1. VEGF levels in plasma in relation to platelet activation, glycemic control, and microvascular complications in type 1 diabetesReinier O. Schlingemann, Cornelis J. F. van Noorden, Mattheus J.M. Diekman, Anna Tiller, Joost C.M. Meijers, Pieter Koolwijk, Wilmar M. Wiersinga, 2013, izvirni znanstveni članek Povzetek: OBJECTIVE
Increased levels of vascular endothelial growth factor (VEGF) in human plasma samples have suggested that circulating VEGF is a cause of endothelial dysfunction in diabetes mellitus. However, artificial release of VEGF from platelets as a source of VEGF in plasma samples, as also occurs in serum samples, has not been ruled out in these studies.
RESEARCH DESIGN AND METHODS
We determined VEGF levels in plasma collected in both citrate and PECT, a medium that inactivates platelets, in a cross-sectional cohort of 21 healthy subjects and 64 patients with type 1 diabetes. In addition, we evaluated whether VEGF levels in both types of plasma correlated with the presence of diabetes, glycemic control, markers of in vivo or ex vivo platelet activation, and degree of diabetic retinopathy and nephropathy.
RESULTS
VEGF levels were invariably low in PECT plasma of both nondiabetic and diabetic subjects and were unrelated to any other diabetes-related variable studied. In contrast, VEGF levels in citrate plasma were 150% higher in diabetic patients than in control subjects and correlated with diabetes-related variables. Multiple linear regression analysis showed that levels of platelet factor 4, a marker for ex vivo platelet activation, and HbA1c were the independent predictors of VEGF levels in citrate plasma. Platelet activation, in vivo and ex vivo, was similar in diabetic persons and control subjects.
CONCLUSIONS
Like serum, citrate plasma is not suitable for reliable measurements of circulating VEGF. The low levels of VEGF in vivo, as represented by measurements in PECT plasma in our study, do not support a role of circulating VEGF in endothelial dysfunction in type 1 diabetes. Higher levels of VEGF in citrate plasma samples of diabetic persons do not represent the in vivo situation, but mainly originate from higher artificial ex vivo release from platelets correlating with the degree of glycemic control. Ključne besede: vascular endothelial growth factor, VEGF, diabetes mellitus Objavljeno v DiRROS: 02.08.2024; Ogledov: 161; Prenosov: 96
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2. Real-world outcomes, treatment patterns and T790M testing rates in non-small cell lung cancer patients treated with first-line first- or second-generation epidermal growth factor receptor tyrosine kinase inhibitors from the Slovenian cohort of the REFLECT studyNina Turnšek, Rok Devjak, Natalija Edelbaher, Ilonka Osrajnik, Mojca Unk, Dušanka Vidovič, Tina Jerič, Urška Janžič, 2022, izvirni znanstveni članek Povzetek: Background. Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are effective treatments for EGFR mutation-positive (EGFRm) non-small cell lung cancer (NSCLC). However, routine clinical practice is different between countries/institutions. Patients and methods. The REFLECT study (NCT04031898) is a retrospective medical chart review that explored real-life treatment and outcomes of EGFRm NSCLC patients receiving first-line (1L) first-/second-generation (1G/2G) EGFR TKIs in 8 countries. This study included adult patients with documented advanced/metastatic EGFRm NSCLC with 1L 1G/2G EGFR TKIs initiated between Jan 2015 – Jun 2018. We reviewed data on clinical characteristics, treatments, EGFR/T790M testing patterns, and survival outcomes. Here, we report data from 120 medical charts in 3 study sites from Slovenia. Results. The Slovenian cohort (median age 70 years, 74% females) received 37% erlotinib, 32% afatinib, 31% gefitinib. At the time of data collection, 94 (78%) discontinuations of 1L TKI, and 89 (74%) progression events on 1L treatment were reported. Among patients progressing on 1L, 73 (82%) were tested for T790M mutation yielding 50 (68%) positive results, and 62 (85%) received 2L treatment. 82% of patients received osimertinib. Attrition rate between 1L and 2L was 10%. The median (95% CI) real-world progression free survival on 1L EGFR TKIs was 15.6 (12.6, 19.2) months; median overall survival (95% CI) was 28.9 (25.0, 34.3) months. Conclusions. This real-world study provides valuable information about 1G/2G EGFR TKIs treatment outcomes and attrition rates in Slovenian EGFRm NSCLC patients. The reduced attrition rate and improved survival outcomes empha-size the importance of 1L treatment decision. Ključne besede: real-world study, non-small cell lung cancer, epidermal growth factor receptor, lung cancer Objavljeno v DiRROS: 25.07.2024; Ogledov: 140; Prenosov: 70
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3. IGF2 and IGF1R identified as novel tip cell genes in primary microvascular endothelial cell monolayersMarchien G. Dallinga, Bahar Yetkin-Arik, Richelle P. Kayser, Ilse M.C. Vogels, Patrycja Nowak-Sliwinska, Arjan W. Griffioen, Cornelis J. F. van Noorden, Ingeborg Klaassen, Reinier O. Schlingemann, 2018, izvirni znanstveni članek Povzetek: Tip cells, the leading cells of angiogenic sprouts, were identified in cultures of human umbilical vein endothelial cells (HUVECs) by using CD34 as a marker. Here, we show that tip cells are also present in primary human microvascular endothelial cells (hMVECs), a more relevant endothelial cell type for angiogenesis. By means of flow cytometry, immunocytochemistry, and qPCR, it is shown that endothelial cell cultures contain a dynamic population of CD34+ cells with many hallmarks of tip cells, including filopodia-like extensions, elevated mRNA levels of known tip cell genes, and responsiveness to stimulation with VEGF and inhibition by DLL4. Furthermore, we demonstrate that our in vitro tip cell model can be exploited to investigate cellular and molecular mechanisms in tip cells and to discover novel targets for anti-angiogenesis therapy in patients. Small interfering RNA (siRNA) was used to knockdown gene expression of the known tip cell genes angiopoietin 2 (ANGPT2) and tyrosine kinase with immunoglobulin-like and EGF-like domains 1 (TIE1), which resulted in similar effects on tip cells and sprouting as compared to inhibition of tip cells in vivo. Finally, we identified two novel tip cell-specific genes in CD34+ tip cells in vitro: insulin-like growth factor 2 (IGF2) and IGF-1-receptor (IGF1R). Knockdown of these genes resulted in a significant decrease in the fraction of tip cells and in the extent of sprouting in vitro and in vivo. In conclusion, this study shows that by using our in vitro tip cell model, two novel essential tip cells genes are identified. Ključne besede: Angiogenesis, tip cells, CD34, IGF2, endothelial cells, cultured cells, endothelial growth factors Objavljeno v DiRROS: 24.07.2024; Ogledov: 160; Prenosov: 136
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4. IGF-binding proteins 3 and 4 are regulators of sprouting angiogenesisMarchien G. Dallinga, Yasmin I. Habani, Richelle P. Kayser, Cornelis J. F. van Noorden, Ingeborg Klaassen, Reinier O. Schlingemann, 2020, izvirni znanstveni članek Povzetek: Purpose
We have previously identified insulin-like growth factor 2 (IGF2) and insulin-like growth factor 1 receptor (IGF1R) as essential proteins for tip cell maintenance and sprouting angiogenesis. In this study, we aim to identify other IGF family members involved in endothelial sprouting angiogenesis.
Methods
Effects on sprouting were analyzed in human umbilical vein endothelial cells (HUVECs) using the spheroid-based sprouting model, and were quantified as mean number of sprouts per spheroid and average sprout length. RNA silencing technology was used to knockdown gene expression. Recombinant forms of the ligands (IGF1 and IGF2, insulin) and the IGF-binding proteins (IGFBP) 3 and 4 were used to induce excess effects. Effects on the tip cell phenotype were analyzed by measuring the fraction of CD34+ tip cells using flow cytometry and immunohistochemistry in a 3D angiogenesis model. Experiments were performed in the presence and absence of serum.
Results
Knockdown of IGF2 inhibited sprouting in HUVECs, in particular when cultured in the absence of serum, suggesting that components in serum influence the signaling of IGF2 in angiogenesis in vitro. We then determined the effects of IGFBP3 and IGFBP4, which are both present in serum, on IGF2-IGF1R signaling in sprouting angiogenesis in the absence of serum: knockdown of IGFBP3 significantly reduced sprouting angiogenesis, whereas knockdown of IGFBP4 resulted in increased sprouting angiogenesis in both flow cytometry analysis and immunohistochemical analysis of the 3D angiogenesis model. Other IGF family members except INSR did not affect IGF2-IGF1R signaling.
Conclusions
Serum components and IGF binding proteins regulate IGF2 effects on sprouting angiogenesis. Whereas IGFBP3 acts as co-factor for IGF2-IGF1R binding, IGFBP4 inhibits IGF2 signaling. Ključne besede: Angiogenesis, tip cells, IGF2, IGF binding proteins, endothelial cells, cultured cells, endothelial growth factors Objavljeno v DiRROS: 23.07.2024; Ogledov: 147; Prenosov: 153
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5. A new network for the advancement of marine biotechnology in Europe and beyondAna Rotter, Ariola Bacu, Michèle Barbier, Francesco Bertoni, Atle M. Bones, M. Leonor Cancela, Jens Carlsson, Maria F. Carvalho, Marta Cegłowska, Meltem Conk Dalay, Jerica Sabotič, 2020, izvirni znanstveni članek Povzetek: Marine organisms produce a vast diversity of metabolites with biological activities useful for humans, e.g., cytotoxic, antioxidant, anti-microbial, insecticidal, herbicidal, anticancer, pro-osteogenic and pro-regenerative, analgesic, anti-inflammatory, anti-coagulant, cholesterol-lowering, nutritional, photoprotective, horticultural or other beneficial properties. These metabolites could help satisfy the increasing demand for alternative sources of nutraceuticals, pharmaceuticals, cosmeceuticals, food, feed, and novel bio-based products. In addition, marine biomass itself can serve as the source material for the production of various bulk commodities (e.g., biofuels, bioplastics, biomaterials). The sustainable exploitation of marine bio-resources and the development of biomolecules and polymers are also known as the growing field of marine biotechnology. Up to now, over 35,000 natural products have been characterized from marine organisms, but many more are yet to be uncovered, as the vast diversity of biota in the marine systems remains largely unexplored. Since marine biotechnology is still in its infancy, there is a need to create effective, operational, inclusive, sustainable, transnational and transdisciplinary networks with a serious and ambitious commitment for knowledge transfer, training provision, dissemination of best practices and identification of the emerging technological trends through science communication activities. A collaborative (net)work is today compelling to provide innovative solutions and products that can be commercialized to contribute to the circular bioeconomy. This perspective article highlights the importance of establishing such collaborative frameworks using the example of Ocean4Biotech, an Action within the European Cooperation in Science and Technology (COST) that connects all and any stakeholders with an interest in marine biotechnology in Europe and beyond. Ključne besede: marine biotechnology, marine natural products, blue growth, marine biodiversity and chemodiversity, responsible research and innovation, stakeholder engagement, science communication, sustainability Objavljeno v DiRROS: 22.07.2024; Ogledov: 168; Prenosov: 88
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6. Learning deep representations of enzyme thermal adaptationGang Li, Filip Buric, Jan Zrimec, Sandra Viknander, Jens Nielsen, Aleksej Zelezniak, Martin K. M. Engqvist, 2022, izvirni znanstveni članek Povzetek: Temperature is a fundamental environmental factor that shapes the evolution of organisms. Learning thermal determinants of protein sequences in evolution thus has profound significance for basic biology, drug discovery, and protein engineering. Here, we use a data set of over 3 million BRENDA enzymes labeled with optimal growth temperatures (OGTs) of their source organisms to train a deep neural network model (DeepET). The protein-temperature representations learned by DeepET provide a temperature-related statistical summary of protein sequences and capture structural properties that affect thermal stability. For prediction of enzyme optimal catalytic temperatures and protein melting temperatures via a transfer learning approach, our DeepET model outperforms classical regression models trained on rationally designed features and other deep-learning-based representations. DeepET thus holds promise for understanding enzyme thermal adaptation and guiding the engineering of thermostable enzymes. Ključne besede: bioinformatics, deep neural networks, enzyme catalytic temperatures, optimal growth temperatures, protein thermostability, transfer learning Objavljeno v DiRROS: 17.07.2024; Ogledov: 194; Prenosov: 150
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7. Transcriptional deregulation of stress-growth balance in Nicotiana benthamiana biofactories producing insect sex pheromonesMojca Juteršek, Marko Petek, Živa Ramšak, Elena Moreno Gimenéz, Silvia Gianoglio, Rubèn Mateos Fernández, Diego Orzaez, Kristina Gruden, Špela Baebler, 2022, izvirni znanstveni članek Povzetek: Plant biofactories are a promising platform for sustainable production of high-value compounds, among which are insect sex pheromones, a green alternative to conventional insecticides in agriculture. Recently, we have constructed transgenic Nicotiana benthamiana plants (“Sexy Plants”, SxP) that successfully produce a blend of moth (Lepidoptera) sex pheromone compounds (Z)-11-hexadecen-1-ol and (Z)-11-hexadecenyl acetate. However, efficient biosynthesis of sex pheromones resulted in growth and developmental penalty, diminishing the potential for commercial use of SxP in biomanufacturing. To gain insight into the underlying molecular responses, we analysed the whole-genome transcriptome and evaluated it in relation to growth and pheromone production in low- and high-producing transgenic plants of v1.0 and v1.2 SxP lines. In our study, high-producing SxPv1.2 plants accumulated the highest amounts of pheromones but still maintained better growth compared to v1.0 high producers. For an in-depth biological interpretation of the transcriptomic data, we have prepared a comprehensive functional N. benthamiana genome annotation as well as gene translations to Arabidopsis thaliana, enabling functional information transfer by using Arabidopsis knowledge networks. Differential gene expression analysis, contrasting pheromone producers to wild-type plants, revealed that while only a few genes were differentially regulated in low-producing plants, high-producing plants exhibited vast transcriptional reprogramming. They showed signs of stress-like response, manifested as downregulation of photosynthesis-related genes and significant differences in expression of hormonal signalling and secondary metabolism-related genes, the latter presumably leading to previously reported volatilome changes. Further network analyses confirmed stress-like response with activation of jasmonic acid and downregulation of gibberellic acid signalling, illuminating the possibility that the observed growth penalty was not solely a consequence of a higher metabolic burden imposed upon constitutive expression of a heterologous biosynthetic pathway, but rather the result of signalling pathway perturbation. Our work presents an example of comprehensive transcriptomic analyses of disadvantageous stress signalling in N. benthamiana biofactory that could be applied to other bioproduction systems. Ključne besede: transcriptomics, plant biotechnology, jasmonic acid, growthstress tradeoffs, network analysis, growth penalty, insect sex pheromone Objavljeno v DiRROS: 17.07.2024; Ogledov: 184; Prenosov: 150
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8. Insulin-like growth factor 1 receptor expression in advanced non-small-cell lung cancer and its impact on overall survivalMojca Humar, Izidor Kern, Gregor Vlačić, Vedran Hadžić, Tanja Čufer, 2017, izvirni znanstveni članek Ključne besede: insulin-like growth factor 1 receptor, type 2 diabetes mellitus, advanced non-small-cell lung cancer, overall survival Objavljeno v DiRROS: 03.06.2024; Ogledov: 226; Prenosov: 159
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9. Too hot to handle : effects of water temperature on the early life stages of Gongolaria barbata (Fucales)Ana Lokovšek, Valentina Pitacco, Annalisa Falace, Domen Trkov, Martina Orlando-Bonaca, 2024, izvirni znanstveni članek Povzetek: Gongolaria barbata plays a crucial role as a habitat-forming Fucales species in the Mediterranean Sea, thriving in shallow, sheltered coastal regions, where it exhibits optimal growth in a temperature range of 10 to 25 °C. In the northern Adriatic Sea, a semi-enclosed part of the Mediterranean, there has been a remarkable increase in seawater temperatures in recent decades, often exceeding 28 °C in summer. These high temperatures pose a significant threat to the vulnerable early life stages of G. barbata. This study delves into the effects of four temperatures (15, 18, 24, and 28 °C) on the growth of G. barbata over its first 16 days, closely monitoring mortality, deformities, and overall survival. Our experiments reveal that higher temperatures can result in deformities and increased mortality of germlings. Notably, a temperature of 28 °C resulted in the death of all germlings within the first week, whereas those exposed to 24 °C survived until the second week, albeit with significant deformities prior to death. In contrast, germlings cultivated at 15 and 18 °C exhibited normal development with minimal deformities. These results highlight the susceptibility of the early life stages of G. barbata to temperature-induced stress and provide valuable insights into the potential consequences of rising seawater temperatures in the Mediterranean. Ključne besede: sea temperature, early stages of growth, deformations, macroalgae, climate change, Mediterranean Sea Objavljeno v DiRROS: 17.05.2024; Ogledov: 334; Prenosov: 373
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10. Release of growth factors after mechanical and chemical pleurodesis for treatment of malignant pleural effusion : a randomized control studyAljaž Hojski, Maja Leitgeb, Anton Crnjac, 2015, izvirni znanstveni članek Povzetek: Growth factors are key inducers of fibrosis but can also mediate inflammatory responses resulting in increasing pleural effusion and acute respiratory distress syndrome. The primary aim of the study was to analyse growth factors release after performing chemical and mechanical pleurodesis in the first 48 hours at the patients with malignant pleural effusion. The secondary endpoints were to evaluate the effectiveness of the both pleurodeses, symptoms release and the quality of life of patients after the treatment. Patients and methods. A prospective randomized study included 36 consecutive female patients with breast carcinoma and malignant pleural effusion in an intention-to-treat analysis. We treated 18 patients by means of thoracoscopic mechanical pleurodesis and 18 patients by chemical pleurodesis with talcum applied over a chest tube. We gathered the pleural fluid and serum samples in the following 48 hours under a dedicated protocol and tested them for growth factors levels. A quality of life and visual analogue pain score surveys were also performed. Results. Median measured serum vascular endothelial growth factor (VEGF) level after chemical pleurodesis was 930.68 pg/ml (95% CI: 388.22-4656.65) and after mechanical pleurodesis 808.54 pg/ml. (95% CI: 463.20-1235.13) (p = 0.103). Median pleural levels of transforming growth factor (TGF) ß1 were higher after performing mechanical pleurodesis (4814.00 pg/ml [95% CI: 2726.51-7292.94]) when compared to those after performing chemical pleurodesis (1976.50 pg/ml [95% CI: 1659.82-5136.26]) (p = 0.078). We observed similar results for fibroblast growth factor (FGF) ß; the serum level was higher after mechanical pleurodesis (30.45 pg/ml [95% CI: 20.40-59.42]), compared to those after chemical pleurodesis (13.39 pg/ml [95% CI: 5.04-74.60]) (p = 0.076). Mechanical pleurodesis was equally effective as chemical pleurodesis in terms of hospital stay, pleural effusion re-accumulation, requiring of additional thoracentesis, median overall survival, but, it shortened the mean thoracic drainage duration (p = 0.030) and resulted in a higher symptoms release and in a better quality of life (p = 0.047). Conclusions. We recorded an increase in serum VEGF levels after chemical pleurodesis, however on the contrary, an increase in the pleural fluid level of TGF%1 and FGF%] after mechanical pleurodesis with respect to compared group. Although the differences did not reach statistical significance, VEGF, TGFß1 and FGFß remain the most interesting parameters for future research. Considering the mechanisms of growth factors action, we conclude that in our study group mechanical pleurodesis might be more efficient in terms of growth factors release, thoracic drainage duration and resulted in a higher symptoms release and in a better quality of life than chemical pleurodesis. Ključne besede: malignant pleural effusion, pleurodesis, growth factors, quality of life Objavljeno v DiRROS: 23.04.2024; Ogledov: 400; Prenosov: 351
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