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This Week in Cell: May 31, 2017

Researchers from Cold Spring Harbor Laboratory and their colleagues in the US, Israel, and Korea explore mutations associated with enhanced branching in tomato plants, which has been implicated in reduced tomato fertility in the past. The team started by screening almost 4,200 wild and domesticated tomato accessions, looking for genotypes, gene expression patterns, or mapping-by-sequencing mutations associated with distinct alterations in inflorescence architecture that were epistatic to beneficial traits. The search led to mutations in two transcription factor genes, leading to leaf-like organs on large tomato fruits, in one case, and fruit drop-resistant joint-free stems in another. "Characterizing and neutralizing similar cases of negative epistasis could improve productivity in many agricultural organisms," the authors note.

A University of Zurich-led team describes findings from an immune profiling analysis of cells from 73 individuals with clear cell renal cell carcinoma (ccRCC) and five healthy controls. The researchers did a series of mass spectrometry experiments on tumor samples, teasing out tumor-associated macrophages and T-cell populations with antibody screening and other techniques before mapping the data in two dimensions. Based on information for 3.5 million cells, they uncovered 17 phenotypes for tumor-associated macrophage cells and nearly two dozen T-cell phenotypes. Moreover, the authors note that "a distinct immune composition correlated with progression-free survival, thereby presenting an in-depth human atlas of the tumor microenvironment in this disease."

Finally, investigators from Emory University and elsewhere describe metabolic phenotypes that seem to track with various responses to the live attenuated shingles vaccine Zostavax. By bringing together blood transcriptomic, plasma metabolomic, plasma cytokine, and cell population profiling data for 33 healthy young individuals under 40-years-old and 44 elderly individuals who received the vaccine, the team put together a so-called multiscale, multifactorial response network that was subsequently considered alongside T-cell and B-cell antibody immune responses. "[W]e measured the magnitude and quality of innate and adaptive immune response to Zostavax vaccination for up to 180 days," the authors say. "Complementing these assays with transcriptomics and metabolomics, our integrative computational analysis reveals a highly interconnected immune network of gene and metabolic pathways that correlate with the later adaptive response."

The Scan

Genetic Ancestry of South America's Indigenous Mapuche Traced

Researchers in Current Biology analyzed genome-wide data from more than five dozen Mapuche individuals to better understand their genetic history.

Study Finds Variants Linked to Diverticular Disease, Presents Polygenic Score

A new study in Cell Genomics reports on more than 150 genetic variants associated with risk of diverticular disease.

Mild, Severe Psoriasis Marked by Different Molecular Features, Spatial Transcriptomic Analysis Finds

A spatial transcriptomics paper in Science Immunology finds differences in cell and signaling pathway activity between mild and severe psoriasis.

ChatGPT Does As Well As Humans Answering Genetics Questions, Study Finds

Researchers in the European Journal of Human Genetics had ChatGPT answer genetics-related questions, finding it was about 68 percent accurate, but sometimes gave different answers to the same question.