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Study Offers Insights Into Role of Structural Variants in Cancer

Combining genomic profiling and genome engineering, a team led by the Salk Institute for Biological Studies' Jesse Dixon has uncovered new details about how some structural variants (SVs) can activate oncogenes to promote cancer. SVs that alter three-dimensional genome organization can lead to enhancer-promoter rewiring and human disease, particularly cancer. But only a small number of SVs are associated with altered gene expression and it is not known why only certain SVs lead to changes in distal gene expression. To investigate, the scientists analyzed Hi-C sequencing data from 92 cancer cell lines and patient samples, finding loci affected by recurrent alterations to 3D genome structure including important oncogenes. As reported in Nature this week, they then used CRISPR/Cas9 genome editing to generate de novo SVs in cell lines and show that oncogene activity can be predicted by using models that consider partner region chromatin contacts and enhancer activity. "Critically, the expression of only a subset of genes is sensitive to these engineered rearrangements, and we observe that only a minority of genes in the genome show evidence of responsiveness to changes in their local enhancer landscape," the study's authors write. "These results indicate that alterations to gene regulatory 3D architecture are a critical mechanism that enables oncogene activation in cancer genomes and sheds light on the essential elements for such gene activation events.

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.