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This Week in Nature: Dec 2, 2010

In a paper published online in advance in Nature this week, researchers at the Children's Hospital of Philadelphia, along with their international colleagues, show that "common polymorphisms at the LMO1 locus are strongly associated with susceptibility to developing neuroblastoma." In a genome-wide association study of 2,251 patients and 6,097 controls, the CHOP-led team found an enriched signal at LMO1 in individuals who had the most aggressive neuroblastomas. In their further analyses of copy number alterations and shRNA-mediated LMO1 depletions, the researchers found that these variants may also "influence the likelihood of further somatic alterations at this locus, leading to malignant progression."

A pair of related papers published online in Nature this week report two research teams' functional investigations of Lkb1. Investigators at the University of Michigan show that the tumor suppressor "regulates cell cycle and energy metabolism in haematopoietic stem cells." The UMich team found that Lkb1-deficient HSCs "exhibited defects in centrosomes and mitotic spindles in culture, and became diploid." Researchers at Harvard Medical School used gene inactivation studies in mice to determine that Lkb1 is "critical for the maintenance of energy homeostasis in haematopoietic cells." Independent of its interactions with AMP-activated protein kinase, the Harvard team writes, Lkb1 works to restrict "HSC entry into cell cycle … broadly maintaining energy homeostasis in haematopoietic cells through a novel metabolic checkpoint."

Harvard researchers have found that "telomerase reactivation reverses tissue degeneration in aged telomerase-deficient mice." More specifically, using a knock-in allele encoding a 4-hydroxytamoxifen-inducible telomerase reverse transcriptase-oestrogen receptor that they designed, the team saw lengthened telomeres in homozygous TERT-ER mice, and, as a result of telomerase reactivation, these animals showed an elimination of "degenerative phenotypes across multiple organs." In a Nature letter published this week, the researchers say that their study provides support for "the development of regenerative strategies designed to restore telomere integrity."

And in Nature Communications this week, a team led by investigators at Cornell University shows that deep re-sequencing can be used to determine the distribution of rare variants associated with human diseases. Using Sanger sequencing and 454 pyrosequencing techniques, the team interrogated the diabetes-associated genes KCNJ11 and HHEX in more than 13,000 individuals. With this method, the authors say they observed "far more variation than would have been predicted on the basis of earlier surveys, which could only capture the distribution of common variants." When considered alongside these previous estimates, the team says its re-sequencing-based data indicates a "clear genetic signal of accelerating population growth, suggesting that humanity harbors a myriad of rare, deleterious variants, and that disease risk and the burden of disease in contemporary populations may be heavily influenced by the distribution of rare variants."

The Scan

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.