1. Long-term survival in glioblastoma : methyl guanine methyl transferase (MGMT) promoter methylation as independent favourable prognostic factorUroš Smrdel, Mara Popović, Matjaž Zwitter, Emanuela Boštjančič, Andrej Zupan, Viljem Kovač, Damjan Glavač, Drago Bokal, Janja Jerebic, 2016, izvirni znanstveni članek Povzetek: In spite of significant improvement after multi-modality treatment, prognosis of most patients with glioblastoma remains poor. Standard clinical prognostic factors (age, gender, extent of surgery and performance status) do not clearly predict long-term survival. The aim of this case-control study was to evaluate immuno-histochemical and genetic characteristics of the tumour as additional prognostic factors in glioblastoma. Long-term survivor group were 40 patients with glioblastoma with survival longer than 30 months. Control group were 40 patients with shorter survival and matched to the long-term survivor group according to the clinical prognostic factors. All patients underwent multimodality treatment with surgery, postoperative conformal radiotherapy and temozolomide during and after radiotherapy. Biopsy samples were tested for the methylation of MGMT promoter (with methylation specific polymerase chain reaction), IDH1 (with immunohistochemistry), IDH2, CDKN2A and CDKN2B (with multiplex ligation-dependent probe amplification), and 1p and 19q mutations (with fluorescent in situ hybridization). Methylation of MGMT promoter was found in 95% and in 36% in the long-term survivor and control groups, respectively (p < 0.001). IDH1 R132H mutated patients had a non-significant lower risk of dying from glioblastoma (p= 0.437), in comparison to patients without this mutation. Other mutations were rare, with no significant difference between the two groups. Molecular and genetic testing offers additional prognostic and predictive information for patients with glioblastoma. The most important finding of our analysis is that in the absence of MGMT promoter methylation, longterm survival is very rare. For patients without this mutation, alternative treatments should be explored.
Ključne besede: glioblastoma, long-term survival, methyl guanine methyl transferase, MGMT, prognostic factor
Objavljeno v DiRROS: 30.04.2024; Ogledov: 48; Prenosov: 15
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2. Application of multivariate statistical methods for determining geochemical trends of elements on the territory of SloveniaRobert Šajn, Mateja Gosar, Jasminka Alijagić, Tamara Teršič, 2024, izvirni znanstveni članek Povzetek: The main objective of this study is to map multi-element geochemical anomalies in soil on a regional scale. We aimed to determine and evaluate the baseline geochemical values and main geochemical trends in soil that may serve as reference values against any future changes. A total of 817 topsoil samples (0–10 cm) were collected in a 5 × 5 km grid and analyzed for 35 elements using ICP-ES after multi-acid digestions (HClO4/HNO3/HCl/HF) and 53 elements using ICP-MS after modified aqua regia digestion (HCl/HNO3/H2O). The analytical results for the two different digestion methods (multi-acid digestion vs. aqua regia) were also compared for each chemical element. Multivariate statistical methods were applied to identify the geochemical trends and main sources of trace elements over the territory of Slovenia. Based on these results, seven natural and one mixed natural/anthropogenic geochemical association were established. The contents and trends of the determined factors are presented according to 8 natural units, 4 drainage areas, and geological units characteristic of Slovenia. The identified anthropogenic geochemical association combines toxic elements (Ag, Bi, Cd, Hg, P, Pb, S, Sn, and Zn). Increased values of these elements can be found in mining areas and metallurgic centers, in Quaternary sediments of the Sava River, and Adriatic Basin as the consequence of past mining activities and in the Julian Alps, where their origin could be connected to the atmospheric deposition.
Ključne besede: soil, geochemical mapping, distribution of geochemical elements, factor analysis, cluster analysis
Objavljeno v DiRROS: 04.01.2024; Ogledov: 208; Prenosov: 54
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3. Candidate pathogenicity factor/effector proteins of ‘Candidatus Phytoplasma solani’ modulate plant carbohydrate metabolism, accelerate the ascorbate–glutathione cycle, and induce autophagosomesMarina Dermastia, Špela Tomaž, Rebeka Strah, Tjaša Lukan, Anna Coll Rius, Barbara Dušak, Timotej Čepin, Aleš Kladnik, Maja Zagorščak, Kristina Gruden, Maruša Pompe Novak, 2023, izvirni znanstveni članek Povzetek: The pathogenicity of intracellular plant pathogenic bacteria is associated with the action of pathogenicity factors/effectors, but their physiological roles for most phytoplasma species, including ‘Candidiatus Phytoplasma solani’ are unknown. Six putative pathogenicity factors/effectors from six different strains of ‘Ca. P. solani’ were selected by bioinformatic analysis. The way in which they manipulate the host cellular machinery was elucidated by analyzing Nicotiana benthamiana leaves after Agrobacterium-mediated transient transformation with the pathogenicity factor/effector constructs using confocal microscopy, pull-down, and co-immunoprecipitation, and enzyme assays. Candidate pathogenicity factors/effectors were shown to modulate plant carbohydrate metabolism and the ascorbate–glutathione cycle and to induce autophagosomes. PoStoSP06, PoStoSP13, and PoStoSP28 were localized in the nucleus and cytosol. The most active effector in the processes studied was PoStoSP06. PoStoSP18 was associated with an increase in phosphoglucomutase activity, whereas PoStoSP28, previously annotated as an antigenic membrane protein StAMP, specifically interacted with phosphoglucomutase. PoStoSP04 induced only the ascorbate–glutathione cycle along with other pathogenicity factors/effectors. Candidate pathogenicity factors/effectors were involved in reprogramming host carbohydrate metabolism in favor of phytoplasma own growth and infection. They were specifically associated with three distinct metabolic pathways leading to fructose-6-phosphate as an input substrate for glycolysis. The possible significance of autophagosome induction by PoStoSP28 is discussed.
Ključne besede: autophagosome, effector, glycolysis, pathogenicity factor, StAMP
Objavljeno v DiRROS: 24.08.2023; Ogledov: 449; Prenosov: 212
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4. Measurements of bridge dynamic amplification factor using bridge weigh-in-motion dataJan Kalin, Aleš Žnidarič, Andrej Anžlin, Maja Kreslin, 2022, izvirni znanstveni članek Povzetek: The dynamic component of bridge traffic loading is commonly taken into account with a Dynamic Amplification Factor (DAF)—the ratio between the dynamic and static load effects on a bridge. In the design codes, this factor is generally more conservative than in reality. Recently a new method of cal- culation of this factor had been developed. Data from 15 different bridges have been analysed since then and this paper presents the results of the analyses. The background for Bridge Weigh-in-Motion is given, and the most recent method for DAF calculation is described. The sites from which the data originated are presented, and the selection of data discussed. The results of the analyses are presented and discussed and some examples of DAF calculations are shown. Data from the considered sites have invariably demonstrated a DAF decrease with increasing axle load. This is a significant result, especially for assessment of existing structures, since it is beneficial to use measured structural param- eters to optimise structural analysis.
Ključne besede: bridge loads, bridge weigh-in-motion, dynamic amplication factor, dynamic analysis, measurement, traffic loading
Objavljeno v DiRROS: 14.07.2023; Ogledov: 300; Prenosov: 160
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5. Private forest owner willingness to mobilise wood from dense, small-diameter tree standsMatevž Triplat, Satu Helenius, Ruben Laina, Nike Krajnc, Thomas Kronholm, Zdenka Ženko, Teppo Hujala, 2023, izvirni znanstveni članek Povzetek: Forests are a source of renewable biomass, and their utilisation will play a vital role in the transition towards a climate-neutral economy. Small-diameter tree management could contribute to this transition via providing renewable biomass for sustainable uses and fostering tree growth towards long-lifecycle bioproducts. The utilisation of small-diameter trees in the EU is still low since new technologies and work models are required to make the operations economically profitable, environmentally sound, and socially attractive. The supply of biomass from small-diameter tree stands is dependent on forest owners with diverse perceptions on their forests and diverse ownership objectives. However, there is scarce research on forest owner perceptions on small-diameter tree management, which encompasses home consumption, self-active work, and commercial forestry services. A survey in four EU countries was designed to identify the main factors affecting the motivation of forest owners to mobilise biomass from small-diameter stands. Factor and clustering analyses were used to identify four forest owner segments: weakly-engaged traders, well-being seekers, self-active profit-seekers, and well-informed service users. The willingness to utilise biomass from small-diameter tree stands and participate in the market was shaped by forest owner knowledge of forestry, economic and socio-cultural motivations, and sensitivity to service offerings. Forest owner preferences for market participation are heterogenous, and thus different policy implementation approaches are needed and proposed.
Ključne besede: customer profiles, factor analysis, forestry services, management objectives, biomass, communication strategies
Objavljeno v DiRROS: 05.01.2023; Ogledov: 673; Prenosov: 266
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6. Mutational burden, MHC-I expression and immune infiltration as limiting factors for in situ vaccination by TNF[alfa] and IL-12 gene electrotransferUrška Kamenšek, Katja Uršič Valentinuzzi, Boštjan Markelc, Maja Čemažar, Vita Šetrajčič Dragoš, Gregor Serša, 2021, izvirni znanstveni članek Povzetek: In situ vaccination is a promising immunotherapeutic approach, where various local ablative therapies are used to induce an immune response against tumor antigens that are released from the therapy-killed tumor cells. We recently proposed using intratumoral gene electrotransfer for concomitant transfection of a cytotoxic cytokine tumor necrosis factor-% (TNF%) to induce in situ vaccination, and an immunostimulatory cytokine interleukin 12 (IL-12) to boost the primed immune response. Here, our aim was to test the local and systemic effectiveness of the approach in tree syngeneic mouse tumor models and associate it with tumor immune profiles, characterized by tumor mutational burden, immune infiltration and expression of PD-L1 and MHC-I on tumor cells. While none of the tested characteristic proved predictive for local effectiveness, high tumor mutational burden, immune infiltration and MHC-I expression were associated with higher abscopal effectiveness. Hence, we have confirmed that both the abundance and presentation of tumor antigens as well as the absence of immunosuppressive mechanisms are important for effective in situ vaccination. These findings provide important indications for future development of in situ vaccination based treatments, and for the selection of tumor types that will most likely benefit from it.
Ključne besede: in situ vaccination, gene electrotransfer, interleukin 12, tumor necrosis factor [alfa]
Objavljeno v DiRROS: 19.09.2022; Ogledov: 549; Prenosov: 182
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7. Real-world testing practices, treatment patterns and clinical outcomes in patients from Central Eastern Europe with EGFR-mutated advanced non-small cell lung cancer : a retrospective chart review study (REFLECT)Urška Janžič, Nina Turnšek, Mircea Dediu, Ivan Shterev Donev, Roxana Lupu, Gabriela Teodorescu, Tudor Ciuleanu, Adam Płużański, 2022, izvirni znanstveni članek Povzetek: The targeted therapy with tyrosine kinase inhibitors (TKIs) against the epidermal growth factor receptor mutation (EGFRm) in advanced non-small cell lung cancer (NSCLC) changed the treatment paradigm. REFLECT study (NCT04031898) explored EGFR/T790M testing and treatment patterns in EGFRm NSCLC patients receiving first- or second-generation (1G/2G) EGFR TKIs as front-line (1L) in eight countries. Pooled data from Central Eastern Europe (CEE) countries from this study (Bulgaria, Poland, Romania, Slovenia) are presented here. This physician-led chart review study was conducted in patients with confirmed-EGFRm NSCLC initiating 1L 1G/2G EGFR TKIs between 2015–2018. The CEE cohort included 389 patients receiving 1L erlotinib (37%), afatinib (34%), and gefitinib (29%). Overall, 320 (82%) patients discontinued 1L, and 298 (77%) progression events were registered. Median progression free survival on 1L TKIs was 14.0 (95% CI: 12.6–15.6) months. Median overall survival from 1L start was 26.6 (95% CI: 24.1–29.0) months. Attrition rate between 1L and next line was 30%. Among patients with 1L progression, 200 (67%) were tested for T790M and 58% were positive. This first CEE analysis of treatments and outcomes in EGFRm NSCLC patients highlights the importance of using the most efficacious therapies currently available in 1L to reduce attrition and improve patient outcomes.
Ključne besede: lung neoplasms, non-small cell lung carcinoma, Eastern Europe, real-world study, REFLECT study, epidermal growth factor receptor, lung cancer
Objavljeno v DiRROS: 09.09.2022; Ogledov: 511; Prenosov: 210
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8. Sequential treatment with afatinib and osimertinib in patients with EGFR mutation-positive non-small-cell lung cancer : an observational studyMaximilian J Hochmair, Alessandro Morabito, Desiree Hao, Cheng-Ta Yang, Ross A Soo, James C-H Yang, Rasim Gucalp, Balazs Halmos, Lara Wang, Amanda Golembesky, Angela Märten, Tanja Čufer, 2018, izvirni znanstveni članek Povzetek: Aim: To assess outcomes in patients with EGFR mutation-positive (Del19, L858R) non-small-cell lung cancer receiving sequential afatinib and osimertinib in a real-world clinical setting. Materials & methods: In this retrospective, observational, multicenter study, patients (n = 204) had T790M-positive disease following first-line afatinib and started osimertinib treatment [>/=]10 months prior to data entry. Primary outcome was time on treatment. Results: Overall median time on treatment was 27.6 months (90% CI: 25.9-31.3), 30.3 months (90% CI: 27.6-44.5) in Del19-positive patients and 46.7 months (90% CI: 26.8-not reached) in Asians. The 2-year overall survival was 78.9%. Conclusion: In real-world clinical practice, sequential afatinib and osimertinib facilitates prolonged, chemotherapy-free treatment in patients with T790M acquired resistance, and is a potentially attractive strategy, especially for Del19-positive tumors.
Ključne besede: lung neoplasms -- therapy, non-small-cell lung cancer, afatinib, osimertinib, epidermal growth factor receptor, EGFR, observational study
Objavljeno v DiRROS: 09.11.2020; Ogledov: 1476; Prenosov: 910
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9. Expression of FGFR1-4 in malignant pleural mesothelioma tissue and corresponding cell lines and its relationship to patient survival and FGFR inhibitor sensitivityGregor Vlačić, Mir Alireza Hoda, Thomas Klikovits, Katharina Sinn, Elisabeth Gschwandtner, Katja Mohorčič, Karin Schelch, Christine Pirker, Barbara Peter-Vörösmarty, Jelena Brankovic, Tanja Čufer, Aleš Rozman, Izidor Kern, 2019, izvirni znanstveni članek Povzetek: Malignant pleural mesothelioma (MPM) is a devastating malignancy with limited therapeutic options. Fibroblast growth factor receptors (FGFR) and their ligands were shown to contribute to MPM aggressiveness and it was suggested that subgroups of MPM patients could benefit from FGFR-targeted inhibitors. In the current investigation, we determined the expression of all four FGFRs (FGFR1-FGFR4) by immunohistochemistry in tissue samples from 94 MPM patients. From 13 of these patients, we were able to establish stable cell lines, which were subjected to FGFR1-4 staining, transcript analysis by quantitative RT-PCR, and treatment with the FGFR inhibitor infigratinib. While FGFR1 and FGFR2 were widely expressed in MPM tissue and cell lines, FGFR3 and FGFR4 showed more restricted expression. FGFR1 and FGFR2 showed no correlation with clinicopathologic data or patient survival, but presence of FGFR3 in 42% and of FGFR4 in 7% of patients correlated with shorter overall survival. Immunostaining in cell lines was more homogenous than in the corresponding tissue samples. Neither transcript nor protein expression of FGFR1-4 correlated with response to infigratinib treatment in MPM cell lines. We conclude that FGFR3 and FGFR4, but not FGFR1 or FGFR2, have prognostic significance in MPM and that FGFR expression is not suffcient to predict FGFR inhibitor response in MPM cell lines.
Ključne besede: malignant pleural mesothelioma, fibroblast growth factor receptors, azbestos, immunotherapy, chemotherapy, genomic analysis, infigratinib
Objavljeno v DiRROS: 07.10.2020; Ogledov: 12120; Prenosov: 1025
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10. Multicenter evaluation of the fully automated PCR-based Idylla EGFR Mutation Assay on formalin-fixed, paraffin-embedded Q1 tissue of human lung cancerSolène M. Evrard, Estelle T. Clermont, Isabelle Rouquette, Samuel Murray, Sebastian Dintner, Yun-Chung Nam-Apostolopoulos, Beatriz Bellosillo, Mar V. Rodriguez, Ernest Nadal, Klaus H. Wiedorn, Mitja Rot, Izidor Kern, 2019, izvirni znanstveni članek Povzetek: Before initiating treatment of advanced nonesmall-cell lung cancer with tyrosine kinase inhibitors (eg, erlotinib, gefitinib, osimertinib, and afatinib), which inhibit the catalytic activity of epidermal growth factor receptor (EGFR), clinical guidelines require determining the EGFR mutational status for activating (EGFR exons 18, 19, 20, or 21) and resistance (EGFR exon 20) mutations. The EGFR resistance mutation T790M should be monitored at cancer progression. The Idylla EGFR Mutation Assay, performed on the Idylla molecular diagnostics platform, is a fully automated (<2.5 hours turnaround time) sample-to-result molecular test to qualitatively detect 51 EGFR oncogene point mutations, deletions, or insertions. In a 15- center evaluation, Idylla results on 449 archived formalin-fixed, paraffin-embedded tissue sections, originating from nonesmall-cell lung cancer biopsies and resection specimens, were compared with data obtained earlier with routine reference methods, including next-generation sequencing, Sanger sequencing, pyrosequencing, mass spectrometry, and PCR-based assays. When results were discordant, a third method of analysis was performed, when possible, to confirm test results. After confirmation testing and excluding invalids/errors and discordant results by design, a concordance of 97.6% was obtained between Idylla and routine test results. Even with <10 mm2 of tissue area, a valid Idylla result was obtained in 98.9% of the cases. The Idylla EGFR Mutation Assay enables sensitive detection of most relevant EGFR mutations in concordance with current guidelines, with minimal molecular expertise or infrastructure.
Ključne besede: non-small cell lung carconima -- diagnosis -- genetics, ErbB receptors, sequence analysis, tyrosine kinase inhibitors, epidermal growth factor receptor
Objavljeno v DiRROS: 07.10.2020; Ogledov: 1381; Prenosov: 982
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