The synergistic interaction landscape of chromatin regulators reveals their epigenetic regulation mechanisms across five cancer cell lines

Cao, Meng; Wang, Liqiang; Xu, Dahua; Bi, Xiaoman; Guo, Shengnan; Xu, Zhizhou; Chen, Liyang; Zheng, Dehua; Li, Peihu; Xu, Jiankai; Zheng, Shaojiang; Wang, Hong; Wang, Bo; Lu, Jianping; Li, Kongning

doi:10.1016/j.csbj.2022.09.008

Cited by 3 publications

(1 citation statement)

References 72 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Generally, the patients of C1 cluster have lower methylation levels than C2 cluster in all 18 chromatin states. Since chromatin states of human genome were regulated by chromatin regulators (CR), we next estimated the expression patterns of these molecules derived from a recent study 35 . In total, 119 CRs (including 69 up-regulated and 51 down-regulated) were identified as differently expressed (Figure 2 H).…”

Section: Resultsmentioning

confidence: 99%

Epigenetically regulated lncRNAs dissect the intratumoural heterogeneity and facilitate immune evasion of glioblastomas

Xu¹,

Cao²,

Wang³

et al. 2023

Theranostics

Self Cite

View full text Add to dashboard Cite

Background: Glioblastomas are the most common and malignant central nervous system (CNS) tumors that occupied a highly heterogeneous tumor microenvironment (TIME). Long noncoding RNAs (lncRNAs), whose expression can be modified by DNA methylation, are emerging as critical regulators in the immune system. However, knowledge about the epigenetic changes in lncRNAs and their contribution to the immune heterogeneity of glioma is still lacking. Methods: In this study, we integrated paired methylome and transcriptome datasets of glioblastomas and identified 2 robust immune subtypes based on lncRNA methylation features. The immune characteristics of glioma subtypes were compared. Furthermore, immune-related lncRNAs were identified and their relationships with immune evasion were evaluated. Results: Glioma immunophenotypes exhibited distinct immune-related characteristics as well as clinical and epigenetic features. 149 epigenetically regulated (ER) lncRNAs were recognized that possessed inverse variation in epigenetic and transcriptional levels between glioma subtypes. Immune-related lncRNAs were further identified through the investigation of their correlation with immune cell infiltrations and immune-related pathways. In particular, the 'Hot' glioma subtype with higher immunoactivity while a worse survival outcome was found to character immune evasion features. We finally prioritized candidate ER lncRNAs associated with immune evasion markers and response to glioma immunotherapy. Among them, CD109-AS1 and LINC02447 were validated as novel immunoevasive biomarkers for glioma through in vitro experiments. Conclusion: In summary, our study systematically reveals the crosstalk among DNA methylation, lncRNA, and immune regulation in glioblastomas, and will facilitate the development of epigenetic immunotherapy approaches.

show abstract

Section: Resultsmentioning

confidence: 99%

Epigenetically regulated lncRNAs dissect the intratumoural heterogeneity and facilitate immune evasion of glioblastomas

Xu¹,

Cao²,

Wang³

et al. 2023

Theranostics

Self Cite

View full text Add to dashboard Cite

show abstract

Identifying the “stripe” transcription factors and cooperative binding related to DNA methylation

Luo,

Zou

2024

Commun Biol

View full text Add to dashboard Cite

Interactomic Analyses and a Reverse Engineering Study Identify Specific Functional Activities of One-to-One Interactions of the S1 Subunit of the SARS-CoV-2 Spike Protein with the Human Proteome

Colonna

2024

Biomolecules

View full text Add to dashboard Cite

The S1 subunit of SARS-CoV-2 Spike is crucial for ACE2 recognition and viral entry into human cells. It has been found in the blood of COVID-19 patients and vaccinated individuals. Using BioGRID, I identified 146 significant human proteins that interact with S1. I then created an interactome model that made it easier to study functional activities. Through a reverse engineering approach, 27 specific one-to-one interactions of S1 with the human proteome were selected. S1 interacts in this manner independently from the biological context in which it operates, be it infection or vaccination. Instead, when it works together with viral proteins, they carry out multiple attacks on single human proteins, showing a different functional engagement. The functional implications and tropism of the virus for human organs/tissues were studied using Cytoscape. The nervous system, liver, blood, and lungs are among the most affected. As a single protein, S1 operates in a complex metabolic landscape which includes 2557 Biological Processes (GO), much more than the 1430 terms controlled when operating in a group. A Data Merging approach shows that the total proteins involved by S1 in the cell are over 60,000 with an average involvement per single biological process of 26.19. However, many human proteins become entangled in over 100 different biological activities each. Clustering analysis showed significant activations of many molecular mechanisms, like those related to hepatitis B infections. This suggests a potential involvement in carcinogenesis, based on a viral strategy that uses the ubiquitin system to impair the tumor suppressor and antiviral functions of TP53, as well as the role of RPS27A in protein turnover and cellular stress responses.

show abstract

The synergistic interaction landscape of chromatin regulators reveals their epigenetic regulation mechanisms across five cancer cell lines

Cited by 3 publications

References 72 publications

Epigenetically regulated lncRNAs dissect the intratumoural heterogeneity and facilitate immune evasion of glioblastomas

Epigenetically regulated lncRNAs dissect the intratumoural heterogeneity and facilitate immune evasion of glioblastomas

Identifying the “stripe” transcription factors and cooperative binding related to DNA methylation

Interactomic Analyses and a Reverse Engineering Study Identify Specific Functional Activities of One-to-One Interactions of the S1 Subunit of the SARS-CoV-2 Spike Protein with the Human Proteome

Contact Info

Product

Resources

About