Transcriptomic analyses of genes differentially expressed by high-risk and low-risk human papilloma virus E6 oncoproteins

Modulation of Epstein-Barr-Virus (EBV)-Associated Cancers by Co-Infections

The oncogenic and persistent Epstein Barr virus (EBV) is carried by more than 95% of the human adult population. While asymptomatic in most of these, EBV can cause a wide variety of malignancies of lymphoid or epithelial cell origin. Some of these are also associated with co-infections that either increase EBV-induced tumorigenesis or weaken its immune control. The respective pathogens include Kaposi-sarcoma-associated herpesvirus (KSHV), Plasmodium falciparum and human immunodeficiency virus (HIV). In this review, I will discuss the respective tumor entities and possible mechanisms by which co-infections increase the EBV-associated cancer burden. A better understanding of the underlying mechanisms could allow us to identify crucial features of EBV-associated malignancies and defects in their immune control. These could then be explored to develop therapies against the respective cancers by targeting EBV and/or the respective co-infections with pathogen-specific therapies or vaccinations.

The Role of CTNNA1 in Malignancies: An Updated Review

Catenin alpha 1 (CTNNA1), encoding α-catenin, is involved in several physiological activities, such as adherens junction synthesis and signal transduction. Recent studies have suggested additional functions for CTNNA1 malignancies. This review systematically summarizes the varying functions of CTNNA1 in different tumors and briefly describes the diverse pathways and mechanisms involved in different types of tumors. CTNNA1 is abnormally expressed in leukemia and solid tumor such as cancers of digestive system, genitourinary system and breast, and it's related to the occurrence, development, and prognosis of tumors. In addition, the possible physiological processes involving CTNNA1, such as methylation, miRNA interference, or regulatory axes, similar to those of CDH1, SETD2, and hsa-miR-30d-5p/GJA1 are also summarized here. The precise mechanism of CTNNA1 in most cancers remains uncertain; hence, additional pre-clinical studies of CTNNA1 are warranted for potential early tumor diagnosis, prognosis, and treatment.

High-Risk Human Papillomavirus and Epstein-Barr Virus Coinfection: A Potential Role in Head and Neck Carcinogenesis

Simple Summary

A subset of carcinomas that arise in the head and neck region show a viral etiology. In fact, a subgroup of oropharyngeal cancers are caused by some types of human papillomavirus (HPV), so-called high-risk (HR)-HPVs, whereas undifferentiated nasopharyngeal carcinomas are etiologically related to Epstein–Barr virus (EBV). However, studies have reported the presence of both HR-HPV and EBV in some types of head and neck cancers. In this review, we discuss the potential contribution and role of HR-HPV/EBV coinfection in head and neck carcinogenesis, as well as the mechanisms that are potentially involved. In addition, HR-HPV/EBV interaction models are proposed.

Abstract

High-risk human papillomaviruses (HR-HPVs) and Epstein–Barr virus (EBV) are recognized oncogenic viruses involved in the development of a subset of head and neck cancers (HNCs). HR-HPVs are etiologically associated with a subset of oropharyngeal carcinomas (OPCs), whereas EBV is a recognized etiological agent of undifferentiated nasopharyngeal carcinomas (NPCs). In this review, we address epidemiological and mechanistic evidence regarding a potential cooperation between HR-HPV and EBV for HNC development. Considering that: (1) both HR-HPV and EBV infections require cofactors for carcinogenesis; and (2) both oropharyngeal and oral epithelium can be directly exposed to carcinogens, such as alcohol or tobacco smoke, we hypothesize possible interaction mechanisms. The epidemiological and experimental evidence suggests that HR-HPV/EBV cooperation for developing a subset of HNCs is plausible and warrants further investigation.

Effect of HPV 16 E6 Oncoprotein Variants on the Alterations of the Proteome of C33A Cells

BACKGROUND/AIM

The E6 genotypic variants of HPV 16 identified in lesions of women with cervical cancer (CC) in Southern of Mexico include the E-G350, AAa, AAc, E-C188/G350, and E-A176/G350, transcriptomic analysis cells transfected with those variants showed to induce differential expression of the host genes involved in the development of CC, the aim of this work was to understand how the over-expression of the E6 oncoprotein and its variants can induce molecular mechanisms that lead to more aggressive HPV 16 phenotypes in cervical cancer and which proteins could be associated with the process.

MATERIALS AND METHODS

Total extracts from C33A, C33A mock, C33A AAa, C33A E-C188/G350, C33A E-A176/G350, and C33A E-prototype cells were analyzed using 2D electrophoresis, PDQuest software and mass spectrometry, validation of results was performed through qPCR.

RESULTS

Statistically significant differential expression of 122 spots was detected, 12 of the identified proteins were associated with metabolism and metabolic programming. Out of these CCT8, ENO and ALDH1A were further validated.

CONCLUSION

CCT8 and ALDH1A were found to be over-expressed in C33A AAa and C33A E-A176/G350, compared to the E prototype. Both proteins could be associated with a most aggressive phenotype due to their relationship with metabolism, protein folding and stemness, mechanisms associated to E6 that could be useful in the design of new therapies.

Lectin-Like Transcript 1 (LLT1) Checkpoint: A Novel Independent Prognostic Factor in HPV-Negative Oropharyngeal Squamous Cell Carcinoma

Lectin-like transcript 1 (LLT1) expression by tumor cells contributes to immune evasion, thereby emerging as a natural killer (NK) cell-mediated immunotherapeutic target. This study is the first to investigate LLT1 expression (encoded by CLEC2D gene) in head and neck cancers to ascertain its impact on patient prognosis. LLT1 expression was analyzed by immunohistochemistry in a homogeneous cohort of human papillomavirus (HPV)-negative oropharyngeal squamous cell carcinomas (OPSCC), and correlated with clinical data. Results were further validated using transcriptomic data from the TCGA database. Tumoral LLT1 expression was detected in 190/221 (86%) OPSCC specimens, whereas normal pharyngeal epithelium was negative. Patients harboring LLT1-positive tumors showed significantly lower disease-specific (DSS) and overall survival (OS) (p = 0.049 and p = 0.036, respectively, log-rank test). High density of LLT1-positive tumor-infiltrating lymphocytes (TIL) was also frequently detected in 160 (73%) OPSCC samples, and significantly associated with better DSS and OS (p < 0.001 and p = 0.007, respectively). Multivariate Cox analysis further revealed that tumoral LLT1 expression and infiltration of LLT1-positive TIL were independent prognostic factors for DSS and OS. CLEC2D mRNA levels are also significantly increased in primary tumors compared to normal tissue. Strikingly, the prognostic impact of CLEC2D mRNA levels varied depending on HPV status in OPSCC, and among distinct cancer types. CLEC2D expression was significantly correlated with NK cell infiltration using the MCP-counter model. These findings uncover LLT1/CLEC2D as an independent prognostic factor in HPV-negative OPSCC, and a potential novel target for immunotherapy.

Analysis of Differentially Expressed Genes in a Chinese Cohort of Esophageal Squamous Cell Carcinoma

Esophageal squamous cell carcinoma (ESCC) is a leading malignancy in China with both high incidence and mortality. Towards improving outcomes, clinically-relevant biomarkers are urgently needed for use as prognostic and treatment targets. Herein we applied RNA-seq for deep sequencing of ten matched pairs of ESCC and adjacent non-cancerous tissues (NT) from Chinese patients. Transcriptomic data mapped to approximately 64% of all annotated genes with 2,047 and 708 unigenes being differentially up-regulated and down-regulated, respectively, between ESCCs and NT samples (p<0.05). Dividing cases by pathological grade revealed significant differentially expressed genes (DEG) between ESCC and NT in both low and high differentiation cases (p<0.05) whereas gene expression differences were not significantly different between high and low differentiation ESCC tissues (p=0.053). Moreover, the majority of ESCC and NT tissues formed clusters in principal component analyses. The veracity of the DEG list was validated in a larger cohort of 45 patient samples, with down-regulated CLIC3, up-regulated CLIC4 and unchanged expression of CLIC2 confirmed in ESCC using quantitative PCR and Western blotting. Our data reveal both previously identified ESCC biomarkers along with novel candidates and represent a ready resource of DEGs in ESCC for further investigation.

Transcriptome analysis of HPV-induced warts and healthy skin in humans

Background

The human papillomaviruses (HPV) are a group of viruses that, depending on the strain, can cause cancer or the formation of benign growths known as warts. Scarce information exists with regard to the genetic nature of non-genital cutaneous warts induced by the human papillomavirus (HPV).

Methods

The main purpose of this study is to investigate the differences between the gene expression profiles of common warts and healthy skin in HPV-positive individuals by RNA sequencing on the Illumina HiSeq 2500. After obtaining shave biopsies of common warts and healthy skin from twelve Arab males, we were able to analyze the transcriptomes of 24 paired cases and controls.

Results

Common warts were found to possess a highly significant and unique molecular signature. Many of the most up-regulated (KRT16, EPGN, and ABCG4) and down-regulated genes (C15orf59, CYB561A3, and FCGRT) in warts were the subject of little investigation in the published literature. Moreover, the top 500 differentially expressed genes were found to be associated with immune and autoimmune pathways, such as the neutrophil degranulation, toll-like receptor 7/8 (TLR 7/8) cascade, toll-like receptor 9 (TLR9) cascade, and toll-like receptor 10 (TLR10) pathways, among others.

Conclusions

Our findings are particularly important because they serve as the most comprehensive to date with regard to the modulation of human skin gene expression by HPV infection.

Expression profiling revealed keratins and interleukins as potential biomarkers in squamous cell carcinoma of horn in Indian bullocks (Bos indicus)

Horn cancer is most prevalent in Bos indicus and poorly defined genetic landscape makes disease diagnosis and treatment difficult. In this study, RNA-Seq and data analysis using CLC Genomics Workbench was employed to identify biomarkers associated with horn cancer. As a result, a total of 149 genes were found significant differentially expressed in horn cancer samples compared to horn normal samples. The study revealed 'keratins' and 'interleukins' as apex groups of significant differentially expressed genes (DEGs). Functional analysis showed that the upregulated keratins support metastasis of tumor via cell proliferation, migration, and affecting cell stability, while downregulated interleukins along with other associated chemokine receptors deprive the immune response to tumor posing clear path for metastasis of horn cancer. Combi-action of both the group facilitates the tumor microenvironment to reproduce tumorigenesis. Analysis of pathways enriched in DEGs and exemplified protein-protein interaction network indicated actual role of DEGs in horn cancer at a fine level. Important effect of deregulated expression of keratin and interleukin genes in horn cancer enrolling their candidacy as potential biomarkers for horn cancer prognosis. This study appraises the possibility to mitigate horn cancer at fine resolution to extract attainable identification of prognostic molecular portraits.

Human papillomavirus 16E6/E7 activates autophagy via Atg9B and LAMP1 in cervical cancer cells

BACKGROUNDS

Although the role of high-risk human papillomavirus (HPV) E6 and E7 in cellular malignant transformation has been elucidated， the function of both genes in cellular homeostasis is still unknown. Autophagy functions in maintenance of cellular homeostasis play a key role in the initiation and development of cancer and infectious disease.

METHODS

Cervical cancer cell lines SiHa and CaSki were utilized in this study.

RESULTS

We found that HPV 16E6/E7 (16E6/E7) downregulation inhibited autophagy, and consequently suppressed cell proliferation and promoted early apoptosis. Transcriptome sequencing demonstrated that Atg9B and LAMP1 were downregulated in 16E6/E7 knockdown cells. Gene function experiments revealed that 16E6/E7 downregulation depressed Atg9B and LAMP1, and Atg9B and LAMP1 overexpression compensated, at least partially, autophagy blockage induced by 16E6/E7 knockdown. Immunoprecipitation assay showed that 16E7 interacted with Atg9B and dual-luciferase reporter system revealed that 16E6 most likely regulated -1750 to -2000 nt in Atg9B and -1800 to -2000 nt in LAMP1 promoter region.

CONCLUSIONS

Our findings verified that 16E6/E7 activated autophagy via accelerating autophagosome formation and degradation, and Atg9B and LAMP1 were involved in the process of 16E6/E7 modulating autophagy, suggesting that targeting autophagy may be a potential approach in cervical cancer therapeutics.

Identifying the differentially expressed microRNAs in esophagus squamous cell carcinoma of Kazakh patients in Xinjiang

Despite improvements in diagnosis and treatment, the survival of patients with advanced stages of esophageal squamous cell carcinoma (ESCC) remains poor. Therefore, novel biomarkers that can assist with early detection of ESCC are required. In the present study, three paired ESCC and normal esophageal tissue samples from Xinjiang Kazakh patients were obtained and microRNA (miRNA) microarray analysis was used to detect the differentially-expressed miRNAs. The target genes of the identified miRNAs were predicted using miRWalk software. A total of 23 miRNAs were differently expressed in Kazakh patients with ESCC. Gene Ontology enrichment analysis demonstrated that the upregulated miRNAs were predominantly associated with the 'vesicle' and 'membrane-bounded vesicle' terms, while the downregulated miRNAs were primarily associated with the term 'negative regulation of integrin-mediated signaling pathway'. The most highly enriched Kyoto Encyclopedia of Genes and Genomes pathway for the differentially-expressed miRNAs was 'Endocrine and other factor-regulated calcium reabsorption'. Protein-protein interaction network analysis revealed that IQ motif containing GTPase activating protein 1, RAB11A, lysine acetyltransferase 2B, catenin α 1 and tight junction protein 2 were hub genes of the network. In conclusion, a number of differentially-expressed miRNAs were identified in ESCC tissues samples from Xinjiang Kazakh patients, which may improve the understanding of the processes of tumorigenesis and development.