Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Holding-on: co-evolution between infant carrying and grasping behaviour in strepsirrhines

The origin and evolution of manual grasping remain poorly understood. The ability to cling requires important grasping abilities and is essential to survive in species where the young are carried in the fur. A previous study has suggested that this behaviour could be a pre-adaptation for the evolution of fine manipulative skills. In this study we tested the co-evolution between infant carrying in the fur and manual grasping abilities in the context of food manipulation. As strepsirrhines vary in the way infants are carried (mouth vs. fur), they are an excellent model to test this hypothesis. Data on food manipulation behaviour were collected for 21 species of strepsirrhines. Our results show that furcarrying species exhibited significantly more frequent manual grasping of food items. This study clearly illustrates the potential novel insights that a behaviour (infant carrying) that has previously been largely ignored in the discussion of the evolution of primate manipulation can bring.peerReviewe

Effect of histamine on lung contractile elements in growing cattle

peer reviewedaudience: researcher, professionalOBJECTIVE: To determine the effect of histamine on the contractile elements of the respiratory tract in neonatal calves and young adult cattle. SAMPLE POPULATION: Samples of trachealis muscle, bronchi, and intrapulmonary arteries and veins dissected from the respiratory tracts of healthy bovids (2 to 8 days and 16 to 20 months old). PROCEDURE: Histamine cumulative concentration-effect curves (10(-6) to 10(-3) M) were constructed in duplicate smooth muscle samples mounted in organ baths. Contractile responses to histamine were compared with reference contractions elicited by methacholine (10(-5) M) for airways or KCl (127 mM) for vessels. RESULTS: In young adult cattle, trachealis muscle had a substantial contractile response to histamine (84% of methacholine-induced contraction), whereas bronchi reacted slightly (15 and 20% for large and small bronchi, respectively). Although contractile responses to KCl were comparable in arteries and veins, histamine-induced contractions were greater for intrapulmonary veins than for arteries (202 vs 48% of KCl-induced contraction). In neonatal calves, histamine-induced contraction of veins also exceeded that of arteries (230 vs 54% of KCl-induced contraction); however, unlike in young adult cattle, histamine produced notable contraction of large and small bronchi (48 and 60% of methacholine-induced contraction, respectively). CONCLUSIONS AND CLINICAL RELEVANCE: Compared with intrapulmonary arteries, intrapulmonary veins have greater contractile responses to histamine in neonatal and young adult cattle. Data suggest loss of histamine responsiveness in bronchial smooth muscle as neonatal calves grow to young adults. Venodilation may be useful in treatment of lung edema in cattle

An Atypical Parvovirus Drives Chronic Tubulointerstitial Nephropathy and Kidney Fibrosis

© 2018 Elsevier Inc. The occurrence of a spontaneous nephropathy with intranuclear inclusions in laboratory mice has puzzled pathologists for over 4 decades, because its etiology remains elusive. The condition is more severe in immunodeficient animals, suggesting an infectious cause. Using metagenomics, we identify the causative agent as an atypical virus, termed “mouse kidney parvovirus” (MKPV), belonging to a divergent genus of Parvoviridae. MKPV was identified in animal facilities in Australia and North America, is transmitted via a fecal-oral or urinary-oral route, and is controlled by the adaptive immune system. Detailed analysis of the clinical course and histopathological features demonstrated a stepwise progression of pathology ranging from sporadic tubular inclusions to tubular degeneration and interstitial fibrosis and culminating in renal failure. In summary, we identify a widely distributed pathogen in laboratory mice and establish MKPV-induced nephropathy as a new tool for elucidating mechanisms of tubulointerstitial fibrosis that shares molecular features with chronic kidney disease in humans. A kidney parvovirus found in multiple laboratory mouse colonies causes spontaneous nephropathy and represents a new tool for studying chronic kidney disease