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

Significant association of cutaneous adverse events with hydroxyurea: results from a prospective non-interventional study in BCR-ABL1-negative myeloproliferative neoplasms (MPN) - on behalf of the German Study Group-MPN

Despite the successes achieved with molecular targeted inhibition of the oncogenic driver Bcr-Abl in chronic myeloid leukemia (CML), the majority of patients still require lifelong tyrosine kinase inhibitor (TKI) therapy. This is primarily caused by resisting leukemic stem cells (LSCs), which prevent achievement of treatment-free remission in all patients. Here we describe the ITIM (immunoreceptor tyrosine-based inhibition motif)-containing Fc gamma receptor IIb (FcγRIIb, CD32b) for being critical in LSC resistance and show that targeting FcγRIIb downstream signaling, by using a Food and Drug Administration-approved BTK inhibitor, provides a successful therapeutic approach. First, we identified FcγRIIb upregulation in primary CML stem cells. FcγRIIb depletion caused reduced serial re-plaiting efficiency and cell proliferation in malignant cells. FcγRIIb targeting in both a transgenic and retroviral CML mouse model provided in vivo evidence for successful LSC reduction. Subsequently, we identified BTK as a main downstream mediator and targeting the Bcr-Abl-FcγRIIb-BTK axis in primary CML CD3

Publisher Correction: Significant association of cutaneous adverse events with hydroxyurea: results from a prospective non-interventional study in BCR-ABL1-negative myeloproliferative neoplasms (MPN) - on behalf of the German Study Group-MPN

Stegelmann F, Wille K, Marchi H, et al. Publisher Correction: Significant association of cutaneous adverse events with hydroxyurea: results from a prospective non-interventional study in BCR-ABL1-negative myeloproliferative neoplasms (MPN) - on behalf of the German Study Group-MPN. Leukemia. 2021

Combining Rigid Cellulose Nanocrystals and Soft Silk Proteins: Revealing Interactions and Alignment in Shear

Abstract Natural materials, such as silk and cellulose, have an inspiring set of properties, which have evolved over hundreds of millions of years. In this study, cellulose nanocrystals (CNCs) and regenerated silk fibroin (RSF) are combined to evaluate their suitability for filament formation. This is assessed by tuning and characterizing the interactions between these two materials and finally by studying the alignment of the mixtures under shear. To modify the interactions between CNCs and silk, CNCs with varying surface functionalities (sulfate and/or aminosilane groups) are used. The interactions and compatibility of the two components are investigated using quartz crystal microbalance with dissipation monitoring (QCM‐D) and photothermal atomic force microscopy (AFM‐IR), which show that ionic interactions induce sufficient binding between the two components. Then, the alignment of the CNC and silk mixtures is evaluated by shear‐induced polarized light imaging, which indicates that silk can orientate with the CNCs when not covalently bound. Finally, the potential of the materials for filament formation is tentatively demonstrated using an industrial dry‐spinning environment, where CNCs are expected to bring order and alignment, whereas RSF provides soft and more mobile regions to further facilitate the alignment of the final filament structure

Solvent-free preparation of high-toughness epoxy-SWNT composite materials

Multicomponent nanocomposite materials based on a high-performance epoxy system and single-walled carbon nanotubes (SWNTs) have been prepared. The noncovalent wrapping of nitric acid-treated SWNTs with a PEO-based amphiphilic block copolymer leads to a highly disaggregated filler with a boosted miscibility in the epoxy matrix, allowing its dispersion without organic solvents. Although direct dispersion of acid-treated SWNTs results in modestly improved epoxy matrix mechanical properties, the incorporation of wrapped SWNTs produces a huge increase in toughness (276% improvement at 0.5 wt % loading) and impact strength (193% at 0.5 wt % loading) with no detrimental effect on the elastic properties. A synergistic effect between SWNTs and the block copolymer is revealed on the basis of tensile and impact strength results. Atomic force microscopy has been applied, obtaining stiffness mappings that identify nanostructure features responsible of the dynamic mechanical behavior. The electrical percolation threshold is greatly reduced, from 0.31 to 0.03 wt % SWNTs when block copolymer-wrapped SWNTs are used, and all the measured conductivity values increased up to a maximum of 7 orders of magnitude with respect to the baseline matrix (1 wt % wrapped-SWNTs loading). This approach provides an efficient way to disperse barely dispersible SWNTs without solvents into an epoxy matrix, and to generate substantial improvements with small amounts of SWNTs. \ua9 2011 American Chemical Society.Peer reviewed: YesNRC publication: Ye