Jovanović, Ivan G.

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orcid::0000-0001-7932-9463
  • Jovanović, Ivan G. (12)
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Author's Bibliography

The Effects of Aronia melanocarpa Juice Consumption on the mRNA Expression Profile in Peripheral Blood Mononuclear Cells in Subjects at Cardiovascular Risk

Stojković, Ljiljana S.; Jovanović, Ivan G.; Živković, Maja; Zec, Manja; Đurić, Tamara; Životić, Ivan; Kuveljić, Jovana; Kolaković, Ana; Kolić, Ivana; Đorđević, Ana; Glibetić, Marija; Alavantić, Dragan; Stanković, Aleksandra

(2020)

TY  - JOUR
AU  - Stojković, Ljiljana S.
AU  - Jovanović, Ivan G.
AU  - Živković, Maja
AU  - Zec, Manja
AU  - Đurić, Tamara
AU  - Životić, Ivan
AU  - Kuveljić, Jovana
AU  - Kolaković, Ana
AU  - Kolić, Ivana
AU  - Đorđević, Ana
AU  - Glibetić, Marija
AU  - Alavantić, Dragan
AU  - Stanković, Aleksandra
PY  - 2020
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/8683
AB  - Foods and food products that contain polyphenols are proposed to modulate risk of cardiovascular disease. The aim of this three-arm, crossover, randomized, double-blind, placebo-controlled intervention study was to examine the impact of Aronia melanocarpa juice (AMJ), high-polyphenol (AMJ treatment, 1.17 g/100 mL polyphenols) and low-polyphenol (dAMJ treatment, 0.29 g/100 mL polyphenols) dose, on the transcriptome in peripheral blood mononuclear cells (PBMC) of 19 subjects at cardiovascular risk. Transcriptome data were obtained by microarray. Bioinformatic functional annotation analysis was performed on both the whole transcriptome datasets and the differentially expressed genes (DEGs). Expression of selected DEGs was validated by RT-qPCR. Administration of AMJ and dAMJ treatments during the two consecutive four-week treatment periods had additive effects on PBMC transcriptome profiles, with the most pronounced and specific effect noticed for AMJ in the last treatment period (TP3) of the trial. Between the high-dose and low-dose treatments in TP3, there was a multitude of overlapping DEGs and DEG-enriched biological processes and pathways, which primarily included immunomodulation and regulation of cell proliferation/death. Increased expression of TNF, IL1B, IL8, RGS1, OSM, and DUSP2 in TP3 was confirmed by RT-qPCR. The results suggest the immunomodulatory effects of prolonged habitual consumption of polyphenol-rich aronia juice in individuals at cardiovascular risk.
T2  - Nutrients
T1  - The Effects of Aronia melanocarpa Juice Consumption on the mRNA Expression Profile in Peripheral Blood Mononuclear Cells in Subjects at Cardiovascular Risk
VL  - 12
IS  - 5
SP  - 1484
DO  - 10.3390/nu12051484
ER  - 
@article{
author = "Stojković, Ljiljana S. and Jovanović, Ivan G. and Živković, Maja and Zec, Manja and Đurić, Tamara and Životić, Ivan and Kuveljić, Jovana and Kolaković, Ana and Kolić, Ivana and Đorđević, Ana and Glibetić, Marija and Alavantić, Dragan and Stanković, Aleksandra",
year = "2020",
abstract = "Foods and food products that contain polyphenols are proposed to modulate risk of cardiovascular disease. The aim of this three-arm, crossover, randomized, double-blind, placebo-controlled intervention study was to examine the impact of Aronia melanocarpa juice (AMJ), high-polyphenol (AMJ treatment, 1.17 g/100 mL polyphenols) and low-polyphenol (dAMJ treatment, 0.29 g/100 mL polyphenols) dose, on the transcriptome in peripheral blood mononuclear cells (PBMC) of 19 subjects at cardiovascular risk. Transcriptome data were obtained by microarray. Bioinformatic functional annotation analysis was performed on both the whole transcriptome datasets and the differentially expressed genes (DEGs). Expression of selected DEGs was validated by RT-qPCR. Administration of AMJ and dAMJ treatments during the two consecutive four-week treatment periods had additive effects on PBMC transcriptome profiles, with the most pronounced and specific effect noticed for AMJ in the last treatment period (TP3) of the trial. Between the high-dose and low-dose treatments in TP3, there was a multitude of overlapping DEGs and DEG-enriched biological processes and pathways, which primarily included immunomodulation and regulation of cell proliferation/death. Increased expression of TNF, IL1B, IL8, RGS1, OSM, and DUSP2 in TP3 was confirmed by RT-qPCR. The results suggest the immunomodulatory effects of prolonged habitual consumption of polyphenol-rich aronia juice in individuals at cardiovascular risk.",
journal = "Nutrients",
title = "The Effects of Aronia melanocarpa Juice Consumption on the mRNA Expression Profile in Peripheral Blood Mononuclear Cells in Subjects at Cardiovascular Risk",
volume = "12",
number = "5",
pages = "1484",
doi = "10.3390/nu12051484"
}
Stojković, L. S., Jovanović, I. G., Živković, M., Zec, M., Đurić, T., Životić, I., Kuveljić, J., Kolaković, A., Kolić, I., Đorđević, A., Glibetić, M., Alavantić, D.,& Stanković, A.. (2020). The Effects of Aronia melanocarpa Juice Consumption on the mRNA Expression Profile in Peripheral Blood Mononuclear Cells in Subjects at Cardiovascular Risk. in Nutrients, 12(5), 1484.
https://doi.org/10.3390/nu12051484
Stojković LS, Jovanović IG, Živković M, Zec M, Đurić T, Životić I, Kuveljić J, Kolaković A, Kolić I, Đorđević A, Glibetić M, Alavantić D, Stanković A. The Effects of Aronia melanocarpa Juice Consumption on the mRNA Expression Profile in Peripheral Blood Mononuclear Cells in Subjects at Cardiovascular Risk. in Nutrients. 2020;12(5):1484.
doi:10.3390/nu12051484 .
Stojković, Ljiljana S., Jovanović, Ivan G., Živković, Maja, Zec, Manja, Đurić, Tamara, Životić, Ivan, Kuveljić, Jovana, Kolaković, Ana, Kolić, Ivana, Đorđević, Ana, Glibetić, Marija, Alavantić, Dragan, Stanković, Aleksandra, "The Effects of Aronia melanocarpa Juice Consumption on the mRNA Expression Profile in Peripheral Blood Mononuclear Cells in Subjects at Cardiovascular Risk" in Nutrients, 12, no. 5 (2020):1484,
https://doi.org/10.3390/nu12051484 . .
4

Perimatrix of middle ear cholesteatoma: A granulation tissue with a specific transcriptomic signature

Jovanović, Ivan G.; Živković, Maja; Đurić, Tamara; Stojković, Ljiljana S.; Ješić, Snežana; Stanković, Aleksandra

(2020)

TY  - JOUR
AU  - Jovanović, Ivan G.
AU  - Živković, Maja
AU  - Đurić, Tamara
AU  - Stojković, Ljiljana S.
AU  - Ješić, Snežana
AU  - Stanković, Aleksandra
PY  - 2020
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/8684
AB  - Objectives/Hypothesis: To establish comprehensive transcriptomic profiles of cholesteatoma perimatrix tissue and granulation tissue from chronic otitis media (COM) that did not develop cholesteatoma, which can indicate molecular pathways involved in the cholesteatoma perimatrix pathology and invasiveness. Study Design: Retrospective Case Series. Methods: Transcriptome data were obtained from cholesteatoma perimatrix tissue and COM granulation tissue by an Illumina iScan microarray. Differentially expressed genes (DEGs) were subsequently analyzed using both bioinformatical functional annotation and network analysis. Expression of candidate genes (MMP9 and LCN2) was validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) on a larger group of samples. Results: Analysis of the transcriptome led to the identification of 169 differentially expressed genes between investigated tissues. Bioinformatic analysis suggested that most significant biological processes involving DEGs were previously described in cholesteatoma pathology. Network analysis identified ERBB2, TFAP2A, and TP63 as major hubs of the DEGs molecular network. Furthermore, it was observed that the cellular component most significantly enriched in DEGs was extracellular space containing 47 DEGs. Using qRT-PCR, it was confirmed that mRNA levels of the major extracellular hub (MMP9) are increased, whereas its interacting molecule (LCN2) mRNA levels were decreased in cholesteatoma perimatrix tissue compared to COM granulation tissue. Conclusions: The current study approach offers an overall look at molecular mechanisms that describe the cholesteatoma entity by focusing exclusively on the perimatrix processes in comparison to COM granulation tissue. The observed differences in gene expression between cholesteatoma perimatrix and COM granulation tissue could suggest novel markers potentially influenced by the perimatrix–matrix molecular interplay, which is not present in COM without cholesteatoma. Level of Evidence: NA. Laryngoscope, 130:E220–E227, 2020. © 2019 The American Laryngological, Rhinological and Otological Society, Inc.
T2  - The Laryngoscope
T1  - Perimatrix of middle ear cholesteatoma: A granulation tissue with a specific transcriptomic signature
VL  - 130
IS  - 4
SP  - E220
EP  - E227
DO  - 10.1002/lary.28084
ER  - 
@article{
author = "Jovanović, Ivan G. and Živković, Maja and Đurić, Tamara and Stojković, Ljiljana S. and Ješić, Snežana and Stanković, Aleksandra",
year = "2020",
abstract = "Objectives/Hypothesis: To establish comprehensive transcriptomic profiles of cholesteatoma perimatrix tissue and granulation tissue from chronic otitis media (COM) that did not develop cholesteatoma, which can indicate molecular pathways involved in the cholesteatoma perimatrix pathology and invasiveness. Study Design: Retrospective Case Series. Methods: Transcriptome data were obtained from cholesteatoma perimatrix tissue and COM granulation tissue by an Illumina iScan microarray. Differentially expressed genes (DEGs) were subsequently analyzed using both bioinformatical functional annotation and network analysis. Expression of candidate genes (MMP9 and LCN2) was validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) on a larger group of samples. Results: Analysis of the transcriptome led to the identification of 169 differentially expressed genes between investigated tissues. Bioinformatic analysis suggested that most significant biological processes involving DEGs were previously described in cholesteatoma pathology. Network analysis identified ERBB2, TFAP2A, and TP63 as major hubs of the DEGs molecular network. Furthermore, it was observed that the cellular component most significantly enriched in DEGs was extracellular space containing 47 DEGs. Using qRT-PCR, it was confirmed that mRNA levels of the major extracellular hub (MMP9) are increased, whereas its interacting molecule (LCN2) mRNA levels were decreased in cholesteatoma perimatrix tissue compared to COM granulation tissue. Conclusions: The current study approach offers an overall look at molecular mechanisms that describe the cholesteatoma entity by focusing exclusively on the perimatrix processes in comparison to COM granulation tissue. The observed differences in gene expression between cholesteatoma perimatrix and COM granulation tissue could suggest novel markers potentially influenced by the perimatrix–matrix molecular interplay, which is not present in COM without cholesteatoma. Level of Evidence: NA. Laryngoscope, 130:E220–E227, 2020. © 2019 The American Laryngological, Rhinological and Otological Society, Inc.",
journal = "The Laryngoscope",
title = "Perimatrix of middle ear cholesteatoma: A granulation tissue with a specific transcriptomic signature",
volume = "130",
number = "4",
pages = "E220-E227",
doi = "10.1002/lary.28084"
}
Jovanović, I. G., Živković, M., Đurić, T., Stojković, L. S., Ješić, S.,& Stanković, A.. (2020). Perimatrix of middle ear cholesteatoma: A granulation tissue with a specific transcriptomic signature. in The Laryngoscope, 130(4), E220-E227.
https://doi.org/10.1002/lary.28084
Jovanović IG, Živković M, Đurić T, Stojković LS, Ješić S, Stanković A. Perimatrix of middle ear cholesteatoma: A granulation tissue with a specific transcriptomic signature. in The Laryngoscope. 2020;130(4):E220-E227.
doi:10.1002/lary.28084 .
Jovanović, Ivan G., Živković, Maja, Đurić, Tamara, Stojković, Ljiljana S., Ješić, Snežana, Stanković, Aleksandra, "Perimatrix of middle ear cholesteatoma: A granulation tissue with a specific transcriptomic signature" in The Laryngoscope, 130, no. 4 (2020):E220-E227,
https://doi.org/10.1002/lary.28084 . .
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4
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4

Expression of LEP, LEPR and PGC1A genes is altered in peripheral blood mononuclear cells of patients with relapsing-remitting multiple sclerosis

Kolić, Ivana; Stojković, Ljiljana S.; Dinčić, Evica; Jovanović, Ivan G.; Stanković, Aleksandra; Živković, Maja

(2020)

TY  - JOUR
AU  - Kolić, Ivana
AU  - Stojković, Ljiljana S.
AU  - Dinčić, Evica
AU  - Jovanović, Ivan G.
AU  - Stanković, Aleksandra
AU  - Živković, Maja
PY  - 2020
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/8618
AB  - Leptin (LEP) may contribute to the pathogenesis of multiple sclerosis (MS) by its immunomodulatory, proinflammatory and prooxidant effects. Therefore, plasma LEP levels and mRNA expression of five genes related to the LEP signaling pathway (LEP, LEP receptor (LEPR), peroxisome proliferator-activated receptor-gamma coactivator 1-alpha (PGC1A), superoxide dismutase 2, tumor necrosis factor-alpha) were investigated in relapsing-remitting MS. In patients (N = 64), compared to healthy subjects (N = 62), relative LEP mRNA levels were significantly increased (p = 0,01), while LEPR and PGC1A mRNA levels were decreased (p = 0,001 and p = 0,04, respectively). Significant positive correlation was observed between LEPR mRNA levels and clinical parameters of MS progression (EDSS, MSSS). © 2019
T2  - Journal of Neuroimmunology
T1  - Expression of LEP, LEPR and PGC1A genes is altered in peripheral blood mononuclear cells of patients with relapsing-remitting multiple sclerosis
VL  - 338
SP  - 577090
DO  - 10.1016/j.jneuroim.2019.577090
ER  - 
@article{
author = "Kolić, Ivana and Stojković, Ljiljana S. and Dinčić, Evica and Jovanović, Ivan G. and Stanković, Aleksandra and Živković, Maja",
year = "2020",
abstract = "Leptin (LEP) may contribute to the pathogenesis of multiple sclerosis (MS) by its immunomodulatory, proinflammatory and prooxidant effects. Therefore, plasma LEP levels and mRNA expression of five genes related to the LEP signaling pathway (LEP, LEP receptor (LEPR), peroxisome proliferator-activated receptor-gamma coactivator 1-alpha (PGC1A), superoxide dismutase 2, tumor necrosis factor-alpha) were investigated in relapsing-remitting MS. In patients (N = 64), compared to healthy subjects (N = 62), relative LEP mRNA levels were significantly increased (p = 0,01), while LEPR and PGC1A mRNA levels were decreased (p = 0,001 and p = 0,04, respectively). Significant positive correlation was observed between LEPR mRNA levels and clinical parameters of MS progression (EDSS, MSSS). © 2019",
journal = "Journal of Neuroimmunology",
title = "Expression of LEP, LEPR and PGC1A genes is altered in peripheral blood mononuclear cells of patients with relapsing-remitting multiple sclerosis",
volume = "338",
pages = "577090",
doi = "10.1016/j.jneuroim.2019.577090"
}
Kolić, I., Stojković, L. S., Dinčić, E., Jovanović, I. G., Stanković, A.,& Živković, M.. (2020). Expression of LEP, LEPR and PGC1A genes is altered in peripheral blood mononuclear cells of patients with relapsing-remitting multiple sclerosis. in Journal of Neuroimmunology, 338, 577090.
https://doi.org/10.1016/j.jneuroim.2019.577090
Kolić I, Stojković LS, Dinčić E, Jovanović IG, Stanković A, Živković M. Expression of LEP, LEPR and PGC1A genes is altered in peripheral blood mononuclear cells of patients with relapsing-remitting multiple sclerosis. in Journal of Neuroimmunology. 2020;338:577090.
doi:10.1016/j.jneuroim.2019.577090 .
Kolić, Ivana, Stojković, Ljiljana S., Dinčić, Evica, Jovanović, Ivan G., Stanković, Aleksandra, Živković, Maja, "Expression of LEP, LEPR and PGC1A genes is altered in peripheral blood mononuclear cells of patients with relapsing-remitting multiple sclerosis" in Journal of Neuroimmunology, 338 (2020):577090,
https://doi.org/10.1016/j.jneuroim.2019.577090 . .
1
2
2
1

MicroRNA meta-signature of oral cancer: evidence from a meta-analysis

Željić, Katarina; Jovanović, Ivan G.; Jovanović, Jasmina; Magić, Zvonko; Stanković, Aleksandra; Šupić, Gordana

(2018)

TY  - JOUR
AU  - Željić, Katarina
AU  - Jovanović, Ivan G.
AU  - Jovanović, Jasmina
AU  - Magić, Zvonko
AU  - Stanković, Aleksandra
AU  - Šupić, Gordana
PY  - 2018
UR  - https://www.tandfonline.com/doi/full/10.1080/03009734.2018.1439551
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/7630
AB  - Aim: It was the aim of the study to identify commonly deregulated miRNAs in oral cancer patients by performing a meta-analysis of previously published miRNA expression profiles in cancer and matched normal non-cancerous tissue in such patients. Material and methods: Meta-analysis included seven independent studies analyzed by a vote-counting method followed by bioinformatic enrichment analysis. Results: Amongst seven independent studies included in the meta-analysis, 20 miRNAs were found to be deregulated in oral cancer when compared with non-cancerous tissue. Eleven miRNAs were consistently up-regulated in three or more studies (miR-21-5p, miR-31-5p, miR-135b-5p, miR-31-3p, miR-93-5p, miR-34b-5p, miR-424-5p, miR-18a-5p, miR-455-3p, miR-450a-5p, miR-21-3p), and nine were down-regulated (miR-139-5p, miR-30a-3p, miR-376c-3p, miR-885-5p, miR-375, miR-486-5p, miR-411-5p, miR-133a-3p, miR-30a-5p). The meta-signature of identified miRNAs was functionally characterized by KEGG enrichment analysis. Twenty-four KEGG pathways were significantly enriched, and TGF-beta signaling was the most enriched signaling pathway. The highest number of meta-signature miRNAs was involved in the sphingolipid signaling pathway. Natural killer cell-mediated cytotoxicity was the pathway with most genes regulated by identified miRNAs. The rest of the enriched pathways in our miRNA list describe different malignancies and signaling. Conclusions: The identified miRNA meta-signature might be considered as a potential battery of biomarkers when distinguishing oral cancer tissue from normal, non-cancerous tissue. Further mechanistic studies are warranted in order to confirm and fully elucidate the role of deregulated miRNAs in oral cancer.
T2  - Upsala Journal of Medical Sciences
T1  - MicroRNA meta-signature of oral cancer: evidence from a meta-analysis
VL  - 123
IS  - 1
SP  - 43
EP  - 49
DO  - 10.1080/03009734.2018.1439551
ER  - 
@article{
author = "Željić, Katarina and Jovanović, Ivan G. and Jovanović, Jasmina and Magić, Zvonko and Stanković, Aleksandra and Šupić, Gordana",
year = "2018",
abstract = "Aim: It was the aim of the study to identify commonly deregulated miRNAs in oral cancer patients by performing a meta-analysis of previously published miRNA expression profiles in cancer and matched normal non-cancerous tissue in such patients. Material and methods: Meta-analysis included seven independent studies analyzed by a vote-counting method followed by bioinformatic enrichment analysis. Results: Amongst seven independent studies included in the meta-analysis, 20 miRNAs were found to be deregulated in oral cancer when compared with non-cancerous tissue. Eleven miRNAs were consistently up-regulated in three or more studies (miR-21-5p, miR-31-5p, miR-135b-5p, miR-31-3p, miR-93-5p, miR-34b-5p, miR-424-5p, miR-18a-5p, miR-455-3p, miR-450a-5p, miR-21-3p), and nine were down-regulated (miR-139-5p, miR-30a-3p, miR-376c-3p, miR-885-5p, miR-375, miR-486-5p, miR-411-5p, miR-133a-3p, miR-30a-5p). The meta-signature of identified miRNAs was functionally characterized by KEGG enrichment analysis. Twenty-four KEGG pathways were significantly enriched, and TGF-beta signaling was the most enriched signaling pathway. The highest number of meta-signature miRNAs was involved in the sphingolipid signaling pathway. Natural killer cell-mediated cytotoxicity was the pathway with most genes regulated by identified miRNAs. The rest of the enriched pathways in our miRNA list describe different malignancies and signaling. Conclusions: The identified miRNA meta-signature might be considered as a potential battery of biomarkers when distinguishing oral cancer tissue from normal, non-cancerous tissue. Further mechanistic studies are warranted in order to confirm and fully elucidate the role of deregulated miRNAs in oral cancer.",
journal = "Upsala Journal of Medical Sciences",
title = "MicroRNA meta-signature of oral cancer: evidence from a meta-analysis",
volume = "123",
number = "1",
pages = "43-49",
doi = "10.1080/03009734.2018.1439551"
}
Željić, K., Jovanović, I. G., Jovanović, J., Magić, Z., Stanković, A.,& Šupić, G.. (2018). MicroRNA meta-signature of oral cancer: evidence from a meta-analysis. in Upsala Journal of Medical Sciences, 123(1), 43-49.
https://doi.org/10.1080/03009734.2018.1439551
Željić K, Jovanović IG, Jovanović J, Magić Z, Stanković A, Šupić G. MicroRNA meta-signature of oral cancer: evidence from a meta-analysis. in Upsala Journal of Medical Sciences. 2018;123(1):43-49.
doi:10.1080/03009734.2018.1439551 .
Željić, Katarina, Jovanović, Ivan G., Jovanović, Jasmina, Magić, Zvonko, Stanković, Aleksandra, Šupić, Gordana, "MicroRNA meta-signature of oral cancer: evidence from a meta-analysis" in Upsala Journal of Medical Sciences, 123, no. 1 (2018):43-49,
https://doi.org/10.1080/03009734.2018.1439551 . .
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MicroRNA meta-signature of oral cancer: evidence from a meta-analysis

Željić, Katarina; Jovanović, Ivan G.; Jovanović, Jasmina; Magić, Zvonko; Stanković, Aleksandra; Šupić, Gordana

(2018)

TY  - GEN
AU  - Željić, Katarina
AU  - Jovanović, Ivan G.
AU  - Jovanović, Jasmina
AU  - Magić, Zvonko
AU  - Stanković, Aleksandra
AU  - Šupić, Gordana
PY  - 2018
UR  - https://figshare.com/articles/MicroRNA_meta-signature_of_oral_cancer_evidence_from_a_meta-analysis/5926675
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/7843
AB  - Aim: It was the aim of the study to identify commonly deregulated miRNAs in oral cancer patients by performing a meta-analysis of previously published miRNA expression profiles in cancer and matched normal non-cancerous tissue in such patients. Material and methods: Meta-analysis included seven independent studies analyzed by a vote-counting method followed by bioinformatic enrichment analysis. Results: Amongst seven independent studies included in the meta-analysis, 20 miRNAs were found to be deregulated in oral cancer when compared with non-cancerous tissue. Eleven miRNAs were consistently up-regulated in three or more studies (miR-21-5p, miR-31-5p, miR-135b-5p, miR-31-3p, miR-93-5p, miR-34b-5p, miR-424-5p, miR-18a-5p, miR-455-3p, miR-450a-5p, miR-21-3p), and nine were down-regulated (miR-139-5p, miR-30a-3p, miR-376c-3p, miR-885-5p, miR-375, miR-486-5p, miR-411-5p, miR-133a-3p, miR-30a-5p). The meta-signature of identified miRNAs was functionally characterized by KEGG enrichment analysis. Twenty-four KEGG pathways were significantly enriched, and TGF-beta signaling was the most enriched signaling pathway. The highest number of meta-signature miRNAs was involved in the sphingolipid signaling pathway. Natural killer cell-mediated cytotoxicity was the pathway with most genes regulated by identified miRNAs. The rest of the enriched pathways in our miRNA list describe different malignancies and signaling. Conclusions: The identified miRNA meta-signature might be considered as a potential battery of biomarkers when distinguishing oral cancer tissue from normal, non-cancerous tissue. Further mechanistic studies are warranted in order to confirm and fully elucidate the role of deregulated miRNAs in oral cancer.
T2  - Upsala Journal of Medical Sciences
T1  - MicroRNA meta-signature of oral cancer: evidence from a meta-analysis
VL  - 123
IS  - 1
SP  - 43
EP  - 49
DO  - 10.6084/m9.figshare.5926675
ER  - 
@misc{
author = "Željić, Katarina and Jovanović, Ivan G. and Jovanović, Jasmina and Magić, Zvonko and Stanković, Aleksandra and Šupić, Gordana",
year = "2018",
abstract = "Aim: It was the aim of the study to identify commonly deregulated miRNAs in oral cancer patients by performing a meta-analysis of previously published miRNA expression profiles in cancer and matched normal non-cancerous tissue in such patients. Material and methods: Meta-analysis included seven independent studies analyzed by a vote-counting method followed by bioinformatic enrichment analysis. Results: Amongst seven independent studies included in the meta-analysis, 20 miRNAs were found to be deregulated in oral cancer when compared with non-cancerous tissue. Eleven miRNAs were consistently up-regulated in three or more studies (miR-21-5p, miR-31-5p, miR-135b-5p, miR-31-3p, miR-93-5p, miR-34b-5p, miR-424-5p, miR-18a-5p, miR-455-3p, miR-450a-5p, miR-21-3p), and nine were down-regulated (miR-139-5p, miR-30a-3p, miR-376c-3p, miR-885-5p, miR-375, miR-486-5p, miR-411-5p, miR-133a-3p, miR-30a-5p). The meta-signature of identified miRNAs was functionally characterized by KEGG enrichment analysis. Twenty-four KEGG pathways were significantly enriched, and TGF-beta signaling was the most enriched signaling pathway. The highest number of meta-signature miRNAs was involved in the sphingolipid signaling pathway. Natural killer cell-mediated cytotoxicity was the pathway with most genes regulated by identified miRNAs. The rest of the enriched pathways in our miRNA list describe different malignancies and signaling. Conclusions: The identified miRNA meta-signature might be considered as a potential battery of biomarkers when distinguishing oral cancer tissue from normal, non-cancerous tissue. Further mechanistic studies are warranted in order to confirm and fully elucidate the role of deregulated miRNAs in oral cancer.",
journal = "Upsala Journal of Medical Sciences",
title = "MicroRNA meta-signature of oral cancer: evidence from a meta-analysis",
volume = "123",
number = "1",
pages = "43-49",
doi = "10.6084/m9.figshare.5926675"
}
Željić, K., Jovanović, I. G., Jovanović, J., Magić, Z., Stanković, A.,& Šupić, G.. (2018). MicroRNA meta-signature of oral cancer: evidence from a meta-analysis. in Upsala Journal of Medical Sciences, 123(1), 43-49.
https://doi.org/10.6084/m9.figshare.5926675
Željić K, Jovanović IG, Jovanović J, Magić Z, Stanković A, Šupić G. MicroRNA meta-signature of oral cancer: evidence from a meta-analysis. in Upsala Journal of Medical Sciences. 2018;123(1):43-49.
doi:10.6084/m9.figshare.5926675 .
Željić, Katarina, Jovanović, Ivan G., Jovanović, Jasmina, Magić, Zvonko, Stanković, Aleksandra, Šupić, Gordana, "MicroRNA meta-signature of oral cancer: evidence from a meta-analysis" in Upsala Journal of Medical Sciences, 123, no. 1 (2018):43-49,
https://doi.org/10.6084/m9.figshare.5926675 . .
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Transcriptome-driven integrative exploration of functional state of ureter tissue affected by CAKUT

Jovanović, Ivan G.; Živković, Maja; Kostić, Mirjana M.; Krstić, Zoran; Đurić, Tamara; Licastro, Danilo; Meroni, Germana; Alavantić, Dragan; Stanković, Aleksandra

(2018)

TY  - JOUR
AU  - Jovanović, Ivan G.
AU  - Živković, Maja
AU  - Kostić, Mirjana M.
AU  - Krstić, Zoran
AU  - Đurić, Tamara
AU  - Licastro, Danilo
AU  - Meroni, Germana
AU  - Alavantić, Dragan
AU  - Stanković, Aleksandra
PY  - 2018
UR  - https://linkinghub.elsevier.com/retrieve/pii/S0024320518305940
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/7891
AB  - Aims: (1) to identify the most dysregulated genes in ureter tissue affected by congenital anomalies of the kidney and urinary tract (CAKUT) and to extract the biological meaning of these markers; (2) to describe the key molecular networks in CAKUT and to provide expression validation of the genes selected from these networks. Main methods: Transcriptome data was obtained from ureter samples of CAKUT patients and controls by Illumina iScan microarray. Identification of differentially expressed genes was coupled with subsequent bioinformatics analyses. Expression of candidate genes was validated by qRT-PCR. Key findings: Analysis of the transcriptome led to the identification of 78 commonly dysregulated genes in CAKUT tissue compared to controls. Integrative bioinformatic analyses of differentially expressed genes identified 7 major networks. The targets for qRT-PCR validation were selected as members of the major molecular networks in CAKUT, which had both, the significant high fold change and biological relevance for CAKUT. By qRT-PCR the substantial increase of LCN2, PROM1, SOSTDC1, and decrease of INA, RASD1 and TAC3 mRNA levels was confirmed. Significance: Since CAKUT is a leading cause of end-stage renal disease in children, the search for molecular targets for postnatal therapy is of particular interest. Data described in this study represents the gene expression profile and significant molecular networks specific to human ureter affected by CAKUT. The discovery of impaired molecular factors and processes is the step towards the uncovering of the key mechanisms that reflect CAKUT postnatally and could lead to the affected tissue deterioration and end organ damage. © 2018 Elsevier Inc.
T2  - Life Sciences
T1  - Transcriptome-driven integrative exploration of functional state of ureter tissue affected by CAKUT
VL  - 212
SP  - 1
EP  - 8
DO  - 10.1016/j.lfs.2018.09.042
ER  - 
@article{
author = "Jovanović, Ivan G. and Živković, Maja and Kostić, Mirjana M. and Krstić, Zoran and Đurić, Tamara and Licastro, Danilo and Meroni, Germana and Alavantić, Dragan and Stanković, Aleksandra",
year = "2018",
abstract = "Aims: (1) to identify the most dysregulated genes in ureter tissue affected by congenital anomalies of the kidney and urinary tract (CAKUT) and to extract the biological meaning of these markers; (2) to describe the key molecular networks in CAKUT and to provide expression validation of the genes selected from these networks. Main methods: Transcriptome data was obtained from ureter samples of CAKUT patients and controls by Illumina iScan microarray. Identification of differentially expressed genes was coupled with subsequent bioinformatics analyses. Expression of candidate genes was validated by qRT-PCR. Key findings: Analysis of the transcriptome led to the identification of 78 commonly dysregulated genes in CAKUT tissue compared to controls. Integrative bioinformatic analyses of differentially expressed genes identified 7 major networks. The targets for qRT-PCR validation were selected as members of the major molecular networks in CAKUT, which had both, the significant high fold change and biological relevance for CAKUT. By qRT-PCR the substantial increase of LCN2, PROM1, SOSTDC1, and decrease of INA, RASD1 and TAC3 mRNA levels was confirmed. Significance: Since CAKUT is a leading cause of end-stage renal disease in children, the search for molecular targets for postnatal therapy is of particular interest. Data described in this study represents the gene expression profile and significant molecular networks specific to human ureter affected by CAKUT. The discovery of impaired molecular factors and processes is the step towards the uncovering of the key mechanisms that reflect CAKUT postnatally and could lead to the affected tissue deterioration and end organ damage. © 2018 Elsevier Inc.",
journal = "Life Sciences",
title = "Transcriptome-driven integrative exploration of functional state of ureter tissue affected by CAKUT",
volume = "212",
pages = "1-8",
doi = "10.1016/j.lfs.2018.09.042"
}
Jovanović, I. G., Živković, M., Kostić, M. M., Krstić, Z., Đurić, T., Licastro, D., Meroni, G., Alavantić, D.,& Stanković, A.. (2018). Transcriptome-driven integrative exploration of functional state of ureter tissue affected by CAKUT. in Life Sciences, 212, 1-8.
https://doi.org/10.1016/j.lfs.2018.09.042
Jovanović IG, Živković M, Kostić MM, Krstić Z, Đurić T, Licastro D, Meroni G, Alavantić D, Stanković A. Transcriptome-driven integrative exploration of functional state of ureter tissue affected by CAKUT. in Life Sciences. 2018;212:1-8.
doi:10.1016/j.lfs.2018.09.042 .
Jovanović, Ivan G., Živković, Maja, Kostić, Mirjana M., Krstić, Zoran, Đurić, Tamara, Licastro, Danilo, Meroni, Germana, Alavantić, Dragan, Stanković, Aleksandra, "Transcriptome-driven integrative exploration of functional state of ureter tissue affected by CAKUT" in Life Sciences, 212 (2018):1-8,
https://doi.org/10.1016/j.lfs.2018.09.042 . .
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Analiza ekspresije celokupnog genoma u cilju identifikacije ključnih gena i mikroRNK za nastanak urođenih anomalija bubrega i urinarnog trakta čoveka

Jovanović, Ivan G.

(Универзитет у Београду, Биолошки факултет, 2016)

TY  - THES
AU  - Jovanović, Ivan G.
PY  - 2016
UR  - http://eteze.bg.ac.rs/application/showtheses?thesesId=4808
UR  - https://fedorabg.bg.ac.rs/fedora/get/o:15112/bdef:Content/download
UR  - http://vbs.rs/scripts/cobiss?command=DISPLAY&base=70036&RID=1025149106
UR  - http://nardus.mpn.gov.rs/123456789/7884
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/7316
AB  - Urođene anomalije bubrega i urinarnog trakta (engl. Congenital Anomalies of the Kidney and Urinary Tract – CAKUT) su razlog nastanka čak polovine slučajeva terminalne bubrežne insuficijencije ali patofiziološka osnova ove bolesti još uvek nije poznata u potpunosti pa je samim tim otežana prevencija i terapija. U ovoj studiji je, upoređivanjem ekspresije celokupnog genoma u tkivu uretera pacijenata sa CAKUT-om i zdravih kontrola, identifikovano 78 diferencijalno eksprimiranih gena. Bioinformatičkom analizom je po prvi put zaključeno da postoji visok nivo kompleksnosti bioloških procesa i molekularnih puteva u tkivu čoveka koji su u CAKUT-u diferencijalno regulisani i čije važne interakcije se mogu predstaviti sa sedam molekularnih mreža, od kojih četiri sadrže gene sa funkcijama koje se direktno mogu asocirati sa CAKUT-om. Eksperimentalnom validacijom ključnih mreža qRT-PCR metodom utvrđen je povišen nivo iRNK za gene LCN2 (7,6 puta), PROM1 (8 puta) i SOSTDC1 (5,6 puta) i snižen nivo iRNK za gene RASD1 (4,5 puta), INA (3,3 puta) i TAC3 (6,6 puta) u tkivu uretera pacijenata u poređenju sa kontrolnim tkivom, koji mogu biti molekularni markeri za CAKUT. Ove mreže su ujedno i prikaz interakcija ključnih molekula u CAKUT-u i predstavljaju temelj budućih funkcionalnih studija. Primenom metode koja povezuje podatke sa genskog ekspresionog čipa i predikcije vezujućih mesta različitih miRNK iz više predikcionih algoritama, sa unapređenom rezolucijom, identifikovane su miRNK sa potencijalno povišenom ekspresijom u CAKUT-u u odnosu na zdrave kontrole. Validacijom ključnih miRNK qRT-PCR metodom je identifikovan povišen nivo miR-144 (5,7 puta) u tkivu uretera pacijenata u odnosu na kontrole, koji može biti molekularni marker za CAKUT.
AB  - Congenital anomalies of the kidney and urinary tract (CAKUT) are the cause for half of the cases with renal failure, but pathophysiological basis of this disease is not fully known. Therefore, the therapy and prevention of the disease is difficult. In this study, by comparing the whole-genome expression in the ureter tissue of patients with CAKUT and healthy controls, 78 differentially expressed genes were identified. By employing bioinformatical analysis it was concluded that there is a high level of complexity of biological processes and molecular pathways, differentialy regulated in CAKUT, whose important interactions can be represented with seven molecular networks, of which four contain genes with functions that can be directly associated with CAKUT. Experimental validation of key networks by qRT-PCR method identified elevated mRNA levels of LCN2 (7.6 fold), PROM1 (8 fold) and SOSTDC1 (5.6 fold), and decreased mRNA levels of RASD1 (4.5 fold), INA (3.3 fold) and TAC3 (6.6 fold) in the ureter tissue of the patients compared to control tissue, which may be molecular markers for CAKUT. These networks display the interactions of key molecules in CAKUT and provide the basis for future functional studies, as well. By applying the method that links microarray gene expression data and prediction of miRNA binding sites from several prediction algorithms, with enhanced resolution, miRNAs with potentialy upregulated expression in CAKUT compared to healthy controls were identified. Validation of key miRNAs by qRT-PCR method identified increased level of miR-144 (5.7 fold) in the ureter tissue of the patients compared to controls, which may be a molecular marker for CAKUT.
PB  - Универзитет у Београду, Биолошки факултет
T2  - Универзитет у Београду
T1  - Analiza ekspresije celokupnog genoma u cilju identifikacije ključnih gena i mikroRNK za nastanak urođenih anomalija bubrega i urinarnog trakta čoveka
ER  - 
@phdthesis{
author = "Jovanović, Ivan G.",
year = "2016",
abstract = "Urođene anomalije bubrega i urinarnog trakta (engl. Congenital Anomalies of the Kidney and Urinary Tract – CAKUT) su razlog nastanka čak polovine slučajeva terminalne bubrežne insuficijencije ali patofiziološka osnova ove bolesti još uvek nije poznata u potpunosti pa je samim tim otežana prevencija i terapija. U ovoj studiji je, upoređivanjem ekspresije celokupnog genoma u tkivu uretera pacijenata sa CAKUT-om i zdravih kontrola, identifikovano 78 diferencijalno eksprimiranih gena. Bioinformatičkom analizom je po prvi put zaključeno da postoji visok nivo kompleksnosti bioloških procesa i molekularnih puteva u tkivu čoveka koji su u CAKUT-u diferencijalno regulisani i čije važne interakcije se mogu predstaviti sa sedam molekularnih mreža, od kojih četiri sadrže gene sa funkcijama koje se direktno mogu asocirati sa CAKUT-om. Eksperimentalnom validacijom ključnih mreža qRT-PCR metodom utvrđen je povišen nivo iRNK za gene LCN2 (7,6 puta), PROM1 (8 puta) i SOSTDC1 (5,6 puta) i snižen nivo iRNK za gene RASD1 (4,5 puta), INA (3,3 puta) i TAC3 (6,6 puta) u tkivu uretera pacijenata u poređenju sa kontrolnim tkivom, koji mogu biti molekularni markeri za CAKUT. Ove mreže su ujedno i prikaz interakcija ključnih molekula u CAKUT-u i predstavljaju temelj budućih funkcionalnih studija. Primenom metode koja povezuje podatke sa genskog ekspresionog čipa i predikcije vezujućih mesta različitih miRNK iz više predikcionih algoritama, sa unapređenom rezolucijom, identifikovane su miRNK sa potencijalno povišenom ekspresijom u CAKUT-u u odnosu na zdrave kontrole. Validacijom ključnih miRNK qRT-PCR metodom je identifikovan povišen nivo miR-144 (5,7 puta) u tkivu uretera pacijenata u odnosu na kontrole, koji može biti molekularni marker za CAKUT., Congenital anomalies of the kidney and urinary tract (CAKUT) are the cause for half of the cases with renal failure, but pathophysiological basis of this disease is not fully known. Therefore, the therapy and prevention of the disease is difficult. In this study, by comparing the whole-genome expression in the ureter tissue of patients with CAKUT and healthy controls, 78 differentially expressed genes were identified. By employing bioinformatical analysis it was concluded that there is a high level of complexity of biological processes and molecular pathways, differentialy regulated in CAKUT, whose important interactions can be represented with seven molecular networks, of which four contain genes with functions that can be directly associated with CAKUT. Experimental validation of key networks by qRT-PCR method identified elevated mRNA levels of LCN2 (7.6 fold), PROM1 (8 fold) and SOSTDC1 (5.6 fold), and decreased mRNA levels of RASD1 (4.5 fold), INA (3.3 fold) and TAC3 (6.6 fold) in the ureter tissue of the patients compared to control tissue, which may be molecular markers for CAKUT. These networks display the interactions of key molecules in CAKUT and provide the basis for future functional studies, as well. By applying the method that links microarray gene expression data and prediction of miRNA binding sites from several prediction algorithms, with enhanced resolution, miRNAs with potentialy upregulated expression in CAKUT compared to healthy controls were identified. Validation of key miRNAs by qRT-PCR method identified increased level of miR-144 (5.7 fold) in the ureter tissue of the patients compared to controls, which may be a molecular marker for CAKUT.",
publisher = "Универзитет у Београду, Биолошки факултет",
journal = "Универзитет у Београду",
title = "Analiza ekspresije celokupnog genoma u cilju identifikacije ključnih gena i mikroRNK za nastanak urođenih anomalija bubrega i urinarnog trakta čoveka"
}
Jovanović, I. G.. (2016). Analiza ekspresije celokupnog genoma u cilju identifikacije ključnih gena i mikroRNK za nastanak urođenih anomalija bubrega i urinarnog trakta čoveka. in Универзитет у Београду
Универзитет у Београду, Биолошки факултет..
Jovanović IG. Analiza ekspresije celokupnog genoma u cilju identifikacije ključnih gena i mikroRNK za nastanak urođenih anomalija bubrega i urinarnog trakta čoveka. in Универзитет у Београду. 2016;..
Jovanović, Ivan G., "Analiza ekspresije celokupnog genoma u cilju identifikacije ključnih gena i mikroRNK za nastanak urođenih anomalija bubrega i urinarnog trakta čoveka" in Универзитет у Београду (2016).

Transcriptome-wide based identification of miRs in congenital anomalies of the kidney and urinary tract (CAKUT) in children: the significant upregulation of tissue miR-144 expression

Jovanović, Ivan G.; Živković, Maja; Kostić, Mirjana M.; Krstić, Zoran; Đurić, Tamara; Kolić, Ivana; Alavantić, Dragan; Stanković, Aleksandra

(2016)

TY  - JOUR
AU  - Jovanović, Ivan G.
AU  - Živković, Maja
AU  - Kostić, Mirjana M.
AU  - Krstić, Zoran
AU  - Đurić, Tamara
AU  - Kolić, Ivana
AU  - Alavantić, Dragan
AU  - Stanković, Aleksandra
PY  - 2016
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/1182
AB  - Background: The genetic cause of most congenital anomalies of the kidney and urinary tract (CAKUT) cases remains unknown, therefore the novel approaches in searching for the common disease denominators are required. miRs regulate gene expression in humans and therefore have potentially therapeutic and biomarker properties. No studies thus far have attempted to explore the miRs in human CAKUT. We applied a new strategy to identify most specific miRs associated with CAKUT, in pediatric patients. Methods: Data from the whole genome expression, gathered from ureter tissue samples of 19 patients and 7 controls, were used for the bioinformatic prediction of miRs activity in CAKUT. We integrated microarray gene expression data and miR target predictions from multiple prediction algorithms using Co-inertia analysis (CIA) in conjunction with correspondence analysis and between group analysis, to produce a ranked list of miRs associated with CAKUT. The CIA included five different sequence based miR target prediction algorithms and the Co-expression Meta-analysis of miR Targets. For the experimental validation of expression of miRs identified by the CIA we used tissue from 36 CAKUT patients and 9 controls. The results of gene ontology (GO) analysis on co-expressed targets of miRs associated with CAKUT were used for the selection of putative biological processes relevant to CAKUT. Results: We identified 7 miRs with a potential role in CAKUT. The top ranked miRs from miRCos communities 4, 1 and 7 were chosen for experimental validation of expression in CAKUT tissue. The 5.7 fold increase of hsa-miR-144 expression in human tissue from CAKUT patients compared to controls (p = 0.005) was observed. From the GO we selected 7 biological processes that could contribute to CAKUT, which genes are potentially influenced by hsa-miR-144. The hsa-miR-200a, hsa-miR-183 and hsa-miR-375 werent differentially expressed in CAKUT. Conclusions: This study shows that integrative approach applied here was useful in identification of the miRs associated with CAKUT. The hsa-miR-144, first time identified in CAKUT, could be connected with biological processes crucial for normal development of kidney and urinary tract. Further functional analysis must follow to reveal the impact of hsa-miR-144 on CAKUT occurrence.
T2  - Journal of Translational Medicine
T1  - Transcriptome-wide based identification of miRs in congenital anomalies of the kidney and urinary tract (CAKUT) in children: the significant upregulation of tissue miR-144 expression
VL  - 14
DO  - 10.1186/s12967-016-0955-0
ER  - 
@article{
author = "Jovanović, Ivan G. and Živković, Maja and Kostić, Mirjana M. and Krstić, Zoran and Đurić, Tamara and Kolić, Ivana and Alavantić, Dragan and Stanković, Aleksandra",
year = "2016",
abstract = "Background: The genetic cause of most congenital anomalies of the kidney and urinary tract (CAKUT) cases remains unknown, therefore the novel approaches in searching for the common disease denominators are required. miRs regulate gene expression in humans and therefore have potentially therapeutic and biomarker properties. No studies thus far have attempted to explore the miRs in human CAKUT. We applied a new strategy to identify most specific miRs associated with CAKUT, in pediatric patients. Methods: Data from the whole genome expression, gathered from ureter tissue samples of 19 patients and 7 controls, were used for the bioinformatic prediction of miRs activity in CAKUT. We integrated microarray gene expression data and miR target predictions from multiple prediction algorithms using Co-inertia analysis (CIA) in conjunction with correspondence analysis and between group analysis, to produce a ranked list of miRs associated with CAKUT. The CIA included five different sequence based miR target prediction algorithms and the Co-expression Meta-analysis of miR Targets. For the experimental validation of expression of miRs identified by the CIA we used tissue from 36 CAKUT patients and 9 controls. The results of gene ontology (GO) analysis on co-expressed targets of miRs associated with CAKUT were used for the selection of putative biological processes relevant to CAKUT. Results: We identified 7 miRs with a potential role in CAKUT. The top ranked miRs from miRCos communities 4, 1 and 7 were chosen for experimental validation of expression in CAKUT tissue. The 5.7 fold increase of hsa-miR-144 expression in human tissue from CAKUT patients compared to controls (p = 0.005) was observed. From the GO we selected 7 biological processes that could contribute to CAKUT, which genes are potentially influenced by hsa-miR-144. The hsa-miR-200a, hsa-miR-183 and hsa-miR-375 werent differentially expressed in CAKUT. Conclusions: This study shows that integrative approach applied here was useful in identification of the miRs associated with CAKUT. The hsa-miR-144, first time identified in CAKUT, could be connected with biological processes crucial for normal development of kidney and urinary tract. Further functional analysis must follow to reveal the impact of hsa-miR-144 on CAKUT occurrence.",
journal = "Journal of Translational Medicine",
title = "Transcriptome-wide based identification of miRs in congenital anomalies of the kidney and urinary tract (CAKUT) in children: the significant upregulation of tissue miR-144 expression",
volume = "14",
doi = "10.1186/s12967-016-0955-0"
}
Jovanović, I. G., Živković, M., Kostić, M. M., Krstić, Z., Đurić, T., Kolić, I., Alavantić, D.,& Stanković, A.. (2016). Transcriptome-wide based identification of miRs in congenital anomalies of the kidney and urinary tract (CAKUT) in children: the significant upregulation of tissue miR-144 expression. in Journal of Translational Medicine, 14.
https://doi.org/10.1186/s12967-016-0955-0
Jovanović IG, Živković M, Kostić MM, Krstić Z, Đurić T, Kolić I, Alavantić D, Stanković A. Transcriptome-wide based identification of miRs in congenital anomalies of the kidney and urinary tract (CAKUT) in children: the significant upregulation of tissue miR-144 expression. in Journal of Translational Medicine. 2016;14.
doi:10.1186/s12967-016-0955-0 .
Jovanović, Ivan G., Živković, Maja, Kostić, Mirjana M., Krstić, Zoran, Đurić, Tamara, Kolić, Ivana, Alavantić, Dragan, Stanković, Aleksandra, "Transcriptome-wide based identification of miRs in congenital anomalies of the kidney and urinary tract (CAKUT) in children: the significant upregulation of tissue miR-144 expression" in Journal of Translational Medicine, 14 (2016),
https://doi.org/10.1186/s12967-016-0955-0 . .
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CXCL16 Haplotypes in Patients with Human Carotid Atherosclerosis: Preliminary Results

Živković, Maja; Đurić, Tamara; Stojković, Ljiljana S.; Jovanović, Ivan G.; Končar, Igor; Davidović, Lazar; Veljković, Nevena V.; Alavantić, Dragan; Stanković, Aleksandra

(2015)

TY  - JOUR
AU  - Živković, Maja
AU  - Đurić, Tamara
AU  - Stojković, Ljiljana S.
AU  - Jovanović, Ivan G.
AU  - Končar, Igor
AU  - Davidović, Lazar
AU  - Veljković, Nevena V.
AU  - Alavantić, Dragan
AU  - Stanković, Aleksandra
PY  - 2015
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/481
AB  - Aim: Chemokine CXC ligand 16 (CXCL16) has chemoattractive, adhesive and scavenging properties and may play a role in the formation of atherosclerotic lesions. However, studies of CXCL16 polymorphisms in patients with atherosclerosis are scarce. The missense polymorphisms I123T and A181V are potentially important factors in the regulation of presentation and shedding of the CXCL16 chemokine domain. The aim of this study was to analyze the association between I123T and A181V polymorphism haplotypes and the accumulation of carotid plaque as well as the effect of the haplotype on the CXCL16 mRNA expression in carotid plaques in patients with advanced atherosclerosis. Additionally, we performed a bioinformatic prediction analysis of the impact of CXCL16 protein sequence variation on CXCL16-CXCR6 interactions and analyzed the soluble CXCL16 plasma levels according to the CXCL16 haplotype. Methods: This study evaluated a total of 733 participants, including 283 controls and 450 patients with carotid atherosclerosis (CA) undergoing endarterectomy. Analyses of the polymorphisms and the gene expression were performed using real-time PCR. The soluble CXCL16 levels were measured with ELISA. Results: The missense allele haplotype, T123V181, was found to be significantly and independently associated with the occurrence of CA plaque (OR=1.27; 1.02-1.57, p=0.03). This haplotype was predicted to significantly change the CXCL16-CXCR6 interaction, compared to I123A181. Neither the CXCL16 mRNA expression in the human plaques nor the soluble CXCL16 plasma levels differed according to the haplotype. Conclusions: These results indicate that the CXCL16 T123V181 haplotype is a moderate genetic risk factor for the development of carotid plaque. Further functional and replication studies are needed to clarify the mechanisms by which this combination of alleles promotes advanced CA and validate its impact on disease progression.
T2  - Journal of Atherosclerosis and Thrombosis
T1  - CXCL16 Haplotypes in Patients with Human Carotid Atherosclerosis: Preliminary Results
VL  - 22
IS  - 1
SP  - 10
EP  - 20
DO  - 10.5551/jat.24299
ER  - 
@article{
author = "Živković, Maja and Đurić, Tamara and Stojković, Ljiljana S. and Jovanović, Ivan G. and Končar, Igor and Davidović, Lazar and Veljković, Nevena V. and Alavantić, Dragan and Stanković, Aleksandra",
year = "2015",
abstract = "Aim: Chemokine CXC ligand 16 (CXCL16) has chemoattractive, adhesive and scavenging properties and may play a role in the formation of atherosclerotic lesions. However, studies of CXCL16 polymorphisms in patients with atherosclerosis are scarce. The missense polymorphisms I123T and A181V are potentially important factors in the regulation of presentation and shedding of the CXCL16 chemokine domain. The aim of this study was to analyze the association between I123T and A181V polymorphism haplotypes and the accumulation of carotid plaque as well as the effect of the haplotype on the CXCL16 mRNA expression in carotid plaques in patients with advanced atherosclerosis. Additionally, we performed a bioinformatic prediction analysis of the impact of CXCL16 protein sequence variation on CXCL16-CXCR6 interactions and analyzed the soluble CXCL16 plasma levels according to the CXCL16 haplotype. Methods: This study evaluated a total of 733 participants, including 283 controls and 450 patients with carotid atherosclerosis (CA) undergoing endarterectomy. Analyses of the polymorphisms and the gene expression were performed using real-time PCR. The soluble CXCL16 levels were measured with ELISA. Results: The missense allele haplotype, T123V181, was found to be significantly and independently associated with the occurrence of CA plaque (OR=1.27; 1.02-1.57, p=0.03). This haplotype was predicted to significantly change the CXCL16-CXCR6 interaction, compared to I123A181. Neither the CXCL16 mRNA expression in the human plaques nor the soluble CXCL16 plasma levels differed according to the haplotype. Conclusions: These results indicate that the CXCL16 T123V181 haplotype is a moderate genetic risk factor for the development of carotid plaque. Further functional and replication studies are needed to clarify the mechanisms by which this combination of alleles promotes advanced CA and validate its impact on disease progression.",
journal = "Journal of Atherosclerosis and Thrombosis",
title = "CXCL16 Haplotypes in Patients with Human Carotid Atherosclerosis: Preliminary Results",
volume = "22",
number = "1",
pages = "10-20",
doi = "10.5551/jat.24299"
}
Živković, M., Đurić, T., Stojković, L. S., Jovanović, I. G., Končar, I., Davidović, L., Veljković, N. V., Alavantić, D.,& Stanković, A.. (2015). CXCL16 Haplotypes in Patients with Human Carotid Atherosclerosis: Preliminary Results. in Journal of Atherosclerosis and Thrombosis, 22(1), 10-20.
https://doi.org/10.5551/jat.24299
Živković M, Đurić T, Stojković LS, Jovanović IG, Končar I, Davidović L, Veljković NV, Alavantić D, Stanković A. CXCL16 Haplotypes in Patients with Human Carotid Atherosclerosis: Preliminary Results. in Journal of Atherosclerosis and Thrombosis. 2015;22(1):10-20.
doi:10.5551/jat.24299 .
Živković, Maja, Đurić, Tamara, Stojković, Ljiljana S., Jovanović, Ivan G., Končar, Igor, Davidović, Lazar, Veljković, Nevena V., Alavantić, Dragan, Stanković, Aleksandra, "CXCL16 Haplotypes in Patients with Human Carotid Atherosclerosis: Preliminary Results" in Journal of Atherosclerosis and Thrombosis, 22, no. 1 (2015):10-20,
https://doi.org/10.5551/jat.24299 . .
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CXCL16 in Vascular Pathology Research: from Macro Effects to microRNAs

Jovanović, Ivan G.; Živković, Maja; Đurić, Tamara; Popović, Milan; Alavantić, Dragan; Stanković, Aleksandra

(2015)

TY  - JOUR
AU  - Jovanović, Ivan G.
AU  - Živković, Maja
AU  - Đurić, Tamara
AU  - Popović, Milan
AU  - Alavantić, Dragan
AU  - Stanković, Aleksandra
PY  - 2015
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/818
AB  - Chemokines and their receptors have become significant factors in atherosclerosis research. CXCL16 is a multifunctional agent located on a separate locus to all other known chemokines and binds only to its unique receptor named CXCR6. As a scavenger receptor, adhesion molecule, and chemokine, it quickly became an interesting target in atherosclerosis research as all its functions have a role in vascular pathology. The investigation of the role of CXCL16 in atherosclerosis, although shown in in vitro studies, animal knockout models, and CXCL16 gene polymorphisms, haplotypes, and circulating levels, still shows puzzling results. Genetic and epigenetic studies have just scratched the surface of research necessary for a better assessment of the significance and perspective of this marker in plaque development and progression. In this review, we will summarize current knowledge about CXCL16 in atherosclerosis. Additionally, we will point out the importance of bioinformatics tools for the detection of potentially new CXCL16 regulatory networks through microRNA activity. This review aims to provide a better understanding of the underlying mechanisms, define more specific biomarkers, and discover new therapeutic targets.
T2  - Journal of Atherosclerosis and Thrombosis
T1  - CXCL16 in Vascular Pathology Research: from Macro Effects to microRNAs
VL  - 22
IS  - 10
SP  - 1012
EP  - 1024
DO  - 10.5551/jat.29942
ER  - 
@article{
author = "Jovanović, Ivan G. and Živković, Maja and Đurić, Tamara and Popović, Milan and Alavantić, Dragan and Stanković, Aleksandra",
year = "2015",
abstract = "Chemokines and their receptors have become significant factors in atherosclerosis research. CXCL16 is a multifunctional agent located on a separate locus to all other known chemokines and binds only to its unique receptor named CXCR6. As a scavenger receptor, adhesion molecule, and chemokine, it quickly became an interesting target in atherosclerosis research as all its functions have a role in vascular pathology. The investigation of the role of CXCL16 in atherosclerosis, although shown in in vitro studies, animal knockout models, and CXCL16 gene polymorphisms, haplotypes, and circulating levels, still shows puzzling results. Genetic and epigenetic studies have just scratched the surface of research necessary for a better assessment of the significance and perspective of this marker in plaque development and progression. In this review, we will summarize current knowledge about CXCL16 in atherosclerosis. Additionally, we will point out the importance of bioinformatics tools for the detection of potentially new CXCL16 regulatory networks through microRNA activity. This review aims to provide a better understanding of the underlying mechanisms, define more specific biomarkers, and discover new therapeutic targets.",
journal = "Journal of Atherosclerosis and Thrombosis",
title = "CXCL16 in Vascular Pathology Research: from Macro Effects to microRNAs",
volume = "22",
number = "10",
pages = "1012-1024",
doi = "10.5551/jat.29942"
}
Jovanović, I. G., Živković, M., Đurić, T., Popović, M., Alavantić, D.,& Stanković, A.. (2015). CXCL16 in Vascular Pathology Research: from Macro Effects to microRNAs. in Journal of Atherosclerosis and Thrombosis, 22(10), 1012-1024.
https://doi.org/10.5551/jat.29942
Jovanović IG, Živković M, Đurić T, Popović M, Alavantić D, Stanković A. CXCL16 in Vascular Pathology Research: from Macro Effects to microRNAs. in Journal of Atherosclerosis and Thrombosis. 2015;22(10):1012-1024.
doi:10.5551/jat.29942 .
Jovanović, Ivan G., Živković, Maja, Đurić, Tamara, Popović, Milan, Alavantić, Dragan, Stanković, Aleksandra, "CXCL16 in Vascular Pathology Research: from Macro Effects to microRNAs" in Journal of Atherosclerosis and Thrombosis, 22, no. 10 (2015):1012-1024,
https://doi.org/10.5551/jat.29942 . .
2
13
13
11

The co-inertia approach in identification of specific microRNA in early and advanced atherosclerosis plaque

Jovanović, Ivan G.; Živković, Maja; Jovanović, Jasmina; Đurić, Tamara; Stanković, Aleksandra

(2014)

TY  - JOUR
AU  - Jovanović, Ivan G.
AU  - Živković, Maja
AU  - Jovanović, Jasmina
AU  - Đurić, Tamara
AU  - Stanković, Aleksandra
PY  - 2014
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/6047
AB  - MicroRNAs (miRs) are short, non-coding RNAs that regulate gene expression by absolute or partial binding to mRNA, which results in transcript degradation and translation blocking. Atherosclerosis, as a complex and progressive disease, represents one of the main causes of cardiovascular clinical complications and even death. We applied co-inertia analysis (CIA) as a novel computation method, to determine which miRs are potentially associated with differences in gene expression levels originating from microarray data of early and advanced atherosclerotic plaque. As the CIA has not been applied in the field of atherosclerosis yet, we hypothesized that using CIA we can get novel information about the miRs that have significant role in early phase of disease or in severe phase of disease. The characteristic split in the data along the axes of performed CIA showed the difference in the gene expression pattern between early atherosclerosis and advanced atherosclerotic plaque. The advanced atherosclerotic plaques showed more homogenous gene expression pattern than early atherosclerosis samples. In early carotid lesions five out of five algorithms predicted miR-24, four out of five predicted miR-155, miR-145, and miR-100 as early active miRs. These miRs could be protective in plaque evolution context because they were not active in advanced plaques according to our results. They were reported previously as atheroprotective, which in a way represents confirmation of CIA application in atherosclerosis. We detected 13 new miRs which could be active in early plaque phenotype according to CIA prediction. In the advanced plaques we predicted miR-221, miR-222, miR-127 and miR-146 which were previously revealed to have atherogenic properties. In addition to miRs that have literature support, we also found new 8 miRs that, with described function so far, could present a novelty in research of atherosclerotic plaque evolution. All of these examples show that CIA results have a great potential to be of interest in future research in atherosclerotic plaque progression. We validated the applicability of CIA in the field of atherosclerosis, but we also found new interesting miR competitors that have strong potential to serve as markers and plaque development factors. These results should be experimentally confirmed in further research with ultimate goal to discover new mediators and blood markers, which could improve the prevention and therapy of this complex disease. (C) 2014 Elsevier Ltd. All rights reserved.
T2  - Medical Hypotheses
T1  - The co-inertia approach in identification of specific microRNA in early and advanced atherosclerosis plaque
VL  - 83
IS  - 1
SP  - 11
EP  - 15
DO  - 10.1016/j.mehy.2014.04.019
ER  - 
@article{
author = "Jovanović, Ivan G. and Živković, Maja and Jovanović, Jasmina and Đurić, Tamara and Stanković, Aleksandra",
year = "2014",
abstract = "MicroRNAs (miRs) are short, non-coding RNAs that regulate gene expression by absolute or partial binding to mRNA, which results in transcript degradation and translation blocking. Atherosclerosis, as a complex and progressive disease, represents one of the main causes of cardiovascular clinical complications and even death. We applied co-inertia analysis (CIA) as a novel computation method, to determine which miRs are potentially associated with differences in gene expression levels originating from microarray data of early and advanced atherosclerotic plaque. As the CIA has not been applied in the field of atherosclerosis yet, we hypothesized that using CIA we can get novel information about the miRs that have significant role in early phase of disease or in severe phase of disease. The characteristic split in the data along the axes of performed CIA showed the difference in the gene expression pattern between early atherosclerosis and advanced atherosclerotic plaque. The advanced atherosclerotic plaques showed more homogenous gene expression pattern than early atherosclerosis samples. In early carotid lesions five out of five algorithms predicted miR-24, four out of five predicted miR-155, miR-145, and miR-100 as early active miRs. These miRs could be protective in plaque evolution context because they were not active in advanced plaques according to our results. They were reported previously as atheroprotective, which in a way represents confirmation of CIA application in atherosclerosis. We detected 13 new miRs which could be active in early plaque phenotype according to CIA prediction. In the advanced plaques we predicted miR-221, miR-222, miR-127 and miR-146 which were previously revealed to have atherogenic properties. In addition to miRs that have literature support, we also found new 8 miRs that, with described function so far, could present a novelty in research of atherosclerotic plaque evolution. All of these examples show that CIA results have a great potential to be of interest in future research in atherosclerotic plaque progression. We validated the applicability of CIA in the field of atherosclerosis, but we also found new interesting miR competitors that have strong potential to serve as markers and plaque development factors. These results should be experimentally confirmed in further research with ultimate goal to discover new mediators and blood markers, which could improve the prevention and therapy of this complex disease. (C) 2014 Elsevier Ltd. All rights reserved.",
journal = "Medical Hypotheses",
title = "The co-inertia approach in identification of specific microRNA in early and advanced atherosclerosis plaque",
volume = "83",
number = "1",
pages = "11-15",
doi = "10.1016/j.mehy.2014.04.019"
}
Jovanović, I. G., Živković, M., Jovanović, J., Đurić, T.,& Stanković, A.. (2014). The co-inertia approach in identification of specific microRNA in early and advanced atherosclerosis plaque. in Medical Hypotheses, 83(1), 11-15.
https://doi.org/10.1016/j.mehy.2014.04.019
Jovanović IG, Živković M, Jovanović J, Đurić T, Stanković A. The co-inertia approach in identification of specific microRNA in early and advanced atherosclerosis plaque. in Medical Hypotheses. 2014;83(1):11-15.
doi:10.1016/j.mehy.2014.04.019 .
Jovanović, Ivan G., Živković, Maja, Jovanović, Jasmina, Đurić, Tamara, Stanković, Aleksandra, "The co-inertia approach in identification of specific microRNA in early and advanced atherosclerosis plaque" in Medical Hypotheses, 83, no. 1 (2014):11-15,
https://doi.org/10.1016/j.mehy.2014.04.019 . .
3
24
17
16

The angiotensin II type 2 receptor-1332 A/G gene polymorphism (rs1403543) is associated with stroke in males patients with carotid atherosclerosis

Kolaković, Ana; Živković, Maja; Končar, Igor; Jovanović, Ivan G.; Đurić, Tamara; Stanković, Aleksandra

(2013)

TY  - CONF
AU  - Kolaković, Ana
AU  - Živković, Maja
AU  - Končar, Igor
AU  - Jovanović, Ivan G.
AU  - Đurić, Tamara
AU  - Stanković, Aleksandra
PY  - 2013
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/5821
C3  - Cerebrovascular Diseases
T1  - The angiotensin II type 2 receptor-1332 A/G gene polymorphism (rs1403543) is associated with stroke in males patients with carotid atherosclerosis
VL  - 35
SP  - 536
EP  - 536
ER  - 
@conference{
author = "Kolaković, Ana and Živković, Maja and Končar, Igor and Jovanović, Ivan G. and Đurić, Tamara and Stanković, Aleksandra",
year = "2013",
journal = "Cerebrovascular Diseases",
title = "The angiotensin II type 2 receptor-1332 A/G gene polymorphism (rs1403543) is associated with stroke in males patients with carotid atherosclerosis",
volume = "35",
pages = "536-536"
}
Kolaković, A., Živković, M., Končar, I., Jovanović, I. G., Đurić, T.,& Stanković, A.. (2013). The angiotensin II type 2 receptor-1332 A/G gene polymorphism (rs1403543) is associated with stroke in males patients with carotid atherosclerosis. in Cerebrovascular Diseases, 35, 536-536.
Kolaković A, Živković M, Končar I, Jovanović IG, Đurić T, Stanković A. The angiotensin II type 2 receptor-1332 A/G gene polymorphism (rs1403543) is associated with stroke in males patients with carotid atherosclerosis. in Cerebrovascular Diseases. 2013;35:536-536..
Kolaković, Ana, Živković, Maja, Končar, Igor, Jovanović, Ivan G., Đurić, Tamara, Stanković, Aleksandra, "The angiotensin II type 2 receptor-1332 A/G gene polymorphism (rs1403543) is associated with stroke in males patients with carotid atherosclerosis" in Cerebrovascular Diseases, 35 (2013):536-536.