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  - 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  - 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  - 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 .