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  - 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  - 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  - 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, 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  - 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  - 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  - 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 . .