Transcriptomic response to differentiation induction

Background  

Microarrays used for gene expression studies yield large amounts of data. The processing of such data typically leads to lists of differentially-regulated genes. A common terminal data analysis step is to map pathways of potentially interrelated genes.     

Synthesis and Characterization of Novel Quinazoline Type Inhibitors for Mutant and Wild-Type EGFR and RICK Kinases

The development of selective protein kinase inhibitors has become an important area of drug discovery for the treatment of different diseases. We report the synthesis and characterization of a series of novel quinazoline derivatives against three therapeutically important and pharmacologically related kinases: 1) epidermal growth factor receptor (EGFR; wild type and mutant) in the field of cancer, 2) receptor-interacting caspase-like apoptosis-regulatory kinase (RICK) in the field of inflammation, and 3) pUL97 of human cytomegalovirus (HCMV). For reference purpose we have synthesized the four clinically relevant quinazolines, including the lead compounds, which we previously identified for RICK and pUL97. A total of 52 quinazoline derivatives were synthesized and tested on the basis of these leads to specifically target the hydrophobic pocket of the ATP-binding site. Selected compounds were tested on wild-type and mutant forms of EGFR, RICK, and pUL97 kinases; their logP and logS values for assessing suitability as drugs were calculated and hit or lead compounds identified.     

Anti-carbamylated protein antibodies in the pre-symptomatic phase of rheumatoid arthritis,their relationship with multiple anti-citrulline peptide antibodies and association with radiological damage

IntroductionThe presence of a new autoantibody system, anti-carbamylated protein (anti-CarP) antibodies, has been identified in rheumatoid arthritis (RA). The presence of anti-CarP antibodies was evaluated in samples taken from individuals who subsequently developed RA before and after onset of symptoms and related to previously analysed antibodies against citrullinated peptides (ACPA specificities) and anti-CCP2.MethodsA total of 252 individuals, with 423 samples from before onset of symptoms of RA, and 197 population controls were identified as donors to the Medical Biobank of Northern Sweden; 192 of them were also sampled at the time of diagnosis. All samples were analysed for anti-CarP IgG and anti-CCP2 antibodies using ELISAs. Ten different antibody reactivities against citrullinated antigens (ACPA specificities) were analysed using a custom-made microarray based on the ImmunoCAP ISAC system (Phadia).ResultsThe concentration of anti-CarP antibodies was significantly increased in the pre-symptomatic individuals compared with controls (P <0.001) and also increased significantly after disease onset (P <0.001). The sensitivity for anti-CarP antibodies in the pre-symptomatic individuals was 13.9% (95% CI: 11 to 17.6) and 42.2% (95% CI: 35.4 to 49.3) following development of RA. Anti-CarP antibody positivity was found in 5.1% to 13.3% of individuals negative for anti-CCP2 or ACPA specificities. Presence of anti-CarP antibodies was significantly related to radiological destruction at baseline, at 24 months and also to radiological change (P <0.05, all).ConclusionsThe results indicate that anti-CarP antibodies are associated with disease development, even after adjusting for the presence of different ACPA fine specificities, and in anti-CCP2 negative individuals and contribute to the identification of a subset of patients with worse radiological progression of the disease independent of ACPA.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0536-2) contains supplementary material, which is available to authorized users.     

Photoactivation of lysosomally sequestered sunitinib after angiostatic treatment causes vascular occlusion and enhances tumor growth inhibition

The angiogenesis inhibitor sunitinib is a tyrosine kinase inhibitor that acts mainly on the VEGF and PDGF pathways. We have previously shown that sunitinib is sequestered in the lysosomes of exposed tumor and endothelial cells. This phenomenon is part of the drug-induced resistance observed in the clinic. Here, we demonstrate that when exposed to light, sequestered sunitinib causes immediate destruction of the lysosomes, resulting in the release of sunitinib and cell death. We hypothesized that this photoactivation of sunitinib could be used as a vaso-occlusive vascular-targeting approach to treating cancer. Spectral properties of sunitinib and its lysosomal accumulation were measured in vitro. The human A2780 ovarian carcinoma transplanted onto the chicken chorioallantoic membrane (CAM) and the Colo-26 colorectal carcinoma model in Balb/c mice were used to test the effects of administrating sunitinib and subsequently exposing tumor tissue to light. Tumors were subsequently resected and subject to immunohistochemical analysis. In A2780 ovarian carcinoma tumors, treatment with sunitinib+light resulted in immediate specific angio-occlusion, leading to a necrotic tumor mass 24 h after treatment. Tumor growth was inhibited by 70% as compared with the control group (**P<0.0001). Similar observations were made in the Colo-26 colorectal carcinoma, where light exposure of the sunitinib-treated mice inhibited tumor growth by 50% as compared with the control and by 25% as compared with sunitinib-only-treated tumors (N≥4; P=0.0002). Histology revealed that photoactivation of sunitinib resulted in a change in tumor vessel architecture. The current results suggest that the spectral properties of sunitinib can be exploited for application against certain cancer indications.Angiogenesis inhibitors are currently firmly implemented in the clinical management of cancer. For example, sunitinib has been approved for the treatment of advanced renal cell carcinoma (RCC),¹ gastrointestinal stromal tumors (GIST)² and pancreatic neuroendocrine tumors.³ Studies assessing its activity against other tumor types are currently underway.⁴ Sunitinib was developed as an angiogenesis inhibitor⁵ and revolutionized the management of advanced RCC and GIST. Its mode of action is based on the suppression of the tyrosine kinase activity of several growth factor receptors, mainly VEGFR2 and PDGFR (alpha and beta).⁶ It has been previously shown that sunitinib is sequestered by tumor cells in their lysosomal compartments.⁷ This sequestration, which limits the exposure of other parts of the cell to sunitinib, is part of a drug-induced resistance mechanism that has also been clinically observed.⁷ The sequestration and accumulation of sunitinib in the lysosomes is similar to a phenomenon that has been described for certain other chemotherapeutics^{8, 9} or photosensitizing compounds,¹⁰ and depends, at least to some extent, on the hydrophobic and weak basic features of the molecule. We discovered a particular characteristic of sunitinib based on its optical properties, which may be helpful in the treatment of certain cancers. On the basis of the spectral features of sunitinib, we hypothesized that the drug may have photosensitizer-like properties.¹¹ If so, exposure to light of an appropriate wavelength could lead to the disruption of the lysosomal membrane, the release of sunitinib and re-exposure of the cell to this molecule. This could lead to further cell damage and eventually cell death. In this study, we show that the exposure of sunitinib-treated cells to light of an appropriate wavelength excites the molecule, which leads to the generation of reactive oxygen species (ROS). We show in two tumor models, that is, human ovarian carcinoma (A2780) xenografted on the chorioallantoic membrane of the chicken embryo (chicken chorioallantoic membrane (CAM)) and in colorectal carcinoma in Balb/c mice, that treatment with sunitinib and its subsequent photoexcitation leads to significant occlusion of the vasculature and inhibition of tumor growth. Our results indicate that additional antitumor activity can be obtained after the normal use of sunitinib through its use as a photosensitizer and the application of light. The combination of classical sunitinib-induced angiostasis with the re-exposure of tumor cells to sunitinib after the destruction of lysosomes and photodynamic vessel obstruction can lead to a strategy that may be applicable in patients.     

A basal sphenodontian (Lepidosauria) from the Jurassic of Patagonia: new insights on the phylogeny and biogeography of Gondwanan rhynchocephalians

Herein we describe a new rhynchocephalian taxon from the Middle Jurassic of Patagonia, Argentina, representing the first Jurassic record of the group in South America. The new taxon, consisting of a complete dentary, is ascribed to Sphenodontia based on the presence of a deep and wide Meckelian groove, long posterior process, well‐developed coronoid process, and acrodont teeth showing dental regionalization including successional, alternate hatchling, and additional series. This allocation is reinforced by a phylogenetic analysis that places the new taxon in a basal position within a clade of sphenodontians that excludes Diphydontosaurus and Planocephalosaurus. Additionally, the new taxon clusters within a Gondwanan clade with the Indian Godavarisaurus from the Jurassic Kota Formation, sharing the presence of recurved and relatively large posterior successional teeth that are ribbed and bear a peculiar anterolingual groove. This sister‐group relationship is intriguing from a palaeobiogeographical viewpoint, as it suggests some degree of endemism during the initial stages of the breakup of Pangaea. We also discuss the ontogenetic stage of the new taxon and provide insights on the evolution of successional dentition in rhynchocephalians. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 342–360.