Ten Years of EWAS

Epigenome-wide association study (EWAS) has been applied to analyze DNA methylation variation in complex diseases for a decade, and epigenome as a research target has gradually become a hot topic of current studies. The DNA methylation microarrays, next-generation, and third-generation sequencing technologies have prepared a high-quality platform for EWAS. Here, the progress of EWAS research is reviewed, its contributions to clinical applications, and mainly describe the achievements of four typical diseases. Finally, the challenges encountered by EWAS and make bold predictions for its future development are presented.

Epigenetic dysregulation of immune-related pathways in cancer: bioinformatics tools and visualization

Cancer immune evasion is one of the hallmarks of carcinogenesis. Cancer cells employ multiple mechanisms to avoid immune recognition and suppress antitumor immune responses. Recently, accumulating evidence has indicated that immune-related pathways are epigenetically dysregulated in cancer. Most importantly, the epigenetic footprint of immune-related pathways is associated with the patient outcome, underscoring the crucial need to understand this process. In this review, we summarize the current evidence for epigenetic regulation of immune-related pathways in cancer and describe bioinformatics tools, informative visualization techniques, and resources to help decipher the cancer epigenome.

Abnormal patterns of genomic chemical modification help tumors elude immunological destruction, but sophisticated computational tools could help identify and overcome these survival mechanisms. Immunotherapy can be a potent weapon against cancer, but many tumors evolve the ability to protect themselves by subduing the immune response. Sungjune Kim and colleagues at the Moffitt Cancer Center, Tampa, USA, have reviewed efforts to study how chemical alterations to DNA that affect gene expression contribute to this process. Considerable evidence indicates a role for a modification called methylation in this immune evasion, and researchers now have access to vast repositories of tumor-specific gene methylation profiles. The authors describe these data resources, and highlight some of the software tools that are helping oncologists to identify patterns in the data that might lead to better therapies.