Previous studies have established that a subset of head and neck tumors contains human papillomavirus (HPV) sequences and that HPV-driven head and neck cancers display distinct biological and clinical features. HPV is known to drive cancer by the actions of the E6 and E7 oncoproteins, but the molecular architecture of HPV infection and its interaction with the host genome in head and neck cancers have not been comprehensively described. We profiled a cohort of 279 head and neck cancers with next generation RNA and DNA sequencing and show that 35 (12.5%) tumors displayed evidence of high-risk HPV types 16, 33, or 35. Twentyfive cases had integration of the viral genome into one or more locations in the human genome with statistical enrichment for genic regions. Integrations had a marked impact on the human genome and were associated with alterations in DNA copy number, mRNA transcript abundance and splicing, and both inter-and intrachromosomal rearrangements. Many of these events involved genes with documented roles in cancer. Cancers with integrated vs. nonintegrated HPV displayed different patterns of DNA methylation and both human and viral gene expressions. Together, these data provide insight into the mechanisms by which HPV interacts with the human genome beyond expression of viral oncoproteins and suggest that specific integration events are an integral component of viral oncogenesis.cancer | head and neck | papilloma virus | genome rearrangement | integration sites H ead and neck cancer (HNC) is a heterogeneous group of tumors characterized by a common anatomic origin, and most such tumors develop from within the mucosa and are classified as head and neck squamous cell carcinomas (HNSCCs) (1). HNSCC, the sixth most common cancer diagnosed worldwide and the eighth most common cause of cancer death (2), is frequently associated with human papillomavirus (HPV) infection (3, 4). Depending on the anatomic site of the tumor, HPV prevalence is estimated at 23-36% (5). HPV-positive HNSCCs form a distinct subset of HNCs that differs from HPV-negative HNSCCs in tumor biology and clinical characteristics, including superior clinical outcomes (6-9).The molecular pathogenesis of HPV-driven HNSCC also seems distinct from HPV-negative tumors, with previous studies showing a divergent spectrum of alterations in gene expression, mutations, amplifications, and deletions as well as distinct epigenome alterations (10-15). HPV is known to drive tumorigenesis through the actions of its major oncoproteins E6 and E7, which target numerous cellular pathways, including inactivation of p53 and the retinoblastoma (Rb) protein (16-18). Together with E5, they also play an important role in immune evasion, being involved in both innate and adaptive immunity (19,20).Initially after infection, HPV is identified in circular extrachromosomal particles or episomes. A critical step in progression to cancer is the integration of viral DNA into the host cell Significance A significant proportion of head and neck cancer is driven by human papil...

Abstract.Two results on site percolation on the d-dimensional lattice, d^l arbitrary, are presented. In the first theorem, we show that for stationary underlying probability measures, each infinite cluster has a well-defined density with probability one. The second theorem states that if in addition, the probability measure satisfies the finite energy condition of Newman and Schulman, then there can be at most one infinite cluster with probability one. The simple arguments extend to a broad class of finite-dimensional models, including bond percolation and regular lattices.Our notation is as follows. Let Z d be the d-dimensional lattice, with d^.1. Finite d-dimensional boxes in Z d whose sides are parallel to the coordinate directions are called rectangles. The number of points in a finite set F is denoted by φ (F). We set and we let μ denote a probability measure on X which is stationary, i.e. invariant under translation by each element of Z d . For each xεX, the connected components of the nearest neighbor graph whose set of vertices is

Let G be a finite graph or an infinite graph on which Z Z d acts with finite fundamental domain. If G is finite, let T be a random spanning tree chosen uniformly from all spanning trees of G; if G is infinite, methods from [Pem] show that this still makes sense, producing a random essential spanning forest of G. A method for calculating local characteristics (i.e. finite-dimensional marginals) of T from the transfer-impedance matrix is presented. This differs from the classical matrix-tree theorem in that only small pieces of the matrix (n-dimensional minors) are needed to compute small (n-dimensional) marginals. Calculation of the matrix entries relies on the calculation of the Green's function for G, which is not a local calculation. However, it is shown how the calculation of the Green's function may be reduced to a finite computation in the case when G is an infinite graph admitting a Z d -action with finite quotient. The same computation also gives the entropy of the law of T.These results are applied to the problem of tiling certain lattices by dominos -the so-called dimer problem. Another application of these results is to prove modified versions of conjectures of Aldous [Al2] on the limiting distribution of degrees of a vertex and on the local structure near a vertex of a uniform random spanning tree in a lattice whose dimension is going to infinity. Included is a generalization of moments to tree-valued random variables and criteria for these generalized moments to determine a distribution.

Vertical, seasonal and geographical patterns in ocean microbial communities have been observed in many studies, but the resolution of community dynamics has been limited by the scope of data sets, which are seldom up to the task of illuminating the highly structured and rhythmic patterns of change found in ocean ecosystems. We studied vertical and temporal patterns in the microbial community composition in a set of 412 samples collected from the upper 300 m of the water column in the northwestern Sargasso Sea, on cruises between 1991 and 2004. The region sampled spans the extent of deep winter mixing and the transition between the euphotic and the upper mesopelagic zones, where most carbon fixation and reoxidation occurs. A bioinformatic pipeline was developed to de-noise, normalize and align terminal restriction fragment length polymorphism (T-RFLP) data from three restriction enzymes and link T-RFLP peaks to microbial clades. Non-metric multidimensional scaling statistics resolved three microbial communities with distinctive composition during seasonal stratification: a surface community in the region of lowest nutrients, a deep chlorophyll maximum community and an upper mesopelagic community. A fourth microbial community was associated with annual spring blooms of eukaryotic phytoplankton that occur in the northwestern Sargasso Sea as a consequence of winter convective mixing that entrains nutrients to the surface. Many bacterial clades bloomed in seasonal patterns that shifted with the progression of stratification. These richly detailed patterns of community change suggest that highly specialized adaptations and interactions govern the success of microbial populations in the oligotrophic ocean.

No abstract