Identification of an immune classification for cervical cancer and integrative analysis of multiomics data

The role of transforming growth factor-β (TGF-β) in the formation of exhausted CD8 + T cells

CD8 + T cells exert a critical role in eliminating cancers and chronic infections, and can provide long-term protective immunity. However, under the exposure of persistent antigen, CD8 + T cells can differentiate into terminally exhausted CD8 + T cells and lose the ability of immune surveillance and disease clearance. New insights into the molecular mechanisms of T-cell exhaustion suggest that it is a potential way to improve the efficacy of immunotherapy by restoring the function of exhausted CD8 + T cells. Transforming growth factor-β (TGF-β) is an important executor of immune homeostasis and tolerance, inhibiting the expansion and function of many components of the immune system. Recent studies have shown that TGF-β is one of the drivers for the development of exhausted CD8 + T cells. In this review, we summarized the role and mechanisms of TGF-β in the formation of exhausted CD8 + T cells and discussed ways to target those to ultimately enhance the efficacy of immunotherapy.

Sequencing-based transcriptome analysis reveals diversification of immune response- and angiogenesis-related expression patterns of early-stage cervical carcinoma as compared with high-grade CIN

Background

Molecular diversity of virus-associated cervical cancer remains a relatively underexplored issue, and interrelations of immunologic and angiogenic features during the establishment of a particular landscape of the cervical cancer microenvironment are not well-characterized, especially for its earliest clinical stages, although this may provide insight into the mechanisms behind the differences in tumor aggressiveness, treatment responsiveness and prognosis. In this research, we were aimed at identifying transcriptomic landscapes of early-stage cervical carcinoma that differ substantially in their immune-related characteristics, patterns of signaling pathways and composition of the microenvironment in comparison with immediate precursor (intraepithelial) lesions.

Methods

We performed the Illumina platform-based RNA sequencing using a panel of fresh tissue samples that included human papillomavirus-positive cervical intraepithelial neoplastic lesions (CIN), invasive squamous carcinoma of the cervix of FIGO IA1-IIB stages, and morphologically normal epithelium. The derived transcriptomic profiles were bioinformatically analyzed and compared by patterns of signaling pathway activation, distribution of tumor-infiltrating cell populations, and genomic regions involved.

Result

According to hierarchical cluster analysis of the whole-transcriptome profiles, tissue samples were distributed between three groups, or gene expression patterns (the one comprising most pre-cancer cases and the other two encompassing mostly early-stage invasive cancer cases). Differentially expressed genes were retrieved in each intergroup pairwise comparison followed by Gene Ontology analysis. Gene set enrichment analysis of the two groups of tumor samples in comparison with the CIN group identified substantial differences in immunological and angiogenic properties between tumorous groups suggesting the development of different molecular phenotypes. Cell composition analysis confirmed the diverse changes in the abundancies of immune and non-immune populations and, accordingly, different impacts of the immune and stromal compartments on the tumor microenvironment in these two groups of tumors compared to CIN. Positional gene expression analysis demonstrated that the identified transcriptomic differences were linked to different chromosomal regions and co-localized with particular gene families implicated in immune regulation, inflammation, cell differentiation, and tumor invasion.

Conclusions

Overall, detection of different transcriptomic patterns of invasive cervical carcinoma at its earliest stages supports the diverse impacts of immune response- and angiogenesis-related mechanisms on the onset of tumor invasion and progression. This may provide new options for broadening the applicability and increasing the efficiency of target anti-angiogenic and immune-based therapy of virus-associated cervical carcinoma.

Integrative analysis of gene expression and DNA methylation to identify biomarkers of non-genital warts induced by low-risk human papillomaviruses infection

Background

Human papillomaviruses have been shown to dysregulate the gene expression and DNA methylation profiles of their host cells over the course of infection. However, there is a lack of information on the impact of low-risk HPV infection and wart formation on host cell's expression and methylation patterns. Therefore, the objective of this study is to analyse the genome and methylome of common warts using an integrative approach.

Methods

In the present study, gene expression (GSE136347) and methylation (GSE213888) datasets of common warts were obtained from the GEO database. Identification of the differentially expressed and differentially methylated genes was carried out using the RnBeads R package and the edgeR Bioconductor package. Next, functional annotation of the identified genes was obtained using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). Network construction and analyses of the gene-gene, protein-protein, and signaling interactions of the differentially expressed and differentially methylated genes was performed using the GeneMANIA web interface, the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, and the Signaling Network Open Resource 2.0 (SIGNOR 2.0), respectively. Lastly, significant hub genes were identified using the Cytoscape application CytoHubba.

Results

A total of 276 genes were identified as differentially expressed and differentially methylated in common warts, with 52% being upregulated and hypermethylated. Functional enrichment analysis identified extracellular components as the most enriched annotations, while network analyses identified ELN, ITGB1, TIMP1, MMP2, LGALS3, COL1A1 and ANPEP as significant hub genes.

Conclusions

To the best knowledge of the authors, this is the first integrative study to be carried out on non-genital warts induced by low-risk HPV types. Future studies are required to re-validate the findings in larger populations using alternative approaches.

Upregulated X-C motif chemokine ligand 2 (XCL2) is associated with poor prognosis and increased immune infiltration in clear cell renal cell carcinoma

BACKGROUND

Clear cell renal cell carcinoma (ccRCC) is one of the most popular malignant carcinomas in the genitourinary system. As a novel tumor-related gene, X-C Motif Chemokine Ligand 2 (XCL2) was up-regulated in ccRCC. The current study aims to reveal the functional activity of XCL2 in ccRCC.

METHODS

The transcriptome profiling, clinical parameters, and simple nucleotide variation profiles of ccRCC samples were obtained from the Cancer Genome Atlas (TCGA) database. The survival analysis, multivariate/univariate Cox analysis, correlation analysis, gene set enrichment analysis (GSEA), and tumor mutation burden (TMB) analysis were performed. Next, immune cell infiltration and immune functions were analyzed. Finally, the functions of XCL2 were investigated in Caki-1 and 786-O cells.

RESULTS

Upregulated XCL2 was associated with worse overall survival of ccRCC and correlated to age, grade, stage, and T stage. Age, grade, and XCL2 were independent prognostic factors. Significant enrichment in apoptosis, DNA replication, and immune response was demonstrated by GSEA. XCL2 was not only tightly associated with immune cell infiltration, but also significantly linked with several immune functions. Moreover, patients, who had higher XCL2 expression, owned higher levels of TMB. Interestingly, XCL2 was positively correlated with common immune checkpoints. In vitro, XCL2 could inhibit apoptosis, and promote proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) of Caki-1 and 786-O cells.

CONCLUSIONS

In general, the current study suggested that XCL2 may participate in the progression of ccRCC. Importantly, XCL2 may be a potential new target of immunotherapy.

Netie: inferring the evolution of neoantigen-T cell interactions in tumors

Neoantigens are the key targets of antitumor immune responses from cytotoxic T cells and play a critical role in affecting tumor progressions and immunotherapy treatment responses. However, little is known about how the interaction between neoantigens and T cells ultimately affects the evolution of cancerous masses. Here, we develop a hierarchical Bayesian model, named neoantigen-T cell interaction estimation (netie) to infer the history of neoantigen-CD8⁺ T cell interactions in tumors. Netie was systematically validated and applied to examine the molecular patterns of 3,219 tumors, compiled from a panel of 18 cancer types. We showed that tumors with an increase in immune selection pressure over time are associated with T cells that have an activation-related expression signature. We also identified a subset of exhausted cytotoxic T cells postimmunotherapy associated with tumor clones that newly arise after treatment. These analyses demonstrate how netie enables the interrogation of the relationship between individual neoantigen repertoires and the tumor molecular profiles. We found that a T cell inflammation gene expression profile (TIGEP) is more predictive of patient outcomes in the tumors with an increase in immune pressure over time, which reveals a curious synergy between T cells and neoantigen distributions. Overall, we provide a new tool that is capable of revealing the imprints left by neoantigens during each tumor's developmental process and of predicting how tumors will progress under further pressure of the host's immune system.

The Detection and Verification of Two Heterogeneous Subgroups and a Risk Model Based on Ferroptosis-Related Genes in Hepatocellular Carcinoma

^#Background. Because of the heterogeneity of hepatocellular carcinoma (HCC) and the complex nature of the tumor microenvironment (TME), the long-term efficacy of therapy continues to be a clinical challenge. It is necessary to classify and refine the appropriate treatment intervention decision-making in this kind of tumor. Methods. We used “ConsensusClusterPlus” to establish a stable molecular classification based on the ferroptosis-related genes (FRGs) expression obtained from FerrDb. The clinical features, immune infiltration, DNA damage, and genomic changes of different subclasses were evaluated. The least absolute shrinkage and selection operator regression (LASSO) method and univariate Cox regression were utilized to construct the ferroptosis-related prognosis risk score (FPRS) model, and the association between the FPRS model and HCC molecular characteristics, immune features, and immunotherapy was studied. Results. We identified two ferroptosis subclasses, C1 with poor prognosis and a higher proportion of patients in the middle and late stages infected with HBV and HCV, having higher DNA damage including aneuploidy, HRD, fraction altered, and the number of segments, and higher probability of gene mutation and copy number mutation. FPRS model was constructed on the basis of differentially expressed genes (DEGs) between C1 and C2, which showed a higher area under the curve (AUC) in predicting overall survival rate in the training set and independent verification cohort and could reflect the clinical characteristics and response to immunotherapy of different patients, being an independent prognostic factor of HCC. Conclusion. Here, we revealed two novel molecular subgroups based on FRGs and develop an FPRS model consisting of six genes that can help predict prognosis and select patients suitable for immunotherapy.

piRNA-14633 promotes cervical cancer cell malignancy in a METTL14-dependent m6A RNA methylation manner

Background

Cervical cancer (CC) is one of the most common gynecological tumors that threatens women's health and lives. Aberrant expression of PIWI-interacting RNA (piRNA) is closely related with a range of cancers and can serve as a tumor promoter or suppressor in proliferation, migration and invasion. In this study, the aim was not only to discover differential expression of piRNA in CC tissue (CC cells) and normal cervical tissue (normal cervical epithelium cells), but also to investigate the biological function and action mechanism of piRNA in CC.

Methods

The DESeq2 approach was used to estimate fold change in piRNA between CC tissue and normal cervical tissue. The relative expressions of piRNAs (piRNA-20657, piRNA-20497, piRNA-14633 and piRNA-13350) and RNA m6A methyltransferases/demethylases were detected using RT-qPCR. After intervention with piRNA-14633 and METTL14 expression, the viability of CaSki cells and SiHa cells was detected by CCK8. CC cell proliferation was detected by colony formation assay. Apoptosis rate and cell cycle were detected by flow cytometry. Transwell assay was performed to detect cell migration and invasion. EpiQuik m6A RNA Methylation Quantification Kit was used to evaluate m6A RNA methylation levels. Expression of methyltransferase-like protein 14 (METTL14), PIWIL-proteins and CYP1B1 were detected by RT-qPCR and western blot. The effect of piRNA-14633 on METTL14 was evaluated by a dual-luciferase reporter assay. The in vivo effects of piRNA-14633 on CC was assessed by nude mice experiments.

Results

piRNA-14633 showed high expression in CC tissues and cells, piRNA-14633 mimic (piRNA-14633 overexpression) promoted viability, proliferation, migration and invasion of CaSki cells and SiHa cells. Besides, piRNA-14633 mimic increased m6A RNA methylation levels and METTL14 mRNA stability. Results of dual luciferase reporter assays indicated that METTL14 was a directed target gene of piRNA-14633. Knockdown of METTL14 with siRNA attenuated proliferation, migration and invasion of CC cells. piRNA-14633 increased CYP1B1 expression, while silencing of METTL14 impaired its expression. The effect of piRNA overexpression on METTL14 expression has concentration-dependent characteristics. Results from in vivo experiment indicated that piRNA-14633 promoted cervical tumor growth.

Conclusion

piRNA-14633 promotes proliferation, migration and invasion of CC cells by METTL14/CYP1B1 signaling axis, highlighting the important role of piRNA-14633 in CC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-022-03257-2.