Treatments database are used as the training cohort. A prognostic signature based on two FR_miRNAs (miR-635 and miR-593) is developed using univariate Cox regression, least absolute shrinkage and selection operator regression, and multivariate Cox regression analyses. The area under the curve values of the prognostic signature to predict the 1-year, 2-year, 3-year, and 5-year overall survival rates in patients with osteosarcoma are 0.782, 0.781, 0.722, and 0.777, respectively, indicating a good predictive ability. Based on the risk score, patients are divided into low-risk and high-risk groups. Patients with high-risk scores are associated with poor survival. The risk level is determined to be an independent prognostic factor. A nomogram is established for predicting prognosis. The expression levels of PRNP (miR-635-related ferroptosis-related gene (FRG); P=0.024) and HILPDA (miR-593-related FRG; P=0.025) are significantly different between the low-risk and high-risk groups. All results are validated in an external cohort (GSE39040). The results of the functional assay reveal that miR-635 mimics inhibit osteosarcoma (OS) cell proliferation and migration, whereas miR-593 overexpression exerts the opposite effect. In conclusion, miR-635 and miR-593 exert contrasting regulatory effects on OS cell proliferation and migration.

Identification and verification of m6A-related miRNAs correlated with prognosis and immune microenvironment in colorectal cancer

It's well known that N6-methyladenosine (m6A) modification is the most abundant modification in multiple RNA species. miRNAs play important roles in m6A modification and are closely related with occurrence and development of colorectal cancer (CRC). Thus, the aim of this study was to identify the prognostic value of m6A-related miRNAs and explore the correlation between the miRNAs and immune microenvironment in CRC. The differentially expressed m6A regulators and differentially expressed miRNAs between CRC tissues and adjacent normal tissues were identified based on TCGA dataset, and the m6A-related miRNAs were screened. The CRC patients from TCGA were randomized (1:1) into training set and validation set, and the risk score was established in the training set. Next, risk score was verified in the validation set and GSE92928 from GEO datasets. Besides, the relationship among tumor mutational burden, immune microenvironment and risk score were analyzed. What's more, RT-qPCR were used to explore the expression levels of the miRNAs in risk score between SW480 and SW620. A total of 29 m6A-related miRNAs were screened out, and a 5-differentially expressed miRNAs risk score was established. Kaplan-Meier analysis and ROC curves revealed the risk score could predict the prognosis of CRC, accurately. Similarly, the patients in the high-risk group had shorter overall survival in GSE92928. The risk score was relevant with the tumor mutational burden and immune infiltration, and the expression of HAVCR2 was significant difference between 2 risk groups. The expression levels of miR-328-3p, miR-3934-5p, miR-664b-5p and miR-3677-3p were down-regulated in SW620 compared with SW480, only the expression level of miR-200c-5p was up-regulated in SW620. The findings provided the new insights into the correlation between miRNAs and m6A regulators. The m6A-related miRNAs could predict the prognosis of CRC and provide the valuable information of immunotherapy in CRC patients.

Comprehensive Analysis of mTORC1 Signaling Pathway–Related Genes in the Prognosis of HNSCC and the Response to Chemotherapy and Immunotherapy

Objective: The mammalian target of the rapamycin complex 1 (mTORC1) signaling pathway has emerged as a crucial player in the oncogenesis and development of head and neck squamous cell carcinoma (HNSCC), however, to date, no relevant gene signature has been identified. Therefore, we aimed to construct a novel gene signature based on the mTORC1 pathway for predicting the outcomes of patients with HNSCC and their response to treatment.

Methods: The gene expression and clinical data were retrieved from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The key prognostic genes associated with the mTORC1 pathway were screened by univariate Cox regression analyses. A prognostic signature was then established based on significant factors identified in the multivariate Cox regression analysis. The performance of the multigene signature was evaluated by the Kaplan–Meier (K–M) survival analysis and receiver operating characteristic (ROC) analysis. Based on the median risk score, patients were categorized into high- and low-risk groups. Subsequently, a hybrid prognostic nomogram was constructed and estimated by a calibration plot and decision curve analysis. Furthermore, immune cell infiltration and therapeutic responses were compared between the two risk groups. Finally, we measured the expression levels of seven genes by quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC).

Results: The mTORC1 pathway–based signature was constructed using the seven identified genes (SEC11A, CYB5B, HPRT1, SLC2A3, SC5D, CORO1A, and PIK3R3). Patients in the high-risk group exhibited a lower overall survival (OS) rate than those in the low-risk group in both datasets. Through the univariate and multivariate Cox regression analyses, this gene signature was confirmed to be an independent prognostic risk factor for HNSCC. The constructed nomogram based on age, American Joint Committee on Cancer (AJCC) stage, and the risk score exhibited satisfactory performance in predicting the OS. In addition, immune cell infiltration and chemotherapeutic and immunotherapeutic responses differed significantly between the two risk groups. The expression levels of SEC11A and CYB5B were higher in HNSCC tissues than in normal tissues.

Conclusion: Our study established and verified an mTORC1 signaling pathway–related gene signature that could be used as a novel prognostic factor for HNSCC.

MED10 Drives the Oncogenicity and Refractory Phenotype of Bladder Urothelial Carcinoma Through the Upregulation of hsa-miR-590

Background

Dysfunctional transcription machinery with associated dysregulated transcription characterizes many malignancies. Components of the mediator complex, a principal modulator of transcription, are increasingly implicated in cancer. The mediator complex subunit 10 (MED10), a vital kinase module of the mediator, plays a critical role in bladder physiology and pathology. However, its role in the oncogenicity, metastasis, and disease recurrence in bladder cancer (BLCA) remains unclear.

Objective

Thus, we investigated the role of dysregulated or aberrantly expressed MED10 in the enhanced onco-aggression, disease progression, and recurrence of bladder urothelial carcinoma (UC), as well as the underlying molecular mechanism.

Methods

Using an array of multi-omics big data analyses of clinicopathological data, in vitro expression profiling and functional assays, and immunocytochemical staining, we assessed the probable roles of MED10 in the progression and prognosis of BLCA/UC.

Results

Our bioinformatics-aided gene expression profiling showed that MED10 is aberrantly expressed in patients with BLCA, is associated with high-grade disease, is positively correlated with tumor stage, and confers significant survival disadvantage. Reanalyzing the TCGA BLCA cohort (n = 454), we showed that aberrantly expressed MED10 expression is associated with metastatic and recurrent disease, disease progression, immune suppression, and therapy failure. Interestingly, we demonstrated that MED10 interacts with and is co-expressed with the microRNA, hsa-miR-590, and that CRISPR-mediated knockout of MED10 elicits the downregulation of miR-590 preferentially in metastatic UC cells, compared to their primary tumor peers. More so, silencing MED10 in SW1738 and JMSU1 UC cell lines significantly attenuates their cell proliferation, migration, invasion, clonogenicity, and tumorsphere formation (primary and secondary), with the associated downregulation of BCL-xL, MKI67, VIM, SNAI1, OCT4, and LIN28A but upregulated BAX protein expression. In addition, we showed that high MED10 expression is a non-inferior biomarker of urothelial recurrence compared with markers of cancer stemness; however, MED10 is a better biomarker of local recurrence than any of the stemness markers.

Conclusion

These data provide preclinical evidence that dysregulated MED10/MIR590 signaling drives onco-aggression, disease progression, and recurrence of bladder UC and that this oncogenic signal is therapeutically actionable for repressing the metastatic/recurrent phenotypes, enhancing therapy response, and shutting down stemness-driven disease progression and relapse in patients with BLCA/UC.

Identification of miR-203a, mir-10a, and miR-194 as predictors for risk of lymphovascular invasion in head and neck cancers

Lymphovascular invasion (LVI) is an important prognostic indicator of lymph node metastasis and disease aggressiveness but clear molecular mechanisms mediating this in head and neck cancers (HNSC) remain undefined. To identify important microRNAs (miRNAs) in HNSC that associate with and are also predictive of increased risk of LVI, we used a combination of clustering algorithms, multiple regression analyses and machine learning approaches and analyzed miRNA expression profiles in the TCGA HNSC database. As the first step, we identified miRNAs with increased association with LVI as a binary variable. In order to determine whether the identified miRNAs would show functional clusters that are also indicative of increased risk for LVI, we carried out unsupervised as well as supervised clustering. Our results identified distinct clusters of miRNAs that are predictive of increased LVI. We further refined these findings using a Random forest approach, and miR-203a-3p, mir-10a-5p, and miR-194-5p to be most strongly associated with LVI. Pathway enrichment analysis showed these miRNAs targeted genes involved in Hippo signaling and fatty acid oxidation pathways that are mediators of lymph node metastasis. Specific association was also identified between the miRNAs associated with LVI and expression of several lymphangiogenic genes that could be critical for determination of therapeutic strategies.

MicroRNA-1: Diverse role of a small player in multiple cancers

The process of cancer initiation and development is a dynamic and complex mechanism involving multiple genetic and non-genetic variations. With the development of high throughput techniques like next-generation sequencing, the field of cancer biology extended beyond the protein-coding genes. It brought the functional role of noncoding RNAs into cancer-associated pathways. MicroRNAs (miRNAs) are one such class of noncoding RNAs regulating different cancer development aspects, including progression and metastasis. MicroRNA-1 (miR-1) is a highly conserved miRNA with a functional role in developing skeletal muscle precursor cells and cardiomyocytes and acts as a consistent tumor suppressor gene. In humans, two discrete genes, MIR-1-1 located on 20q13.333 and MIR-1-2 located on 18q11.2 loci encode for a single mature miR-1. Downregulation of miR-1 has been demonstrated in multiple cancers, including lung, breast, liver, prostate, colorectal, pancreatic, medulloblastoma, and gastric cancer. A vast number of studies have shown that miR-1 affects the hallmarks of cancer like proliferation, invasion and metastasis, apoptosis, angiogenesis, chemosensitization, and immune modulation. The potential therapeutic applications of miR-1 in multiple cancer pathways provide a novel platform for developing anticancer therapies. This review focuses on the different antitumorigenic and therapeutic aspects of miR-1, including how it regulates tumor development and associated immunomodulatory functions.

Construction of a Prognostic Gene Signature Associated with Immune Infiltration in Glioma: A Comprehensive Analysis Based on the CGGA

Background

Tumor microenvironment (TME) is closely related to the progression of glioma and the therapeutic effect of drugs on this cancer. The aim of this study was to develop a signature associated with the tumor immune microenvironment using machine learning.

Methods

We downloaded the transcriptomic and clinical data of glioma patients from the Chinese Glioma Genome Atlas (CGGA) databases (mRNAseq_693). The single-sample Gene Set Enrichment Analysis (ssGSEA) database was used to quantify the relative abundance of immune cells. We divided patients into two different infiltration groups via unsupervised clustering analysis of immune cells and then selected differentially expressed genes (DEGs) between the two groups. Survival-related genes were determined using Cox regression analysis. We next randomly divided patients into a training set and a testing set at a ratio of 7 : 3. By integrating the DEGs into least absolute shrinkage and selection operator (LASSO) regression analysis in the training set, we were able to construct a 15-gene signature, which was validated in the testing and total sets. We further validated the signature in the mRNAseq_325 dataset of CGGA.

Results

We identified 74 DEGs associated with tumor immune infiltration, 70 of which were significantly associated with overall survival (OS). An immune-related gene signature was established, consisting of 15 key genes: adenosine triphosphate (ATP)-binding cassette subfamily C member 3 (ABCC3), collagen type IV alpha 1 chain (COL4A1), podoplanin (PDPN), annexin A1 (ANXA1), COL4A2, insulin-like growth factor binding protein 2 (IGFBP2), serpin family A member 3 (SERPINA3), CXXC-type zinc finger protein 11 (CXXC11), junctophilin 3 (JPH3), secretogranin III (SCG3), secreted protein acidic and rich in cysteine (SPARC)-related modular calcium-binding protein 1 (SMOC1), Cluster of Differentiation 14 (CD14), COL1A1, S100 calcium-binding protein A4 (S100A4), and transforming growth factor beta 1 (TGF-β1). The OS of patients in the high-risk group was worse than that of patients in the low-risk group. GSEA showed that interleukin-6 (IL-6)/Janus kinase (JAK)/signal transducer and activator of transcription (STAT3) signaling, interferon gamma (IFN-γ) response, angiogenesis, and coagulation were more highly enriched in the high-risk group and that oxidative phosphorylation was more highly enriched in the low-risk group.

Conclusion

We constructed a stable gene signature associated with immune infiltration to predict the survival rates of glioma patients.