Zuzana Varchulova Novakova
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Previous Organizations / Institutes
The organizations / institutes from the scholar's other articles in the past ten years
Research Subjects
Research Interests
Zuzana Varchulova Novakova has a total of 34 co-authors. Here are the top co-authors by number of shared publications:
- Lubos Danisovic
Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia
7 shared publications - Stanislav Ziaran
Department of Urology, Faculty of Medicine, Comenius University in Bratislava, 826 06 Bratislava, Slovakia
5 shared publications - Stefan Harsanyi
Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, 811 08 Bratislava, Slovakia
4 shared publications - Katarina Bevizova
Institute of Anatomy, Faculty of Medicine, Comenius University in Bratislava, 811 08 Bratislava, Slovakia
3 shared publications - Andreas Nicodemou
Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia
2 shared publications - Martina Culenova
Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia
2 shared publications
Latest Publications
- Open Access
- 2 January 2026
- Published by MDPI AG in Journal of Clinical Medicine
- Vol. 15 (1) , 338
Optimizing Ki-67 and E-Cadherin Thresholds for Improved Grade and Stage Classification in Urothelial Bladder Cancer
Background: Bladder cancer exhibits substantial heterogeneity, and accurate discrimination between non-muscle-invasive (NMIBC) and muscle-invasive disease (MIBC), as well as between low-grade (LG) and high-grade (HG) tumors, remains essential for appropriate clinical management. Established immunohistochemical (IHC) markers, such as p53, Ki-67, and E-cadherin, could be used in a new setting, but standardized cut-off values and their combined predictive value remain unclear. This study aimed to identify optimal cut-offs for these markers and to evaluate whether biomarker combinations enhance the discrimination of tumor grade and stage. Methods: A retrospective dataset of 568 cases of bladder cancer was analyzed. For each case, the expression of p53, Ki-67, and E-cadherin was quantified, and tumors were classified as NMIBC or MIBC, and as LG or HG. ROC-based cut-off selection was performed using Youden’s J criterion with 10-fold stratified cross-validation. E-cadherin was modelled using an inverted scale to reflect biological loss. Logistic regression models were used to evaluate the discriminatory performance of single markers, two-marker combinations, and a three-marker model. Cross-validated AUC values and optimal thresholds were reported. Results: Ki-67 showed the strongest single-marker performance for predicting both MIBC (AUC 0.842) and HG disease (AUC 0.813), with optimal cut-offs of ≥40% and ≥30%, respectively. p53 demonstrated moderate discrimination (AUC 0.778 for MIBC and 0.776 for HG), while E-cadherin, evaluated on an inverted scale, showed acceptable performance (AUC 0.746 for MIBC; 0.780 for HG). Combining markers yielded modest improvements, with the best performance observed for Ki-67 + E-cadherin (AUCs of 0.851 for MIBC and 0.838 for HG). Conclusions: Ki-67 is the most effective single biomarker for distinguishing invasive and HG bladder cancer, while E-cadherin provides complementary value. A two-marker panel combining Ki-67 and E-cadherin, using appropriate cut-offs, offers the highest overall performance and may serve as a practical tool for enhanced pathological stratification.
- 2 January 2026
- Published by MDPI AG in Journal of Clinical Medicine
- Vol. 15 (1) , 338
Open AccessOptimizing Ki-67 and E-Cadherin Thresholds for Improved Grade and Stage Classification in Urothelial Bladder Cancer
Background: Bladder cancer exhibits substantial heterogeneity, and accurate discrimination between non-muscle-invasive (NMIBC) and muscle-invasive disease (MIBC), as well as between low-grade (LG) and high-grade (HG) tumors, remains essential for appropriate clinical management. Established immunohistochemical (IHC) markers, such as p53, Ki-67, and E-cadherin, could be used in a new setting, but standardized cut-off values and their combined predictive value remain unclear. This study aimed to identify optimal cut-offs for these markers and to evaluate whether biomarker combinations enhance the discrimination of tumor grade and stage. Methods: A retrospective dataset of 568 cases of bladder cancer was analyzed. For each case, the expression of p53, Ki-67, and E-cadherin was quantified, and tumors were classified as NMIBC or MIBC, and as LG or HG. ROC-based cut-off selection was performed using Youden’s J criterion with 10-fold stratified cross-validation. E-cadherin was modelled using an inverted scale to reflect biological loss. Logistic regression models were used to evaluate the discriminatory performance of single markers, two-marker combinations, and a three-marker model. Cross-validated AUC values and optimal thresholds were reported. Results: Ki-67 showed the strongest single-marker performance for predicting both MIBC (AUC 0.842) and HG disease (AUC 0.813), with optimal cut-offs of ≥40% and ≥30%, respectively. p53 demonstrated moderate discrimination (AUC 0.778 for MIBC and 0.776 for HG), while E-cadherin, evaluated on an inverted scale, showed acceptable performance (AUC 0.746 for MIBC; 0.780 for HG). Combining markers yielded modest improvements, with the best performance observed for Ki-67 + E-cadherin (AUCs of 0.851 for MIBC and 0.838 for HG). Conclusions: Ki-67 is the most effective single biomarker for distinguishing invasive and HG bladder cancer, while E-cadherin provides complementary value. A two-marker panel combining Ki-67 and E-cadherin, using appropriate cut-offs, offers the highest overall performance and may serve as a practical tool for enhanced pathological stratification.
- Open Access
- 31 December 2025
- Published by MDPI AG in Clinics and Practice
- Vol. 16 (1) , 9
Comment on Hasan et al. Clinico-Pathological Features and Immunohistochemical Comparison of p16, p53, and Ki-67 Expression in Muscle-Invasive and Non-Muscle-Invasive Conventional Urothelial Bladder Carcinoma. Clin. Pract. 2023, 13, 806–819
We read with great interest the article Clinico-Pathological Features and Immunohistochemical Comparison of p16, p53, and Ki-67 Expression in Muscle-Invasive and Non-Muscle-Invasive Conventional Urothelial Bladder Carcinoma by Hasan et al
- 31 December 2025
- Published by MDPI AG in Clinics and Practice
- Vol. 16 (1) , 9
Open AccessComment on Hasan et al. Clinico-Pathological Features and Immunohistochemical Comparison of p16, p53, and Ki-67 Expression in Muscle-Invasive and Non-Muscle-Invasive Conventional Urothelial Bladder Carcinoma. Clin. Pract. 2023, 13, 806–819
We read with great interest the article Clinico-Pathological Features and Immunohistochemical Comparison of p16, p53, and Ki-67 Expression in Muscle-Invasive and Non-Muscle-Invasive Conventional Urothelial Bladder Carcinoma by Hasan et al
- Open Access
- 18 November 2024
- Published by MDPI AG in International Journal of Molecular Sciences
- Vol. 25 (22) , 12361
Effects of Two Decellularization Protocols on the Mechanical Behavior and Structural Properties of the Human Urethra
This study evaluates the effects of two decellularization protocols, enzyme-detergent (ED) and detergent-detergent (DD), on the structural and biomechanical properties of human urethral tissue. Urethral samples from 18 individuals were divided into ED (n = 7) and DD (n = 11) groups, with native samples (n = 3) serving as controls. Histological and ultrastructural analyses confirmed that both protocols effectively removed cellular content while preserving essential extracellular matrix (ECM) elements, such as collagen and elastic fibers. Immunohistochemical staining for collagen IV and fibronectin revealed no significant differences between decellularized and native tissues, indicating intact ECM structure. Biomechanical testing demonstrated that DD-treated tissues had significantly lower Cauchy stress (1494.8 ± 518.4 kPa) when compared to native tissues (2439.7 ± 578.7 kPa, p = 0.013), while ED-treated tissues were similar to both groups. Both decellularized groups exhibited reduced stretch at failure and elastic modulus compared to native tissues. Cytotoxicity assays using adipose-derived stem cells demonstrated no signs of toxicity in either protocol. Overall, both ED and DD protocols effectively preserved the urethral ECM structure and mechanical properties, making them suitable for potential use in tissue-engineered grafts and for biobanking purposes. Further research is needed to refine and optimize decellularization methods to improve scaffold recellularization and ensure clinical safety and efficacy.
- 18 November 2024
- Published by MDPI AG in International Journal of Molecular Sciences
- Vol. 25 (22) , 12361
Open AccessEffects of Two Decellularization Protocols on the Mechanical Behavior and Structural Properties of the Human Urethra
This study evaluates the effects of two decellularization protocols, enzyme-detergent (ED) and detergent-detergent (DD), on the structural and biomechanical properties of human urethral tissue. Urethral samples from 18 individuals were divided into ED (n = 7) and DD (n = 11) groups, with native samples (n = 3) serving as controls. Histological and ultrastructural analyses confirmed that both protocols effectively removed cellular content while preserving essential extracellular matrix (ECM) elements, such as collagen and elastic fibers. Immunohistochemical staining for collagen IV and fibronectin revealed no significant differences between decellularized and native tissues, indicating intact ECM structure. Biomechanical testing demonstrated that DD-treated tissues had significantly lower Cauchy stress (1494.8 ± 518.4 kPa) when compared to native tissues (2439.7 ± 578.7 kPa, p = 0.013), while ED-treated tissues were similar to both groups. Both decellularized groups exhibited reduced stretch at failure and elastic modulus compared to native tissues. Cytotoxicity assays using adipose-derived stem cells demonstrated no signs of toxicity in either protocol. Overall, both ED and DD protocols effectively preserved the urethral ECM structure and mechanical properties, making them suitable for potential use in tissue-engineered grafts and for biobanking purposes. Further research is needed to refine and optimize decellularization methods to improve scaffold recellularization and ensure clinical safety and efficacy.
- Open Access
- 1 November 2023
- Published by MDPI AG in International Journal of Molecular Sciences
- Vol. 24 (21) , 15856
Rheumatoid Synovial Fluid and Acidic Extracellular pH Modulate the Immunomodulatory Activity of Urine-Derived Stem Cells
Urine-derived stem cells (UdSCs) possess a remarkable anti-inflammatory and immune-modulating activity. However, the clinical significance of UdSCs in autoimmune inflammatory diseases such as rheumatoid arthritis (RA) is yet to be explored. Hence, we tested the UdSCs response to an articular RA microenvironment. To simulate the inflamed RA joint more authentically in vitro, we treated cells with rheumatoid synovial fluids (RASFs) collected from RA patients, serum deprivation, acidosis (pH 7.0 and 6.5), and their combinations. Firstly, the RASFs pro-inflammatory status was assessed by cytokine quantification. Then, UdSCs were exposed to the RA environmental factors for 48 h and cell proliferation, gene expression and secretion of immunomodulatory factors were evaluated. The immunosuppressive potential of pre-conditioned UdSCs was also assessed via co-cultivation with activated peripheral blood mononuclear cells (PBMCs). In all experimental conditions, UdSCs’ proliferation was not affected. Conversely, extracellular acidosis considerably impaired the viability/proliferation of adipose tissue-derived stem cells (ATSCs). In the majority of cases, exposure to RA components led to the upregulated expression of IL-6, TSG6, ICAM-1, VCAM-1, and PD-L1, all involved in immunomodulation. Upon RASFs and acidic stimulation, UdSCs secreted higher levels of immunomodulatory cytokines: IL-6, IL-8, MCP-1, RANTES, GM-CSF, and IL-4. Furthermore, RASFs and combined pretreatment with RASFs and acidosis promoted the UdSCs-mediated immunosuppression and the proliferation of activated PBMCs was significantly inhibited. Altogether, our data indicate that the RA microenvironment certainly has the capacity to enhance UdSCs’ immunomodulatory function. For potential preclinical/clinical applications, the intra-articular injection might be a reasonable approach to maximize UdSCs’ therapeutic efficiency in the RA treatment.
- 1 November 2023
- Published by MDPI AG in International Journal of Molecular Sciences
- Vol. 24 (21) , 15856
Open AccessRheumatoid Synovial Fluid and Acidic Extracellular pH Modulate the Immunomodulatory Activity of Urine-Derived Stem Cells
Urine-derived stem cells (UdSCs) possess a remarkable anti-inflammatory and immune-modulating activity. However, the clinical significance of UdSCs in autoimmune inflammatory diseases such as rheumatoid arthritis (RA) is yet to be explored. Hence, we tested the UdSCs response to an articular RA microenvironment. To simulate the inflamed RA joint more authentically in vitro, we treated cells with rheumatoid synovial fluids (RASFs) collected from RA patients, serum deprivation, acidosis (pH 7.0 and 6.5), and their combinations. Firstly, the RASFs pro-inflammatory status was assessed by cytokine quantification. Then, UdSCs were exposed to the RA environmental factors for 48 h and cell proliferation, gene expression and secretion of immunomodulatory factors were evaluated. The immunosuppressive potential of pre-conditioned UdSCs was also assessed via co-cultivation with activated peripheral blood mononuclear cells (PBMCs). In all experimental conditions, UdSCs’ proliferation was not affected. Conversely, extracellular acidosis considerably impaired the viability/proliferation of adipose tissue-derived stem cells (ATSCs). In the majority of cases, exposure to RA components led to the upregulated expression of IL-6, TSG6, ICAM-1, VCAM-1, and PD-L1, all involved in immunomodulation. Upon RASFs and acidic stimulation, UdSCs secreted higher levels of immunomodulatory cytokines: IL-6, IL-8, MCP-1, RANTES, GM-CSF, and IL-4. Furthermore, RASFs and combined pretreatment with RASFs and acidosis promoted the UdSCs-mediated immunosuppression and the proliferation of activated PBMCs was significantly inhibited. Altogether, our data indicate that the RA microenvironment certainly has the capacity to enhance UdSCs’ immunomodulatory function. For potential preclinical/clinical applications, the intra-articular injection might be a reasonable approach to maximize UdSCs’ therapeutic efficiency in the RA treatment.
- 23 October 2023
- Published by Institute of Physiology of the Czech Academy of Sciences in Physiological Research
- Vol. 72 (S3) , S247-S256
Molecular Biomarkers of Bladder Cancer: A Mini-Review
Cancers are quite common, but mostly very serious diseases and therefore belong to the most important areas of scientific research activity. Bladder cancer is one of the most common malignancies, it is a heterogeneous disease with significant diagnostic, therapeutic, and prognostic problems. It represents a disease with a variable course and a different response to therapy. The “conventional” prognostic markers used so far cannot reliably predict the natural course of the disease or estimate the tumor response to the chosen type of treatment. Molecular markers can provide us with the opportunity to diagnose a bladder tumor early, identify patients who are at risk of recurrence, or predict how tumors will respond to therapeutic approaches. As a result, diagnostics are found to help clinicians find the best therapeutic options for patients with bladder cancer. In this study, we focused on a brief description of potential molecular markers in bladder tumors in the context of precise diagnostics. Last but not least, we also focused on a new approach to the treatment of cancer using nanomaterials.
- 23 October 2023
- Published by Institute of Physiology of the Czech Academy of Sciences in Physiological Research
- Vol. 72 (S3) , S247-S256
Molecular Biomarkers of Bladder Cancer: A Mini-Review
Cancers are quite common, but mostly very serious diseases and therefore belong to the most important areas of scientific research activity. Bladder cancer is one of the most common malignancies, it is a heterogeneous disease with significant diagnostic, therapeutic, and prognostic problems. It represents a disease with a variable course and a different response to therapy. The “conventional” prognostic markers used so far cannot reliably predict the natural course of the disease or estimate the tumor response to the chosen type of treatment. Molecular markers can provide us with the opportunity to diagnose a bladder tumor early, identify patients who are at risk of recurrence, or predict how tumors will respond to therapeutic approaches. As a result, diagnostics are found to help clinicians find the best therapeutic options for patients with bladder cancer. In this study, we focused on a brief description of potential molecular markers in bladder tumors in the context of precise diagnostics. Last but not least, we also focused on a new approach to the treatment of cancer using nanomaterials.
- Open Access
- 30 October 2022
- Published by MDPI AG in International Journal of Molecular Sciences
- Vol. 23 (21) , 13206
Biomarkers of Bladder Cancer: Cell-Free DNA, Epigenetic Modifications and Non-Coding RNAs
Bladder cancer (BC) is the 10th most frequent cancer in the world. The initial diagnosis and surveillance of BC require a combination of invasive and non-invasive methods, which are costly and suffer from several limitations. Cystoscopy with urine cytology and histological examination presents the standard diagnostic approach. Various biomarkers (e.g., proteins, genes, and RNAs) have been extensively studied in relation to BC. However, the new trend of liquid biopsy slowly proves to be almost equally effective. Cell-free DNA, non-coding RNA, and other subcellular structures are now being tested for the best predictive and diagnostic value. In this review, we focused on published gene mutations, especially in DNA fragments, but also epigenetic modifications, and non-coding RNA (ncRNA) molecules acquired by liquid biopsy. We performed an online search in PubMed/Medline, Scopus, and Web of Science databases using the terms “bladder cancer”, in combination with “markers” or “biomarkers” published until August 2022. If applicable, we set the sensitivity and specificity threshold to 80%. In the era of precision medicine, the development of complex laboratory techniques fuels the search and development of more sensitive and specific biomarkers for diagnosis, follow-up, and screening of BC. Future efforts will be focused on the validation of their sensitivity, specificity, predictive value, and their utility in everyday clinical practice.
- 30 October 2022
- Published by MDPI AG in International Journal of Molecular Sciences
- Vol. 23 (21) , 13206
Open AccessBiomarkers of Bladder Cancer: Cell-Free DNA, Epigenetic Modifications and Non-Coding RNAs
Bladder cancer (BC) is the 10th most frequent cancer in the world. The initial diagnosis and surveillance of BC require a combination of invasive and non-invasive methods, which are costly and suffer from several limitations. Cystoscopy with urine cytology and histological examination presents the standard diagnostic approach. Various biomarkers (e.g., proteins, genes, and RNAs) have been extensively studied in relation to BC. However, the new trend of liquid biopsy slowly proves to be almost equally effective. Cell-free DNA, non-coding RNA, and other subcellular structures are now being tested for the best predictive and diagnostic value. In this review, we focused on published gene mutations, especially in DNA fragments, but also epigenetic modifications, and non-coding RNA (ncRNA) molecules acquired by liquid biopsy. We performed an online search in PubMed/Medline, Scopus, and Web of Science databases using the terms “bladder cancer”, in combination with “markers” or “biomarkers” published until August 2022. If applicable, we set the sensitivity and specificity threshold to 80%. In the era of precision medicine, the development of complex laboratory techniques fuels the search and development of more sensitive and specific biomarkers for diagnosis, follow-up, and screening of BC. Future efforts will be focused on the validation of their sensitivity, specificity, predictive value, and their utility in everyday clinical practice.
- Open Access
- 19 November 2021
- Published by MDPI AG in International Journal of Molecular Sciences
- Vol. 22 (22) , 12503
Isolation, Culture and Comprehensive Characterization of Biological Properties of Human Urine-Derived Stem Cells
Mesenchymal stem cells (MSCs) represent an attractive source within the field of tissue engineering. However, their harvesting often requires invasive medical procedures. Urine-derived stem cells (UDSCs) display similar properties to MSCs, and their obtention and further processing is non-invasive for the donors as well as low cost. Here, we offer a comprehensive analysis of their biological properties. The goal of this study was to analyze their morphology, stemness, differentiation potential and cytokine profile. We have successfully isolated UDSCs from 25 urine samples. First colonies emerged up to 9 days after the initial seeding. Cell doubling time was 45 ± 0.24 SD, and when seeded at the density of 100 cells/cm2, they formed 42 ± 6.5 SD colonies within 10 days. Morphological analyzes revealed that two different types of the cell populations have been present. The first type had a rice-grain shape and the second one was characterized by a polyhedral shape. In several cell cultures, dome-shaped cells were observed as well. All examined UDSCs expressed typical MSC-like surface markers, CD73, CD90 and CD105. Moreover, conditioned media from UDSCs were harvested, and cytokine profile has been evaluated showing a significantly higher secretory rate of IL-8, IL-6 and chemokines MCP-1 and GM-CSF. We have also successfully induced human UDSCs into chondrogenic, osteogenic and myogenic cell lineages. Our findings indicate that UDSCs might have immense potential in the regeneration of the damaged tissues.
- 19 November 2021
- Published by MDPI AG in International Journal of Molecular Sciences
- Vol. 22 (22) , 12503
Open AccessIsolation, Culture and Comprehensive Characterization of Biological Properties of Human Urine-Derived Stem Cells
Mesenchymal stem cells (MSCs) represent an attractive source within the field of tissue engineering. However, their harvesting often requires invasive medical procedures. Urine-derived stem cells (UDSCs) display similar properties to MSCs, and their obtention and further processing is non-invasive for the donors as well as low cost. Here, we offer a comprehensive analysis of their biological properties. The goal of this study was to analyze their morphology, stemness, differentiation potential and cytokine profile. We have successfully isolated UDSCs from 25 urine samples. First colonies emerged up to 9 days after the initial seeding. Cell doubling time was 45 ± 0.24 SD, and when seeded at the density of 100 cells/cm2, they formed 42 ± 6.5 SD colonies within 10 days. Morphological analyzes revealed that two different types of the cell populations have been present. The first type had a rice-grain shape and the second one was characterized by a polyhedral shape. In several cell cultures, dome-shaped cells were observed as well. All examined UDSCs expressed typical MSC-like surface markers, CD73, CD90 and CD105. Moreover, conditioned media from UDSCs were harvested, and cytokine profile has been evaluated showing a significantly higher secretory rate of IL-8, IL-6 and chemokines MCP-1 and GM-CSF. We have also successfully induced human UDSCs into chondrogenic, osteogenic and myogenic cell lineages. Our findings indicate that UDSCs might have immense potential in the regeneration of the damaged tissues.
- Open Access
- 8 August 2019
- Published by MDPI AG in Proceedings
- Vol. 22 (1) , 48
Antibacterial N-Arylcinnamamides as Anti-inflammatory Agents
A series of ring-substituted N-arylcinnamamides was prepared, characterized, and investigated for their antimicrobial efficacy in detail
- 8 August 2019
- Published by MDPI AG in Proceedings
- Vol. 22 (1) , 48
Open AccessAntibacterial N-Arylcinnamamides as Anti-inflammatory Agents
A series of ring-substituted N-arylcinnamamides was prepared, characterized, and investigated for their antimicrobial efficacy in detail