Tumor-intrinsic and Cancer-associated Fibroblast Subtypes Independently Predict Outcomes in Pancreatic Cancer.

OBJECTIVE: To assess the utility of tumor-intrinsic and cancer-associated fibroblast (CAF) subtypes of pancreatic ductal adenocarcinoma (PDAC) in predicting response to neoadjuvant therapy (NAT) and overall survival. BACKGROUND: PDAC remains a deadly disease with limited treatment options, and both the tumor as well as the microenvironment play an important role in pathogenesis. Gene expression-based tumor-intrinsic subtypes (classical and basal-like) have been shown to predict outcomes, but tumor microenvironment subtypes are still evolving. METHODS: RNA-sequencing was performed on 114 deidentified resected PDAC tumors. Clinical data were collected by retrospective chart review. Single sample classifiers (SSCs) were used to determine classical and basal-like subtypes as well as tumor-permissive permCAF and tumor-restraining restCAF subtypes. Survival was analyzed using log-rank test. RESULTS: Patients who received NAT had an increase in overall survival (OS), with median survival of 27.9 months compared to 20.1 months for those who did not receive NAT, but the difference did not reach statistical significance (HR 0.64, P=0.076). Either tumor-intrinsic or CAF subtypes alone were associated with OS regardless of NAT or no NAT, and patients with classical or restCAF subtype had the best outcomes. When evaluated together, patients with classical-restCAF subtype had the best OS and basal-permCAF the worst OS (P<0.0001). NAT patients with classical-restCAF subtype demonstrated the longest OS compared to the other groups (P=0.00041). CONCLUSIONS: CAF subtypes have an additive effect over tumor-intrinsic subtypes in predicting survival with or without neoadjuvant FOLFIRINOX in PDAC. Molecular subtyping of both tumor and CAF compartments of PDAC may be important steps in selecting first-line systemic therapy.

EndoPRS: Incorporating Endophenotype Information to Improve Polygenic Risk Scores for Clinical Endpoints.

Polygenic risk score (PRS) prediction of complex diseases can be improved by leveraging related phenotypes. This has motivated the development of several multi-trait PRS methods that jointly model information from genetically correlated traits. However, these methods do not account for vertical pleiotropy between traits, in which one trait acts as a mediator for another. Here, we introduce endoPRS, a weighted lasso model that incorporates information from relevant endophenotypes to improve disease risk prediction without making assumptions about the genetic architecture underlying the endophenotype-disease relationship. Through extensive simulation analysis, we demonstrate the robustness of endoPRS in a variety of complex genetic frameworks. We also apply endoPRS to predict the risk of childhood onset asthma in UK Biobank by leveraging a paired GWAS of eosinophil count, a relevant endophenotype. We find that endoPRS significantly improves prediction compared to many existing PRS methods, including multi-trait PRS methods, MTAG and wMT-BLUP, which suggests advantages of endoPRS in real-life clinical settings.

Determination of permissive and restraining cancer-associated fibroblast (DeCAF) subtypes.

Cancer-associated fibroblast (CAF) subpopulations in pancreatic ductal adenocarcinoma (PDAC) have been identified using single-cell RNA sequencing (scRNAseq) with divergent characteristics, but their clinical relevance remains unclear. We translate scRNAseq-derived CAF cell-subpopulation-specific marker genes to bulk RNAseq data, and develop a single- sample classifier, DeCAF, for the classification of clinically rest raining and perm issive CAF subtypes. We validate DeCAF in 19 independent bulk transcriptomic datasets across four tumor types (PDAC, mesothelioma, bladder and renal cell carcinoma). DeCAF subtypes have distinct histology features, immune landscapes, and are prognostic and predict response to therapy across cancer types. We demonstrate that DeCAF is clinically replicable and robust for the classification of CAF subtypes in patients for multiple tumor types, providing a better framework for the future development and translation of therapies against permissive CAF subtypes and preservation of restraining CAF subtypes. Significance: We introduce a replicable and robust classifier, DeCAF, that delineates the significance of the role of permissive and restraining CAF subtypes in cancer patients. DeCAF is clinically tractable, prognostic and predictive of treatment response in multiple cancer types and lays the translational groundwork for the preclinical and clinical development of CAF subtype specific therapies.

Extensive research of conductivity in the fluorite-like KLn4Mo3O15F (Ln = La, Pr, Nd) rare earth molybdates: theoretical and experimental data.

The conductive properties of fluorite-like structures KLn4Mo3O15F (Ln = La, Pr, Nd: KLM, KPM, KNM) have been studied theoretically and experimentally. Theoretical studies included the geometrical-topological analysis of voids and channels available for migration of working ions; bond valence site energy calculations of the oxygen ions' migration energy; quantum-chemical calculations for the estimation of the oxygen vacancies formation energy. Experimental measurements of conductivity were made using impedance spectroscopy and as a function of oxygen partial pressure. The total conductivity was ∼10-3 S cm-1 for KLM and ∼10-2 S cm-1 for KPM and KNM at 800 °C. Measurements with changes in partial pressure proved the mixed nature of electric transport in KLM, KPM, and KNM phases, with predominantly ionic conductivity. The measured ion transference numbers in air reached approximately 0.9 at 800 °C for the KPM and KNM ceramics. Also, evaluated proton transfer numbers were less than 10%, indicating a small contribution to the total conductivity.

Rapid and Cost-Efficient Detection of RET Rearrangements in a Large Consecutive Series of Lung Carcinomas.

RET-kinase-activating gene rearrangements occur in approximately 1-2% of non-small-cell lung carcinomas (NSCLCs). Their reliable detection requires next-generation sequencing (NGS), while conventional methods, such as immunohistochemistry (IHC), fluorescence in situ hybridization (FISH) or variant-specific PCR, have significant limitations. We developed an assay that compares the level of RNA transcripts corresponding to 5'- and 3'-end portions of the RET gene; this test relies on the fact that RET translocations result in the upregulation of the kinase domain of the gene and, therefore, the 5'/3'-end expression imbalance. The present study included 16,106 consecutive NSCLC patients, 14,449 (89.7%) of whom passed cDNA quality control. The 5'/3'-end unbalanced RET expression was observed in 184 (1.3%) tumors, 169 of which had a sufficient amount of material for the identification of translocation variants. Variant-specific PCR revealed RET rearrangements in 155/169 (91.7%) tumors. RNA quality was sufficient for RNA-based NGS in 10 cases, 8 of which carried exceptionally rare or novel (HOOK1::RET and ZC3H7A::RET) RET translocations. We also applied variant-specific PCR for eight common RET rearrangements in 4680 tumors, which emerged negative upon the 5'/3'-end unbalanced expression test; 33 (0.7%) of these NSCLCs showed RET fusion. While the combination of the analysis of 5'/3'-end RET expression imbalance and variant-specific PCR allowed identification of RET translocations in approximately 2% of consecutive NSCLCs, this estimate approached 120/2361 (5.1%) in EGFR/KRAS/ALK/ROS1/BRAF/MET-negative carcinomas. RET-rearranged tumors obtained from females, but not males, had a decreased level of expression of thymidylate synthase (p < 0.00001), which is a known predictive marker of the efficacy of pemetrexed. The results of our study provide a viable alternative for RET testing in facilities that do not have access to NGS due to cost or technical limitations.

A New Look at the Chemical Recycling of Polypropylene: Thermal Oxidative Destruction in Aqueous Oxygen-Enriched Medium.

Recycling of plastic waste, in particular polypropylene, represents one of the most pressing challenges facing humanity. Despite the promise of chemical methods for recycling polypropylene, they usually require a high temperature and are energy-intensive. In this work, we investigated the oxidative thermolysis of polypropylene in aqueous media. This approach rendered it possible to carry out the decomposition of the polymer at a comparatively low temperature (150 °C). It was shown that among the tested, the most promising aqueous medium for the decomposition of polypropylene is water saturated with gaseous oxygen at an elevated pressure (14 bar) and at a temperature of 150 °C. In such an environment, polypropylene was converted mostly to acetic acid (up to 1.3 g/g acetic acid to starting polypropylene mass ratio). Moreover, methanol, formic acid, and propionic acid were also detected as the products. Finally, the applicability of the proposed recycling method to real polypropylene waste was shown.

Green nanocomposite gels based on binary network of sodium alginate and percolating halloysite clay nanotubes for 3D printing.

Alginate hydrogels with embedded rigid percolating network of halloysite clay nanotubes were evaluated as a novel ink for 3D printing. Hydrophilic alginate macromolecules adsorbing on halloysite stabilize the network of the nanotubes and form their own network of interlaced polymer chains. The effect of halloysite content on the structure and properties of the hydrogels was studied by rheometry, thermogravimetric analysis, FTIR-spectroscopy, dynamic light scattering, transmission electron microscopy, and 3D cryo-electron microscopy. Hydrogels demonstrate a very pronounced shear-thinning at extrusion and rather quick viscosity recovery after extrusion assigned to rapid rearrangement of the network structure promoted by mobile alginate chains. Even at low volume fractions (up to 0.054) the nanotubes reinforce the hydrogel increasing its storage modulus up to 650 Pa and inducing the appearance of yield stress. These properties make the alginate/halloysite hydrogels promising for the application in 3D printing for fabrication of green and sustainable nanocomposite materials made from natural components.

Microstructured Macromaterials Based on IPN Microgels.

This study investigates the formation of microstructured macromaterials from thermo- and pH-sensitive microgels based on interpenetrating networks of poly-N-isopropylacrylamide (PNIPAM) and polyacrylic acid (PAA). Macromaterials are produced as a result of the deposition of microgel particles and subsequent crosslinking of polyacrylic acid subnetworks to each other due to the formation of the anhydride bonds during annealing. Since both PNIPAM and PAA are environment-sensitive polymers, one can expect that their conformational state during material development will affect its resulting properties. Thus, the influence of conditions of preparation for annealing (pH of the solution, the temperature of preliminary drying) on the swelling behavior, pH- and thermosensitivity, and macromaterial inner structure was investigated. In parallel, the study of the effect of the relative conformations of the IPN microgel subnetworks on the formation of macromaterials was carried out by the computer simulations method. It was shown that the properties of the prepared macromaterials strongly depend both on the temperature and pH of the PNIPAM-PAA IPN microgel dispersions. This opens up new opportunities to obtain materials with pre-chosen characteristics and environmental sensitivity.

Green approach for fabrication of bacterial cellulose-chitosan composites in the solutions of carbonic acid under high pressure CO2.

The functionalization of the bacterial cellulose (BC) surface with a chitosan biopolymer to expand the areas of possible applications of the modified BC is an important scientific task. The creation of such composites in the carbonic acid solutions that were performed in this work has several advantages in terms of being biocompatible and eco-friendly. Quantitative analysis of chitosan content in the composite was conducted by tritium-labeled chitosan radioactivity detection method and this showed three times increased chitosan loading. Different physicochemical methods showed successful incorporation of chitosan into the BC matrix and interaction with it through hydrogen bonds. Microscopy results showed that the chitosan coating with a thickness of around 10 nm was formed in the bulk of BC, covering each microfibril. It was found that the inner specific surface area increased 1.5 times on deposition of chitosan from the solutions in carbonic acid.

Iridium-Catalyzed Silylation of Five-Membered Heteroarenes: High Sterically Derived Selectivity from a Pyridyl-Imidazoline Ligand.

The steric effects of substituents on five-membered rings are less pronounced than those on six-membered rings because of the difference in bond angles. Thus, the regioselectivities of reactions that occur with selectivities dictated by steric effects, such as the borylation of C-H bonds, have been poor in many cases. We report that the silylation of five-membered ring heteroarenes occurs with high sterically derived regioselectivity when catalyzed by the combination of [Ir(cod)(OMe)]2 and a phenanthroline ligand or a new pyridyl-imidazoline ligand that further increases the regioselectivity. The silylation reactions with these catalysts produce high yields of heteroarylsilanes from functionalization at the most sterically accessible C-H bonds of these rings under conditions that the borylation of C-H bonds with previously reported catalysts formed mixtures of products or products that are unstable. The heteroarylsilane products undergo cross-coupling reactions and substitution reactions with ipso selectivity to generate heteroarenes that bear halogen, aryl and perfluoroalkyl substituents.

Synthesis, structure and properties of layered Pr2MoO6-based oxymolybdates doped with Mg.

Undoped and Mg-doped Pr2MoO6 oxymolybdate polycrystals and single crystals have been prepared by solid-state reactions and flux growth. The compounds have been characterized by powder X-ray diffraction, energy-dispersive spectroscopy, inductively coupled plasma mass spectrometry, scanning transmission electron microscopy, single crystal X-ray structure analysis, differential scanning calorimetry and thermogravimetry. The (MgO)x(Pr2O3)y(MoO3)z (x + y + z = 1) solid solution series has been shown to extend to x = 0.03. The structure of the Mg-doped Pr2MoO6 single crystals can be represented as superimposed lattices of the main matrix (Pr2MoO6) and lattices in which Mo atoms are partially replaced by Mg. The incorporation of Mg atoms into the structure of Pr2MoO6 results in the disordering of the praseodymium and oxygen lattices. Both the polycrystalline and single-crystal Mg-doped samples are hygroscopic.

Structural organization of bacterial cellulose: The origin of anisotropy and layered structures.

In this paper, we perform a systematic analysis of the structural organization of bacterial cellulose (BC). We report four types of organization of the BC mass, produced by Gluconacetobacter hansenii that occur depending on cultivation conditions. Two of those, particularly, plywood type one and layers of micro-sized tubes were observed and described for the first time. In spherical BC particles (pellets), we found the layered structure that had previously been reported for planar geometry only. We suggest a model explaining why layers form in BC films and attempt to reveal the impact of different factors on the BC microscale morphology. We assume that the main factor that has direct impact on the type of structure formed is the rate of BC mass accumulation.

Iridium-Catalyzed Silylation of Five-Membered Heteroarenes: High Sterically Derived Selectivity from a Pyridyl-Imidazoline Ligand.

The steric effects of substituents on five-membered rings are less pronounced than those on six-membered rings because of the difference in bond angles. Thus, the regioselectivities of reactions of five-membered heteroarenes that occur with selectivities dictated by steric effects, such as the borylation of C-H bonds, have been poor in many cases. We report that the silylation of five-membered-ring heteroarenes occurs with high sterically derived regioselectivity when catalyzed by the combination of [Ir(cod)(OMe)]2 (cod=1,5-cyclooctadiene) and a phenanthroline ligand or a new pyridyl-imidazoline ligand that further increases the regioselectivity. The silylation reactions with these catalysts produce high yields of heteroarylsilanes from functionalization at the most sterically accessible C-H bonds of these rings under conditions that the borylation of C-H bonds with previously reported catalysts formed mixtures of products or products that are unstable. The heteroarylsilane products undergo cross-coupling reactions and substitution reactions with ipso selectivity to generate heteroarenes that bear halogen, aryl, and perfluoroalkyl substituents.

Structure of fluorite-like compound based on Nd5Mo3O16 with lead partly substituting for neodymium.

A single crystal of Nd5Mo3O16 with lead partly substituting for neodymium, which has a fluorite-like structure, was studied by precision X-ray diffraction, high-resolution transmission microscopy and EDX microanalysis. The crystal structure is determined in the space group Pn3¯n. It was found that the Pb atoms substitute in part for Nd atoms in the structure and are located in the vicinity of Nd2 positions. Partial substitutions of Mo cations for Nd positions and of Nd for Mo positions in crystals of the Ln5Mo3O16 oxide family are corroborated by X-ray diffraction for the first time. The first experimental verification of the location of an additional oxygen ion in the voids abutting MoO4 tetrahedra was obtained.

X-ray diffraction study of oxygen-conducting compounds Ln2Mo2O9 (Ln = La, Pr).

The La2Mo2O9 (LM) and Pr2Mo2O9 (PM) single crystals are studied using precision X-ray diffraction and high-resolution transmission microscopy at room temperature. The crystal structures are determined in the space group P2(1)3. La and Pr atoms, as well as Mo1 and O1 atoms, are located in the vicinity of the threefold axes rather than on the axes as in the high-temperature cubic phase. In both structures studied, the O2 and O3 positions are partially occupied. The coexistence of different configurations of the Mo coordination environment facilitates the oxygen-ion migration in the structure. Based on the X-ray data, the activation energies of O atoms are calculated and the migration paths of oxygen ions in the structures are analysed. The conductivity of PM crystals is close to that of LM crystals. The O2 and O3 atoms are the main contributors to the ion conductivity of LM and PM.

Novel composite Zr/PBI-O-PhT membranes for HT-PEFC applications.

Novel composite membranes for high temperature polymer-electrolyte fuel cells (HT-PEFC) based on a poly[oxy-3,3-bis(4'-benzimidazol-2″-ylphenyl)phtalide-5″(6″)-diyl] (PBI-O-PhT) polymer with small amounts of added Zr were prepared. It was shown in a model reaction between zirconium acetylacetonate (Zr(acac)4) and benzimidazole (BI) that Zr-atoms are capable to form chemical bonds with BI. Thus, Zr may be used as a crosslinking agent for PBI membranes. The obtained Zr/PBI-O-PhT composite membranes were examined by means of SAXS, thermomechanical analysis (TMA), and were tested in operating fuel cells by means of stationary voltammetry and impedance spectroscopy. The new membranes showed excellent stability in a 2000-hour fuel cell (FC) durability test. The modification of the PBI-O-PhT films with Zr facilitated an increase of the phosphoric acid (PA) uptake by the membranes, which resulted in an up to 2.5 times increased proton conductivity. The existence of an optimal amount of Zr content in the modified PBI-O-PhT film was shown. Larger amounts of Zr lead to a lower PA doping level and a reduced conductivity due to an excessively high degree of crosslinking.

Cell attachment on poly(3-hydroxybutyrate)-poly(ethylene glycol) copolymer produced by Azotobacter chroococcum 7B.

BACKGROUND: The improvement of biomedical properties, e.g. biocompatibility, of poly(3-hydroxyalkanoates) (PHAs) by copolymerization is a promising trend in bioengineering. We used strain Azotobacter chroococcum 7B, an effective producer of PHAs, for biosynthesis of not only poly(3-hydroxybutyrate) (PHB) and its main copolymer, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHB-HV), but also alternative copolymer, poly(3-hydroxybutyrate)-poly(ethylene glycol) (PHB-PEG). RESULTS: In biosynthesis we used sucrose as the primary carbon source and valeric acid or poly(ethylene glycol) 300 (PEG 300) as additional carbon sources. The chemical structure of PHB-PEG and PHB-HV was confirmed by 1H nuclear-magnetic resonance (1H NMR) analysis. The physico-chemical properties (molecular weight, crystallinity, hydrophilicity, surface energy) and surface morphology of films from PHB copolymers were studied. To study copolymers biocompatibility in vitro the protein adsorption and COS-1 fibroblasts growth on biopolymer films by XTT assay were analyzed. Both copolymers had changed physico-chemical properties compared to PHB homopolymer: PHB-HV and PHB-PEG had less crystallinity than PHB; PHB-HV was more hydrophobic than PHB in contrast to PHB-PEG appeared to have greater hydrophilicity than PHB; whereas the morphology of polymer films did not differ significantly. The protein adsorption to PHB-PEG was greater and more uniform than to PHB and PHB-PEG copolymer promoted better growth of COS-1 fibroblasts compared with PHB homopolymer. CONCLUSIONS: Thus, despite low EG-monomers content in bacterial origin PHB-PEG copolymer, this polymer demonstrated significant improvement in biocompatibility in contrast to PHB and PHB-HV copolymers, which may be coupled with increased protein adsorption and hydrophilicity of PEG-containing copolymer.

The terpolymer produced by Azotobacter chroococcum 7B: effect of surface properties on cell attachment.

The copolymerization of poly(3-hydroxybutyrate) (PHB) is a promising trend in bioengineering to improve biomedical properties, e.g. biocompatibility, of this biodegradable polymer. We used strain Azotobacter chroococcum 7B, an effective producer of PHB, for biosynthesis of not only homopolymer and its main copolymer, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHB-HV), but also novel terpolymer, poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-poly(ethylene glycol) (PHB-HV-PEG), using sucrose as the primary carbon source and valeric acid and poly(ethylene glycol) 300 (PEG 300) as additional carbon sources. The chemical structure of PHB-HV-PEG was confirmed by (1)H nuclear-magnetic resonance analysis. The physico-chemical properties (molecular weight, crystallinity, hydrophilicity, surface energy) of produced biopolymer, the protein adsorption to the terpolymer, and cell growth on biopolymer films were studied. Despite of low EG-monomers content in bacterial-origin PHB-HV-PEG polymer, the terpolymer demonstrated significant improvement in biocompatibility in vitro in contrast to PHB and PHB-HV polymers, which may be coupled with increased protein adsorption, hydrophilicity and surface roughness of PEG-containing copolymer.