Volume 46 Issue 6, June 2014

Proper control of cyclin-dependent kinases ensures coordinated cell cycle progression and guards against tumorigenesis. A new study identifies the PARK2 E3 ubiquitin ligase as an important coordinator of G1/S-phase cyclin turnover and explains how mutations targeting this key cell cycle regulatory node contribute to a range of cancers.

Prader-Willi syndrome (PWS) is caused by loss of paternally expressed genes at an imprinted locus on chromosome 15, including the long noncoding RNA IPW. A new study identifies a critical role for IPW in modulating the expression of maternally expressed genes in trans, which has important implications for the understanding of imprinted gene networks.

Although silent transposons in plants can be reactivated by stress or during development, their potential deleterious effects are prevented by transposon-derived epigenetically activated small interfering RNAs (easiRNAs). A new study shows how serendipitous interactions between reactivated transposons and endogenous microRNAs might initiate easiRNA biogenesis, establishing an unexpected link between these two classes of silencing small RNAs.

Wei Zheng and colleagues report the results of a large-scale genome-wide association study of colorectal cancer in East Asians. They identify six new susceptibility loci, including variants near TCF7L2 and TGFB1.

Nicole Soranzo, Tim Spector, Gabi Kastenmüller and colleagues report a large-scale analysis of genetic variants influencing human blood metabolite levels. They identify genome-wide significant associations at 145 loci, providing a framework for exploring relationships between genetic variation, metabolism and complex disease.

Nissim Benvenisty and colleagues use induced pluripotent stem cells (iPSCs) derived from individuals with Prader-Willi syndrome (PWS) to model PWS in vitro. By comparison to parthenogenetic human iPSCs, they find that the PWS-associated noncoding RNA IPW regulates maternally expressed genes at the DLK1-DIO3 imprinted region through its effect on H3K9me3 histone marks in that region.

Piero Carninci and colleagues report the discovery of a large class of noncoding RNAs, non-annotated stem cell transcripts (NASTs), which are implicated in the regulation of stem cell properties. The authors identify 8,873 mouse and 3,042 human NASTs and functionally validate 4 as having an important role in the maintenance of pluripotency.

Yu-Xian Zhu, Jun Wang, Shuxun Yu and colleagues report sequencing and assembly of the genome of cultivated cotton, Gossypium arboreum. Comparison with the Gossypium raimondii genome sequence provides insights into genome evolution and speciation, and identifies two shared whole-genome duplication events occurring before the speciation event around 2–13 million years ago.

Suet Yi Leung, Mao Mao and colleagues report whole-genome sequencing of 100 gastric cancers and DNA copy number, gene expression and methylation profiling of these tumors. They identify new recurrently mutated genes and find mutation of RHOA in 14% of diffuse-type gastric cancers.

Shumpei Ishikawa and colleagues report the identification of recurrent gain-of-function mutations in RHOA in diffuse-type gastric carcinomas.

Timothy Chan and colleagues show that the PARK2 tumor suppressor is a master regulator of G1 and S phase cyclins and is critical for proper cell cycle regulation. PARK2 genetic alterations are common across many human cancers as well as in hereditary Parkinson's disease.

Marc Ladanyi and colleagues identify a recurrent somatic mutation in MYOD1 in a subset of rhabdomyosarcomas with poor outcome. The mutation alters the DNA binding and transactivation properties of MYOD1 and promotes a switch from differentiation to proliferation.

Jonathan Fletcher and colleagues describe highly recurrent deletions of the large muscular dystrophy–associated gene DMD in gastrointestinal stromal tumors, rhabdomyosarcomas and leiomyosarcomas, all cancers with muscle differentiation. Re-expression of DMD in these tumor cells inhibits aspects of their metastatic phenotypes.

Jérôme Bertherat, Aurélien de Reyniès and colleagues perform integrated genomic analyses of adrenocortical carcinomas. They discover recurrent alterations in several new driver genes, including ZNRF3, DAXX, TERT and MED12, and identify two distinct molecular subgroups with opposite clinical outcomes.

Richard Lifton and colleagues identify a recurrent activating mutation in PRKACA, which encodes the catalytic subunit of protein kinase A, in cortisol-producing adrenal tumors. They further show that the mutation results in loss of binding by the regulatory subunit PRKAR1A, leading to increased phosphorylation of downstream targets.

David Weinstock and colleagues identify a triplication at chromosome 21q22 that is associated with development of B cell acute lymphoblastic leukemia (B-ALL) that causes B cell self renewal in vitro. They further demonstrate that this triplication leads to overexpression of the nucleosome remodeling protein HMGN1 and loss of H3K27me3, implicating these changes in B-ALL.

Lars Forsberg, Jan Dumanski and colleagues report that age-related loss of chromosome Y in peripheral blood is associated with increased risks of all-cause mortality, cancer mortality and non-hematological cancer mortality.

Guillaume Lettre, Alexander Reiner, George Diaz and colleagues use an exome array to identify rare and low-frequency coding variants influencing hematological traits. They find several missense variants in CXCR2 associated with reduced white blood cell counts, and, in a separate family-based study, they identify a homozygous CXCR2 frameshift mutation in two siblings with congenital neutropenia.

Bruce Gelb and colleagues identify rare RAF1 mutations in individuals with childhood-onset dilated cardiomyopathy in three cohorts from South India, North India and Japan. Variant RAF1 proteins show altered kinase activity that causes AKT hyperactivation.

Christel Depienne, Eric LeGuern and colleagues report the identification of 5 de novo missense mutations in HCN1 in individuals with early-onset epileptic encephalopathy. Functional studies confirmed the pathogenic nature of these mutations.

Heymut Omran and colleagues show that biallelic mutations in CCNO cause a chronic destructive lung disease resulting from loss of multiple motile cilia from the surface of respiratory epithelial cells. Subcellular analyses suggest that CCNO deficiency leads to defective centriole amplification and migration, leading to reduced ciliogenesis.

Xiangdong Fu and colleagues show that variation in DEP1, which encodes a G protein subunit known to influence rice panicle architecture, underlies a major quantitative trait locus for nitrogen-use efficiency. These findings suggest that modulating heterotrimeric G protein activity could contribute to environmentally sustainable increases in rice grain yield.