TY  - CONF
AU  - Perić, Jelena
AU  - Pavlović, Dunja
AU  - Dragičević, Sandra
AU  - Miladinov, Marko
AU  - Djikić-Rom, Aleksandra
AU  - Bjelanović, Jasna
AU  - Kovač, Jelena
AU  - Despotović, Jovana
AU  - Babić, Tamara
AU  - Rosic, Jovana
AU  - Dimitrijević, Ivan
AU  - Marković, Velimir
AU  - Barisic, Goran
AU  - Nikolić, Aleksandra
PY  - 2023
UR  - https://2023.eshg.org/
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2061
AB  - The cornerstone in the treatment of locally advanced rectal cancer (LARC) is neoadjuvant
chemoradiotherapy (nCRT) followed by total mesorectal excision. Reliable predictors of
response to nCRT in LARC remain an unmet need in colorectal cancer research. This study
used high throughput DNA analysis to investigate genetic differences between highly
responsive tumors and tumors resistant to nCRT.
C3  - ESHG 2023
T1  - Genetic determinants of response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer identified by whole exome sequencing
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2061
ER  - 

@conference{
author = "Perić, Jelena and Pavlović, Dunja and Dragičević, Sandra and Miladinov, Marko and Djikić-Rom, Aleksandra and Bjelanović, Jasna and Kovač, Jelena and Despotović, Jovana and Babić, Tamara and Rosic, Jovana and Dimitrijević, Ivan and Marković, Velimir and Barisic, Goran and Nikolić, Aleksandra",
year = "2023",
abstract = "The cornerstone in the treatment of locally advanced rectal cancer (LARC) is neoadjuvant
chemoradiotherapy (nCRT) followed by total mesorectal excision. Reliable predictors of
response to nCRT in LARC remain an unmet need in colorectal cancer research. This study
used high throughput DNA analysis to investigate genetic differences between highly
responsive tumors and tumors resistant to nCRT.",
journal = "ESHG 2023",
title = "Genetic determinants of response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer identified by whole exome sequencing",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2061"
}

Perić, J., Pavlović, D., Dragičević, S., Miladinov, M., Djikić-Rom, A., Bjelanović, J., Kovač, J., Despotović, J., Babić, T., Rosic, J., Dimitrijević, I., Marković, V., Barisic, G.,& Nikolić, A.. (2023). Genetic determinants of response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer identified by whole exome sequencing. in ESHG 2023.
https://hdl.handle.net/21.15107/rcub_imagine_2061

Perić J, Pavlović D, Dragičević S, Miladinov M, Djikić-Rom A, Bjelanović J, Kovač J, Despotović J, Babić T, Rosic J, Dimitrijević I, Marković V, Barisic G, Nikolić A. Genetic determinants of response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer identified by whole exome sequencing. in ESHG 2023. 2023;.
https://hdl.handle.net/21.15107/rcub_imagine_2061 .

Perić, Jelena, Pavlović, Dunja, Dragičević, Sandra, Miladinov, Marko, Djikić-Rom, Aleksandra, Bjelanović, Jasna, Kovač, Jelena, Despotović, Jovana, Babić, Tamara, Rosic, Jovana, Dimitrijević, Ivan, Marković, Velimir, Barisic, Goran, Nikolić, Aleksandra, "Genetic determinants of response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer identified by whole exome sequencing" in ESHG 2023 (2023),
https://hdl.handle.net/21.15107/rcub_imagine_2061 .

TY  - CONF
AU  - Ljubičić, Jelena
AU  - Bogdanović, Aleksandar
AU  - Babić, Tamara
AU  - Despotović, Jovana
AU  - Dugalić, Vladimir
AU  - Nikolić, Aleksandra
PY  - 2023
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2100
AB  - Background: Our previous study has identified variant rs745430558 in the SMAD4 gene promoter as potential biomarker for adenocarcinoma of the pancreas. The allele delTT (10T instead of 12T) was present in malignant pancreatic tissue with a prevalence of 88%. As analysis of cfDNA in liquid biopsy represents a noninvasive approach for the diagnosis and monitoring of malignancies, the aim of this study was to determine the presence of 12T and 10T alleles in the peripheral blood of patients with suspected pancreatic malignancy. Material and Methods: The study was performed using cell-free DNA (cfDNA) isolated from the serum of 15 patients with morphological alterations of the pancreas. The presence of 12T and 10T alleles was assessed by allele specific quantitative real-time PCR. Results: Of 15 analyzed samples, 13 were diagnosed with adenocarcinoma of the pancreas (AcP), 1 with neuroendocrine tumor (NET), and 1 with pancreatitis. The 10T allele was present in 84.7% of cases with AcP and also in the sample from the patient with NET. In patient with pancreatitis only the 12T allele was detected. Conclusion: Our research has shown that the results of liquid biopsy of patients with AcP are in agreement with tissue specimens analysis. Targeted detection of the rs745430558 10T variant in patients with suspected pancreatic malignancies could be a potential biomarker for diagnosis of AcP in the future.
PB  - Belgrade :  Serbian Association on for Cancer Research
C3  - 6th Congress of the Serbian Association for Cancer Research (SDIR)
T1  - Variant rs745430558 in the SMAD4 gene promoter as a biomarker for adenocarcinoma of the pancreas
EP  - 85
IS  - 1
SP  - 85
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2100
ER  - 

@conference{
author = "Ljubičić, Jelena and Bogdanović, Aleksandar and Babić, Tamara and Despotović, Jovana and Dugalić, Vladimir and Nikolić, Aleksandra",
year = "2023",
abstract = "Background: Our previous study has identified variant rs745430558 in the SMAD4 gene promoter as potential biomarker for adenocarcinoma of the pancreas. The allele delTT (10T instead of 12T) was present in malignant pancreatic tissue with a prevalence of 88%. As analysis of cfDNA in liquid biopsy represents a noninvasive approach for the diagnosis and monitoring of malignancies, the aim of this study was to determine the presence of 12T and 10T alleles in the peripheral blood of patients with suspected pancreatic malignancy. Material and Methods: The study was performed using cell-free DNA (cfDNA) isolated from the serum of 15 patients with morphological alterations of the pancreas. The presence of 12T and 10T alleles was assessed by allele specific quantitative real-time PCR. Results: Of 15 analyzed samples, 13 were diagnosed with adenocarcinoma of the pancreas (AcP), 1 with neuroendocrine tumor (NET), and 1 with pancreatitis. The 10T allele was present in 84.7% of cases with AcP and also in the sample from the patient with NET. In patient with pancreatitis only the 12T allele was detected. Conclusion: Our research has shown that the results of liquid biopsy of patients with AcP are in agreement with tissue specimens analysis. Targeted detection of the rs745430558 10T variant in patients with suspected pancreatic malignancies could be a potential biomarker for diagnosis of AcP in the future.",
publisher = "Belgrade :  Serbian Association on for Cancer Research",
journal = "6th Congress of the Serbian Association for Cancer Research (SDIR)",
title = "Variant rs745430558 in the SMAD4 gene promoter as a biomarker for adenocarcinoma of the pancreas",
pages = "85-85",
number = "1",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2100"
}

Ljubičić, J., Bogdanović, A., Babić, T., Despotović, J., Dugalić, V.,& Nikolić, A.. (2023). Variant rs745430558 in the SMAD4 gene promoter as a biomarker for adenocarcinoma of the pancreas. in 6th Congress of the Serbian Association for Cancer Research (SDIR)
Belgrade :  Serbian Association on for Cancer Research.(1), 85-85.
https://hdl.handle.net/21.15107/rcub_imagine_2100

Ljubičić J, Bogdanović A, Babić T, Despotović J, Dugalić V, Nikolić A. Variant rs745430558 in the SMAD4 gene promoter as a biomarker for adenocarcinoma of the pancreas. in 6th Congress of the Serbian Association for Cancer Research (SDIR). 2023;(1):85-85.
https://hdl.handle.net/21.15107/rcub_imagine_2100 .

Ljubičić, Jelena, Bogdanović, Aleksandar, Babić, Tamara, Despotović, Jovana, Dugalić, Vladimir, Nikolić, Aleksandra, "Variant rs745430558 in the SMAD4 gene promoter as a biomarker for adenocarcinoma of the pancreas" in 6th Congress of the Serbian Association for Cancer Research (SDIR), no. 1 (2023):85-85,
https://hdl.handle.net/21.15107/rcub_imagine_2100 .

TY  - JOUR
AU  - Jovanović, Emilija
AU  - Babić, Tamara
AU  - Dragičević, Sandra
AU  - Kmezic, Stefan
AU  - Nikolić, Aleksandra
PY  - 2023
UR  - https://onlinelibrary.wiley.com/doi/abs/10.1002/cbf.3890
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2223
AB  - The role of tetraspanin CD81 in malignant transformation is best studied in colorectal cancer, and it appears that other transcripts beside the fully coding mRNA may also be dysregulated in malignant cells. Recent data from a comprehensive pan-cancer transcriptome analysis demonstrated differential activity of two alternative CD81 gene promoters in malignant versus nonmalignant gut mucosa. The promoter active in gut mucosa gives rise to transcripts CD81-203 and CD81-213, while the promoter active in colon and rectal cancer gives rise to transcripts CD81-205 and CD81-215. Our study aimed to explore the biomarker potential of the transcripts from the alternative CD81 gene promoters in colon cancer, as well as to investigate their structure and potential function using in silico tools. The analysis of the transcripts' expression in several colon cell lines cultivated in 2D and 3D and a set of colon cancer and healthy gut mucosa samples by qPCR and RNA sequencing suggested their low expression and stromal origin. Expression patterns in tumor and nontumor tissue along with in silico data suppose that the transcript CD81-215 may be a noncoding RNA of stromal origin with possible involvement in signaling related to malignant transformation.
T2  - Cell Biochemistry and Function
T1  - Transcript CD81-215 may be a long noncoding RNA of stromal origin with tumor-promoting role in colon cancer
IS  - n/a
VL  - n/a
DO  - 10.1002/cbf.3890
ER  - 

@article{
author = "Jovanović, Emilija and Babić, Tamara and Dragičević, Sandra and Kmezic, Stefan and Nikolić, Aleksandra",
year = "2023",
abstract = "The role of tetraspanin CD81 in malignant transformation is best studied in colorectal cancer, and it appears that other transcripts beside the fully coding mRNA may also be dysregulated in malignant cells. Recent data from a comprehensive pan-cancer transcriptome analysis demonstrated differential activity of two alternative CD81 gene promoters in malignant versus nonmalignant gut mucosa. The promoter active in gut mucosa gives rise to transcripts CD81-203 and CD81-213, while the promoter active in colon and rectal cancer gives rise to transcripts CD81-205 and CD81-215. Our study aimed to explore the biomarker potential of the transcripts from the alternative CD81 gene promoters in colon cancer, as well as to investigate their structure and potential function using in silico tools. The analysis of the transcripts' expression in several colon cell lines cultivated in 2D and 3D and a set of colon cancer and healthy gut mucosa samples by qPCR and RNA sequencing suggested their low expression and stromal origin. Expression patterns in tumor and nontumor tissue along with in silico data suppose that the transcript CD81-215 may be a noncoding RNA of stromal origin with possible involvement in signaling related to malignant transformation.",
journal = "Cell Biochemistry and Function",
title = "Transcript CD81-215 may be a long noncoding RNA of stromal origin with tumor-promoting role in colon cancer",
number = "n/a",
volume = "n/a",
doi = "10.1002/cbf.3890"
}

Jovanović, E., Babić, T., Dragičević, S., Kmezic, S.,& Nikolić, A.. (2023). Transcript CD81-215 may be a long noncoding RNA of stromal origin with tumor-promoting role in colon cancer. in Cell Biochemistry and Function, n/a(n/a).
https://doi.org/10.1002/cbf.3890

Jovanović E, Babić T, Dragičević S, Kmezic S, Nikolić A. Transcript CD81-215 may be a long noncoding RNA of stromal origin with tumor-promoting role in colon cancer. in Cell Biochemistry and Function. 2023;n/a(n/a).
doi:10.1002/cbf.3890 .

Jovanović, Emilija, Babić, Tamara, Dragičević, Sandra, Kmezic, Stefan, Nikolić, Aleksandra, "Transcript CD81-215 may be a long noncoding RNA of stromal origin with tumor-promoting role in colon cancer" in Cell Biochemistry and Function, n/a, no. n/a (2023),
https://doi.org/10.1002/cbf.3890 . .

TY  - CONF
AU  - Dragičević, Sandra
AU  - Babić, Tamara
AU  - Miladinov, Marko
AU  - Kmezić, Stefan
AU  - Nikolić, Aleksandra
PY  - 2023
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2098
AB  - The activity profi le of alternative promoters may be an indicator of tumor characteristics. Alternative promoters of CD81 gene were shown to be differentially active in colon and rectal cancer tissue. The promoter active in colon and rectal cancer gives rise to transcripts CD81-205 and CD81-215, while the promoter active in normal gut mucosa gives rise to transcripts CD81-203 and CD81-213. This study aimed to analyze the relative abundance of the CD81 gene transcripts in colorectal cancer.
PB  - Belgrade : Serbian Association on for Cancer Research
C3  - 6th Congress of the Serbian AssociaƟ on for Cancer Research (SDIR)
T1  - Expression profile of CD81 gene transcripts in colorectal cancer
EP  - 81
IS  - 1
SP  - 81
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2098
ER  - 

@conference{
author = "Dragičević, Sandra and Babić, Tamara and Miladinov, Marko and Kmezić, Stefan and Nikolić, Aleksandra",
year = "2023",
abstract = "The activity profi le of alternative promoters may be an indicator of tumor characteristics. Alternative promoters of CD81 gene were shown to be differentially active in colon and rectal cancer tissue. The promoter active in colon and rectal cancer gives rise to transcripts CD81-205 and CD81-215, while the promoter active in normal gut mucosa gives rise to transcripts CD81-203 and CD81-213. This study aimed to analyze the relative abundance of the CD81 gene transcripts in colorectal cancer.",
publisher = "Belgrade : Serbian Association on for Cancer Research",
journal = "6th Congress of the Serbian AssociaƟ on for Cancer Research (SDIR)",
title = "Expression profile of CD81 gene transcripts in colorectal cancer",
pages = "81-81",
number = "1",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2098"
}

Dragičević, S., Babić, T., Miladinov, M., Kmezić, S.,& Nikolić, A.. (2023). Expression profile of CD81 gene transcripts in colorectal cancer. in 6th Congress of the Serbian AssociaƟ on for Cancer Research (SDIR)
Belgrade : Serbian Association on for Cancer Research.(1), 81-81.
https://hdl.handle.net/21.15107/rcub_imagine_2098

Dragičević S, Babić T, Miladinov M, Kmezić S, Nikolić A. Expression profile of CD81 gene transcripts in colorectal cancer. in 6th Congress of the Serbian AssociaƟ on for Cancer Research (SDIR). 2023;(1):81-81.
https://hdl.handle.net/21.15107/rcub_imagine_2098 .

Dragičević, Sandra, Babić, Tamara, Miladinov, Marko, Kmezić, Stefan, Nikolić, Aleksandra, "Expression profile of CD81 gene transcripts in colorectal cancer" in 6th Congress of the Serbian AssociaƟ on for Cancer Research (SDIR), no. 1 (2023):81-81,
https://hdl.handle.net/21.15107/rcub_imagine_2098 .

TY  - CONF
AU  - Ignjatović, Sofija
AU  - Pavlović, Dunja
AU  - Babić, Tamara
AU  - Dragičević, Sandra
AU  - Nikolić, Aleksandra
PY  - 2023
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2136
AB  - Introduction: A recent comprehensive pan-cancer transcriptome analysis revealed differential activity
of two alternative promoters of the gene PHF19 in malignant and non-malignant gut mucosa. Transcription from the promoter which is up-regulated in colorectal cancer results in the synthesis of transcript PHF19-207. This finding indicates that transcript PHF19-207 could potentially be used as a
biomarker for this disease. Our study aimed to assess the expression profile of the PHF19 gene in colon
cancer.
Methods: Immortalized colonic epithelial cell line isolated from healthy tissue (HCEC-1CT) as well as a
set of colon cancer cell lines (DLD1, SW620, HCT116) were used for transcriptional profiling of PHF19 in
cells cultivated in 3D. The transcriptional profile was obtained using RNA sequencing and the function
of transcript PHF19-207 was evaluated using in silico tools.
Results: Our analysis confirmed the up-regulation of transcript PHF19-207 in all malignant cell cultures
in comparison to the healthy cell line HCEC-1CT. The expression of transcript PHF19-207 was more notable in cell lines that originated from colon cancer in later stages. Coding Potential Calculator tool classifies this transcript as non-coding, with a probability of 0.2. Annolnc tool shows the up-regulation of
thistranscript in colorectal cancer cell lines and its down-regulation in healthy samples. Also, thistool predicts that transcript PHF19-207 localizes in the nucleus.
Conclusion: We conclude that transcript PHF19-207 could serve as a biomarker for colorectal cancer.
Also, we hypothesize that thistranscript is a lncRNA with a role in gene expression regulation and could
be linked to oncogenesis.
PB  - Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade
C3  - CoMBoS2 – the Second Congress of Molecular Biologists of Serbia, Abstract Book – Trends in Molecular Biology, Special issue 06-08 October 2023, Belgrade, Serbia
T1  - Transcriptional profiling of PHF19 gene in colon cancer cell lines cultivated in 3D
EP  - 178
SP  - 178
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2136
ER  - 

@conference{
author = "Ignjatović, Sofija and Pavlović, Dunja and Babić, Tamara and Dragičević, Sandra and Nikolić, Aleksandra",
year = "2023",
abstract = "Introduction: A recent comprehensive pan-cancer transcriptome analysis revealed differential activity
of two alternative promoters of the gene PHF19 in malignant and non-malignant gut mucosa. Transcription from the promoter which is up-regulated in colorectal cancer results in the synthesis of transcript PHF19-207. This finding indicates that transcript PHF19-207 could potentially be used as a
biomarker for this disease. Our study aimed to assess the expression profile of the PHF19 gene in colon
cancer.
Methods: Immortalized colonic epithelial cell line isolated from healthy tissue (HCEC-1CT) as well as a
set of colon cancer cell lines (DLD1, SW620, HCT116) were used for transcriptional profiling of PHF19 in
cells cultivated in 3D. The transcriptional profile was obtained using RNA sequencing and the function
of transcript PHF19-207 was evaluated using in silico tools.
Results: Our analysis confirmed the up-regulation of transcript PHF19-207 in all malignant cell cultures
in comparison to the healthy cell line HCEC-1CT. The expression of transcript PHF19-207 was more notable in cell lines that originated from colon cancer in later stages. Coding Potential Calculator tool classifies this transcript as non-coding, with a probability of 0.2. Annolnc tool shows the up-regulation of
thistranscript in colorectal cancer cell lines and its down-regulation in healthy samples. Also, thistool predicts that transcript PHF19-207 localizes in the nucleus.
Conclusion: We conclude that transcript PHF19-207 could serve as a biomarker for colorectal cancer.
Also, we hypothesize that thistranscript is a lncRNA with a role in gene expression regulation and could
be linked to oncogenesis.",
publisher = "Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade",
journal = "CoMBoS2 – the Second Congress of Molecular Biologists of Serbia, Abstract Book – Trends in Molecular Biology, Special issue 06-08 October 2023, Belgrade, Serbia",
title = "Transcriptional profiling of PHF19 gene in colon cancer cell lines cultivated in 3D",
pages = "178-178",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2136"
}

Ignjatović, S., Pavlović, D., Babić, T., Dragičević, S.,& Nikolić, A.. (2023). Transcriptional profiling of PHF19 gene in colon cancer cell lines cultivated in 3D. in CoMBoS2 – the Second Congress of Molecular Biologists of Serbia, Abstract Book – Trends in Molecular Biology, Special issue 06-08 October 2023, Belgrade, Serbia
Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade., 178-178.
https://hdl.handle.net/21.15107/rcub_imagine_2136

Ignjatović S, Pavlović D, Babić T, Dragičević S, Nikolić A. Transcriptional profiling of PHF19 gene in colon cancer cell lines cultivated in 3D. in CoMBoS2 – the Second Congress of Molecular Biologists of Serbia, Abstract Book – Trends in Molecular Biology, Special issue 06-08 October 2023, Belgrade, Serbia. 2023;:178-178.
https://hdl.handle.net/21.15107/rcub_imagine_2136 .

Ignjatović, Sofija, Pavlović, Dunja, Babić, Tamara, Dragičević, Sandra, Nikolić, Aleksandra, "Transcriptional profiling of PHF19 gene in colon cancer cell lines cultivated in 3D" in CoMBoS2 – the Second Congress of Molecular Biologists of Serbia, Abstract Book – Trends in Molecular Biology, Special issue 06-08 October 2023, Belgrade, Serbia (2023):178-178,
https://hdl.handle.net/21.15107/rcub_imagine_2136 .

TY  - CONF
AU  - Pruner, Iva
AU  - Nikolić, Aleksandra
PY  - 2023
UR  - https://belbi.bg.ac.rs/
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2034
AB  - Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. Lack
of specific CRC symptoms is a challenge for clinicians, as the symptoms overlap with other
non-cancerous diseases, leading to 20-25% of newly diagnosed CRC patients already
having liver metastasis. Thus, discovering reliable early-disease biomarkers is of high
importance. Non-coding RNAs (ncRNAs) have been demonstrated to be involved in CRC
development and progression. Long non-coding RNAs (lncRNAs) can interact with RNA,
DNA and proteins, forming complexes that are involved in regulation of gene expression
via multiple mechanisms, affecting every stage of colon carcinogenesis and making them
top candidates for novel biomarker discovery.
The aim of our study was to conduct data mining of Gene Expression Omnibus (GEO)
database by using “colon cancer” and “ncRNA” keywords, and identify differentially
expressed lnRNAs present in different GEO datasets.
GEO database which collects submitted high-throughput gene expression data was queried
for all datasets that studied colon cancer and ncRNA. Over 60 datasets were manually
inspected in order to identify those where analysis of colon and normal tissue originating
from the same patient was done. Each dataset was analyzed by GEO2R software to
discover differentially expressed lncRNAs. LncRNAs were considered significant if they
appeared in more than one GEO dataset. Parts of lncRNAs sequences available in GEO2R
analysis results were run through BLAST in order to identify full length lncRNAs.
Five GEO datasets matched our criteria. We discovered 12 sequences that appeared in
more than one dataset and we identified them through BLAST analysis. Six sequences
originated from lncRNAs (RYR3 divergent transcript, long intergenic non-protein coding
RNA 595, TOX divergent transcript, FLVCR2 antisense RNA 1, LHRI_LNC744.1 lncRNA
gene, and ELFN1 antisense RNA 1), while six sequences represented partial sequences
of various mRNAs. Four lncRNAs were down-regulated in colon cancer; one was upregulated,
while one showed different expression patterns in different GEO datasets.
In this study, we have identified six lncRNAs that have potential significance for colorectal
cancer etiology and will be a subject of further in silico and in vitro study.
PB  - Belgrade : Institute of molecular genetics and genetic engineering
C3  - 4th Belgrade Bioinformatics Conference
T1  - Data mining for long-non coding RNAs deregulated in colon cancer through analysis of Gene Expression Omnibus database
EP  - 89
SP  - 89
VL  - 4
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2034
ER  - 

@conference{
author = "Pruner, Iva and Nikolić, Aleksandra",
year = "2023",
abstract = "Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. Lack
of specific CRC symptoms is a challenge for clinicians, as the symptoms overlap with other
non-cancerous diseases, leading to 20-25% of newly diagnosed CRC patients already
having liver metastasis. Thus, discovering reliable early-disease biomarkers is of high
importance. Non-coding RNAs (ncRNAs) have been demonstrated to be involved in CRC
development and progression. Long non-coding RNAs (lncRNAs) can interact with RNA,
DNA and proteins, forming complexes that are involved in regulation of gene expression
via multiple mechanisms, affecting every stage of colon carcinogenesis and making them
top candidates for novel biomarker discovery.
The aim of our study was to conduct data mining of Gene Expression Omnibus (GEO)
database by using “colon cancer” and “ncRNA” keywords, and identify differentially
expressed lnRNAs present in different GEO datasets.
GEO database which collects submitted high-throughput gene expression data was queried
for all datasets that studied colon cancer and ncRNA. Over 60 datasets were manually
inspected in order to identify those where analysis of colon and normal tissue originating
from the same patient was done. Each dataset was analyzed by GEO2R software to
discover differentially expressed lncRNAs. LncRNAs were considered significant if they
appeared in more than one GEO dataset. Parts of lncRNAs sequences available in GEO2R
analysis results were run through BLAST in order to identify full length lncRNAs.
Five GEO datasets matched our criteria. We discovered 12 sequences that appeared in
more than one dataset and we identified them through BLAST analysis. Six sequences
originated from lncRNAs (RYR3 divergent transcript, long intergenic non-protein coding
RNA 595, TOX divergent transcript, FLVCR2 antisense RNA 1, LHRI_LNC744.1 lncRNA
gene, and ELFN1 antisense RNA 1), while six sequences represented partial sequences
of various mRNAs. Four lncRNAs were down-regulated in colon cancer; one was upregulated,
while one showed different expression patterns in different GEO datasets.
In this study, we have identified six lncRNAs that have potential significance for colorectal
cancer etiology and will be a subject of further in silico and in vitro study.",
publisher = "Belgrade : Institute of molecular genetics and genetic engineering",
journal = "4th Belgrade Bioinformatics Conference",
title = "Data mining for long-non coding RNAs deregulated in colon cancer through analysis of Gene Expression Omnibus database",
pages = "89-89",
volume = "4",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2034"
}

Pruner, I.,& Nikolić, A.. (2023). Data mining for long-non coding RNAs deregulated in colon cancer through analysis of Gene Expression Omnibus database. in 4th Belgrade Bioinformatics Conference
Belgrade : Institute of molecular genetics and genetic engineering., 4, 89-89.
https://hdl.handle.net/21.15107/rcub_imagine_2034

Pruner I, Nikolić A. Data mining for long-non coding RNAs deregulated in colon cancer through analysis of Gene Expression Omnibus database. in 4th Belgrade Bioinformatics Conference. 2023;4:89-89.
https://hdl.handle.net/21.15107/rcub_imagine_2034 .

Pruner, Iva, Nikolić, Aleksandra, "Data mining for long-non coding RNAs deregulated in colon cancer through analysis of Gene Expression Omnibus database" in 4th Belgrade Bioinformatics Conference, 4 (2023):89-89,
https://hdl.handle.net/21.15107/rcub_imagine_2034 .

TY  - CONF
AU  - Ignjatović, Sofija
AU  - Pavlović, Dunja
AU  - Babić, Tamara
AU  - Dragičević, Sandra
AU  - Nikolić, Aleksandra
PY  - 2023
UR  - https://febs.onlinelibrary.wiley.com/doi/10.1002/1878-0261.13471
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1971
AB  - Introduction: Recent data from a comprehensive pan-cancer
transcriptome analysis demonstrated differential activity of
two alternative PHF19 gene promoters in malignant vs.
non-malignant gut mucosa. The promoter found to be upregulated
in colon and rectal cancer gives rise to the
transcript PHF19-207. This finding has pointed to the
biomarker potential and possible tumor-promoting role of
this transcript. Our study aimed to evaluate the expression
of PHF19-207 in colon cancer, as well as to investigate its
potential function using in silico tools.
PB  - Wiley
C3  - Molecular oncology
T1  - Biomarker potential of the transcript PHF19-207 in colon cancer
IS  - Supplement 1
SP  - 70
SP  - 70
VL  - 17
DO  - doi.org/10.1002/1878-0261.13471
ER  - 

@conference{
author = "Ignjatović, Sofija and Pavlović, Dunja and Babić, Tamara and Dragičević, Sandra and Nikolić, Aleksandra",
year = "2023",
abstract = "Introduction: Recent data from a comprehensive pan-cancer
transcriptome analysis demonstrated differential activity of
two alternative PHF19 gene promoters in malignant vs.
non-malignant gut mucosa. The promoter found to be upregulated
in colon and rectal cancer gives rise to the
transcript PHF19-207. This finding has pointed to the
biomarker potential and possible tumor-promoting role of
this transcript. Our study aimed to evaluate the expression
of PHF19-207 in colon cancer, as well as to investigate its
potential function using in silico tools.",
publisher = "Wiley",
journal = "Molecular oncology",
title = "Biomarker potential of the transcript PHF19-207 in colon cancer",
number = "Supplement 1",
pages = "70-70",
volume = "17",
doi = "doi.org/10.1002/1878-0261.13471"
}

Ignjatović, S., Pavlović, D., Babić, T., Dragičević, S.,& Nikolić, A.. (2023). Biomarker potential of the transcript PHF19-207 in colon cancer. in Molecular oncology
Wiley., 17(Supplement 1), 70.
https://doi.org/doi.org/10.1002/1878-0261.13471

Ignjatović S, Pavlović D, Babić T, Dragičević S, Nikolić A. Biomarker potential of the transcript PHF19-207 in colon cancer. in Molecular oncology. 2023;17(Supplement 1):70.
doi:doi.org/10.1002/1878-0261.13471 .

Ignjatović, Sofija, Pavlović, Dunja, Babić, Tamara, Dragičević, Sandra, Nikolić, Aleksandra, "Biomarker potential of the transcript PHF19-207 in colon cancer" in Molecular oncology, 17, no. Supplement 1 (2023):70,
https://doi.org/doi.org/10.1002/1878-0261.13471 . .

TY  - JOUR
AU  - Rosić, Jovana
AU  - Miladinov, Marko
AU  - Dragičević, Sandra
AU  - Erić, Katarina
AU  - Bogdanović, Aleksandar
AU  - Krivokapić, Zoran
AU  - Nikolić, Aleksandra
PY  - 2023
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1769
AB  - Considering the impact of SMAD7 deregulation in colorectal cancer (CRC) progression and the
significance of single nucleotide variant (SNV)-mediated disruptions of microRNA (miRNA)-dependent regulation
for cancer susceptibility, our study aimed to analyze genetic variation in the SMAD7 3′ untranslated region (
3′UTR) in CRC, measure differences in allelic mRNA expression, and evaluate its interference with miRNAmediated
post-transcriptional regulation.
Patients and Methods: This study included 80 patients with different CRC stages and six human colon cancer cell
lines of various histological origins. SMAD7 3′ UTR was analyzed by direct sequencing, followed by the relative
quantification of differential allelic expression of detected variants by allele-specific qRT-PCR. In silico tools were
employed for predictions of regulatory consequences of detected variants.
Results: A total of four different SNVs in one cell line and nine patients were found, among which were a novel
somatic point variant and three already known germline variants (rs16950113, rs1050799536, and
rs1043778717). All evaluated SNVs exhibited variable extents of allelic imbalance in expression. In silico analysis
predicted significant effects of SNVs on miRNA binding efficiency, with each SNV disrupting existing and
creating new target sites for one or more miRNAs.
Conclusion: Imbalance observed in the expression of SNV alleles altering miRNA binding suggests that all
investigated SNVs are potential contributing factors impacting SMAD7 expression regulation in CRC that further
studies should investigate.
PB  - Elsevier
T2  - Gene
T1  - Genetic analysis and allele-specific expression of SMAD7 3′UTR variants in human colorectal cancer reveal a novel somatic variant exhibiting allelic imbalance
SP  - 147217
VL  - 859
DO  - doi.org/10.1016/j.gene.2023.147217
ER  - 

@article{
author = "Rosić, Jovana and Miladinov, Marko and Dragičević, Sandra and Erić, Katarina and Bogdanović, Aleksandar and Krivokapić, Zoran and Nikolić, Aleksandra",
year = "2023",
abstract = "Considering the impact of SMAD7 deregulation in colorectal cancer (CRC) progression and the
significance of single nucleotide variant (SNV)-mediated disruptions of microRNA (miRNA)-dependent regulation
for cancer susceptibility, our study aimed to analyze genetic variation in the SMAD7 3′ untranslated region (
3′UTR) in CRC, measure differences in allelic mRNA expression, and evaluate its interference with miRNAmediated
post-transcriptional regulation.
Patients and Methods: This study included 80 patients with different CRC stages and six human colon cancer cell
lines of various histological origins. SMAD7 3′ UTR was analyzed by direct sequencing, followed by the relative
quantification of differential allelic expression of detected variants by allele-specific qRT-PCR. In silico tools were
employed for predictions of regulatory consequences of detected variants.
Results: A total of four different SNVs in one cell line and nine patients were found, among which were a novel
somatic point variant and three already known germline variants (rs16950113, rs1050799536, and
rs1043778717). All evaluated SNVs exhibited variable extents of allelic imbalance in expression. In silico analysis
predicted significant effects of SNVs on miRNA binding efficiency, with each SNV disrupting existing and
creating new target sites for one or more miRNAs.
Conclusion: Imbalance observed in the expression of SNV alleles altering miRNA binding suggests that all
investigated SNVs are potential contributing factors impacting SMAD7 expression regulation in CRC that further
studies should investigate.",
publisher = "Elsevier",
journal = "Gene",
title = "Genetic analysis and allele-specific expression of SMAD7 3′UTR variants in human colorectal cancer reveal a novel somatic variant exhibiting allelic imbalance",
pages = "147217",
volume = "859",
doi = "doi.org/10.1016/j.gene.2023.147217"
}

Rosić, J., Miladinov, M., Dragičević, S., Erić, K., Bogdanović, A., Krivokapić, Z.,& Nikolić, A.. (2023). Genetic analysis and allele-specific expression of SMAD7 3′UTR variants in human colorectal cancer reveal a novel somatic variant exhibiting allelic imbalance. in Gene
Elsevier., 859, 147217.
https://doi.org/doi.org/10.1016/j.gene.2023.147217

Rosić J, Miladinov M, Dragičević S, Erić K, Bogdanović A, Krivokapić Z, Nikolić A. Genetic analysis and allele-specific expression of SMAD7 3′UTR variants in human colorectal cancer reveal a novel somatic variant exhibiting allelic imbalance. in Gene. 2023;859:147217.
doi:doi.org/10.1016/j.gene.2023.147217 .

Rosić, Jovana, Miladinov, Marko, Dragičević, Sandra, Erić, Katarina, Bogdanović, Aleksandar, Krivokapić, Zoran, Nikolić, Aleksandra, "Genetic analysis and allele-specific expression of SMAD7 3′UTR variants in human colorectal cancer reveal a novel somatic variant exhibiting allelic imbalance" in Gene, 859 (2023):147217,
https://doi.org/doi.org/10.1016/j.gene.2023.147217 . .

TY  - CONF
AU  - Pavlović, Dunja
AU  - Babić, Tamara
AU  - Nikolić, Aleksandra
PY  - 2023
UR  - https://www.nature.com/articles/s41431-023-01339-3#Sec859
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1973
AB  - Background/Objectives: The transcriptional regulation of
PRKAR1B is controlled by alternative promoters, and previous in
silico analysis has indicated their differential activity in colon and
rectal cancer tissue in comparison to normal gut mucosa. The aim
of this study was to investigate PRKAR1B promoters and transcripts
potentially involved in cancer.
Methods: The sequences of PRKAR1B alternative promoters
were retrieved from Ensembl database: promoter A 752209 and
promoter B 767287 bases upstream from the translation start site.
Bioinformatic tools Alggen, AliBaba, CiiiDER, and TFBIND were
used to predict binding of transcriptional regulators. Primer
extension assay was performed on RNA isolated from malignant
colon cell lines using an oligonucleotide probe binding to the
sequence at the exon2/exon3 junction common for all PRKAR1B
transcripts.
Results: Based on analyzed elements, both PRKAR1B promoters
were found to have atypical structure. According to the prediction,
promoter A that encodes transcript PRKAR1B-201 binds several
factors involved in cell proliferation, while promoter B that encodes
transcript PRKAR1B-203 binds mostly pro-apoptotic factors. In primer
extension experiments, a single signal corresponding to the
transcript PRKAR1B-212 was observed in malignant cells.
Conclusion: The differential activity of alternative PRKAR1B
promoters in colorectal cancer can be explained by in silico
results, predicting that promoter sequences bind sets of transcriptional
regulators with opposing roles. However, experiments
point to the transcript unrelated to either of the investigated
promoters as potential cancer biomarker and it should be further
characterized.
PB  - Springer Nature
C3  - European Journal of Human Genetic
T1  - Analysis of transcripts from alternative PRKAR1B gene promoters in colorectal cancer
EP  - 249
IS  - Supplement S1
SP  - 249
VL  - 31
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1973
ER  - 

@conference{
author = "Pavlović, Dunja and Babić, Tamara and Nikolić, Aleksandra",
year = "2023",
abstract = "Background/Objectives: The transcriptional regulation of
PRKAR1B is controlled by alternative promoters, and previous in
silico analysis has indicated their differential activity in colon and
rectal cancer tissue in comparison to normal gut mucosa. The aim
of this study was to investigate PRKAR1B promoters and transcripts
potentially involved in cancer.
Methods: The sequences of PRKAR1B alternative promoters
were retrieved from Ensembl database: promoter A 752209 and
promoter B 767287 bases upstream from the translation start site.
Bioinformatic tools Alggen, AliBaba, CiiiDER, and TFBIND were
used to predict binding of transcriptional regulators. Primer
extension assay was performed on RNA isolated from malignant
colon cell lines using an oligonucleotide probe binding to the
sequence at the exon2/exon3 junction common for all PRKAR1B
transcripts.
Results: Based on analyzed elements, both PRKAR1B promoters
were found to have atypical structure. According to the prediction,
promoter A that encodes transcript PRKAR1B-201 binds several
factors involved in cell proliferation, while promoter B that encodes
transcript PRKAR1B-203 binds mostly pro-apoptotic factors. In primer
extension experiments, a single signal corresponding to the
transcript PRKAR1B-212 was observed in malignant cells.
Conclusion: The differential activity of alternative PRKAR1B
promoters in colorectal cancer can be explained by in silico
results, predicting that promoter sequences bind sets of transcriptional
regulators with opposing roles. However, experiments
point to the transcript unrelated to either of the investigated
promoters as potential cancer biomarker and it should be further
characterized.",
publisher = "Springer Nature",
journal = "European Journal of Human Genetic",
title = "Analysis of transcripts from alternative PRKAR1B gene promoters in colorectal cancer",
pages = "249-249",
number = "Supplement S1",
volume = "31",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1973"
}

Pavlović, D., Babić, T.,& Nikolić, A.. (2023). Analysis of transcripts from alternative PRKAR1B gene promoters in colorectal cancer. in European Journal of Human Genetic
Springer Nature., 31(Supplement S1), 249-249.
https://hdl.handle.net/21.15107/rcub_imagine_1973

Pavlović D, Babić T, Nikolić A. Analysis of transcripts from alternative PRKAR1B gene promoters in colorectal cancer. in European Journal of Human Genetic. 2023;31(Supplement S1):249-249.
https://hdl.handle.net/21.15107/rcub_imagine_1973 .

Pavlović, Dunja, Babić, Tamara, Nikolić, Aleksandra, "Analysis of transcripts from alternative PRKAR1B gene promoters in colorectal cancer" in European Journal of Human Genetic, 31, no. Supplement S1 (2023):249-249,
https://hdl.handle.net/21.15107/rcub_imagine_1973 .

TY  - JOUR
AU  - Nikolić, Aleksandra
AU  - Mark, Kevin J.
AU  - Dragičević, Sandra
AU  - Babić, Tamara
AU  - Milošević, Katarina
AU  - Nestorović, Branimir
AU  - Beskoski, Vladimir
PY  - 2023
UR  - https://www.eurekaselect.com/article/129606
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2058
AB  - Background: Leukocytes are key cellular effectors of inflammation in asthma and understandingtheir function in this disease is of crucial importance. Blood leukocytes reflect the actions oftheir counterparts in the lungs and they can be obtained through minimal invasive procedures as partof the peripheral blood.Objective: The aim of the study was to identify proteins in blood leukocyte proteomes that respond toex vivo treatment by prednisone in order to pinpoint candidates for predictive biomarkers in corticosteroid-responsive asthma.Methods: The study included five children diagnosed with asthma and five healthy children. After theex vivo treatment of blood samples with prednisone, lysis of erythrocytes was performed and proteinswere extracted from the remaining leukocytes by ultrasonic disintegration. Protein extracts were analyzedby reversed phase nano-liquidchromatography–tandem mass spectrometry (LC–MS/MS).Results: The stimulation of asthmatics' leukocytes with prednisone has led to an increase in the levelsof FYB (fold change 3.4) and LYZ (fold change 2.2) with a statistical significance of p
T2  - Current Proteomics
T1  - Pilot Study of the Ex Vivo Blood Leukocytes’ Proteomic Response to Prednisone Stimulation in Corticosteroid-responsive Asthma
EP  - 18
IS  - 1
SP  - 12
VL  - 20
DO  - 10.2174/1570164620666230220112500
ER  - 

@article{
author = "Nikolić, Aleksandra and Mark, Kevin J. and Dragičević, Sandra and Babić, Tamara and Milošević, Katarina and Nestorović, Branimir and Beskoski, Vladimir",
year = "2023",
abstract = "Background: Leukocytes are key cellular effectors of inflammation in asthma and understandingtheir function in this disease is of crucial importance. Blood leukocytes reflect the actions oftheir counterparts in the lungs and they can be obtained through minimal invasive procedures as partof the peripheral blood.Objective: The aim of the study was to identify proteins in blood leukocyte proteomes that respond toex vivo treatment by prednisone in order to pinpoint candidates for predictive biomarkers in corticosteroid-responsive asthma.Methods: The study included five children diagnosed with asthma and five healthy children. After theex vivo treatment of blood samples with prednisone, lysis of erythrocytes was performed and proteinswere extracted from the remaining leukocytes by ultrasonic disintegration. Protein extracts were analyzedby reversed phase nano-liquidchromatography–tandem mass spectrometry (LC–MS/MS).Results: The stimulation of asthmatics' leukocytes with prednisone has led to an increase in the levelsof FYB (fold change 3.4) and LYZ (fold change 2.2) with a statistical significance of p",
journal = "Current Proteomics",
title = "Pilot Study of the Ex Vivo Blood Leukocytes’ Proteomic Response to Prednisone Stimulation in Corticosteroid-responsive Asthma",
pages = "18-12",
number = "1",
volume = "20",
doi = "10.2174/1570164620666230220112500"
}

Nikolić, A., Mark, K. J., Dragičević, S., Babić, T., Milošević, K., Nestorović, B.,& Beskoski, V.. (2023). Pilot Study of the Ex Vivo Blood Leukocytes’ Proteomic Response to Prednisone Stimulation in Corticosteroid-responsive Asthma. in Current Proteomics, 20(1), 12-18.
https://doi.org/10.2174/1570164620666230220112500

Nikolić A, Mark KJ, Dragičević S, Babić T, Milošević K, Nestorović B, Beskoski V. Pilot Study of the Ex Vivo Blood Leukocytes’ Proteomic Response to Prednisone Stimulation in Corticosteroid-responsive Asthma. in Current Proteomics. 2023;20(1):12-18.
doi:10.2174/1570164620666230220112500 .

Nikolić, Aleksandra, Mark, Kevin J., Dragičević, Sandra, Babić, Tamara, Milošević, Katarina, Nestorović, Branimir, Beskoski, Vladimir, "Pilot Study of the Ex Vivo Blood Leukocytes’ Proteomic Response to Prednisone Stimulation in Corticosteroid-responsive Asthma" in Current Proteomics, 20, no. 1 (2023):12-18,
https://doi.org/10.2174/1570164620666230220112500 . .

TY  - JOUR
AU  - Jovanović, Ljubiša
AU  - Nikolić, Aleksandra
AU  - Dragičević, Sandra
AU  - Jović, Milena
AU  - Janković, Radmila
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2300
AB  - Aim To analyze the expression of autophagy markers p62,
LC3, and Beclin1 in ovarian cancer tissue and evaluate the
prognostic potential of these markers.
Methods The study enrolled 328 patients: 122 with epithelial ovarian carcinoma, 42 with atypical proliferative tumor, and 164 with benign epithelial ovarian tumor. The expression of p62, LC3, and Beclin1 was analyzed in central
and invasive tumor segments with immunohistochemistry
combined with tissue microarray. The expression levels of
the analyzed markers were correlated with relevant histopathology parameters.
Results The expression of all analyzed markers was most
remarkable in epithelial ovarian carcinoma. There was a
strong positive correlation between the expressions of p62
and LC3, while these two markers negatively correlated
with Beclin1. High-grade serous carcinoma had higher p62
and LC3 levels, and lower Beclin1 levels than other tumor
types. This expression profile was also observed in more
advanced tumor stages.
Conclusion Prominent p62 and LC3 expression in combination with weak Beclin1 expression in high-grade serous
carcinoma indicates potential for the application of autophagy inhibitors in patients with this tumor subtype.
PB  - Medicinska naklada (Croatia)
T2  - Croatian Medical Journal
T1  - Prognostic relevance of autophagy-related markers p62, LC3, and Beclin1 in ovarian cancer
EP  - 460
IS  - 5
SP  - 453
VL  - 63
DO  - 10.3325/cmj.2022.63.453
ER  - 

@article{
author = "Jovanović, Ljubiša and Nikolić, Aleksandra and Dragičević, Sandra and Jović, Milena and Janković, Radmila",
year = "2022",
abstract = "Aim To analyze the expression of autophagy markers p62,
LC3, and Beclin1 in ovarian cancer tissue and evaluate the
prognostic potential of these markers.
Methods The study enrolled 328 patients: 122 with epithelial ovarian carcinoma, 42 with atypical proliferative tumor, and 164 with benign epithelial ovarian tumor. The expression of p62, LC3, and Beclin1 was analyzed in central
and invasive tumor segments with immunohistochemistry
combined with tissue microarray. The expression levels of
the analyzed markers were correlated with relevant histopathology parameters.
Results The expression of all analyzed markers was most
remarkable in epithelial ovarian carcinoma. There was a
strong positive correlation between the expressions of p62
and LC3, while these two markers negatively correlated
with Beclin1. High-grade serous carcinoma had higher p62
and LC3 levels, and lower Beclin1 levels than other tumor
types. This expression profile was also observed in more
advanced tumor stages.
Conclusion Prominent p62 and LC3 expression in combination with weak Beclin1 expression in high-grade serous
carcinoma indicates potential for the application of autophagy inhibitors in patients with this tumor subtype.",
publisher = "Medicinska naklada (Croatia)",
journal = "Croatian Medical Journal",
title = "Prognostic relevance of autophagy-related markers p62, LC3, and Beclin1 in ovarian cancer",
pages = "460-453",
number = "5",
volume = "63",
doi = "10.3325/cmj.2022.63.453"
}

Jovanović, L., Nikolić, A., Dragičević, S., Jović, M.,& Janković, R.. (2022). Prognostic relevance of autophagy-related markers p62, LC3, and Beclin1 in ovarian cancer. in Croatian Medical Journal
Medicinska naklada (Croatia)., 63(5), 453-460.
https://doi.org/10.3325/cmj.2022.63.453

Jovanović L, Nikolić A, Dragičević S, Jović M, Janković R. Prognostic relevance of autophagy-related markers p62, LC3, and Beclin1 in ovarian cancer. in Croatian Medical Journal. 2022;63(5):453-460.
doi:10.3325/cmj.2022.63.453 .

Jovanović, Ljubiša, Nikolić, Aleksandra, Dragičević, Sandra, Jović, Milena, Janković, Radmila, "Prognostic relevance of autophagy-related markers p62, LC3, and Beclin1 in ovarian cancer" in Croatian Medical Journal, 63, no. 5 (2022):453-460,
https://doi.org/10.3325/cmj.2022.63.453 . .

TY  - CONF
AU  - Velimirov, Luka
AU  - Babić, Tamara
AU  - Dragičević, Sandra
AU  - Nikolić, Aleksandra
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2084
AB  - Gene LDLRAD4 plays a role in cell proliferation, apoptosis, immunosuppression and cancer
progression. Transcription of LDLRAD4 is regulated by several alternative promoters, two of which
were indicated by in silico analyses to be differentially active in rectal cancer. Promoter A encodes for a
truncated protein-coding transcript and is down-regulated in rectal cancer. Promoter B encodes for a
non-coding transcript up-regulated in rectal cancer identified as lnc-RNMT-2:5. The aim of this study
was to characterize the two alternative promoters in silico in order to explain their differential activity
and to investigate the profile of LDLRAD4 transcripts in colon cell lines. Nucleotide sequences used in
the analyses were downloaded from the Ensemble genome database (reference GRCh37). Three
bioinformatics tools were used for core promoter element prediction: GPMiner, YAPP and
CNNPromoter. Four bioinformatics tools were used for transcription factor binding site prediction:
PROMO, TFBIND, CiiiDER and Tfsitescan. Only the predictions made by two or more tools were
considered. Primer extension followed by fragment analysis was used to characterize LDLRAD4
transcripts present in colon cell lines. The promoter element predictions showed that the promoter A is
typical, while promoter B has most typical elements and lacks GC boxes. The transcription binding site
predictions indicate that three different transcription factors bind only to the promoter A (NF-kB,
EGR1 and IRF-7), while four different transcription factors bind only to the promoter B (HNF1,
POU2F1, POU2F2 and PTF1). The predicted transcription factors are mostly involved in regulation of
cell differentiation and proliferation. The primer extension experiment performed with primer specific
for exon 2-exon 3 junction produced multiple signals of relatively low intensity, indicating the presence
of multiple LDLRAD4 transcripts in colon cell lines. The results obtained by in silico analysis may
explain promoter B activation in rectal cancer. However, based on the results of primer extension, neither
of the LDLRAD4 transcripts is dominant in colon cell lines. Considering that promoter B generates
long non-coding RNA that can exert its function even at low expression level, it can serve as potential
colorectal cancer biomarker and its potential role in carcinogenesis should be investigated.
PB  - Croatian Association for Cancer Research, Zagreb, Croatia
C3  - “HDIR-6: Targeting Cancer” The 6th Meeting of the Croatian Association for Cancer Research with International Participation – Book of Abstracts
T1  - Analysis of Alternative LDLRAD4 Gene Promoters and Transcripts in Colorectal Cancer
EP  - 35
SP  - 35
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2084
ER  - 

@conference{
author = "Velimirov, Luka and Babić, Tamara and Dragičević, Sandra and Nikolić, Aleksandra",
year = "2022",
abstract = "Gene LDLRAD4 plays a role in cell proliferation, apoptosis, immunosuppression and cancer
progression. Transcription of LDLRAD4 is regulated by several alternative promoters, two of which
were indicated by in silico analyses to be differentially active in rectal cancer. Promoter A encodes for a
truncated protein-coding transcript and is down-regulated in rectal cancer. Promoter B encodes for a
non-coding transcript up-regulated in rectal cancer identified as lnc-RNMT-2:5. The aim of this study
was to characterize the two alternative promoters in silico in order to explain their differential activity
and to investigate the profile of LDLRAD4 transcripts in colon cell lines. Nucleotide sequences used in
the analyses were downloaded from the Ensemble genome database (reference GRCh37). Three
bioinformatics tools were used for core promoter element prediction: GPMiner, YAPP and
CNNPromoter. Four bioinformatics tools were used for transcription factor binding site prediction:
PROMO, TFBIND, CiiiDER and Tfsitescan. Only the predictions made by two or more tools were
considered. Primer extension followed by fragment analysis was used to characterize LDLRAD4
transcripts present in colon cell lines. The promoter element predictions showed that the promoter A is
typical, while promoter B has most typical elements and lacks GC boxes. The transcription binding site
predictions indicate that three different transcription factors bind only to the promoter A (NF-kB,
EGR1 and IRF-7), while four different transcription factors bind only to the promoter B (HNF1,
POU2F1, POU2F2 and PTF1). The predicted transcription factors are mostly involved in regulation of
cell differentiation and proliferation. The primer extension experiment performed with primer specific
for exon 2-exon 3 junction produced multiple signals of relatively low intensity, indicating the presence
of multiple LDLRAD4 transcripts in colon cell lines. The results obtained by in silico analysis may
explain promoter B activation in rectal cancer. However, based on the results of primer extension, neither
of the LDLRAD4 transcripts is dominant in colon cell lines. Considering that promoter B generates
long non-coding RNA that can exert its function even at low expression level, it can serve as potential
colorectal cancer biomarker and its potential role in carcinogenesis should be investigated.",
publisher = "Croatian Association for Cancer Research, Zagreb, Croatia",
journal = "“HDIR-6: Targeting Cancer” The 6th Meeting of the Croatian Association for Cancer Research with International Participation – Book of Abstracts",
title = "Analysis of Alternative LDLRAD4 Gene Promoters and Transcripts in Colorectal Cancer",
pages = "35-35",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2084"
}

Velimirov, L., Babić, T., Dragičević, S.,& Nikolić, A.. (2022). Analysis of Alternative LDLRAD4 Gene Promoters and Transcripts in Colorectal Cancer. in “HDIR-6: Targeting Cancer” The 6th Meeting of the Croatian Association for Cancer Research with International Participation – Book of Abstracts
Croatian Association for Cancer Research, Zagreb, Croatia., 35-35.
https://hdl.handle.net/21.15107/rcub_imagine_2084

Velimirov L, Babić T, Dragičević S, Nikolić A. Analysis of Alternative LDLRAD4 Gene Promoters and Transcripts in Colorectal Cancer. in “HDIR-6: Targeting Cancer” The 6th Meeting of the Croatian Association for Cancer Research with International Participation – Book of Abstracts. 2022;:35-35.
https://hdl.handle.net/21.15107/rcub_imagine_2084 .

Velimirov, Luka, Babić, Tamara, Dragičević, Sandra, Nikolić, Aleksandra, "Analysis of Alternative LDLRAD4 Gene Promoters and Transcripts in Colorectal Cancer" in “HDIR-6: Targeting Cancer” The 6th Meeting of the Croatian Association for Cancer Research with International Participation – Book of Abstracts (2022):35-35,
https://hdl.handle.net/21.15107/rcub_imagine_2084 .

TY  - CONF
AU  - Jovanović, I.
AU  - Nikolić, Aleksandra
AU  - Dragičević, Sandra
AU  - Jović, M.
AU  - Janković, R.
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2082
AB  - Background & objectives: Autophagy is a crucial cellular mechanism that coordinates various physiological processes. Many cancers can activate autophagy and make the tumour more aggressive. In this study, we analysed autophagy in ovarian cancers. Methods: We included 122 patients with ovarian cancers. Tissue microarray was made for immunohistochemical analysis of p62, LC3, and Beclin1 expressions. Their expressions were correlated with tumour histology type, differentiation, and stage. The percentage of positive tumour cells was estimated from the total number of tumour cells. Samples with positive cells were stratified into three ranges of positivity: <10%; 10–50%; >50%. Results: There was a strong positive correlation between p62 and LC3 expression, while both markers were in negative correlation with Beclin1. The expression of each analysed marker showed a statistically significant association with tumour histological type, stage, and differentiation (p<0.001). While p62 and LC3 were more prominently expressed in patients with high-grade serous ovarian cancer (HGSOC), Beclin 1 expression was lower in HGSOC and more prominent in other histology types. A higher expression of  p62 and LC3 was observed in later tumour stages, while the oppo- site was observed for Beclin1 expression. Tumour differentiation  positively correlated with p62 and LC3 expression, and negatively with Beclin1 expression.  Conclusion: The expression of p62 and LC3 was more promi- nent in HGSOC in comparison to other histology types, while  Beclin1 expression was more prominent in carcinomas other than in HGSOC. While p62 and LC3 expression was associated with higher tumour stages and tumour grades, the opposite was found for Beclin1. Prominent p62 and LC3 expression in combination with weak Beclin1 expression in HGSOC indicate the potential for application of autophagy inhibitors in patients with this tumour subtype.
PB  - Springer
C3  - Virchows Archiv, 34 th European Congress of Pathology - Abstracts
T1  - Expression of autophagy markers in ovarian cancer
EP  - S256
IS  - Supplement 1
SP  - S256
SP  - E-PS-09-003
VL  - 481
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2082
ER  - 

@conference{
author = "Jovanović, I. and Nikolić, Aleksandra and Dragičević, Sandra and Jović, M. and Janković, R.",
year = "2022",
abstract = "Background & objectives: Autophagy is a crucial cellular mechanism that coordinates various physiological processes. Many cancers can activate autophagy and make the tumour more aggressive. In this study, we analysed autophagy in ovarian cancers. Methods: We included 122 patients with ovarian cancers. Tissue microarray was made for immunohistochemical analysis of p62, LC3, and Beclin1 expressions. Their expressions were correlated with tumour histology type, differentiation, and stage. The percentage of positive tumour cells was estimated from the total number of tumour cells. Samples with positive cells were stratified into three ranges of positivity: <10%; 10–50%; >50%. Results: There was a strong positive correlation between p62 and LC3 expression, while both markers were in negative correlation with Beclin1. The expression of each analysed marker showed a statistically significant association with tumour histological type, stage, and differentiation (p<0.001). While p62 and LC3 were more prominently expressed in patients with high-grade serous ovarian cancer (HGSOC), Beclin 1 expression was lower in HGSOC and more prominent in other histology types. A higher expression of  p62 and LC3 was observed in later tumour stages, while the oppo- site was observed for Beclin1 expression. Tumour differentiation  positively correlated with p62 and LC3 expression, and negatively with Beclin1 expression.  Conclusion: The expression of p62 and LC3 was more promi- nent in HGSOC in comparison to other histology types, while  Beclin1 expression was more prominent in carcinomas other than in HGSOC. While p62 and LC3 expression was associated with higher tumour stages and tumour grades, the opposite was found for Beclin1. Prominent p62 and LC3 expression in combination with weak Beclin1 expression in HGSOC indicate the potential for application of autophagy inhibitors in patients with this tumour subtype.",
publisher = "Springer",
journal = "Virchows Archiv, 34 th European Congress of Pathology - Abstracts",
title = "Expression of autophagy markers in ovarian cancer",
pages = "S256-S256-E-PS-09-003",
number = "Supplement 1",
volume = "481",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2082"
}

Jovanović, I., Nikolić, A., Dragičević, S., Jović, M.,& Janković, R.. (2022). Expression of autophagy markers in ovarian cancer. in Virchows Archiv, 34 th European Congress of Pathology - Abstracts
Springer., 481(Supplement 1), S256-S256.
https://hdl.handle.net/21.15107/rcub_imagine_2082

Jovanović I, Nikolić A, Dragičević S, Jović M, Janković R. Expression of autophagy markers in ovarian cancer. in Virchows Archiv, 34 th European Congress of Pathology - Abstracts. 2022;481(Supplement 1):S256-S256.
https://hdl.handle.net/21.15107/rcub_imagine_2082 .

Jovanović, I., Nikolić, Aleksandra, Dragičević, Sandra, Jović, M., Janković, R., "Expression of autophagy markers in ovarian cancer" in Virchows Archiv, 34 th European Congress of Pathology - Abstracts, 481, no. Supplement 1 (2022):S256-S256,
https://hdl.handle.net/21.15107/rcub_imagine_2082 .

TY  - CONF
AU  - Jovanović, Emilija
AU  - Dragičević, Sandra
AU  - Babić, Tamara
AU  - Nikolić, Aleksandra
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1741
AB  - Transkripcija gena CD81, čiji proteinski produkt ostvaruje brojne biološke
uloge i uključen je u razvoj maligniteta, regulisana je alternativnim
promotorima. U prethodnoj in silico studiji pokazali smo da se regulatorni
proteini diferencijalno vezuju za alternativne promotore gena CD81 označene
kao A i B, za koje je prethodno pokazano da su diferencijalno aktivni u
kolorektalnom karcinomu.1,2 Cilj ovog rada bio je da se u kolorektalnom
karcinomu in vitro analiziraju transkripti koji nastaju usled aktivnosti ovih
promotora. Ekspresija alternativnih transkripata, kao i ukupna ekspresija gena
CD81 analizirane su u humanim ćelijskim linijama kolona metodom PCR u
realnom vremenu. Pokazano je da alternativni promotori doprinose ukupnoj
ekspresiji gena CD81 sa relativno malim udelom: promotor A 0,43-12,86%, a
promotor B 0,40-4,13%. U nemalignoj ćelijskoj liniji HCEC-1CT, pokazan je
približno jednak nivo ekspresije transkripata oba promotora, dok je u malignim
ćelijskim linijama HT29, Caco-2, HCT116, SW480 i SW620, ekspresija
transkipata promotora A bila veća u odnosu na promotor B, što je očekivano na
osnovu prethodnih in silico studija. Dobijeni rezultati ukazuju na potencijal
alternativnih transkripata gena CD81 kao biomarkera za kolorektalni karcinom.
Kako uloga transkripata nije poznata, njihova struktura i ekspresija sugerišu da
treba ispitati mogućnost da neki od njih mogu biti duge nekodirajuće RNK.
AB  - Транскрипција гена CD81, чији протеински продукт остварује бројне биолошке
улоге и укључен је у развој малигнитета, регулисана је алтернативним
промоторима. У претходној in silico студији показали смо да се регулаторни
протеини диференцијално везују за алтернативне промоторе гена CD81 означене
као А и Б, за које је претходно показано да су диференцијално активни у
колоректалном карциному.1,2 Циљ овог рада био је да се у колоректалном
карциному in vitro анализирају транскрипти који настају услед активности ових
промотора. Експресија алтернативних транскрипата, као и укупна експресија гена
CD81 анализиране су у хуманим ћелијским линијама колона методом ПЦР у
реaлном времену. Показано је да алтернативни промотори доприносе укупној
експресији гена CD81 са релативно малим уделом: промотор А 0,43-12,86%, а
промотор Б 0,40-4,13%. У немалигној ћелијској линији HCEC-1CT, показан је
приближно једнак ниво експресије транскрипата оба промотора, док је у малигним
ћелијским линијама HT29, Caco-2, HCT116, SW480 и SW620, експресија
транскипата промотора А била већа у односу на промотор Б, што је очекивано на
основу претходних in silico студија. Добијени резултати указују на потенцијал
алтернативних транскрипата гена CD81 као биомаркера за колоректални карцином.
Како улога транскрипата није позната, њихова структура и експресија сугеришу да
треба испитати могућност да неки од њих могу бити дуге некодирајуће РНК.
PB  - Treći kongres biologa Srbije
C3  - Treći kongres biologa Srbije
T1  - Analiza alternativnih transkripata gena CD81 u kolorektalnom karcinomu
T1  - Анализа алтернативних транскрипата гена CD81 у колоректалном карциному
EP  - 303
SP  - 303
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1741
ER  - 

@conference{
author = "Jovanović, Emilija and Dragičević, Sandra and Babić, Tamara and Nikolić, Aleksandra",
year = "2022",
abstract = "Transkripcija gena CD81, čiji proteinski produkt ostvaruje brojne biološke
uloge i uključen je u razvoj maligniteta, regulisana je alternativnim
promotorima. U prethodnoj in silico studiji pokazali smo da se regulatorni
proteini diferencijalno vezuju za alternativne promotore gena CD81 označene
kao A i B, za koje je prethodno pokazano da su diferencijalno aktivni u
kolorektalnom karcinomu.1,2 Cilj ovog rada bio je da se u kolorektalnom
karcinomu in vitro analiziraju transkripti koji nastaju usled aktivnosti ovih
promotora. Ekspresija alternativnih transkripata, kao i ukupna ekspresija gena
CD81 analizirane su u humanim ćelijskim linijama kolona metodom PCR u
realnom vremenu. Pokazano je da alternativni promotori doprinose ukupnoj
ekspresiji gena CD81 sa relativno malim udelom: promotor A 0,43-12,86%, a
promotor B 0,40-4,13%. U nemalignoj ćelijskoj liniji HCEC-1CT, pokazan je
približno jednak nivo ekspresije transkripata oba promotora, dok je u malignim
ćelijskim linijama HT29, Caco-2, HCT116, SW480 i SW620, ekspresija
transkipata promotora A bila veća u odnosu na promotor B, što je očekivano na
osnovu prethodnih in silico studija. Dobijeni rezultati ukazuju na potencijal
alternativnih transkripata gena CD81 kao biomarkera za kolorektalni karcinom.
Kako uloga transkripata nije poznata, njihova struktura i ekspresija sugerišu da
treba ispitati mogućnost da neki od njih mogu biti duge nekodirajuće RNK., Транскрипција гена CD81, чији протеински продукт остварује бројне биолошке
улоге и укључен је у развој малигнитета, регулисана је алтернативним
промоторима. У претходној in silico студији показали смо да се регулаторни
протеини диференцијално везују за алтернативне промоторе гена CD81 означене
као А и Б, за које је претходно показано да су диференцијално активни у
колоректалном карциному.1,2 Циљ овог рада био је да се у колоректалном
карциному in vitro анализирају транскрипти који настају услед активности ових
промотора. Експресија алтернативних транскрипата, као и укупна експресија гена
CD81 анализиране су у хуманим ћелијским линијама колона методом ПЦР у
реaлном времену. Показано је да алтернативни промотори доприносе укупној
експресији гена CD81 са релативно малим уделом: промотор А 0,43-12,86%, а
промотор Б 0,40-4,13%. У немалигној ћелијској линији HCEC-1CT, показан је
приближно једнак ниво експресије транскрипата оба промотора, док је у малигним
ћелијским линијама HT29, Caco-2, HCT116, SW480 и SW620, експресија
транскипата промотора А била већа у односу на промотор Б, што је очекивано на
основу претходних in silico студија. Добијени резултати указују на потенцијал
алтернативних транскрипата гена CD81 као биомаркера за колоректални карцином.
Како улога транскрипата није позната, њихова структура и експресија сугеришу да
треба испитати могућност да неки од њих могу бити дуге некодирајуће РНК.",
publisher = "Treći kongres biologa Srbije",
journal = "Treći kongres biologa Srbije",
title = "Analiza alternativnih transkripata gena CD81 u kolorektalnom karcinomu, Анализа алтернативних транскрипата гена CD81 у колоректалном карциному",
pages = "303-303",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1741"
}

Jovanović, E., Dragičević, S., Babić, T.,& Nikolić, A.. (2022). Analiza alternativnih transkripata gena CD81 u kolorektalnom karcinomu. in Treći kongres biologa Srbije
Treći kongres biologa Srbije., 303-303.
https://hdl.handle.net/21.15107/rcub_imagine_1741

Jovanović E, Dragičević S, Babić T, Nikolić A. Analiza alternativnih transkripata gena CD81 u kolorektalnom karcinomu. in Treći kongres biologa Srbije. 2022;:303-303.
https://hdl.handle.net/21.15107/rcub_imagine_1741 .

Jovanović, Emilija, Dragičević, Sandra, Babić, Tamara, Nikolić, Aleksandra, "Analiza alternativnih transkripata gena CD81 u kolorektalnom karcinomu" in Treći kongres biologa Srbije (2022):303-303,
https://hdl.handle.net/21.15107/rcub_imagine_1741 .

TY  - JOUR
AU  - Jendrišek, Gorana
AU  - Nikolić, Aleksandra
AU  - Dragičević, Sandra
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1512
AB  - Montelukast, a leukotriene receptor antagonist, is the most prescribed nonsteroidal anti-inflammatory drug used as an add-on therapy for asthma. Besides its effect on blocking leukotriene action, montelukast has been proposed to have secondary anti-inflammatory properties. This study aimed to investigate the modulatory effect of montelukast on the expression of major genes involved in airway inflammation (TNF, IL6) and remodeling (MMP9, TGFB1) in response to lipopolysaccharide (LPS) in vitro. The expression of selected genes was measured by quantitative real-time polymerase chain reaction 0h and 24h after LPS stimulation in cells pretreated with montelukast. Montelukast was found to significantly attenuate increased TNF and IL6 gene expression, to have a mild effect on MMP9 and have no effect on TGFB1 expression upon stimulation with LPS. The results of our study indicate that patients on montelukast therapy would have an adequate response to acute microorganism-induced inflammation, so additional anti-inflammatory effects of montelukast should be better exploited.
PB  - Univerzitet u Kragujevcu - Prirodno-matematički fakultet, Kragujevac
T2  - Kragujevac Journal of Science
T1  - Inflammatory modulation of the response of bronchial epithelial cells to lipopolysaccharide with pretreatment by montelukast
EP  - 125
IS  - 44
SP  - 115
DO  - 10.5937/KgJSci2244115J
ER  - 

@article{
author = "Jendrišek, Gorana and Nikolić, Aleksandra and Dragičević, Sandra",
year = "2022",
abstract = "Montelukast, a leukotriene receptor antagonist, is the most prescribed nonsteroidal anti-inflammatory drug used as an add-on therapy for asthma. Besides its effect on blocking leukotriene action, montelukast has been proposed to have secondary anti-inflammatory properties. This study aimed to investigate the modulatory effect of montelukast on the expression of major genes involved in airway inflammation (TNF, IL6) and remodeling (MMP9, TGFB1) in response to lipopolysaccharide (LPS) in vitro. The expression of selected genes was measured by quantitative real-time polymerase chain reaction 0h and 24h after LPS stimulation in cells pretreated with montelukast. Montelukast was found to significantly attenuate increased TNF and IL6 gene expression, to have a mild effect on MMP9 and have no effect on TGFB1 expression upon stimulation with LPS. The results of our study indicate that patients on montelukast therapy would have an adequate response to acute microorganism-induced inflammation, so additional anti-inflammatory effects of montelukast should be better exploited.",
publisher = "Univerzitet u Kragujevcu - Prirodno-matematički fakultet, Kragujevac",
journal = "Kragujevac Journal of Science",
title = "Inflammatory modulation of the response of bronchial epithelial cells to lipopolysaccharide with pretreatment by montelukast",
pages = "125-115",
number = "44",
doi = "10.5937/KgJSci2244115J"
}

Jendrišek, G., Nikolić, A.,& Dragičević, S.. (2022). Inflammatory modulation of the response of bronchial epithelial cells to lipopolysaccharide with pretreatment by montelukast. in Kragujevac Journal of Science
Univerzitet u Kragujevcu - Prirodno-matematički fakultet, Kragujevac.(44), 115-125.
https://doi.org/10.5937/KgJSci2244115J

Jendrišek G, Nikolić A, Dragičević S. Inflammatory modulation of the response of bronchial epithelial cells to lipopolysaccharide with pretreatment by montelukast. in Kragujevac Journal of Science. 2022;(44):115-125.
doi:10.5937/KgJSci2244115J .

Jendrišek, Gorana, Nikolić, Aleksandra, Dragičević, Sandra, "Inflammatory modulation of the response of bronchial epithelial cells to lipopolysaccharide with pretreatment by montelukast" in Kragujevac Journal of Science, no. 44 (2022):115-125,
https://doi.org/10.5937/KgJSci2244115J . .

TY  - JOUR
AU  - Despotović, Jovana
AU  - Bogdanović, Aleksandar
AU  - Dragičević, Sandra
AU  - Galun, Danijel
AU  - Krivokapić, Zoran
AU  - Nikolić, Aleksandra
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1588
AB  - This study aimed to examine the expression pattern of tumoral and circulating miR-93-5p in patients with colorectal cancer (CRC) liver metastasis (CRLM) and to explore its predictive and prognostic potential. CRLM tissue, surrounding non-tumor liver tissue, and serum were obtained from 35 patients with CRLM. The expression pattern of tissue and circulating miR-93-5p in patients with CRLM was determined using quantitative polymerase chain reaction, using miR-16-5p for normalization. Sample-based cut-off values for CRLM and serum miR-93-5p expression were calculated using Receiver Operating Characteristic curve analysis to stratify the patients into high and low miR-93-5p expression groups which were that compared with patients??? clinicopathological data, therapy response, one-year disease-free survival, and disease recurrence. Relative miR-93-5p expression was higher in CRLM in comparison to the non-metastatic liver tissue (p lt 0.001). CRLM miR-93-5p expression showed moderate negative correlation with carcinoembryonic antigen levels (r=???0.406; p=0.016). There were no differences in high-/low-miR-93-5p expression and therapy responders vs. non-responders, which was confirmed in vitro using metastatic and normal colonic cells SW620 and HCEC-1CT, respectively. No difference was observed in one-year recurrence-free survival in patients with high vs. low miR-93-5p expression in CRLM or serum. However, high miR-93-5p serum levels were significantly associated with early disease recurrence (p=0.035). In conclusion, miR-93-5p serum levels could be potentially used as a prognostic factor for early disease recurrence in CRLM patients.
PB  - Aepress Sro, Bratislava
T2  - Neoplasma
T1  - Prognostic potential of circulating miR-93-5p in patients with colorectal cancer liver metastases
EP  - 442
IS  - 2
SP  - 430
VL  - 69
DO  - 10.4149/neo_2021_210603N749
ER  - 

@article{
author = "Despotović, Jovana and Bogdanović, Aleksandar and Dragičević, Sandra and Galun, Danijel and Krivokapić, Zoran and Nikolić, Aleksandra",
year = "2022",
abstract = "This study aimed to examine the expression pattern of tumoral and circulating miR-93-5p in patients with colorectal cancer (CRC) liver metastasis (CRLM) and to explore its predictive and prognostic potential. CRLM tissue, surrounding non-tumor liver tissue, and serum were obtained from 35 patients with CRLM. The expression pattern of tissue and circulating miR-93-5p in patients with CRLM was determined using quantitative polymerase chain reaction, using miR-16-5p for normalization. Sample-based cut-off values for CRLM and serum miR-93-5p expression were calculated using Receiver Operating Characteristic curve analysis to stratify the patients into high and low miR-93-5p expression groups which were that compared with patients??? clinicopathological data, therapy response, one-year disease-free survival, and disease recurrence. Relative miR-93-5p expression was higher in CRLM in comparison to the non-metastatic liver tissue (p lt 0.001). CRLM miR-93-5p expression showed moderate negative correlation with carcinoembryonic antigen levels (r=???0.406; p=0.016). There were no differences in high-/low-miR-93-5p expression and therapy responders vs. non-responders, which was confirmed in vitro using metastatic and normal colonic cells SW620 and HCEC-1CT, respectively. No difference was observed in one-year recurrence-free survival in patients with high vs. low miR-93-5p expression in CRLM or serum. However, high miR-93-5p serum levels were significantly associated with early disease recurrence (p=0.035). In conclusion, miR-93-5p serum levels could be potentially used as a prognostic factor for early disease recurrence in CRLM patients.",
publisher = "Aepress Sro, Bratislava",
journal = "Neoplasma",
title = "Prognostic potential of circulating miR-93-5p in patients with colorectal cancer liver metastases",
pages = "442-430",
number = "2",
volume = "69",
doi = "10.4149/neo_2021_210603N749"
}

Despotović, J., Bogdanović, A., Dragičević, S., Galun, D., Krivokapić, Z.,& Nikolić, A.. (2022). Prognostic potential of circulating miR-93-5p in patients with colorectal cancer liver metastases. in Neoplasma
Aepress Sro, Bratislava., 69(2), 430-442.
https://doi.org/10.4149/neo_2021_210603N749

Despotović J, Bogdanović A, Dragičević S, Galun D, Krivokapić Z, Nikolić A. Prognostic potential of circulating miR-93-5p in patients with colorectal cancer liver metastases. in Neoplasma. 2022;69(2):430-442.
doi:10.4149/neo_2021_210603N749 .

Despotović, Jovana, Bogdanović, Aleksandar, Dragičević, Sandra, Galun, Danijel, Krivokapić, Zoran, Nikolić, Aleksandra, "Prognostic potential of circulating miR-93-5p in patients with colorectal cancer liver metastases" in Neoplasma, 69, no. 2 (2022):430-442,
https://doi.org/10.4149/neo_2021_210603N749 . .

TY  - JOUR
AU  - Babić, Tamara
AU  - Dragičević, Sandra
AU  - Miladinov, Marko
AU  - Krivokapić, Zoran
AU  - Nikolić, Aleksandra
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1532
AB  - Background: Transcripts with alternative 5'-untranslated regions (UTRs) result from the activity of alternative promoters and they can determine gene expression by influencing its stability and translational efficiency, thus executing complex regulation of developmental, physiological and pathological processes. Transcriptional regulation of human SMAD4, a key tumor suppressor deregulated in most gastrointestinal cancers, entails four alternative promoters. These promoters and alternative transcripts they generate remain unexplored as contributors to the SMAD4 deregulation in cancer. The aim of this study was to investigate the relative abundance of the transcript SMAD4-201 in colorectal cell lines and tissues in order to establish if its fluctuations may be associated with colorectal cancer (CRC). Methods: Relative abundance of SMAD4-201 in total SMAD4 mRNA was analyzed using quantitative PCR in a set of permanent human colon cell lines and tumor and corresponding healthy tissue samples from patients with CRC. Results: The relative abundance of SMAD4-201 in analyzed cell lines varied between 16 and 47%. A similar relative abundance of SMAD4-201 transcript was found in the majority of analyzed human tumor tissue samples, and it was averagely 20% lower in non-malignant in comparison to malignant tissue samples (p = 0.001). Transcript SMAD4-202 was not detectable in any of the analyzed samples, so the observed fluctuations in the composition of SMAD4 transcripts can be attributed to transcripts other than SMAD4-201 and SMAD4-202. Conclusion: The expression profile of SMAD4-201 in human tumor and non-tumor tissue samples may indicate the translational potential of this molecule in CRC, but further research is needed to clarify its usability as a potential biomarker for early diagnosis.
PB  - BMC, London
T2  - Bmc Cancer
T1  - SMAD4-201 transcript as a putative biomarker in colorectal cancer
IS  - 1
VL  - 22
DO  - 10.1186/s12885-022-09186-z
ER  - 

@article{
author = "Babić, Tamara and Dragičević, Sandra and Miladinov, Marko and Krivokapić, Zoran and Nikolić, Aleksandra",
year = "2022",
abstract = "Background: Transcripts with alternative 5'-untranslated regions (UTRs) result from the activity of alternative promoters and they can determine gene expression by influencing its stability and translational efficiency, thus executing complex regulation of developmental, physiological and pathological processes. Transcriptional regulation of human SMAD4, a key tumor suppressor deregulated in most gastrointestinal cancers, entails four alternative promoters. These promoters and alternative transcripts they generate remain unexplored as contributors to the SMAD4 deregulation in cancer. The aim of this study was to investigate the relative abundance of the transcript SMAD4-201 in colorectal cell lines and tissues in order to establish if its fluctuations may be associated with colorectal cancer (CRC). Methods: Relative abundance of SMAD4-201 in total SMAD4 mRNA was analyzed using quantitative PCR in a set of permanent human colon cell lines and tumor and corresponding healthy tissue samples from patients with CRC. Results: The relative abundance of SMAD4-201 in analyzed cell lines varied between 16 and 47%. A similar relative abundance of SMAD4-201 transcript was found in the majority of analyzed human tumor tissue samples, and it was averagely 20% lower in non-malignant in comparison to malignant tissue samples (p = 0.001). Transcript SMAD4-202 was not detectable in any of the analyzed samples, so the observed fluctuations in the composition of SMAD4 transcripts can be attributed to transcripts other than SMAD4-201 and SMAD4-202. Conclusion: The expression profile of SMAD4-201 in human tumor and non-tumor tissue samples may indicate the translational potential of this molecule in CRC, but further research is needed to clarify its usability as a potential biomarker for early diagnosis.",
publisher = "BMC, London",
journal = "Bmc Cancer",
title = "SMAD4-201 transcript as a putative biomarker in colorectal cancer",
number = "1",
volume = "22",
doi = "10.1186/s12885-022-09186-z"
}

Babić, T., Dragičević, S., Miladinov, M., Krivokapić, Z.,& Nikolić, A.. (2022). SMAD4-201 transcript as a putative biomarker in colorectal cancer. in Bmc Cancer
BMC, London., 22(1).
https://doi.org/10.1186/s12885-022-09186-z

Babić T, Dragičević S, Miladinov M, Krivokapić Z, Nikolić A. SMAD4-201 transcript as a putative biomarker in colorectal cancer. in Bmc Cancer. 2022;22(1).
doi:10.1186/s12885-022-09186-z .

Babić, Tamara, Dragičević, Sandra, Miladinov, Marko, Krivokapić, Zoran, Nikolić, Aleksandra, "SMAD4-201 transcript as a putative biomarker in colorectal cancer" in Bmc Cancer, 22, no. 1 (2022),
https://doi.org/10.1186/s12885-022-09186-z . .

TY  - JOUR
AU  - Andjelic, Jelic M.
AU  - Radojković, Dragica
AU  - Nikolić, Aleksandra
AU  - Rakićević, Ljiljana
AU  - Babić, Tamara
AU  - Jelic, D.
AU  - Lalic, N. M.
PY  - 2022
UR  - https://sciendo.com/article/10.2478/bjmg-2022-0001
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1787
AB  - AbstractVascular complications are the leading cause of increased morbidity and mortality of diabetic patients. It has been postulated that matrix metalloproteinases MMP-2 and MMP-9, zinc-dependent endopeptidases through remodeling of the extracellular matrix, can contribute to the onset and progression of diabetic vascular complications. The aim of our study was to assess whether there is a major difference in single nucleotide polymorphisms in the MMP-2 (at position -1306C˃T) and MMP-9 (at position -1562C˃T) gene in type 2 diabetic patients and healthy controls and to determine whether there is an association of these gene variants with the presence of microvascular complications in diabetic patients. Our study included 102 type 2 diabetes patients and a control group which was comprised of 56 healthy controls. All diabetic patients were screened for microvascular diabetes complications. Genotypes were detected by polymerase chain reactions followed by restriction analyses with specific endonucleases and their frequencies were determined. The MMP-2 variant -1306C>T showed a negative correlation with type 2 diabetes (p=0.028). It was also shown that the presence of the -1306C allele increases the probability of developing type 2 diabetes. This was a 2.2 fold increase and that the -1306 T allele has a protective role in regards to
PB  - Sciendo
T2  - Balkan Journal of Medical Genetics
T2  - Balkan Journal of Medical Genetics
T1  - Matrix metalloproteinase-2 (MMP-2) and-9 (MMP-9) gene variants and microvascular complications in type 2 diabetes patients
EP  - 40
IS  - 1
SP  - 35
VL  - 25
DO  - 10.2478/bjmg-2022-0001
ER  - 

@article{
author = "Andjelic, Jelic M. and Radojković, Dragica and Nikolić, Aleksandra and Rakićević, Ljiljana and Babić, Tamara and Jelic, D. and Lalic, N. M.",
year = "2022",
abstract = "AbstractVascular complications are the leading cause of increased morbidity and mortality of diabetic patients. It has been postulated that matrix metalloproteinases MMP-2 and MMP-9, zinc-dependent endopeptidases through remodeling of the extracellular matrix, can contribute to the onset and progression of diabetic vascular complications. The aim of our study was to assess whether there is a major difference in single nucleotide polymorphisms in the MMP-2 (at position -1306C˃T) and MMP-9 (at position -1562C˃T) gene in type 2 diabetic patients and healthy controls and to determine whether there is an association of these gene variants with the presence of microvascular complications in diabetic patients. Our study included 102 type 2 diabetes patients and a control group which was comprised of 56 healthy controls. All diabetic patients were screened for microvascular diabetes complications. Genotypes were detected by polymerase chain reactions followed by restriction analyses with specific endonucleases and their frequencies were determined. The MMP-2 variant -1306C>T showed a negative correlation with type 2 diabetes (p=0.028). It was also shown that the presence of the -1306C allele increases the probability of developing type 2 diabetes. This was a 2.2 fold increase and that the -1306 T allele has a protective role in regards to",
publisher = "Sciendo",
journal = "Balkan Journal of Medical Genetics, Balkan Journal of Medical Genetics",
title = "Matrix metalloproteinase-2 (MMP-2) and-9 (MMP-9) gene variants and microvascular complications in type 2 diabetes patients",
pages = "40-35",
number = "1",
volume = "25",
doi = "10.2478/bjmg-2022-0001"
}

Andjelic, J. M., Radojković, D., Nikolić, A., Rakićević, L., Babić, T., Jelic, D.,& Lalic, N. M.. (2022). Matrix metalloproteinase-2 (MMP-2) and-9 (MMP-9) gene variants and microvascular complications in type 2 diabetes patients. in Balkan Journal of Medical Genetics
Sciendo., 25(1), 35-40.
https://doi.org/10.2478/bjmg-2022-0001

Andjelic JM, Radojković D, Nikolić A, Rakićević L, Babić T, Jelic D, Lalic NM. Matrix metalloproteinase-2 (MMP-2) and-9 (MMP-9) gene variants and microvascular complications in type 2 diabetes patients. in Balkan Journal of Medical Genetics. 2022;25(1):35-40.
doi:10.2478/bjmg-2022-0001 .

Andjelic, Jelic M., Radojković, Dragica, Nikolić, Aleksandra, Rakićević, Ljiljana, Babić, Tamara, Jelic, D., Lalic, N. M., "Matrix metalloproteinase-2 (MMP-2) and-9 (MMP-9) gene variants and microvascular complications in type 2 diabetes patients" in Balkan Journal of Medical Genetics, 25, no. 1 (2022):35-40,
https://doi.org/10.2478/bjmg-2022-0001 . .

TY  - JOUR
AU  - Nikolić, Aleksandra
AU  - Despotović, Jovana
AU  - Babić, Tamara
AU  - Antić, Jadranka
AU  - Marković, Srdjan
AU  - Krivokapić, Zoran
AU  - Radojković, Dragica
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1595
AB  - In colorectal cancer (CRC), inactivation of SMAD4 occurs early in the disease development and SMAD4 represents one of key driver genes in progression and metastasis. Loss of SMAD4 protein expression is a relatively common feature of sporadic colorectal cancers, and it was observed to be even more frequent in tumors of patients with early onset disease and also more frequent in microsatellite stable tumors. Pathogenic variants in the SMAD4 gene are usually missense or nonsense mutations, and they are more frequent in the C-terminal domain. The aim of this study was to perform genetic analysis of SMAD4 C-terminal domain in colorectal cancer patients with early onset disease and microsatellite stable tumors. This pilot study was conducted with a purpose of investigating if such genetic screening strategy would be useful for diagnostic purposes in this specific subgroup of CRC patients. The study was conducted in a selected set of DNA samples extracted from the tumors of CRC patients who had less than 50 years at the time of diagnosis. Genetic analysis of C-terminal domain has encompassed analysis of exons 9, 10, 11 and 12 of the SMAD4 gene by PCR and direct DNA sequencing. Among the twenty analyzed tumor DNAs, one sample was found to harbor a SMAD4 variant: NC_000018.9:g.48591918C  gt  T; (NM005359.5: c.1081C  gt  T; Arg361Cys). The variant was discovered in exon 9, affecting the codon 361, which represents a mutational hot spot within the SMAD4 gene. This variant was discovered in homozygous state in the tumor of a 47 yr old female with T3 stage carcinoma of the right colon. Considering the incidence and functional consequences of SMAD4 exon 9 variants, the screening of this region could be a useful low cost strategy for the genetic analysis of colorectal tumors from patients with early onset disease, as well as for susceptibility testing.
PB  - Pleiades Publishing Inc, New York
T2  - Cytology and Genetics
T1  - SMAD4 Gene Analysis in Patients with Early Onset Colorectal Cancer: A Pilot Study
EP  - 276
IS  - 3
SP  - 273
VL  - 56
DO  - 10.3103/S0095452722030082
ER  - 

@article{
author = "Nikolić, Aleksandra and Despotović, Jovana and Babić, Tamara and Antić, Jadranka and Marković, Srdjan and Krivokapić, Zoran and Radojković, Dragica",
year = "2022",
abstract = "In colorectal cancer (CRC), inactivation of SMAD4 occurs early in the disease development and SMAD4 represents one of key driver genes in progression and metastasis. Loss of SMAD4 protein expression is a relatively common feature of sporadic colorectal cancers, and it was observed to be even more frequent in tumors of patients with early onset disease and also more frequent in microsatellite stable tumors. Pathogenic variants in the SMAD4 gene are usually missense or nonsense mutations, and they are more frequent in the C-terminal domain. The aim of this study was to perform genetic analysis of SMAD4 C-terminal domain in colorectal cancer patients with early onset disease and microsatellite stable tumors. This pilot study was conducted with a purpose of investigating if such genetic screening strategy would be useful for diagnostic purposes in this specific subgroup of CRC patients. The study was conducted in a selected set of DNA samples extracted from the tumors of CRC patients who had less than 50 years at the time of diagnosis. Genetic analysis of C-terminal domain has encompassed analysis of exons 9, 10, 11 and 12 of the SMAD4 gene by PCR and direct DNA sequencing. Among the twenty analyzed tumor DNAs, one sample was found to harbor a SMAD4 variant: NC_000018.9:g.48591918C  gt  T; (NM005359.5: c.1081C  gt  T; Arg361Cys). The variant was discovered in exon 9, affecting the codon 361, which represents a mutational hot spot within the SMAD4 gene. This variant was discovered in homozygous state in the tumor of a 47 yr old female with T3 stage carcinoma of the right colon. Considering the incidence and functional consequences of SMAD4 exon 9 variants, the screening of this region could be a useful low cost strategy for the genetic analysis of colorectal tumors from patients with early onset disease, as well as for susceptibility testing.",
publisher = "Pleiades Publishing Inc, New York",
journal = "Cytology and Genetics",
title = "SMAD4 Gene Analysis in Patients with Early Onset Colorectal Cancer: A Pilot Study",
pages = "276-273",
number = "3",
volume = "56",
doi = "10.3103/S0095452722030082"
}

Nikolić, A., Despotović, J., Babić, T., Antić, J., Marković, S., Krivokapić, Z.,& Radojković, D.. (2022). SMAD4 Gene Analysis in Patients with Early Onset Colorectal Cancer: A Pilot Study. in Cytology and Genetics
Pleiades Publishing Inc, New York., 56(3), 273-276.
https://doi.org/10.3103/S0095452722030082

Nikolić A, Despotović J, Babić T, Antić J, Marković S, Krivokapić Z, Radojković D. SMAD4 Gene Analysis in Patients with Early Onset Colorectal Cancer: A Pilot Study. in Cytology and Genetics. 2022;56(3):273-276.
doi:10.3103/S0095452722030082 .

Nikolić, Aleksandra, Despotović, Jovana, Babić, Tamara, Antić, Jadranka, Marković, Srdjan, Krivokapić, Zoran, Radojković, Dragica, "SMAD4 Gene Analysis in Patients with Early Onset Colorectal Cancer: A Pilot Study" in Cytology and Genetics, 56, no. 3 (2022):273-276,
https://doi.org/10.3103/S0095452722030082 . .

TY  - JOUR
AU  - Nikolić, Aleksandra
AU  - Krivokapić, Zoran
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1562
AB  - The progress that has been made in the treatment of rectal cancer has mostly resulted from multimodality strategy approach that combines surgery, chemotherapy and radiotherapy. In locally advanced rectal cancer (LARC), surgery remains the primary treatment, while neoadjuvant chemoradiotherapy (nCRT) is used to downsize or downstage the tumor before surgical resection. Highly variable response to nCRT observed in LARC patients raises the need for biomarkers to enable prediction and evaluation of treatment response in a more efficient and timely manner than currently available tools. The search for predictive biomarkers continues beyond blood proteins, which have failed in subsequent validation studies. This review presents nucleic acids based markers and their predictive potential in LARC patients. Most of the candidate biomarkers come from relatively small single-institution studies. The only candidate biomarker that emerged as relevant in more than a single study was elevated levels of Fusobacterium nucleatum nucleic acids in tumor tissue. Considering that this marker is easily accessible through non-invasive analysis of faecal samples, its predictive potential is worth further validation. The other candidate nucleic acid-based biomarkers require more consistent studies on larger cohorts before they can be considered for use in clinical setting.
PB  - Elsevier Sci Ltd, Oxford
T2  - Surgical Oncology-Oxford
T1  - Nucleic acid-based markers of response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer
VL  - 41
DO  - 10.1016/j.suronc.2022.101743
ER  - 

@article{
author = "Nikolić, Aleksandra and Krivokapić, Zoran",
year = "2022",
abstract = "The progress that has been made in the treatment of rectal cancer has mostly resulted from multimodality strategy approach that combines surgery, chemotherapy and radiotherapy. In locally advanced rectal cancer (LARC), surgery remains the primary treatment, while neoadjuvant chemoradiotherapy (nCRT) is used to downsize or downstage the tumor before surgical resection. Highly variable response to nCRT observed in LARC patients raises the need for biomarkers to enable prediction and evaluation of treatment response in a more efficient and timely manner than currently available tools. The search for predictive biomarkers continues beyond blood proteins, which have failed in subsequent validation studies. This review presents nucleic acids based markers and their predictive potential in LARC patients. Most of the candidate biomarkers come from relatively small single-institution studies. The only candidate biomarker that emerged as relevant in more than a single study was elevated levels of Fusobacterium nucleatum nucleic acids in tumor tissue. Considering that this marker is easily accessible through non-invasive analysis of faecal samples, its predictive potential is worth further validation. The other candidate nucleic acid-based biomarkers require more consistent studies on larger cohorts before they can be considered for use in clinical setting.",
publisher = "Elsevier Sci Ltd, Oxford",
journal = "Surgical Oncology-Oxford",
title = "Nucleic acid-based markers of response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer",
volume = "41",
doi = "10.1016/j.suronc.2022.101743"
}

Nikolić, A.,& Krivokapić, Z.. (2022). Nucleic acid-based markers of response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer. in Surgical Oncology-Oxford
Elsevier Sci Ltd, Oxford., 41.
https://doi.org/10.1016/j.suronc.2022.101743

Nikolić A, Krivokapić Z. Nucleic acid-based markers of response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer. in Surgical Oncology-Oxford. 2022;41.
doi:10.1016/j.suronc.2022.101743 .

Nikolić, Aleksandra, Krivokapić, Zoran, "Nucleic acid-based markers of response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer" in Surgical Oncology-Oxford, 41 (2022),
https://doi.org/10.1016/j.suronc.2022.101743 . .

TY  - CONF
AU  - Babić, Tamara
AU  - Dragičević, Sandra
AU  - Miladinov, Marko
AU  - Krivokapić, Zoran
AU  - Nikolić, Aleksandra
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1563
PB  - Springernature, London
C3  - European Journal of Human Genetics
T1  - SMAD4 gene coding transcripts with alternative 5 ' ends as colorectal cancer biomarkers
EP  - 556
IS  - SUPPL 1
SP  - 556
VL  - 30
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1563
ER  - 

@conference{
author = "Babić, Tamara and Dragičević, Sandra and Miladinov, Marko and Krivokapić, Zoran and Nikolić, Aleksandra",
year = "2022",
publisher = "Springernature, London",
journal = "European Journal of Human Genetics",
title = "SMAD4 gene coding transcripts with alternative 5 ' ends as colorectal cancer biomarkers",
pages = "556-556",
number = "SUPPL 1",
volume = "30",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1563"
}

Babić, T., Dragičević, S., Miladinov, M., Krivokapić, Z.,& Nikolić, A.. (2022). SMAD4 gene coding transcripts with alternative 5 ' ends as colorectal cancer biomarkers. in European Journal of Human Genetics
Springernature, London., 30(SUPPL 1), 556-556.
https://hdl.handle.net/21.15107/rcub_imagine_1563

Babić T, Dragičević S, Miladinov M, Krivokapić Z, Nikolić A. SMAD4 gene coding transcripts with alternative 5 ' ends as colorectal cancer biomarkers. in European Journal of Human Genetics. 2022;30(SUPPL 1):556-556.
https://hdl.handle.net/21.15107/rcub_imagine_1563 .

Babić, Tamara, Dragičević, Sandra, Miladinov, Marko, Krivokapić, Zoran, Nikolić, Aleksandra, "SMAD4 gene coding transcripts with alternative 5 ' ends as colorectal cancer biomarkers" in European Journal of Human Genetics, 30, no. SUPPL 1 (2022):556-556,
https://hdl.handle.net/21.15107/rcub_imagine_1563 .

TY  - JOUR
AU  - Babić, Tamara
AU  - Lygirou, Vasiliki
AU  - Rosić, Jovana
AU  - Miladinov, Marko
AU  - Rom, Aleksandra Djikic
AU  - Baira, Eirini
AU  - Stroggilos, Rafael
AU  - Pappa, Eftychia
AU  - Zoidakis, Jerome
AU  - Krivokapić, Zoran
AU  - Nikolić, Aleksandra
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1521
AB  - Purpose In the search for candidate predictive biomarkers to evaluate response to neoadjuvant chemoradiotherapy (nCRT) in rectal cancer, only a few studies report proteomic profiles of tumor tissue before and after nCRT. The aim of our study was to determine differentially expressed proteins between responders and non-responders before and after the therapy in order to identify candidate molecules for prediction and follow-up of response to nCRT. Experimental Design The study has included tissue sections of rectal tumor and non-tumor mucosa from five responders and five non-responders taken before and after nCRT from patients with locally advanced rectal cancer. Extracted proteins were analyzed by LC-MS/MS analysis followed by a set of bioinformatics analyses. Result Proteomics analysis provided a mean of approximately 1050 protein identifications per sample. A comparison of proteomic profiles between responders and non-responders has identified 18 differentially expressed proteins. Pathway analysis demonstrated high metabolic activity in non-responders' tumors before nCRT, indicating the presence of intrinsic chemoradioresistance in these subjects. Two proteins associated with poor prognosis in colorectal cancer, ADAM10 and CAD, were identified as candidate predictive biomarkers as they were present in non-responders only. Conclusions and Clinical Relevance Shortlisted proteins from our study should be further validated as candidate biomarkers for response to routinely applied nCRT protocols.
PB  - Wiley-V C H Verlag Gmbh, Weinheim
T2  - Proteomics Clinical Applications
T1  - Pilot proteomic study of locally advanced rectal cancer before and after neoadjuvant chemoradiotherapy indicates high metabolic activity in non-responders' tumor tissue
DO  - 10.1002/prca.202100116
ER  - 

@article{
author = "Babić, Tamara and Lygirou, Vasiliki and Rosić, Jovana and Miladinov, Marko and Rom, Aleksandra Djikic and Baira, Eirini and Stroggilos, Rafael and Pappa, Eftychia and Zoidakis, Jerome and Krivokapić, Zoran and Nikolić, Aleksandra",
year = "2022",
abstract = "Purpose In the search for candidate predictive biomarkers to evaluate response to neoadjuvant chemoradiotherapy (nCRT) in rectal cancer, only a few studies report proteomic profiles of tumor tissue before and after nCRT. The aim of our study was to determine differentially expressed proteins between responders and non-responders before and after the therapy in order to identify candidate molecules for prediction and follow-up of response to nCRT. Experimental Design The study has included tissue sections of rectal tumor and non-tumor mucosa from five responders and five non-responders taken before and after nCRT from patients with locally advanced rectal cancer. Extracted proteins were analyzed by LC-MS/MS analysis followed by a set of bioinformatics analyses. Result Proteomics analysis provided a mean of approximately 1050 protein identifications per sample. A comparison of proteomic profiles between responders and non-responders has identified 18 differentially expressed proteins. Pathway analysis demonstrated high metabolic activity in non-responders' tumors before nCRT, indicating the presence of intrinsic chemoradioresistance in these subjects. Two proteins associated with poor prognosis in colorectal cancer, ADAM10 and CAD, were identified as candidate predictive biomarkers as they were present in non-responders only. Conclusions and Clinical Relevance Shortlisted proteins from our study should be further validated as candidate biomarkers for response to routinely applied nCRT protocols.",
publisher = "Wiley-V C H Verlag Gmbh, Weinheim",
journal = "Proteomics Clinical Applications",
title = "Pilot proteomic study of locally advanced rectal cancer before and after neoadjuvant chemoradiotherapy indicates high metabolic activity in non-responders' tumor tissue",
doi = "10.1002/prca.202100116"
}

Babić, T., Lygirou, V., Rosić, J., Miladinov, M., Rom, A. D., Baira, E., Stroggilos, R., Pappa, E., Zoidakis, J., Krivokapić, Z.,& Nikolić, A.. (2022). Pilot proteomic study of locally advanced rectal cancer before and after neoadjuvant chemoradiotherapy indicates high metabolic activity in non-responders' tumor tissue. in Proteomics Clinical Applications
Wiley-V C H Verlag Gmbh, Weinheim..
https://doi.org/10.1002/prca.202100116

Babić T, Lygirou V, Rosić J, Miladinov M, Rom AD, Baira E, Stroggilos R, Pappa E, Zoidakis J, Krivokapić Z, Nikolić A. Pilot proteomic study of locally advanced rectal cancer before and after neoadjuvant chemoradiotherapy indicates high metabolic activity in non-responders' tumor tissue. in Proteomics Clinical Applications. 2022;.
doi:10.1002/prca.202100116 .

Babić, Tamara, Lygirou, Vasiliki, Rosić, Jovana, Miladinov, Marko, Rom, Aleksandra Djikic, Baira, Eirini, Stroggilos, Rafael, Pappa, Eftychia, Zoidakis, Jerome, Krivokapić, Zoran, Nikolić, Aleksandra, "Pilot proteomic study of locally advanced rectal cancer before and after neoadjuvant chemoradiotherapy indicates high metabolic activity in non-responders' tumor tissue" in Proteomics Clinical Applications (2022),
https://doi.org/10.1002/prca.202100116 . .

TY  - JOUR
AU  - Ugrin, Milena
AU  - Dinić, Jelena
AU  - Jeremić, Sanja
AU  - Dragičević, Sandra
AU  - Banović Đeri, Bojana
AU  - Nikolić, Aleksandra
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1478
AB  - Bacterial nanocellulose (BNC) stands out among polymers as a promising biomaterial due to its mechanical strength, hydrophilicity, biocompatibility, biodegradability, low toxicity and renewability. The use of scaffolds based on BNC for 3D cell culture has been previously demonstrated. The study exploited excellent properties of the BNC to develop an efficient and low-cost in vitro cell migration assay. The BNC scaffold was introduced into a cell culture 24 h after the SW480 cells were seeded, and cells were allowed to enter the scaffold within the next 24-48 h. The cells were stained with different fluorophores either before or after the introduction of the scaffold in the culture. Untreated cells were observed to enter the BNC scaffold in significant numbers, form clusters and retain a high viability after 48 h. To validate the assay's usability for drug development, the treatments of SW480 cells were performed using aspirin, an agent known to reduce the migratory potential of this cell line in culture. This study demonstrates the application of BNC as a scaffold for cell migration testing as a low-cost alternative to commercial assays based on the Boyden chamber principle. The assay could be further developed for routine use in cancer research and anticancer drug development.
PB  - MDPI, Basel
T2  - Nanomaterials
T1  - Bacterial Nanocellulose as a Scaffold for In Vitro Cell Migration Assay
IS  - 9
VL  - 11
DO  - 10.3390/nano11092322
ER  - 

@article{
author = "Ugrin, Milena and Dinić, Jelena and Jeremić, Sanja and Dragičević, Sandra and Banović Đeri, Bojana and Nikolić, Aleksandra",
year = "2021",
abstract = "Bacterial nanocellulose (BNC) stands out among polymers as a promising biomaterial due to its mechanical strength, hydrophilicity, biocompatibility, biodegradability, low toxicity and renewability. The use of scaffolds based on BNC for 3D cell culture has been previously demonstrated. The study exploited excellent properties of the BNC to develop an efficient and low-cost in vitro cell migration assay. The BNC scaffold was introduced into a cell culture 24 h after the SW480 cells were seeded, and cells were allowed to enter the scaffold within the next 24-48 h. The cells were stained with different fluorophores either before or after the introduction of the scaffold in the culture. Untreated cells were observed to enter the BNC scaffold in significant numbers, form clusters and retain a high viability after 48 h. To validate the assay's usability for drug development, the treatments of SW480 cells were performed using aspirin, an agent known to reduce the migratory potential of this cell line in culture. This study demonstrates the application of BNC as a scaffold for cell migration testing as a low-cost alternative to commercial assays based on the Boyden chamber principle. The assay could be further developed for routine use in cancer research and anticancer drug development.",
publisher = "MDPI, Basel",
journal = "Nanomaterials",
title = "Bacterial Nanocellulose as a Scaffold for In Vitro Cell Migration Assay",
number = "9",
volume = "11",
doi = "10.3390/nano11092322"
}

Ugrin, M., Dinić, J., Jeremić, S., Dragičević, S., Banović Đeri, B.,& Nikolić, A.. (2021). Bacterial Nanocellulose as a Scaffold for In Vitro Cell Migration Assay. in Nanomaterials
MDPI, Basel., 11(9).
https://doi.org/10.3390/nano11092322

Ugrin M, Dinić J, Jeremić S, Dragičević S, Banović Đeri B, Nikolić A. Bacterial Nanocellulose as a Scaffold for In Vitro Cell Migration Assay. in Nanomaterials. 2021;11(9).
doi:10.3390/nano11092322 .

Ugrin, Milena, Dinić, Jelena, Jeremić, Sanja, Dragičević, Sandra, Banović Đeri, Bojana, Nikolić, Aleksandra, "Bacterial Nanocellulose as a Scaffold for In Vitro Cell Migration Assay" in Nanomaterials, 11, no. 9 (2021),
https://doi.org/10.3390/nano11092322 . .

TY  - JOUR
AU  - Bogdanović, Aleksandar
AU  - Despotović, Jovana
AU  - Galun, Danijel
AU  - Bidzić, Nemanja
AU  - Nikolić, Aleksandra
AU  - Rosić, Jovana
AU  - Krivokapić, Zoran
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1490
AB  - Purpose: There are limited data on expression of epithelial-mesenchymal transition (EMT) markers in patients with colorectal liver metastases (CRLM). The study aim was to evaluate the expression and prognostic significance of E-cadherin (CDH1), fibronectin (FN1) and vimentin (VIM) in patients with CRLM after curative-intent liver resection. Patients and Methods: Thirty patients with CRLM managed by curative-intent liver resection were included in this prospective pilot study. Blood samples, colorectal liver metastases and surrounding non-tumor liver tissue were collected. Expression of CDH1, FN1 and VIM was analyzed by quantitative real-time polymerase chain reaction. Expression in CRLM and non-tumor liver tissue was compared, while expression in serum was correlated with CRLM expression. One-year recurrence-free survival was compared between patients with low and high CDH1, FN1 and VIM expression. Results: The expression of CDH1 was similar in CRLM and non-tumor liver tissues, while FN1 and VIM expression was significantly lower in metastatic tissue (P=0.003 and pP lt  0.001, respectively). Serum expression of CDH1 and VIM was detected in 66.7% and 93.3% of patients, respectively, while FN1 was not detected in any of the patients. The correlation of CDH1 and VIM expression between CRLM and serum was not statistically significant. Decreased CDH1 expression in CRLM and decreased VIM expression in serum were associated with early recurrence after surgical treatment of CRLM. Conclusion: Lower expression of CDH1 in CRLM and lower serum expression of VIM were found to be associated with early recurrence after liver resection for CRLM.
PB  - Dove Medical Press Ltd, Albany
T2  - Cancer Management and Research
T1  - Prognostic Significance of CDH1, FN1 and VIM for Early Recurrence in Patients with Colorectal Liver Metastasis After Liver Resection
EP  - 171
SP  - 163
VL  - 13
DO  - 10.2147/CMAR.S287974
ER  - 

@article{
author = "Bogdanović, Aleksandar and Despotović, Jovana and Galun, Danijel and Bidzić, Nemanja and Nikolić, Aleksandra and Rosić, Jovana and Krivokapić, Zoran",
year = "2021",
abstract = "Purpose: There are limited data on expression of epithelial-mesenchymal transition (EMT) markers in patients with colorectal liver metastases (CRLM). The study aim was to evaluate the expression and prognostic significance of E-cadherin (CDH1), fibronectin (FN1) and vimentin (VIM) in patients with CRLM after curative-intent liver resection. Patients and Methods: Thirty patients with CRLM managed by curative-intent liver resection were included in this prospective pilot study. Blood samples, colorectal liver metastases and surrounding non-tumor liver tissue were collected. Expression of CDH1, FN1 and VIM was analyzed by quantitative real-time polymerase chain reaction. Expression in CRLM and non-tumor liver tissue was compared, while expression in serum was correlated with CRLM expression. One-year recurrence-free survival was compared between patients with low and high CDH1, FN1 and VIM expression. Results: The expression of CDH1 was similar in CRLM and non-tumor liver tissues, while FN1 and VIM expression was significantly lower in metastatic tissue (P=0.003 and pP lt  0.001, respectively). Serum expression of CDH1 and VIM was detected in 66.7% and 93.3% of patients, respectively, while FN1 was not detected in any of the patients. The correlation of CDH1 and VIM expression between CRLM and serum was not statistically significant. Decreased CDH1 expression in CRLM and decreased VIM expression in serum were associated with early recurrence after surgical treatment of CRLM. Conclusion: Lower expression of CDH1 in CRLM and lower serum expression of VIM were found to be associated with early recurrence after liver resection for CRLM.",
publisher = "Dove Medical Press Ltd, Albany",
journal = "Cancer Management and Research",
title = "Prognostic Significance of CDH1, FN1 and VIM for Early Recurrence in Patients with Colorectal Liver Metastasis After Liver Resection",
pages = "171-163",
volume = "13",
doi = "10.2147/CMAR.S287974"
}

Bogdanović, A., Despotović, J., Galun, D., Bidzić, N., Nikolić, A., Rosić, J.,& Krivokapić, Z.. (2021). Prognostic Significance of CDH1, FN1 and VIM for Early Recurrence in Patients with Colorectal Liver Metastasis After Liver Resection. in Cancer Management and Research
Dove Medical Press Ltd, Albany., 13, 163-171.
https://doi.org/10.2147/CMAR.S287974

Bogdanović A, Despotović J, Galun D, Bidzić N, Nikolić A, Rosić J, Krivokapić Z. Prognostic Significance of CDH1, FN1 and VIM for Early Recurrence in Patients with Colorectal Liver Metastasis After Liver Resection. in Cancer Management and Research. 2021;13:163-171.
doi:10.2147/CMAR.S287974 .

Bogdanović, Aleksandar, Despotović, Jovana, Galun, Danijel, Bidzić, Nemanja, Nikolić, Aleksandra, Rosić, Jovana, Krivokapić, Zoran, "Prognostic Significance of CDH1, FN1 and VIM for Early Recurrence in Patients with Colorectal Liver Metastasis After Liver Resection" in Cancer Management and Research, 13 (2021):163-171,
https://doi.org/10.2147/CMAR.S287974 . .

TY  - JOUR
AU  - Prosenc-Zmrzljak, Ursula
AU  - Kosir, Rok
AU  - Krivokapić, Zoran
AU  - Radojković, Dragica
AU  - Nikolić, Aleksandra
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1494
AB  - Liquid biopsy and cell-free DNA (cfDNA) show great promise in cancer diagnostics. In this study, we designed a custom droplet digital PCR (ddPCR) assay for the quantification and quality control of cfDNA isolated from serum. The assay was validated on a group of locally advanced colorectal cancer (CRC) patients and two control groups-patients with hemorrhoids and healthy individuals. The assay shows a high correlation with Qubit measurement (r = 0.976) but offers a higher dynamic range. Mean concentrations of cfDNA were 12.36 ng/mu L, 5.17 ng/mu L, and 0.29 ng/mu L for CRC, hemorrhoid patients, and healthy controls, respectively. The quality of cfDNA was assessed with the measurement of B-cell DNA contamination. On a subset of CRC patients, we compared the mutation status on KRAS (G12A, G12D, G12V, G13D) and BRAF (V600E) genes in the primary tumor and cfDNA isolated from the serum. A total of 70.6% of primary tumor samples were mutated, and the mean fractional abundance of mutations was 9.50%. The matching serum samples were mutated in 38% cases with an average fractional abundance of 0.23%. We conclude that any decisions based solely on the amount of cfDNA present in patient serum must be interpreted carefully and in the context of co-morbidities. This study explores the potential of ddPCR somatic mutations detection from liquid biopsy as a supplement to tissue biopsy in targeted personalized CRC patient management.
PB  - MDPI, Basel
T2  - Genes
T1  - Detection of Somatic Mutations with ddPCR from Liquid Biopsy of Colorectal Cancer Patients
IS  - 2
VL  - 12
DO  - 10.3390/genes12020289
ER  - 

@article{
author = "Prosenc-Zmrzljak, Ursula and Kosir, Rok and Krivokapić, Zoran and Radojković, Dragica and Nikolić, Aleksandra",
year = "2021",
abstract = "Liquid biopsy and cell-free DNA (cfDNA) show great promise in cancer diagnostics. In this study, we designed a custom droplet digital PCR (ddPCR) assay for the quantification and quality control of cfDNA isolated from serum. The assay was validated on a group of locally advanced colorectal cancer (CRC) patients and two control groups-patients with hemorrhoids and healthy individuals. The assay shows a high correlation with Qubit measurement (r = 0.976) but offers a higher dynamic range. Mean concentrations of cfDNA were 12.36 ng/mu L, 5.17 ng/mu L, and 0.29 ng/mu L for CRC, hemorrhoid patients, and healthy controls, respectively. The quality of cfDNA was assessed with the measurement of B-cell DNA contamination. On a subset of CRC patients, we compared the mutation status on KRAS (G12A, G12D, G12V, G13D) and BRAF (V600E) genes in the primary tumor and cfDNA isolated from the serum. A total of 70.6% of primary tumor samples were mutated, and the mean fractional abundance of mutations was 9.50%. The matching serum samples were mutated in 38% cases with an average fractional abundance of 0.23%. We conclude that any decisions based solely on the amount of cfDNA present in patient serum must be interpreted carefully and in the context of co-morbidities. This study explores the potential of ddPCR somatic mutations detection from liquid biopsy as a supplement to tissue biopsy in targeted personalized CRC patient management.",
publisher = "MDPI, Basel",
journal = "Genes",
title = "Detection of Somatic Mutations with ddPCR from Liquid Biopsy of Colorectal Cancer Patients",
number = "2",
volume = "12",
doi = "10.3390/genes12020289"
}

Prosenc-Zmrzljak, U., Kosir, R., Krivokapić, Z., Radojković, D.,& Nikolić, A.. (2021). Detection of Somatic Mutations with ddPCR from Liquid Biopsy of Colorectal Cancer Patients. in Genes
MDPI, Basel., 12(2).
https://doi.org/10.3390/genes12020289

Prosenc-Zmrzljak U, Kosir R, Krivokapić Z, Radojković D, Nikolić A. Detection of Somatic Mutations with ddPCR from Liquid Biopsy of Colorectal Cancer Patients. in Genes. 2021;12(2).
doi:10.3390/genes12020289 .

Prosenc-Zmrzljak, Ursula, Kosir, Rok, Krivokapić, Zoran, Radojković, Dragica, Nikolić, Aleksandra, "Detection of Somatic Mutations with ddPCR from Liquid Biopsy of Colorectal Cancer Patients" in Genes, 12, no. 2 (2021),
https://doi.org/10.3390/genes12020289 . .