In Nature this week, an international group of researchers led by the Wellcome Trust Sanger Institute's Mike Stratton followed up on their recent publication of lung and melanoma genomes with a paper looking at rearrangements in breast cancer. Using paired-end sequencing, the team found more than 2,000 chromosomal rearrangements in 24 breast cancers — more than expected in breast cancer. As the Times Online reported, the new study also highlights the diversity within breast cancer, suggesting it can be classified as five or more conditions, each with distinct treatment options and prognoses. For example, the team noted, a sub-group of breast cancers tested that were rife with tandem duplications. For more information, check out yesterday's feature story in our sister publication In Sequence.
In another cancer-related paper in Nature's advance, online edition, a Columbia University-led research team used bioinformatics to home in on two transcription factors acting in cahoots to promote the formation and invasion of an aggressive type of glioblastoma multiforme brain tumor that has a so-called mesenchymal gene expression signature. The researchers found that the transcription factors STAT3 and C/EBPbeta spur this transformation, which is linked to poor outcomes for patients. Without the two transcription factors, though, the signature disappears — as does tumor aggressiveness. "These results show that the activation of a small regulatory module is necessary and sufficient to initiate and maintain an aberrant phenotypic state in cancer cells," they write.
Microbes were the focus of a paper by researchers with the Genomic Encyclopedia of Bacteria and Archaea, who reported on the first 56 microbial genomes to be sequenced through that project. The group has already found new proteins and protein families and say their results support the validity of phylogeny-based sequencing — not only learning more about how microbes and microbial communities function, but also for informing future biofuel and other research. "[T]argeting microorganisms for genome sequencing solely on the basis of phylogenetic considerations offers significant far-reaching benefits in diverse areas," senior author Jonathan Eisen and his co-workers write. Our sister publication GenomeWeb Daily News has more here.
A news feature profiles the journal's "Newsmaker of the Year" Steven Chu, a Nobel laureate and US Secretary of Energy. Meanwhile, The Guardian picked up a letter in the correspondence section in which German chemist Thomas Koop takes exception to the flagrant use of "incorrect 'designer' snowflakes" in advertisements and elsewhere. Scientifically accurate snowflakes have six fold symmetry, not eight, Koop explained, owing to "water molecules' hexagonal crystal lattice, held together by a hydrogen-bonding network and the structural form of lowest energy under the ambient cold conditions."