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This Week in Cell: May 30, 2018

Researchers at the BC Cancer Agency, University of British Columbia, and elsewhere explore interactions between malignant and immune cells in dozens of individuals with high-grade serous ovarian cancer, using multi-region sampling and a combination of genome sequencing, immunohistochemistry, expression profiling, immune cell receptor sequencing, and other approaches. Based on data for 212 samples from 38 high-grade serous ovarian cancer patients, for example, they uncovered three main immunologic subtypes, known as "sparse," "stromally restricted," and "epithelial and stromal." The team also documented the immunologic diversity within individuals and retraced relationships between tumor features and specific immune profiles. From these and other findings, the authors suggest "within-patient spatial immune microenvironment variation shapes intraperitoneal malignant spread, provoking new evolutionary perspectives on [high-grade serous ovarian cancer] clonal dispersion."

A Columbia University-led team taps into electronic health record data to estimate the heritability of roughly 500 human traits or diseases. Along with insights into individuals' disease diagnoses, the researchers mined 7.4 million familial relationships from emergency contact data in EHRs at Columbia Medical Center, Weill Cornell Medical Center, and Mount Sinai Health System, verifying the validity of this approach using relationships gleaned from genetic data for more than 1,500 of the individuals. From there, they estimated the heritability for acne, asthma, epilepsy, obesity, colon cancer, and hundreds more conditions. The Scan has more on this, here.

Researchers from the US, Germany, and the Netherlands report on regulatory features found in macrophages from five mouse strains, identifying gene expression shifts that tend to coincide with phenotypic features in the immune cells. Using RNA sequencing, chromatin immunoprecipitation sequencing, and several other sequencing strategies, in combination with gene expression and transcription factor network clues, the team considered genetic variant, chromatin interaction, transcriptome, and regulatory features in resting and activated macrophages. "Integration of strain-specific genomic features indicate that they frequently reside in highly interconnected clusters associated with strain-specific gene expression," the authors write, "suggesting a domain-wide regulatory environment that influences [transcription factor] binding and function."

The Scan

Tara Pacific Expedition Project Team Finds High Diversity Within Coral Reef Microbiome

In papers appearing in Nature Communications and elsewhere, the team reports on findings from the two-year excursion examining coral reefs.

Study Examines Relationship Between Cellular Metabolism, DNA Damage Repair

A new study in Molecular Systems Biology finds that an antioxidant enzyme shifts from mitochondria to the nucleus as part of the DNA damage response.

Stem Cell Systems Target Metastatic Melanoma in Mouse Model

Researchers in Science Translational Medicine describe a pair of stem cell systems aimed at boosting immune responses against metastatic melanoma in the brain.

Open Pediatric Brain Tumor Atlas Team Introduces Genomic Data Collection, Analytical Tools

A study in Cell Genomics outlines open-source methods being used to analyze and translate whole-genome, exome, and RNA sequence data from the Pediatric Brain Tumor Atlas.