Hematopoietic stem and progenitor cells are a distinct HIV reservoir that contributes to persistent viremia in suppressed patients

Long-lived reservoirs of persistent HIV are a major barrier to a cure. CD4+ hematopoietic stem and progenitor cells (HSPCs) have the capacity for lifelong survival, self-renewal, and the generation of daughter cells. Recent evidence shows that they are also susceptible to HIV infection in vitro and in vivo. Whether HSPCs harbor infectious virus or contribute to plasma virus (PV) is unknown. Here, we provide strong evidence that clusters of identical proviruses from HSPCs and their likely progeny often match residual PV. A higher proportion of these sequences match residual PV than proviral genomes from bone marrow and peripheral blood mononuclear cells that are observed only once. Furthermore, an analysis of near-full-length genomes isolated from HSPCs provides evidence that HSPCs harbor functional HIV proviral genomes that often match residual PV. These results support the conclusion that HIV-infected HSPCs form a distinct and functionally significant reservoir of persistent HIV in infected people

Quantitative Fitness Analysis Shows That NMD Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects

To better understand telomere biology in budding yeast, we have performed systematic suppressor/enhancer analyses on yeast strains containing a point mutation in the essential telomere capping gene CDC13 (cdc13-1) or containing a null mutation in the DNA damage response and telomere capping gene YKU70 (yku70Δ). We performed Quantitative Fitness Analysis (QFA) on thousands of yeast strains containing mutations affecting telomere-capping proteins in combination with a library of systematic gene deletion mutations. To perform QFA, we typically inoculate 384 separate cultures onto solid agar plates and monitor growth of each culture by photography over time. The data are fitted to a logistic population growth model; and growth parameters, such as maximum growth rate and maximum doubling potential, are deduced. QFA reveals that as many as 5% of systematic gene deletions, affecting numerous functional classes, strongly interact with telomere capping defects. We show that, while Cdc13 and Yku70 perform complementary roles in telomere capping, their genetic interaction profiles differ significantly. At least 19 different classes of functionally or physically related proteins can be identified as interacting with cdc13-1, yku70Δ, or both. Each specific genetic interaction informs the roles of individual gene products in telomere biology. One striking example is with genes of the nonsense-mediated RNA decay (NMD) pathway which, when disabled, suppress the conditional cdc13-1 mutation but enhance the null yku70Δ mutation. We show that the suppressing/enhancing role of the NMD pathway at uncapped telomeres is mediated through the levels of Stn1, an essential telomere capping protein, which interacts with Cdc13 and recruitment of telomerase to telomeres. We show that increased Stn1 levels affect growth of cells with telomere capping defects due to cdc13-1 and yku70Δ. QFA is a sensitive, high-throughput method that will also be useful to understand other aspects of microbial cell biology

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

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Nanostructured metal oxide thin films for humidity sensors

Capacitive humidity sensors were fabricated using countersunk interdigitated electrodes coated with amorphous nanostructured TiO2, SiO2, and Al2O3 thin films grown by glancing angle deposition. The capacitive response and response times for each sensor were measured. The sensor utilizing TiO2 exhibited the largest change in capacitance, increasing exponentially from ~ 1 nF to ~ 1muF for an increase in relative humidity from 2% to 92%. Adsorption and desorption response times were measured using flow rates of 2.5 l/min and were between 90 ms and 300 ms for the sensors studied here. A simple model of the capacitive response of the devices has been developed and used to calculate the dielectric constant of the combined system of our films and adsorbed water. The obtained dielectric constants are found to be much higher than bulk or literature values for similar systems.Peer reviewed: YesNRC publication: Ye

Polarity-adjustable reversed phase ultrathin-layer chromatography

Reversed phase thin layer chromatography (TLC) or high performance thin layer chromatography (HPTLC) plates modified with C18, C8 or C2 to provide the silica-gel stationary phase with different polarities are available on the market, however, reversed phase plates with tunable polarity have not been reported. Given the limited variety of reversed phase plates, mobile phase composition optimization is necessary to obtain better separation of analytes with similar characteristics, which is often a time consuming step. We present polarity-adjustable reversed phase ultrathin-layer chromatography (UTLC) plates, which simplifies the mobile phase screening process and greatly expands the selection of reversed phase plates. The plates were fabricated on glass substrates with SiO2 nanopillars deposited using the glancing angle deposition (GLAD) technique. SiO2 nanopillars were functionalized with octadecyltrichlorosilane to generate a super hydrophobic stationary phase. Unlike commercial silica-gel based stationary phases, the isolated nanopillar architecture presented here exposes a high surface area to post-fabrication surface treatments. In our work, an O2 plasma treatment at different powers, pressures and exposure times was used to shorten the silane carbon chain and introduce COOH groups to the surface, producing plates with finely tunable polarities. Separation of a model dye mixture of Sudan blue and Sudan IV confirmed the tuning of surface polarities by measurement of retention behavior changes. The dye elution order reversed as a result of the change in surface polarity. When the same plasma treatment process was tested on commercial reversed phase plates, separation behavior did not change because the disordered and tortuous silica gel restricts the accessible surface area. Plasma treatment of GLAD structures with highly accessible surfaces improved control over interfacial properties, producing better reverse phase separations.Peer reviewed: YesNRC publication: Ye

Glancing angle deposition on a roll: towards high-throughput nanostructured thin films

Increasing the throughput of the powerful single-step glancing angle deposition (GLAD) method using a prototype simplified roll-to-roll (R2R) system has been explored. While the conventional GLAD technique is popular for fabricating nanostructured devices in a single deposition step, it is not a high-output process. To evaluate the feasibility of large area GLAD deposition, the authors examined the geometrical considerations required to eventually achieve GLAD in a roll-to-roll manufacturing system. Nominal deposition and rotation angles were mathematically translated to their effective R2R counterparts, allowing for deposition recipes of the archetype GLAD nanostructures (slanted posts, vertical posts, and square spirals) and the mechanics of the phi-sweep technique to be converted to this space. Representative structures were then deposited, and the phi-sweep technique successfully applied, in a prototype single barrel roller R2R experimental system. This prototype system provides a foundation for moving GLAD from the laboratory to mass production. \ua9 2013 American Vacuum Society.Peer reviewed: YesNRC publication: Ye

Glancing angle deposition on a roll: towards high-throughput nanostructured thin films

Increasing the throughput of the powerful single-step glancing angle deposition (GLAD) method using a prototype simplified roll-to-roll (R2R) system has been explored. While the conventional GLAD technique is popular for fabricating nanostructured devices in a single deposition step, it is not a high-output process. To evaluate the feasibility of large area GLAD deposition, the authors examined the geometrical considerations required to eventually achieve GLAD in a roll-to-roll manufacturing system. Nominal deposition and rotation angles were mathematically translated to their effective R2R counterparts, allowing for deposition recipes of the archetype GLAD nanostructures (slanted posts, vertical posts, and square spirals) and the mechanics of the phi-sweep technique to be converted to this space. Representative structures were then deposited, and the phi-sweep technique successfully applied, in a prototype single barrel roller R2R experimental system. This prototype system provides a foundation for moving GLAD from the laboratory to mass production. \ua9 2013 American Vacuum Society.Peer reviewed: YesNRC publication: Ye