Genome-Wide Profiling of Human Papillomavirus DNA Integration into Human Genome and Its Influence on PD-L1 Expression in Chinese Uygur Cervical Cancer Women

Preliminary study of HPV integration status on the occurrence and development of vaginal intraepithelial neoplasia

AIM

The aim of this study was to investigate how the integration status of HPV in the vaginal epithelium affects the development of vaginal intraepithelial neoplasia (VaIN).

METHODS

Twenty-four vaginal tissues were collected before applying high-throughput viral integration detection (HIVID), medical records of them were documented, including age, thin-prep cytologic test (TCT) and HPV test results, colposcopic biopsy pathology, and other clinical data, such as history of total hysterectomy for cervical lesions, whether they were infected with HPV16/18 with a follow-up span of 2 years. We summarized the distribution of HPV integration on the host chromosome and HPV type, as well as the hotspot integration gene and its role in the development of VaIN.

RESULTS

In this study, 24 cases suffered from VaIN were involved. HPV integration was detected in 11 cases; furthermore, we discovered HPV 16 and 73, chromosome 1 and 2 possessed most HPV integration sites while EMBP1, CLO5A1, EHF, ELF5 as dominate hot spots. Taken clinical outcome into account, we found a significant difference between HPV integration occurrence and VaIN (p = 0.011).

CONCLUSION

(1) This study found a statistical difference between HPV integration and the occurrence of VaIN; (2) HPV integration may provide a new clinical predictor for VaIN and facilitate risk assessment and stratified management of high-risk patients.

Identification of m6A-related lncRNAs-based signature for predicting the prognosis of patients with skin cutaneous melanoma

BACKGROUND

Skin cutaneous melanoma (SKCM) is one of the fastest developing malignancies with strong aggressive ability and no proper curative treatments. Numerous studies illustrated the importance of N6-methyladenosine (m6A) RNA modification to tumorigenesis. The aim of this study was to identify novel prognostic signature by using m6A-related lncRNAs, thus to improve the survival for SKCM patients and guide SKCM therapy.

METHODS

We downloaded the Presentational Matrix data from The Cancer Genome Atlas (TCGA) and analyzed all the expressed lncRNAs among 468 SKCM samples. Pearson correlation analysis was performed to assess the correlations between lncRNAs and 29 m6A-related genes. Least absolute shrinkage and selection operator (LASSO), univariate and multivariate Cox regression analysis were performed to construct m6A-related lncRNAs prognostic signature (m6A-LPS). The accuracy and prognostic value of this signature were validated by using receiver operating characteristic (ROC) curves, Kaplan-Meier (K-M) survival analysis, univariate COX or multivariate COX analyses. After calculating risk scores, patients were divided into low- and high-risk subgroups by the median value of risk scores.

RESULTS

A total of 2973 lncRNAs were found expressed among SKCM tissues. Prognostic analysis showed that 98 lncRNAs had a significant effect on the survival of SKCM patients. The m6A-LPS was validated using K-M and ROC analysis and the predictive accuracy of the risk score was also high according to the AUC of the ROC curve in training and testing sets. A nomogram based on tumor stage, gender and risk score that had a strong ability to forecast the 1-, 2-, 3-, 5-year OS of SKCM patients confirmed by calibrations. Enrichment analysis indicated that malignancy-associated biological processes and pathways were more common in the high-risk subgroup.

CONCLUSION

Collectively, m6A-related lncRNAs exert as potential biomarkers for prognostic stratification of SKCM patients and may assist clinicians achieving individualized treatment for SKCM.

Human papillomavirus associated cervical lesion: pathogenesis and therapeutic interventions

Human papillomavirus (HPV) is the most prevalent sexually transmitted virus globally. Persistent high-risk HPV infection can result in cervical precancerous lesions and cervical cancer, with 70% of cervical cancer cases associated with high-risk types HPV16 and 18. HPV infection imposes a significant financial and psychological burden. Therefore, studying methods to eradicate HPV infection and halt the progression of precancerous lesions remains crucial. This review comprehensively explores the mechanisms underlying HPV-related cervical lesions, including the viral life cycle, immune factors, epithelial cell malignant transformation, and host and environmental contributing factors. Additionally, we provide a comprehensive overview of treatment methods for HPV-related cervical precancerous lesions and cervical cancer. Our focus is on immunotherapy, encompassing HPV therapeutic vaccines, immune checkpoint inhibitors, and advanced adoptive T cell therapy. Furthermore, we summarize the commonly employed drugs and other nonsurgical treatments currently utilized in clinical practice for managing HPV infection and associated cervical lesions. Gene editing technology is currently undergoing clinical research and, although not yet employed officially in clinical treatment of cervical lesions, numerous preclinical studies have substantiated its efficacy. Therefore, it holds promise as a precise treatment strategy for HPV-related cervical lesions.

HECW2 promotes the progression and chemoresistance of colorectal cancer via AKT/mTOR signaling activation by mediating the ubiquitin-proteasome degradation of lamin B1

Colorectal cancer (CRC) is among the most common malignancies worldwide. Although a recent study has shown that E3 ubiquitin ligases play a major role in regulating the occurrence and development of CRC, there are few reports on the role of the E3 ubiquitin ligase HECW2(HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2) in CRC progression and chemoresistance. We found that HECW2 is highly expressed in CRC tissues. HECW2 knockdown inhibits CRC progression and chemoresistance, whereas HECW2 overexpression has the opposite effect. Mechanistically, HECW2 activates the AKT/mTOR signaling pathway by mediating the ubiquitin-proteasome degradation of lamin B1, thereby promoting CRC progression and chemoresistance. Our findings suggest that HECW2 may be a promising novel therapeutic target for CRC treatment.

Long-read sequencing reveals oncogenic mechanism of HPV-human fusion transcripts in cervical cancer

Integration of high-risk human papillomavirus (HPV) into the host genome is a crucial event for the development of cervical cancer, however, the underlying mechanism of HPV integration-driven carcinogenesis remains unknown. Here, we performed long-read RNA sequencing on 12 high-grade squamous intraepithelial lesions (HSIL) and cervical cancer patients, including 3 pairs of cervical cancer and corresponding para-cancerous tissue samples to investigate the full-length landscape of cross-species genome integrations. In addition to massive unannotated isoforms, transcriptional regulatory events, and gene chimerism, more importantly, we found that HPV-human fusion events were prevalent in HPV-associated cervical cancers. Combined with the genome data, we revealed the existence of a universal transcription pattern in these fusion events, whereby structurally similar fusion transcripts were generated by specific splicing in E6 and a canonical splicing donor site in E1 linking to various human splicing acceptors. Highly expressed HPV-human fusion transcripts, eg, HPV16 E6*I-E7-E1_SD880-human gene, were the key driver of cervical carcinogenesis, which could trigger overexpression of E6*I and E7, and destroy the transcription of tumor suppressor genes CMAHP, TP63 and P3H2. Finally, evidence from in vitro and in vivo experiments demonstrates that the novel read-through fusion gene mRNA, E1-CMAHP (E1C, formed by the integration of HPV58 E1 with CMAHP), existed in the fusion transcript can promote malignant transformation of cervical epithelial cells via regulating downstream oncogenes to participate in various biological processes. Taken together, we reveal a previously unknown mechanism of HPV integration-driven carcinogenesis and provide a novel target for the diagnosis and treatment of cervical cancer.

Direct Comparison of HPV16 Viral Genomic Integration, Copy Loss, and Structural Variants in Oropharyngeal and Uterine Cervical Cancers Reveal Distinct Relationships to E2 Disruption and Somatic Alteration

Squamous cell carcinoma of the oropharynx caused by HPV type 16 (HPV16+ OPSCC) is the most common HPV-associated malignancy in the USA and has many molecular differences from uterine cervical squamous cell carcinoma (UCSCC). Our understanding of HPV oncogenesis relied on studies of UCSCC revealing a consensus model reliant on HPV integration with a loss of E2. Here, we compare patterns of HPV integration in UCSCC and OPSCC by analysis of affinity capture sequencing of the HPV16 genome in 104 OPSCC and 44 UCSCC tumors. These cohorts were contemporaneously sequenced using an identical strategy. Integration was identified using discordant read pair clustering and assembly-based approaches. Viral integration sites, structural variants, and copy losses were examined. While large-scale deep losses of HPV16 genes were common in UCSCC and were associated with E2 loss, deep copy losses of the HPV16 genome were infrequent in HPV16+ OPSCC. Similarly, structural variants within HPV16 favored E2 loss in UCSCC but not OPSCC. HPV16 integration sites were non-random, with recurrent integration hot-spots identified. OPSCC tumors had many more integration sites per tumor when compared to UCSCC and had more integration sites in genomic regions with high gene density. These data show that viral integration and E2 disruption are distinct in UCSCC and OPSCC. Our findings also add to growing literature suggesting that HPV tumorigenesis in OPSCC does not follow the model developed based on UCSCC.

Modeling HPV-Associated Disease and Cancer Using the Cottontail Rabbit Papillomavirus

Approximately 5% of all human cancers are attributable to human papillomavirus (HPV) infections. HPV-associated diseases and cancers remain a substantial public health and economic burden worldwide despite the availability of prophylactic HPV vaccines. Current diagnosis and treatments for HPV-associated diseases and cancers are predominantly based on cell/tissue morphological examination and/or testing for the presence of high-risk HPV types. There is a lack of robust targets/markers to improve the accuracy of diagnosis and treatments. Several naturally occurring animal papillomavirus models have been established as surrogates to study HPV pathogenesis. Among them, the Cottontail rabbit papillomavirus (CRPV) model has become known as the gold standard. This model has played a pivotal role in the successful development of vaccines now available to prevent HPV infections. Over the past eighty years, the CRPV model has been widely applied to study HPV carcinogenesis. Taking advantage of a large panel of functional mutant CRPV genomes with distinct, reproducible, and predictable phenotypes, we have gained a deeper understanding of viral–host interaction during tumor progression. In recent years, the application of genome-wide RNA-seq analysis to the CRPV model has allowed us to learn and validate changes that parallel those reported in HPV-associated cancers. In addition, we have established a selection of gene-modified rabbit lines to facilitate mechanistic studies and the development of novel therapeutic strategies. In the current review, we summarize some significant findings that have advanced our understanding of HPV pathogenesis and highlight the implication of the development of novel gene-modified rabbits to future mechanistic studies.

Differential Long Non-Coding RNA Expression Analysis in Chronic Non-Atrophic Gastritis, Gastric Mucosal Intraepithelial Neoplasia, and Gastric Cancer Tissues

Gastric cancer (GC) has a high incidence worldwide, and when detected, the majority of patients have already progressed to advanced stages. Long non-coding RNAs (lncRNAs) have a wide range of biological functions and affect tumor occurrence and development. However, the potential role of lncRNAs in GC diagnosis remains unclear. We selected five high-quality samples from each group of chronic non-atrophic gastritis, gastric mucosal intraepithelial neoplasia, and GC tissues for analysis. RNA-seq was used to screen the differentially expressed lncRNAs, and we identified 666 differentially expressed lncRNAs between the chronic non-atrophic gastritis and GC groups, 13 differentially expressed lncRNAs between the gastric mucosal intraepithelial neoplasia and GC groups, and 507 differentially expressed lncRNAs between the chronic non-atrophic gastritis and gastric mucosal intraepithelial neoplasia groups. We also identified six lncRNAs (lncRNA H19, LINC00895, lnc-SRGAP2C-16, lnc-HLA-C-2, lnc-APOC1-1, and lnc-B3GALT2-1) which not only differentially expressed between the chronic non-atrophic gastritis and GC groups, but also differentially expressed between the gastric mucosal intraepithelial neoplasia and GC groups. Furthermore, RT-qPCR was used to verify the differentially co-expressed lncRNAs. LncSEA was used to conduct a functional analysis of differentially expressed lncRNAs. We also predicted the target mRNAs of the differentially expressed lncRNAs through bioinformatics analysis and analyzed targeting correlations between three differentially co-expressed lncRNAs and mRNAs (lncRNA H19, LINC00895, and lnc-SRGAP2C-16). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases were used to explore the functions of target mRNAs of differentially expressed lncRNAs. In conclusion, our study provides a novel perspective on the potential functions of differentially expressed lncRNAs in GC occurrence and development, indicating that the differentially expressed lncRNAs might be new biomarkers for early GC diagnosis.

Exosomes Isolated From Bone Marrow Mesenchymal Stem Cells Exert a Protective Effect on Osteoarthritis via lncRNA LYRM4-AS1-GRPR-miR-6515-5p

Objectives

The aim of this study was to investigate the effects of exosomes isolated from human bone marrow mesenchymal stem cells (BMSCs) on osteoarthritis (OA) and a competitive endogenous RNA (ceRNA) network.

Methods

Exosomes were isolated from human BMSCs and characterized by transmission electron microscopy (TEM), Nanosight (NTA), and western blotting. Chondrocytes were treated with interleukin-1β (IL-1β) and then transfected with exosomes. Cell viability and apoptosis were determined using Cell Counting Kit-8 (CCK-8) and flow cytometry, respectively. Cells with IL-1β and exosomes were sequenced, and differentially expressed lncRNAs (DE-lncRNAs) and miRNAs (DE-miRNAs) were identified. Thereafter, a ceRNA network (LYRM4-AS1-GRPR-miR-6515-5p) was chosen for further validation.

Results

TEM, NTA, and western blotting showed that exosomes were successfully isolated, and PKH67 staining showed that exosomes could be taken up by IL-1β-induced chondrocytes. Compared with the control group, IL-1β significantly decreased cell viability and promoted apoptosis (P < 0.05), while exosomes reversed the changes induced by IL-1β. For MMP3, AKT, and GRPR, IL-1β upregulated their expression, while exosomes downregulated their expression. For PTEN, there was no significant difference in PTEN expression between the control and IL-1β groups; however, exosomes markedly upregulated PTEN expression. By sequencing, 907 DE-lncRNAs and 25 DE-miRNAs were identified, and a ceRNA network was constructed. The dual-luciferase reporter gene indicated that LYRM4-AS1, miR-6515-5, and GRPR interacted with each other. The results of cell experiments showed that LYRM4-AS1 regulated the growth of IL-1β-induced chondrocytes by GRPR/miR-6515-5p.

Conclusion

Exosomes may alleviate OA inflammation by regulating the LYRM4-AS1/GRPR/miR-6515-5p signaling pathway.

HIVID2: an accurate tool to detect virus integrations in the host genome

MOTIVATION

Virus integration in the host genome is frequently reported to be closely associated with many human diseases, and the detection of virus integration is a critically challenging task. However, most existing tools show limited specificity and sensitivity. Therefore, the objective of this study is to develop a method for accurate detection of virus integration into host genomes.

RESULTS

Herein, we report a novel method termed HIVID2 that is a significant upgrade of HIVID. HIVID2 performs a paired-end combination (PE-combination) for potentially integrated reads. The resulting sequences are then remapped onto the reference genomes, and both split and discordant chimeric reads are used to identify accurate integration breakpoints with high confidence. HIVID2 represents a great improvement in specificity and sensitivity, and predicts breakpoints closer to the real integrations, compared with existing methods. The advantage of our method was demonstrated using both simulated and real data sets. HIVID2 uncovered novel integration breakpoints in well-known cervical cancer-related genes, including FHIT and LRP1B, which was verified using protein expression data. In addition, HIVID2 allows the user to decide whether to automatically perform advanced analysis using the identified virus integrations. By analyzing the simulated data and real data tests, we demonstrated that HIVID2 is not only more accurate than HIVID but also better than other existing programs with respect to both sensitivity and specificity. We believe that HIVID2 will help in enhancing future research associated with virus integration.

AVAILABILITY

HIVID2 can be accessed at https://github.com/zengxi-hada/HIVID2/.

CONTACT

Xi Zeng (zengxi@mail.hzau.edu.cn), Linghao Zhao (michael_yifan@126.com).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.