NEW YORK (GenomeWeb News) – A new Nature Methods paper introduces a bioinformatics-based strategy for gauging human stem cell pluripotency. Using gene expression data on hundreds of samples — including 223 human embryonic stem cells and 41 induced pluripotent stem cells — from the so-called "stem cell matrix 2" or SCM2 database, an international team came up with PluriTest. The open-access assay, which relies on data from microarray analyses rather than animal testing, can reportedly distinguish between pluripotent and non-pluripotent cell samples with 98 percent sensitivity and 100 percent specificity.
Researchers from St. Jude Children's Research Hospital and the National Cancer Institute reported online in Nature yesterday that mutations in a histone acetyltransferase and transcriptional co-activator gene called CREBBP are linked to elevated relapse risk in children with acute lymphoblastic leukemia. By first resequencing 300 genes in relapse samples and matched ALL diagnosis samples in nearly two-dozen children, the team found somatic, non-synonymous, ALL-associated mutations affecting 32 genes. Among them: CREBBP and another histone modification-related gene called CTCF. Follow-up studies in more than 70 ALL relapse cases and nearly 300 non-relapse cases also pointed to a role for CREBBP in ALL treatment resistance and relapse, with CREBBP alterations turning up in more than 18 percent of relapse cases tested.
"These results extend the landscape of genetic alterations in leukemia," senior author James Downing, a pathology researcher at St. Jude Children's Research Hospital, and his co-authors wrote, "and identify mutations targeting transcriptional and epigenetic regulation as a mechanism of resistance in ALL."
CREBBP mutations were also detected through another blood cancer study appearing in Nature this week. Investigators from the US and Italy found recurrent structural alterations to CREBBP and a related acetyltransferase gene, EP300, in B-cell non-Hodgkin lymphoma using a combination of exome sequencing, targeted resequencing, and microarray analyses. Roughly 40 percent of the diffuse large B-cell lymphoma and follicular lymphoma cases they tested harbored CREBBP or EP300 deletions or mutations — changes that typically rendered histone acetyltransferase coding bits of these genes useless.
"The findings of this study suggest that the use of histone deacetylase inhibitors has a rational basis in [B-cell non-Hodgkin lymphoma]," Columbia University researcher Riccardo Dalla-Favera and co-authors wrote. "On the other hand, their efficacy should be re-evaluated by stratifying patients based on the presence of [histone acetyltransferase] defects as well as by testing the numerous histone deacetylase and sirtuin inhibitors with target specificity."
In an online paper in Science today, researchers from Massachusetts and New York describe how they tracked spliceosome assembly in yeast cells over time. The group used fluorescence microscopy to follow the steps involved in putting together the small nuclear RNA and protein-containing complex — providing new clues about how it slices and dices pre-messenger RNAs to produce a range of alternative transcripts.
"By looking at individual molecules one at a time we can actually follow the stages of the assembly process," co-corresponding author Jeff Gelles, a biochemistry researcher at Brandeis University, said in a statement. "We can determine whether it happens in the same order on each molecule, or if some spliceosomes assemble differently than others."
Genomics In The Journals is a new weekly feature pointing readers to select, recently published articles involving genomics and related research.