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Cancer Pathways Found With 'Crosstalk' Pathway Enrichment Approach

In Genome Medicine, a team from Nanjing University of Aeronautics, Thomas Jefferson University's Sidney Kimmel Cancer Center, and elsewhere describes a "crosstalk"-based pathway enrichment method known as CTpathway, which rapidly focuses in on key pathways based on data ranging from differential gene expression data to protein and transcription factor interactions based on bulk and/or single-cell RNA sequence and other data. When the researchers used CTpathway to assess thousands of expression profiles representing cancer or blood tissues, for example, they unearthed known cancer risk pathways, along with pathways not linked to the cancer types considered in the past. "CTpathway recapitulates known risk pathways and exclusively identifies several previously unreported critical pathways for individual cancer types," the authors report, noting that the approach "outperforms other methods in identifying risk pathways across all cancer stages, including early-stage cancer with a small number of differentially expressed genes."

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.