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Analysis of Methylation in Esophageal Tumors, Nonmalignant Tissue

Cell type-specific partially methylated domains and differentially methylated domains found in normal cells persist in malignant cells, researchers from Cedars-Sinai Medical Center in Los Angeles and elsewhere report in Genome Biology. They analyzed the whole-genome bisulfite sequencing profiles of 45 esophageal tumors, representing both the squamous cell carcinoma and adenocarcinoma subtypes, and matched nonmalignant tissue. Using a sequence-aware multi-model PMD caller they developed, dubbed MMSeekR, the researchers uncovered a high level of heterogeneity at the methylation level and in the distribution of PMDs across tumor samples. Where these PMDs fall in the genome is present in normal cells, they report, but note that tumor cells exhibit a higher level of loss, and further add that cell-type-specific H3K36me2 deposition may shape how PMDs are distributed throughout the genome. Meanwhile, at the DMR level, the researchers found more than 10,000 hypo-DMRs between the two esophageal cancer types and also note that many of the methylation changes there were also present in normal cells. "To our knowledge, this is the first demonstration of the prominent cell-type specificity of PMDs across normal, precursor, and malignant states," the researchers write.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.