Mechanisms of resistance to a PI3K inhibitor in gastrointestinal stromal tumors: an omic approach to identify novel druggable targets

Background: Gastrointestinal stromal tumors (GISTs) represent a worldwide paradigm of target therapy. The introduction of tyrosine kinase inhibitors has deeply changed the prognosis of GIST patients, however, the majority of them acquire secondary mutations and progress. Unfortunately, besides tyrosine-kinase inhibitors, no other therapeutic options are available. Therefore, it is mandatory to identify novel molecules and/or strategies to overcome the inevitable resistance. In this context, after promising preclinical data on the novel PI3K inhibitor BYL719, the NCT01735968 trial in GIST patients who had previously failed treatment with imatinib and sunitinib started. BYL719 has attracted our attention, and we comprehensively characterized genomic and transcriptomic changes taking place during resistance. Methods: For this purpose, we generated two in vitro GIST models of acquired resistance to BYL719 and performed an omic-based analysis by integrating RNA-sequencing, miRNA, and methylation profiles in sensitive and resistant cells. Results: We identified novel epigenomic mechanisms of pharmacological resistance in GISTs suggesting the existence of pathways involved in drug resistance and alternatively acquired mutations. Therefore, epigenomics should be taken into account as an alternative adaptive mechanism. Conclusion: Despite the fact that currently we do not have patients in treatment with BYL719 to verify this hypothesis, the most intriguing result is the involvement of H19 and PSTA1 in GIST resistance, which might represent druggable targets

Analysis of microbiome in gastrointestinal stromal tumors: Looking for different players in tumorigenesis and novel therapeutic options

Preclinical forms of gastrointestinal stromal tumor (GIST), small asymptomatic lesions, called microGIST, are detected in approximately 30% of the general population. Gastrointestinal stromal tumor driver mutation can be already detected in microGISTs, even if they do not progress into malignant cancer; these mutations are necessary, but insufficient events to foster tumor progression. Here we profiled the tissue microbiota of 60 gastrointestinal specimens in three different patient cohorts—micro, low-risk, and high-risk or metastatic GIST—exploring the compositional structure, predicted function, and microbial networks, with the aim of providing a complete overview of microbial ecology in GIST and its preclinical form. Comparing microGISTs and GISTs, both weighted and unweighted UniFrac and Bray–Curtis dissimilarities showed significant community-level separation between them and a pronounced difference in Proteobacteria, Firmicutes, and Bacteroidota was observed. Through the LEfSe tool, potential microbial biomarkers associated with a specific type of lesion were identified. In particular, GIST samples were significantly enriched in the phylum Proteobacteria compared to microGISTs. Several pathways involved in sugar metabolism were also highlighted in GISTs; this was expected as cancer usually displays high aerobic glycolysis in place of oxidative phosphorylation and rise of glucose flux to promote anabolic request. Our results highlight that specific differences do exist in the tissue microbiome community between GIST and benign lesions and that microbiome restructuration can drive the carcinogenesis process

Spectroscopic and Morphological Studies of Metal-Organic and Metal-Free Dyes onto Titania Films for Dye-Sensitized Solar Cells

We have investigated the spectroscopic behavior of three different sensitizers adsorbed onto titania thin films in order to gain information both on the electron transfer process from dye to titania and on the anchorage of the chromophore onto the semiconductor. We have examined by UV-Vis and fluorescence spectroscopy the widely used ruthenium complex cis-di(thiocyanato)bis(2,2′-bipyridyl-4,4′-dicarboxylato)ruthenium(II) (N719), the more recently developed organic molecular 3-(5-(4-(diphenylamino)styryl)thiophen-2-yl)-2-cyanoacrylic acid (D5), and a push-pull zinc phthalocyanine sensitizer (ZnPc). Three type of titania films with different morphology, characterized by SEM and FT-IR measurement, were considered: a mesoporous transparent film deposited by spin-coating (TiMS), a semiopaque film deposited by doctor-blade from mesoporous titania (TiMS_DB) and a semiopaque film deposited by doctor-blade form commercial P25 titania (P25_DB). The use of TiMS is responsible for the adsorption of a higher amount of dye since the mesoporous structure allows increasing the interfacial area between dye and titania. Moreover, the fluorescence emission peak is weaker when the sensitizers are adsorbed onto TiMS. These findings suggest that mesostructured films could be considered the most promising substrates to realize photoanodes with a fast electron transfer process

Case report: A novel patient presenting TRIM32-related limb-girdle muscular dystrophy

Limb-girdle muscular dystrophy autosomal recessive 8 (LGMDR8) is a rare clinical manifestation caused by the presence of biallelic variants in the TRIM32 gene. We present the clinical, molecular, histopathological, and muscle magnetic resonance findings of a novel 63-years-old LGMDR8 patient of Italian origins, who went undiagnosed for 24 years. Clinical exome sequencing identified two TRIM32 missense variants, c.1181G > A p.(Arg394His) and c.1781G > A p.(Ser594Asp), located in the NHL1 and NHL4 structural domains, respectively, of the TRIM32 protein. We conducted a literature review of the clinical and instrumental data associated to the so far known 26 TRIM32 variants, carried biallelically by 53 LGMDR8 patients reported to date in 20 papers. Our proband's variants were previously identified only in three independent LGMDR8 patients in homozygosis, therefore our case is the first in literature to be described as compound heterozygous for such variants. Our report also provides additional data in support of their pathogenicity, since p.(Arg394His) is currently classified as a variant of uncertain significance, while p.(Ser594Asp) as likely pathogenic. Taken together, these findings might be useful to improve both the genetic counseling and the diagnostic accuracy of this rare neuromuscular condition

Echinoderms from the Museum of Zoology from the Universidad de Costa Rica

El Museo de Zoología de la Universidad de Costa Rica (MZUCR) se funda en 1966 y alberga la colección de organismos vertebrados e invertebrados más completa de Costa Rica. El MZUCR cuenta actualmente con 24 colec-ciones que contienen más de cinco millones de especíme-nes, y más de 13 000 especies identificadas. Las primeras colecciones datan 1960 e incluyen peces, reptiles, anfibios, poliquetos, crustáceos y equinodermos. Para este último grupo, el MZUCR posee un total de 157 especies, en 1 173 lotes y 4 316 ejemplares. Estas 157 especies representan el 54% del total de especies de equinodermos que posee Costa Rica (293 especies). El resto de especies están repar-tidas en las siguientes instituciones: Academia de la Cien-cias de California (CAS) (4.8%), Instituto Oceanográfico Scripps (SIO) (5.2%), en la Colección Nacional de equino-dermos “Dra. Ma. Elena Caso” de la Universidad Nacional Autónoma de México (ICML-UNAM) (12.7%), Museo de Zoología Comparada de Harvard (MZC) (19.2%), y en el Museo Nacional de Historia Natural del Instituto Smithso-niano (USNM) (35.1%). Es posible que haya material de Costa Rica en el Museo de Historia Natural de Dinamarca (NCD) y en el Museo de Historia Natural de los Ángeles (LACM), sin embargo, no hubo acceso a dichas coleccio-nes. A su vez hay 9.6% de especies que no aparecen en ningún museo, pero están reportadas en la literatura. Con base en esta revisión de colecciones se actualizó el listado taxonómico de equinodermos para Costa Rica que consta de 293 especies, 152 géneros, 75 familias, 30 órdenes y cinco clases. La costa Pacífica de Costa Rica posee 153 especies, seguida por la isla del Coco con 134 y la costa Caribe con 65. Holothuria resultó ser el género más rico con 25 especies.The Museum of Zoology, Universidad de Costa Rica (MZUCR) was founded in 1966 and houses the most complete collection of vertebrates and invertebrates in Costa Rica. The MZUCR currently has 24 collections containing more than five million specimens, and more than 13 000 species. The earliest collections date back to 1960 and include fishes, reptiles, amphibians, polychaetes, crustaceans and echinoderms. For the latter group, the MZUCR has a total of 157 species, in 1 173 lots and 4 316 specimens. These 157 species represent 54% of the total species of echino-derms from Costa Rica. The remaining species are distributed in the following institutions: California Academy of Sciences (CAS) (4.8%), Scripps Oceanographic Institute (SIO) (5.2%), National Echinoderm Collection “Dr. Ma. Elena Caso” from the National Autonomous University of Mexico (ICML-UNAM) (12.7%), the National Museum of Natural History, Smithsonian Institute (USNM) (35.1%), and the Harvard Museum of Comparative Zoology (19.2%). There may be material from Costa Rica in the Natural History Museum of Denmark (NCD) and the Natural History Museum of Los Angeles (LACM), however, there was no access to such collections. There are 9.6% that do not appear in museums, but are reported in the literature. Based on this revision, the taxonomic list of echinoderms for Costa Rica is updated to 293 species, 152 genera, 75 families, 30 orders and 5 classes. The Pacific coast of Costa Rica has 153 species, followed by the Isla del Coco with 134 and the Caribbean coast with 65. Holothuria is the most diverse genus with 25 species.UCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de BiologíaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Ciencias del Mar y Limnología (CIMAR)UCR::Vicerrectoría de Investigación::Unidades de Investigación::Artes y Letras::Museo de la Universidad de Costa Ric

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Outdoor operation of small-molecule organic photovoltaics

We measure the diurnal dependence of the operating characteristics of tetraphenyldibenzoperiflanthene (DBP):C70 planar-mixed heterojunction small-molecule organic photovoltaic (OPV) cells with 2,2′,2″-(1,3,5-benzenitryl tris-[1-phenyl-1H-benzimidazole] (TPBi):C70 electron-filtering cathode buffer layers. Over the course of a day, efficiency gradually increases as a result of a concomitant increase in short-circuit current, while the fill factor and open-circuit voltage remain constant. The results are analyzed on the basis of independent measurements of temperature- and intensity-dependent OPV performance. The power conversion efficiency is maximized slightly below 1 sun intensity and at 40 °C, which is beneficial for practical outdoor operation. We attribute the increased short circuit current with temperature to broadening of the absorption spectrum due to population of phonon states along with increased charge mobility, which also results in an increase in fill factor.Peer Reviewe

Phase Transition and Point Defects in the Ferroelectric Molecular Perovskite (MDABCO)(NH₄)I₃

We measured the anelastic, dielectric and structural properties of the metal-free molecular perovskite (ABX3) (MDABCO)(NH4)I3, which has already been demonstrated to become ferroelectric below TC= 448 K. Both the dielectric permittivity measured in air on discs pressed from powder and the complex Young’s modulus measured on resonating bars in a vacuum show that the material starts to deteriorate with a loss of mass just above TC, introducing defects and markedly lowering TC. The elastic modulus softens by 50% when heating through the initial TC, contrary to usual ferroelectrics, which are stiffer in the paraelectric phase. This is indicative of improper ferroelectricity, in which the primary order parameter of the transition is not the electric polarization, but the orientational order of the MDABCO molecules. The degraded material presents thermally activated relaxation peaks in the elastic energy loss, whose intensities increase together with the decrease in TC. The peaks are much broader than pure Debye due to the general loss of crystallinity. This is also apparent from X-ray diffraction, but their relaxation times have parameters typical of point defects. It is argued that the major defects should be of the Schottky type, mainly due to the loss of (MDABCO)2+ and I−, leaving charge neutrality, and possibly (NH4)+ vacancies. The focus is on an anelastic relaxation process peaked around 200 K at ∼1 kHz, whose relaxation time follows the Arrhenius law with τ0 ∼ 10−13 s and E≃0.4 eV. This peak is attributed to I vacancies (VX) hopping around MDABCO vacancies (VA), and its intensity presents a peculiar dependence on the temperature and content of defects. The phenomenology is thoroughly discussed in terms of lattice disorder introduced by defects and partition of VX among sites that are far from and close to the cation vacancies. A method is proposed for calculating the relative concentrations of VX, that are untrapped, paired with VA or forming VX–VA–VX complexes

Influence of Temperature, Pressure, and Humidity on the Stabilities and Transition Kinetics of the Various Polymorphs of FAPbI3

The phase transitions between the various polymorphs of FAPbI3 (FAPI, FA = formamidinium [CH(NH2)2]+) are studied by anelastic, dielectric, and X-ray diffraction measurements on samples pressed from δ-FAPI (2H phase) yellow powder. The samples become orange after application of as little as 0.2 GPa, which has been explained in terms of partial transformations to the other hexagonal polymorphs 4H and 6H. The phenomenon is discussed in the light of what is known about the stability of the various polymorphs of hybrid and inorganic perovskites ABX3 with large A cations and hence a large tolerance factor t. Remarkably, FAPI at room and higher temperatures behaves like a perovskite with a large t, while just below room temperature it behaves like a perovskite with a small t. The kinetics of the transformations between the polymorphs is enhanced by small amounts of intercalated water. It seems therefore worthy to try improving the atomic diffusion and crystallization during synthesis, and hence the final photovoltaic performance, through controlled small amounts of water that should be thoroughly removed after a sufficiently homogeneous and smooth microstructure is achieved

Hormonal Replacement Therapy and Lipids

We evaluated the effect of transdermal norethisterone acetate (NETA) versus oral medroxyprogesterone acetate (MPA) on the lipids of 28 postmenopausal women taking hormonal replacement therapy for climacteric symptoms. All the 28 patients were using conventional patches releasing 0.050 mg of estradiol per day continuously. However, while one group of 14 patients received transdermal NETA (0.25 mg/day) for 14 days of the cycle, the other group of 14 patients received oral MPA (10 mg/day) for the same number of days. The patients were randomly allocated to one of the two groups. The treatment cycles were repeated for 12 months. There was no significant difference between the two treatment groups for compliance and for incidence of side effects. Both hormonal replacement therapies were equally effective in relieving climacteric symptoms. All the patients underwent serum lipid assays twice, the first time before starting treatment and then again during the progestogen phase of the 12th and last cycle. Serum total cholesterol (TC), low-density lipoprotein (LDL-C), and triglyceride levels did not change significantly during both treatments. Transdermal estradiol associated with oral MPA significantly reduced high-density lipoprotein (HDL-C) by 17.9% (p < 0.05) and significantly increased LDL-C/HDL-C and TC/HDL-C risk ratios by 61.7% (p < 0.05) and 33.1% (p < 0.05), respectively. In contrast, administration of the transdermal NETA did not significantly affect HDL-C levels (- 1.9% of decrease) and, consequently, the risk ratios were minimally altered, with 3.3 and 6.0% increases for TC/HDL-C and LDL-C/HDL-C, respectively. There was a statistically significant difference (p < 0.05) in HDL-C net changes between MPA and NETA treatments (+ 8.5 and - 8.0 mg/dl, respectively). We can therefore conclude that the association of transdermal NETA with transdermal estradiol elicits a relatively benign impact on lipoprotein profile in comparison to oral MPA associatio