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1.
CRISPR/Cas9-mediated fine-tuning of miRNA expression in tetraploid potato
Tjaša Lukan, Florian Veillet, Maja Križnik, Anna Coll Rius, Tjaša Mahkovec Povalej, Karmen Pogačar, Katja Stare, Laura Chauvin, Jean-Eric Chauvin, Kristina Gruden, 2022, izvirni znanstveni članek

Povzetek: MicroRNAs (miRNAs) are small noncoding RNAs, which modulate the abundance and spatiotemporal accumulation of target mRNAs at transcriptional and post-transcriptional levels and through that play important roles in several biological processes in plants. Here we show that in polyploid species, CRISPR/Cas9 system can be used for fine-tuning of miRNA expression, which can have broader range of applications compared to knock-out mutants. We established the complete pipeline for CRISPR-Cas9-mediated modulation of miRNA expression in potato. It consists of (1) design and assembly of dual sgRNA CRISPR/Cas9 constructs, (2) transient transfection of protoplasts following fast and efficient screening by high resolution melting analysis to select functional sgRNAs, and (3) stable transformation of potato explants with functional sgRNAs and selection of regenerated transgenic lines with desired mutations and desired miRNA abundance based on sequencing and RT-qPCR. We show that miRNA-editing using dual sgRNA approach results in different types of mutations among transgenic lines but also in different alleles of the same plant, which are target site-dependent. The most frequent were short deletions, but we also detected 1-nt insertions (T or G), deletions between two sgRNAs and larger deletions. miRNA abundance correlates with the frequency and type of introduced mutations, as more extensive mutations in more alleles result in lower miRNA abundance. Interestingly, some mutated loci can generate alternative miRNAs, now novel targets were however predicted for those. In all transgenic lines with Cas9 expression, we detected mutations, suggesting high efficiency of Cas9-editing. We confirmed the miRNA-editing efficiency of our optimised approach in two different potato genotypes and three different loci.
Ključne besede: CRISPR/Cas9, hypersensitive response (HR)-conferred resistance, immune signaling, live cell imaging, Solanum tuberosum (potato), spatiotemporal analysis, stromules, virus resistance
Objavljeno v DiRROS: 17.07.2024; Ogledov: 3; Prenosov: 2
.pdf Celotno besedilo (2,94 MB)
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Nuclear magnetic resonance metabolic fingerprint of bevacizumab in mutant IDH1 glioma cells
Tanja Mesti, Nadia Bouchemal, Claire Banissi, Mohamed N. Triba, Carole Marbeuf-Gueye, Maja Čemažar, Laurence Le Moyec, Antoine F. Carpentier, Philippe Savarin, Janja Ocvirk, 2018, izvirni znanstveni članek

Povzetek: Malignant gliomas are rapidly growing tumours that extensively invade the brain and have bad prognosis. Our study was performed to assess the metabolic effects of bevacizumab on the glioma cells carrying the IDH1 mutation, a mutation, associated with better prognosis and treatment outcome. Bevacizumab is known to inhibit tumour growth by neutralizing the biological activity of vascular endothelial growth factor (VEGF). However, the direct effects of bevacizumab on tumour cells metabolism remain poorly known. Materials and methods The immunoassay and MTT assay were used to assess the concentration of secreted VEGF and cell viability after bevacizumab exposure. Metabolomic studies on cells were performed using high resolution magic angle spinning spectroscopy (HRMAS). Results mIDH1-U87 cells secreted VEGF (13 ng/mL). Regardless, bevacizumab had no cytotoxic effect, even after a 72h exposure and with doses as high as 1 mg/mL. Yet, HRMAS analysis showed a significant effect of bevacizumab (0.1 mg/mL) on the metabolic phenotype of mIDH1-U87 cells with elevation of 2-hydroxyglutarate and changes in glutamine group metabolites (alanine, glutamate, glycine) and lipids (polyunsaturated fatty acids [PUFA], glycerophosphocholine, and phosphocholine). Conclusions In mIDH1-U87 cells, changes in glutamine group metabolites and lipids were identified as metabolic markers of bevacizumab treatment. These data support the possibility of a functional tricarboxylic acid cycle that runs in reductive manner, as a probable mechanism of action of bevacizumab in IDH1 mutated gliomas and propose a new target pathway for effective treatment of malignant gliomas.
Ključne besede: symptomatic pseudoprogression, atypical response, immunotherapy, lung cancer, idh1 mutation, malignant glioma, bevacizumab, metabolic fingerprint
Objavljeno v DiRROS: 11.06.2024; Ogledov: 80; Prenosov: 37
.pdf Celotno besedilo (511,70 KB)

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Immune RECIST criteria and symptomatic pseudoprogression in non-small cell lung cancer patients treated with immunotherapy
Martina Vrankar, Mojca Unk, 2018, pregledni znanstveni članek

Povzetek: Uncommon responses during immunotherapy is a new challenging issue in oncology practice. Recently, new criteria for evaluation of response to immunotherapy immune response evaluation criteria solid tumors (iRECIST) were accepted. According to iRECIST, worsening of performance status (PS) accompanied to pseudoprogression reflects most probably the true progression of the malignant disease. Methods. A systematic review of the literature was made by using several electronic database with the following search criteria: symptomatic pseudoprogression, atypical response, immunotherapy and lung cancer. Results. In the literature, we identified five reports of seven patients treated with immunotherapy that met the inclusion criteria. We also report our experience of patient with pseudoprogression and almost complete response after one dose of immunotherapy. Conclusions. As seen from our review, iRECIST criteria might be insufficient in distinguishing true progression from pseudoprogression in some patients with advanced NSCLC treated with immunotherapy. More precise assessment methods are urgently needed.
Ključne besede: symptomatic pseudoprogression, atypical response, immunotherapy, lung cancer
Objavljeno v DiRROS: 11.06.2024; Ogledov: 94; Prenosov: 31
.pdf Celotno besedilo (426,11 KB)

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Proximity to riverbed influences physiological response of adult pedunculate oak trees
Lazar Kesić, Matjaž Čater, Saša Orlović, Bratislav Matović, Marko Stojanović, Mirjana Bojović, 2023, izvirni znanstveni članek

Povzetek: The pedunculate oak (Quercus robur L.) is economically and ecologically one of the most significant tree species in Serbia, however, little is known about the influence of the riverbed distance and its water supply on ecophysiological responses of this species. Given the limited information on the light-response curve of photosynthesis for oaks in southwest Srem, Serbia, the aim of this paper is to enhance understanding of their ecophysiological responses in this context. Maximum assimilation rate (Amax), the quantum yield (Ф), and light compensation point (LCP) were compared in adult trees situated along the transect from the river: (1) close to the river, (2) intermediate, (3) farthest from the river, and (4) forest reserve (second closest), with the first three transects being managed forests and the last one being an unmanaged forest reserve. The measurements were conducted in July during the first evidence of drought. The highest Amax rates were measured in all light intensities on the site closest to the river and the smallest on the site that was most distant to the water source. The most efficient were trees close to the river and the ones in the forest reserve. No significant difference between compensation points was confirmed for the studied groups of trees, although the forest reserve trees showed slightly higher values. The results demonstrated clear response between transects, which followed the distance from the riverbed. Pedunculate oak's reliance on groundwater is in tight relation with ecophysiological processes in trees; groundwater depletion may threaten its survival in areas distant from the river.
Ključne besede: Quercus robur L., floodplain forest, drought, light-response curves, transects
Objavljeno v DiRROS: 05.06.2024; Ogledov: 1105; Prenosov: 83
.pdf Celotno besedilo (861,11 KB)
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Electrotransfer of plasmid DNA radiosensitizes B16F10 tumors through activation of immune response
Monika Savarin, Urška Kamenšek, Maja Čemažar, Richard Heller, Gregor Serša, 2017, izvirni znanstveni članek

Povzetek: Tumor irradiation combined with adjuvant treatments, either vascular targeted or immunomodulatory, is under intense investigation. Gene electrotransfer of therapeutic genes is one of these approaches. The aim of this study was to determine, whether gene electrotransfer of plasmid encoding shRNA for silencing endoglin, with vascular targeted effectiveness, can radiosensitize melanoma B16F10 tumors. Materials and methods. The murine melanoma B16F10 tumors, growing on the back of C57Bl/6 mice, were treated by triple gene electrotransfer and irradiation. The antitumor effect was evaluated by determination of tumor growth delay and proportion of tumor free mice. Furthermore, histological analysis of tumors (necrosis, apoptosis, proliferation, vascularization, presence of hypoxia and infiltration of immune cells,) was used to evaluate the therapeutic mechanisms. Results. Gene electrotransfer of plasmid silencing endoglin predominantly indicated vascular targeted effects of the therapy, since significant tumor growth delay and 44% of tumor free mice were obtained. In addition, irradiation had minor effects on radioresistant melanoma, with 11% of mice tumor free. The combined treatment resulted in excellent effectiveness with 88% of mice tumor free, with more than half resistant to secondary tumor challenge, which was observed also with the plasmid devoid of the therapeutic gene. Histological analysis of tumors in the combined treatment group, demonstrated similar mode of action of the gene electrotransfer of plasmid encoding shRNA for silencing endoglin and devoid of it, both through the induction of an immune response. Conclusions. The results of this study indicate that irradiation can in radioresistant melanoma tumors, by release of tumor associated antigens, serve as activator of the immune response, besides directly affecting tumor cells and vasculature. The primed antitumor immune response can be further boosted by gene electrotransfer of plasmid, regardless of presence of the therapeutic gene, which was confirmed by the high radiosensitization, resulting in prolonged tumor growth delay and 89% of tumor free mice that were up to 63% resistant to secondary challenge of tumor. In addition, gene electrotransfer of therapeutic plasmid for silencing endoglin has also a direct effect on tumor vasculature and tumors cells; however in combination with radiotherapy this effect was masked by pronounced immune response.
Ključne besede: gene therapy, electrotransfer, plasmid, irradiation, immune response, melanoma
Objavljeno v DiRROS: 24.05.2024; Ogledov: 223; Prenosov: 175
.pdf Celotno besedilo (1,13 MB)

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Response of beech and fir to different light intensities along the Carpathian and Dinaric Mountains
Matjaž Čater, Pia Caroline Adamič, Eva Dařenová, 2024, izvirni znanstveni članek

Povzetek: Predicting global change mitigations based on environmental variables, like temperature and water availability, although yielding insightful hypothesis still lacks the integration of environmental responses. Physiological limits should be assessed to obtain a complete representation of a species’ fundamental niche. Detailed ecophysiological studies on the response of trees along the latitudinal gradient are rare. They could shed light on the behaviour under different light intensities and other studied traits. The forests of the Dinaric Mountains and the Carpathians represent the largest contiguous forest complexes in south-eastern Europe. In uneven-aged Carpathian (8 plots) and Dinaric Mountain (11 plots) forests, net assimilation (Amax) and maximum quantum yield (Φ) were measured for beech and fir in three predefined light intensity categories according to the indirect site factor (ISF%) obtained by the analysis of hemispherical photographs in managed and old growth forests, all located above 800 m a.s.l. The measurements were carried out under fixed environmental conditions in each light category per plot for three consecutive years. Data from the last 50-year average period from the CRU TS 4.01 dataset were used for the comparison between Amax, Φ, and climate. The highest Φ for beech were observed in the central part of the Dinaric Mountains and in the south westernmost and northwesternmost part of the Carpathians for both beech and fir, while they were highest for fir in the Dinaric Mountains in the northwesternmost part of the study area. The Φ-value of beech decreased in both complexes with increasing mean annual temperature and was highest in the open landscape. For fir in the Carpathians, Φ decreased with increasing mean annual temperature, while in the Dinaric Mountains it increased with higher temperature and showed a more scattered response compared to the Carpathians. Short-term ecophysiological responses of beech and fir were consistent to long-term radial growth observations observed on same locations. The results may provide a basis and an indication of the future response of two tree species in their biogeographical range to climate change in terms of competitiveness, existence and consequently forest management decisions.
Ključne besede: silver fir, beech, light response, Carpathian Mountains, Dinaric Mountains, temperature, precipitation
Objavljeno v DiRROS: 08.05.2024; Ogledov: 188; Prenosov: 400
.pdf Celotno besedilo (1,56 MB)
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Effects of electrochemotherapy on immunologically important modifications in tumor cells
Urša Kešar, Boštjan Markelc, Tanja Jesenko, Katja Uršič Valentinuzzi, Maja Čemažar, Primož Strojan, Gregor Serša, 2023, izvirni znanstveni članek

Povzetek: Electrochemotherapy (ECT) is a clinically acknowledged method that combines the use of anticancer drugs and electrical pulses. Electrochemotherapy with bleomycin (BLM) can induce immunogenic cell death (ICD) in certain settings. However, whether this is ubiquitous over different cancer types and for other clinically relevant chemotherapeutics used with electrochemotherapy is unknown. Here, we evaluated in vitro in the B16-F10, 4T1 and CT26 murine tumor cell lines, the electrochemotherapy triggered changes in the ICD-associated damage-associated molecular patterns (DAMPs): Calreticulin (CRT), ATP, High Mobility Group Box 1 (HMGB1), and four immunologically important cellular markers: MHCI, MHC II, PD-L1 and CD40. The changes in these markers were investigated in time up to 48 h after ECT. We showed that electrochemotherapy with all three tested chemotherapeutics induced ICD-associated DAMPs, but the induced DAMP signature was cell line and chemotherapeutic concentration specific. Similarly, electrochemotherapy with CDDP, OXA or BLM modified the expression of MHC I, MHC II, PD-L1 and CD40. The potential of electrochemotherapy to change their expression was also cell line and chemotherapeutic concentration specific. Our results thus put the electrochemotherapy with clinically relevant chemotherapeutics CDDP, OXA and BLM on the map of ICD inducing therapies.
Ključne besede: electrochemotherapy, cisplatin, immune response
Objavljeno v DiRROS: 21.03.2024; Ogledov: 270; Prenosov: 168
.pdf Celotno besedilo (7,17 MB)
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