1. Correlation of the high-resolution computed tomography patterns of intrathoracic sarcoidosis with serum levels of SAA, CA 15.3, SP-D, and other biomarkers of interstitial lung diseaseZala Leštan Ramovš, Snežna Sodin-Šemrl, Katja Lakota, Saša Čučnik, Damjan Manevski, Rok Zbačnik, Mirjana Zupančič, Martin Verbič, Marjeta Terčelj-Zorman, 2023, izvirni znanstveni članek Povzetek: Studies on the serum biomarkers of granulomatous inflammation and pulmonary interstitial disease in intrathoracic sarcoidosis have shown conflicting results. We postulated that differences in the concentrations of serum biomarkers can be explained by the heterogenous patterns of sarcoidosis seen on thoracic HRCT. Serum biomarker levels in 79 consecutive patients, newly diagnosed with intrathoracic sarcoidosis, were compared to our control group of 56 healthy blood donors. An analysis was performed with respect to HRCT characteristics (the presence of lymph node enlargement, perilymphatic or peribronchovascular infiltrates, ground-glass lesions, or fibrosis), CXR, and disease extent. Serum levels of CXCL9, CXCL10, CTO, and CCL18 were statistically significantly increased in all patients compared to controls. Serum levels of CA15.3 were statistically significantly increased in all patients with parenchymal involvement. SAA was increased in patients with ground-glass lesions while SP-D levels were statistically significantly increased in patients with lung fibrosis. Only SP-D and CA15.3 showed a significant correlation to interstitial disease extent. In conclusion, we found that sarcoidosis patients with different HRCT patterns of intrathoracic sarcoidosis have underlying biochemical differences in their serum biomarkers transcending Scadding stages. The stratification of patients based on both radiologic and biochemical characteristics could enable more homogenous patient selection for further prognostic studies. Ključne besede: intrathoracic sarcoidosis, biomarker, HRCT Objavljeno v DiRROS: 10.09.2026; Ogledov: 22; Prenosov: 20
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2. Molecular profiling of inflammatory processes in a mouse model of IC/BPS : from the complete transcriptome to major sex-related histological features of the urinary bladderDominika Peskar, Tadeja Kuret, Katja Lakota, Andreja Erman, 2023, izvirni znanstveni članek Povzetek: Animal models are invaluable in the research of the pathophysiology of interstitial cystitis/bladder pain syndrome (IC/BPS), a chronic aseptic urinary bladder disease of unknown etiology that primarily affects women. Here, a mouse model of IC/BPS was induced with multiple low-dose cyclophosphamide (CYP) applications and thoroughly characterized by RNA sequencing, qPCR, Western blot, and immunolabeling to elucidate key inflammatory processes and sex-dependent differences in the bladder inflammatory response. CYP treatment resulted in the upregulation of inflammatory transcripts such as Ccl8, Eda2r, and Vegfd, which are predominantly involved in innate immunity pathways, recapitulating the crucial findings in the bladder transcriptome of IC/BPS patients. The JAK/STAT signaling pathway was analyzed in detail, and the JAK3/STAT3 interaction was found to be most activated in cells of the bladder urothelium and lamina propria. Sex-based data analysis revealed that cell proliferation was more pronounced in male bladders, while innate immunity and tissue remodeling processes were the most distinctive responses of female bladders to CYP treatment. These processes were also reflected in prominent histological changes in the bladder. The study provides an invaluable reference dataset for preclinical research on IC/BPS and an insight into the sex-specific mechanisms involved in the development of IC/BPS pathology, which may explain the more frequent occurrence of this disease in women. Ključne besede: interstitial cystitis, inflammation, RNA sequencing Objavljeno v DiRROS: 10.09.2026; Ogledov: 19; Prenosov: 19
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3. Longitudinal analysis of antiphospholipid antibody dynamics after infection with SARS-CoV-2 or vaccination with BNT162b2Manca Ogrič, Polona Žigon, Snežna Sodin-Šemrl, Mirjana Zlatković Švenda, Marija Zdravković, Milica Ovuka, Tinka Švec, Katja Lakota, Peter Radšel, Žiga Rotar, Saša Čučnik, 2023, izvirni znanstveni članek Povzetek: Antiphospholipid antibodies (aPL) comprise a group of autoantibodies that reflect prothrombotic risk in antiphospholipid syndrome (APS) but may also be present in a small proportion of healthy individuals. They are often transiently elevated in infections, including SARS-CoV-2, and may also be associated with vaccine-induced autoimmunity. Therefore, we aimed to investigate the dynamics of aPL in COVID-19 patients and in individuals (healthcare professionals—HCPs) after receiving BNT162b2 vaccine and to compare aPL levels and positivity with those found in APS patients. We measured solid-phase identifiable aPL, including anticardiolipin (aCL), anti-β2 glycoprotein I (anti-β2GPI), and anti-prothrombin/phosphatidylserine (aPS/PT) antibodies in 58 HCPs before and after vaccination (at 3 weeks, 3, 6, and 9 months after the second dose, and 3 weeks after the third booster dose), in 45 COVID-19 patients hospitalized in the ICU, in 89 COVID-19 patients hospitalized in the non-ICU (at admission, at hospital discharge, and at follow-up), and in 52 patients with APS. The most frequently induced aPL in COVID-19 patients (hospitalized in non-ICU) were aCL (50.6% of patients had positive levels at at least one time point), followed by anti-β2GPI (21.3% of patients had positive levels at at least one time point). In 9/89 COVID-19 patients, positive aPL levels persisted for three months. One HCP developed aCL IgG after vaccination but the persistence could not be confirmed, and two HCPs developed persistent anti-β2GPI IgG after vaccination with no increase during a 1-year follow-up period. Solid-phase aPL were detected in 84.6% of APS patients, in 49.4% of COVID-19 patients hospitalized in the non-ICU, in 33.3% of COVID-19 patients hospitalized in the ICU, and in only 17.2% of vaccinated HCPs. aPL levels and multiple positivity were significantly lower in both infected groups and in vaccinated individuals compared with APS patients. In conclusion, BNT162b2 mRNA vaccine may have induced aPL in a few individuals, whereas SARS-CoV-2 infection itself results in a higher percentage of aPL induction, but the levels, persistence, and multiple positivity of aPL do not follow the pattern observed in APS. Ključne besede: COVID-19, SARS-CoV-2, BNT162b2 vaccine, autoantibodies, antophospholipid antibodies, healthcare professionalism, APS Objavljeno v DiRROS: 10.09.2026; Ogledov: 18; Prenosov: 20
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4. Disturbed antioxidant capacity in patients with systemic sclerosis associates with lung and gastrointestinal symptomsNeža Brezovec, Katja Perdan-Pirkmajer, Blaž Burja, Žiga Rotar, Joško Osredkar, Snežna Sodin-Šemrl, Katja Lakota, Saša Čučnik, 2023, izvirni znanstveni članek Povzetek: The correct balance between reactive oxygen species and antioxidant defense in an organism is disturbed in oxidative stress. To assess oxidative balance in 36 SSc patients and 26 healthy controls (HCs), we measured reactive oxidative metabolites (ROMs), total antioxidant capacity (TAC), lipid peroxidation (measuring 4-HNE), and DNA oxidative damage (measuring 8-OHdG) in serum. Furthermore, DNA breaks in leukocytes of 35 SSc patients and 32 HCs were evaluated using COMET. While we report high ROMs for both SSc patients and age/sex matched HC samples, there was a significant increase in TAC in SSc patients as compared to HCs, and thus also a significantly higher oxidative stress index in SSc patients. TAC was significantly higher in SSc patients with ILD and gastrointestinal involvement, as well as in patients with anti-topoisomerase antibodies. We observe no difference in serum lipid peroxidation status or oxidative DNA damage. However, SSc patients had significantly more leukocyte DNA breaks than HCs; the most damage was observed in patients treated with immunosuppressives. Thus, our study confirms presence of oxidative stress and increased DNA damage in leukocytes of SSc patients; however, it points toward increased antioxidant capacity, which needs to be further studied. Ključne besede: systemic sclerosis, oxidative stress, reactive oxidative metabolites, antioxidants, lipid peroxidation, DNA damage, DNA breaks Objavljeno v DiRROS: 05.08.2026; Ogledov: 270; Prenosov: 138
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5. Fine-tuning the nanostructured titanium oxide surface for selective biological responseNiharika Rawat, Metka Benčina, Domen Paul, Janez Kovač, Katja Lakota, Polona Žigon, Veronika Kralj-Iglič, Hsin-Chia Ho, Marija Vukomanović, Aleš Iglič, Ita Junkar, 2023, izvirni znanstveni članek Ključne besede: gaseous plasma treatment, hydrothermal treatment, biocompatibility, vascular stent, nanostructured surface Objavljeno v DiRROS: 03.08.2026; Ogledov: 229; Prenosov: 202
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6. Characterization of anti-phospholipid antibodies in lyme borreliosis using in-house developed ELISAsPolona Žigon, Katja Lakota, Katarina Ogrinc, Petra Bogovič, Franc Strle, 2026, izvirni znanstveni članek Povzetek: Objectives: Borrelia burgdorferi sensu lato, a spirochete bacterium responsible for Lyme borreliosis-the most common tick-borne infection in North America and Europe-can trigger the production of antiphospholipid antibodies. These antibodies target host lipids such as cardiolipin (CL), phosphatidic acid (PA), phosphatidylcholine (PC), and phosphatidylserine (PS), which the spirochete incorporates into its membrane from the surrounding environment. Although antiphospholipid antibodies are typically associated with antiphospholipid syndrome (APS), they may also arise during infections, including Lyme borreliosis. This study aimed to develop and optimize several enzyme-linked immunosorbent assays (ELISAs) for measuring various antiphospholipid antibodies in patients with Lyme borreliosis. Methods: Thirty patients diagnosed with Lyme borreliosis were enrolled: ten with solitary erythema migrans (EM), ten with multiple EM (MEM), and ten with late manifestations known as acrodermatitis chronica atrophicans (ACA). Forty healthy blood donors served as controls. Four distinct antiphospholipid antibody ELISAs were developed, each using a different phospholipid coating: CL, PA, PC, and PS. Serum of APS patient was used as a positive control and for standard curve generation. Results: All four ELISAs were successfully established and demonstrated good measurement precision. Significant differences in antiphospholipid antibody levels and positivity rates were observed between Lyme borreliosis patients and healthy blood donors. Notably, levels of antibodies directed against PA (aPA), PC (aPC), and PS (aPS), both IgG and IgM, were significantly higher in patients with late Lyme borreliosis, manifested as ACA, compared to healthy blood donors. In contrast, anti-CL (aCL) levels did not differ significantly between groups. Patients with ACA also showed the highest frequency of multiple antiphospholipid antibody positivity, with 7 out of 10 patients testing positive for three or more antiphospholipid antibodies. Conclusions: Accurate and precise in-house ELISAs for the detection of aCL, aPA, aPC, and aPS using APS sera as standard material were developed and validated for the analysis of samples of patients with Lyme borreliosis. Our data suggest that antiphospholipid antibody levels-specifically aPA, aPC, and aPS-differ across clinical manifestations of Lyme borreliosis, with the greatest increases observed in patients with ACA. Ključne besede: Borrelia burgdorferi sensu lato, lyme borreliosis, anti-phosphatidic acid antibodies, anti-phosphatidylcholine antibodies, anti-phosphatidylserine antibodies, antiphospholipid antibodies Objavljeno v DiRROS: 22.07.2026; Ogledov: 241; Prenosov: 173
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7. Insights into the immunological description of cryoglobulins with regard to detection and characterization in Slovenian rheumatological patientsManca Ogrič, Tinka Švec, Katjuša Mrak Poljšak, Katja Lakota, Eva Podovšovnik, Marie Nathalie Kolopp-Sarda, Alojzija Hočevar, Saša Čučnik, 2024, izvirni znanstveni članek Povzetek: The detection of cryoglobulins (CG) used to diagnose cryoglobulemic vasculitis requires strict adherence to protocol, with emphasis on the preanalytical part. Our main objectives were to introduce a more sensitive and specific protocol for the detection of CG and to characterize CG in Slovenian patients diagnosed with cryoglobulinemic vasculitis, other vasculitides, connective tissue diseases or non-rheumatic diseases examined at the Department of Rheumatology (University Medical Centre Ljubljana). Samples were routinely analyzed for the presence of CG with the protocol using the Folin-Ciocalteu reagent. In the newly introduced protocol, the type of CG was determined by immunofixation on visually observed positive samples, and the concentration of CG in the cryoprecipitate and rheumatoid factor (RF) activity were measured by nephelometry. RF, C3c and C4 were measured in the patients` serum, and decision tree analysis was performed using all results. The agreement between negative and positive results between the two protocols was 86%. Of the 258 patient samples tested, we found 56 patients (21.7%) with positive CG (37.5% - type II, 62.5% - type III). The RF activity was observed in 21.4% of CG positive subjects. The median concentration of type II CG was significantly higher than that of type III CG (67.4 mg/L vs. 45.0 mg/L, p=0.037). Patients with type II had lower C4 concentrations and higher RF activity compared to patients with type III CG. In the decision tree, C4 was the strongest predictor of cryoglobulinemia in patients. With the newly implemented protocol, we were able to improve the detection and quantification of CG in the samples of our rheumatology patients and report the results to adequately support clinicians. Ključne besede: cryoglobulins, cryoglobulinemic vasculitis, rheumatoid factor activity, complement components, cryoglobulin detection, pre-analytical phase Objavljeno v DiRROS: 09.06.2026; Ogledov: 290; Prenosov: 126
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8. Deregulation in adult IgA vasculitis skin as the basis for the discovery of novel serum biomarkersMatija Bajželj, Matjaž Hladnik, Rok Blagus, Vesna Jurčić, Ana Markež, Tanya Deniz Toluay, Snežna Sodin-Šemrl, Alojzija Hočevar, Katja Lakota, 2024, izvirni znanstveni članek Povzetek: Introduction: Immunoglobulin A vasculitis (IgAV) in adults has a variable disease course, with patients often developing gastrointestinal and renal involvement and thus contributing to higher mortality. Due to understudied molecular mechanisms in IgAV currently used biomarkers for IgAV visceral involvement are largely lacking. Our aim was to search for potential serum biomarkers based on the skin transcriptomic signature. Methods: RNA sequencing analysis was conducted on skin biopsies collected from 6 treatment-naïve patients (3 skin only and 3 renal involvement) and 3 healthy controls (HC) to get insight into deregulated processes at the transcriptomic level. 15 analytes were selected and measured based on the transcriptome analysis (adiponectin, lipopolysaccharide binding protein (LBP), matrix metalloproteinase-1 (MMP1), C-C motif chemokine ligand (CCL) 19, kallikrein-5, CCL3, leptin, C-X-C motif chemokine ligand (CXCL) 5, osteopontin, interleukin (IL)-15, CXCL10, angiopoietin-like 4 (ANGPTL4), SERPIN A12/vaspin, IL-18 and fatty acid-binding protein 4 (FABP4)) in sera of 59 IgAV and 22 HC. Machine learning was used to assess the ability of the analytes to predict IgAV and its organ involvement. Results: Based on the gene expression levels in the skin, we were able to differentiate between IgAV patients and HC using principal component analysis (PCA) and a sample-to-sample distance matrix. Differential expression analysis revealed 49 differentially expressed genes (DEGs) in all IgAV patient's vs. HC. Patients with renal involvement had more DEGs than patients with skin involvement only (507 vs. 46 DEGs) as compared to HC, suggesting different skin signatures. Major dysregulated processes in patients with renal involvement were lipid metabolism, acute inflammatory response, and extracellular matrix (ECM)-related processes. 11 of 15 analytes selected based on affected processes in IgAV skin (osteopontin, LBP, ANGPTL4, IL-15, FABP4, CCL19, kallikrein-5, CCL3, leptin, IL-18 and MMP1) were significantly higher (p-adj < 0.05) in IgAV serum as compared to HC. Prediction models utilizing measured analytes showed high potential for predicting adult IgAV. Conclusion: Skin transcriptomic data revealed deregulations in lipid metabolism and acute inflammatory response, reflected also in serum analyte measurements. LBP, among others, could serve as a potential biomarker of renal complications, while adiponectin and CXCL10 could indicate gastrointestinal involvement. Ključne besede: acute inflammatory response, adults, IgA vasculitis, lipid metabolism, machine learning, RNA sequencing, serum biomarkers Objavljeno v DiRROS: 04.06.2026; Ogledov: 325; Prenosov: 229
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9. Enhanced hemocompatibility and cytocompatibility of stainless steelMetka Benčina, Niharika Rawat, Domen Paul, Janez Kovač, Katja Lakota, Polona Žigon, Veronika Kralj-Iglič, Aleš Iglič, Ita Junkar, 2024, izvirni znanstveni članek Ključne besede: surface modifications, electrochemical anodization, non-thermal plasma treatment, altered surface properties, blood platelets, human coronary stents Objavljeno v DiRROS: 03.06.2026; Ogledov: 304; Prenosov: 363
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