Multivalent glycan arrays

Glycan microarrays have become a powerful technology to study biological processes, such as cell–cell interaction, inflammation, and infections. Yet, several challenges, especially in multivalent display, remain. In this introductory lecture we discuss the state-of-the-art glycan microarray technology, with emphasis on novel approaches to access collections of pure glycans and their immobilization on surfaces. Future directions to mimic the natural glycan presentation on an array format, as well as in situ generation of combinatorial glycan collections, are discussed

VaporSPOT: Parallel Synthesis of Oligosaccharides on Membranes

Automated chemical synthesis has revolutionized synthetic access to biopolymers in terms of simplicity and speed. While automated oligosaccharide synthesis has become faster and more versatile, the parallel synthesis of oligosaccharides is not yet possible. Here, a chemical vapor glycosylation strategy (VaporSPOT) is described that enables the simultaneous synthesis of oligosaccharides on a cellulose membrane solid support. Different linkers allow for flexible and straightforward cleavage, purification, and characterization of the target oligosaccharides. This method is the basis for the development of parallel automated glycan synthesis platforms

Automated Laser‐Transfer Synthesis of High‐Density Microarrays for Infectious Disease Screening

Laser-induced forward transfer (LIFT) is a rapid laser-patterning technique for high-throughput combinatorial synthesis directly on glass slides. A lack of automation and precision limits LIFT applications to simple proof-of-concept syntheses of fewer than 100 compounds. Here, an automated synthesis instrument is reported that combines laser transfer and robotics for parallel synthesis in a microarray format with up to 10 000 individual reactions cm−2. An optimized pipeline for amide bond formation is the basis for preparing complex peptide microarrays with thousands of different sequences in high yield with high reproducibility. The resulting peptide arrays are of higher quality than commercial peptide arrays. More than 4800 15-residue peptides resembling the entire Ebola virus proteome on a microarray are synthesized to study the antibody response of an Ebola virus infection survivor. Known and unknown epitopes that serve now as a basis for Ebola diagnostic development are identified. The versatility and precision of the synthesizer is demonstrated by in situ synthesis of fluorescent molecules via Schiff base reaction and multi-step patterning of precisely definable amounts of fluorophores. This automated laser transfer synthesis approach opens new avenues for high-throughput chemical synthesis and biological screening

Functionalization of Pyrene To Prepare Luminescent Materials—Typical Examples of Synthetic Methodology

Pyrene-based π-conjugated materials are considered to be an ideal organic electro-luminescence material for application in semiconductor devices, such as organic light-emitting diodes (OLEDs), organic field-effect transistors (OFETs) and organic photovoltaics (OPVs), and so forth. However, the great drawback of employing pyrene as an organic luminescence material is the formation of excimer emission, which quenches the efficiency at high concentration or in the solid-state. Thus, in order to obtain highly efficient optical devices, scientists have devoted much effort to tuning the structure of pyrene derivatives in order to realize exploitable properties by employing two strategies, 1) introducing a variety of moieties at the pyrene core, and 2) exploring effective and convenient synthetic strategies to functionalize the pyrene core. Over the past decades, our group has mainly focused on synthetic methodologies for functionalization of the pyrene core; we have found that formylation/acetylation or bromination of pyrene can selectly lead to functionalization at K-region by Lewis acid catalysis. Herein, this Minireview highlights the direct synthetic approaches (such as formylation, bromination, oxidation, and de-tert-butylation reactions, etc.) to functionalize the pyrene in order to advance research on luminescent materials for organic electronic applications. Further, this article demonstrates that the future direction of pyrene chemistry is asymmetric functionalization of pyrene for organic semiconductor applications and highlights some of the classical asymmetric pyrenes, as well as the latest breakthroughs. In addition, the photophysical properties of pyrene-based molecules are briefly reviewed. To give a current overview of the development of pyrene chemistry, the review selectively covers some of the latest reports and concepts from the period covering late 2011 to the present day

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Glioneuronal tumor with ATRX alteration, kinase fusion and anaplastic features (GTAKA): a molecularly distinct brain tumor type with recurrent NTRK gene fusions

Glioneuronal tumors are a heterogenous group of CNS neoplasms that can be challenging to accurately diagnose. Molecular methods are highly useful in classifying these tumors-distinguishing precise classes from their histological mimics and identifying previously unrecognized types of tumors. Using an unsupervised visualization approach of DNA methylation data, we identified a novel group of tumors (n = 20) that formed a cluster separate from all established CNS tumor types. Molecular analyses revealed ATRX alterations (in 16/16 cases by DNA sequencing and/or immunohistochemistry) as well as potentially targetable gene fusions involving receptor tyrosine-kinases (RTK; mostly NTRK1-3) in all of these tumors (16/16; 100%). In addition, copy number profiling showed homozygous deletions of CDKN2A/B in 55% of cases. Histological and immunohistochemical investigations revealed glioneuronal tumors with isomorphic, round and often condensed nuclei, perinuclear clearing, high mitotic activity and microvascular proliferation. Tumors were mainly located supratentorially (84%) and occurred in patients with a median age of 19 years. Survival data were limited (n = 18) but point towards a more aggressive biology as compared to other glioneuronal tumors (median progression-free survival 12.5 months). Given their molecular characteristics in addition to anaplastic features, we suggest the term glioneuronal tumor with ATRX alteration, kinase fusion and anaplastic features (GTAKA) to describe these tumors. In summary, our findings highlight a novel type of glioneuronal tumor driven by different RTK fusions accompanied by recurrent alterations in ATRX and homozygous deletions of CDKN2A/B. Targeted approaches such as NTRK inhibition might represent a therapeutic option for patients suffering from these tumors

Tectono-stratigraphic response of the Sandino Forearc Basin (N-Costa Rica and W-Nicaragua) to episodes of rough crust and oblique subduction

The southern Central American active margin is a world-class site where past and present subduction processes have been extensively studied. Tectonic erosion/accretion and oblique/orthogonal subduction are thought to alternate in space and time along the Middle American Trench. These processes may cause various responses in the upper plate, such as uplift/subsidence, deformation, and volcanic arc migration/ shut-off. We present an updated stratigraphic framework of the Late Cretaceous– Cenozoic Sandino Forearc Basin (SFB) which provides evidence of sedimentary response to tectonic events. Since its inception, the basin was predominantly filled with deep-water volcaniclastic deposits. In contrast, shallow-water deposits appeared episodically in the basin record and are considered as tectonic event markers. The SFB stretches for about 300 km and varies in thickness from 5 km (southern part) to about 16 km (northern part). The drastic, along-basin, thickness variation appears to be the result of (1) differential tectonic evolutions and (2) differential rates of sediment supply. (1) The northern SFB did not experience major tectonic events. In contrast, the reduced thickness of the southern SFB (5 km) is the result of at least four uplift phases related to the collision/accretion of bathymetric reliefs on the incoming plate: (i) the accretion of a buoyant oceanic plateau (Nicoya Complex) during the middle Campanian; (ii) the collision of an oceanic plateau (?) during the late Danian–Selandian; (iii) the collision/accretion of seamounts during the late Eocene–early Oligocene; (iv) the collision of seamounts and ridges during the Pliocene–Holocene. (2) The northwestward thickening of the SFB may have been enhanced by high sediment supply in the Fonseca Gulf area which reflects sourcing from wide, high relief drainage basins. In contrast, sedimentary input has possibly been lower along the southern SFB, due to the proximity of the narrow, lowland isthmus of southern Central America. Moreover, two phases of strongly oblique subduction affected the margin, producing strike-slip faulting in the forearc basin: (1) prior to the Farallon Plate breakup, an Oligocene transpressional phase caused deformation and uplift of the basin depocenter, triggering shallowing-upward of the Nicaraguan Isthmus in the central and northern SFB; (2) a Pleistocene–Holocene transtensional phase drives the NW-directed motion of a forearc sliver and reactivation of the graben-bounding faults of the late Neogene Nicaraguan Depression. We discuss arguments in favour of a Pliocene development of the Nicaraguan Depression and propose that the Nicaraguan Isthmus, which is the apparent rift shoulder of the depression, represents a structure inherited from the Oligocene transpressional phase