TY  - CONF
AU  - Đorđević, Marija
AU  - Feuerstein-Akgoz, Clarissa
AU  - Arambašić Jovanović, Jelena
AU  - Tolić, Anja
AU  - Rajić, Jovana
AU  - Sarić, Ana
AU  - Grdović, Nevena
AU  - Dinić, Svetlana
AU  - Uskoković, Aleksandra
AU  - Mihailović, Mirjana
AU  - Gerhauser, Clarissa
AU  - Jurkowski, Tomasz
AU  - Vidaković, Melita
PY  - 2023
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/6307
AB  - Introduction: The Aristaless-related homeobox (Arx) gene plays a key role in the development and maintaining pancreatic alpha cell phenotype, and as such represents an excellent target for alpha cell identity change towards insulin-producing cells. Therefore, this cell switch and increase in beta cell mass could be of potential use in diabetes management.
Methods: On the fifth day after transient transfection with dCas9-Dnmt3a3L-KRAB construct and four gRNAs targeting Arx promoter, αTC1-6 were sorted to collect GFP-positive (transfected) cells (EpiC). The mRNA-seq libraries were pooled in equimolar amounts and sequenced in a single end-setting on the Illumina NextSeq 500 High output machine with 75 bases long reads. KEGG pathway overrepresentation analysis was performed using an application on all significantly up- or downregulated genes using default settings.
Results: Directed induction of DNA methylation on the Arx gene promoter reduces its expression and causes the up-regulation of 357 genes, while 266 genes were down-regulated in EpiC compared to Mock transfected cells. The KEGG pathways analysis of biological processes confirmed several biological pathways associated with genes differentially expressed in EpiC vs. Mock transfected cells at the 5th posttransfection day (pval ≤ 0.05). As the most significant, up-regulated pathways we found Type II diabetes, Insulin secretion, Longevity regulation pathways. As significant, down-regulated pathways pop-up Fatty acid metabolism and PPAR signaling pathway.
Conclusion: Reduction of ArxmRNA level is sufficient to initiate the transdifferentiation process of alpha cells into insulin-producing cells by triggering several biological pathways tight related to insulin secretion and function.
PB  - Belgrade: Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
C3  - Abstract Book: CoMBoS2 - the Second Congress of Molecular Biologists of Serbia; 2023 Oct 6-8; Belgrade, Serbia
T1  - Changes in up and down regulated gene expression after transient suppression of Arx gene in pancreatic alphaTC1-6 cell line
SP  - 151
EP  - 151
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_6307
ER  - 

@conference{
author = "Đorđević, Marija and Feuerstein-Akgoz, Clarissa and Arambašić Jovanović, Jelena and Tolić, Anja and Rajić, Jovana and Sarić, Ana and Grdović, Nevena and Dinić, Svetlana and Uskoković, Aleksandra and Mihailović, Mirjana and Gerhauser, Clarissa and Jurkowski, Tomasz and Vidaković, Melita",
year = "2023",
abstract = "Introduction: The Aristaless-related homeobox (Arx) gene plays a key role in the development and maintaining pancreatic alpha cell phenotype, and as such represents an excellent target for alpha cell identity change towards insulin-producing cells. Therefore, this cell switch and increase in beta cell mass could be of potential use in diabetes management.
Methods: On the fifth day after transient transfection with dCas9-Dnmt3a3L-KRAB construct and four gRNAs targeting Arx promoter, αTC1-6 were sorted to collect GFP-positive (transfected) cells (EpiC). The mRNA-seq libraries were pooled in equimolar amounts and sequenced in a single end-setting on the Illumina NextSeq 500 High output machine with 75 bases long reads. KEGG pathway overrepresentation analysis was performed using an application on all significantly up- or downregulated genes using default settings.
Results: Directed induction of DNA methylation on the Arx gene promoter reduces its expression and causes the up-regulation of 357 genes, while 266 genes were down-regulated in EpiC compared to Mock transfected cells. The KEGG pathways analysis of biological processes confirmed several biological pathways associated with genes differentially expressed in EpiC vs. Mock transfected cells at the 5th posttransfection day (pval ≤ 0.05). As the most significant, up-regulated pathways we found Type II diabetes, Insulin secretion, Longevity regulation pathways. As significant, down-regulated pathways pop-up Fatty acid metabolism and PPAR signaling pathway.
Conclusion: Reduction of ArxmRNA level is sufficient to initiate the transdifferentiation process of alpha cells into insulin-producing cells by triggering several biological pathways tight related to insulin secretion and function.",
publisher = "Belgrade: Institute of Molecular Genetics and Genetic Engineering, University of Belgrade",
journal = "Abstract Book: CoMBoS2 - the Second Congress of Molecular Biologists of Serbia; 2023 Oct 6-8; Belgrade, Serbia",
title = "Changes in up and down regulated gene expression after transient suppression of Arx gene in pancreatic alphaTC1-6 cell line",
pages = "151-151",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_6307"
}

Đorđević, M., Feuerstein-Akgoz, C., Arambašić Jovanović, J., Tolić, A., Rajić, J., Sarić, A., Grdović, N., Dinić, S., Uskoković, A., Mihailović, M., Gerhauser, C., Jurkowski, T.,& Vidaković, M.. (2023). Changes in up and down regulated gene expression after transient suppression of Arx gene in pancreatic alphaTC1-6 cell line. in Abstract Book: CoMBoS2 - the Second Congress of Molecular Biologists of Serbia; 2023 Oct 6-8; Belgrade, Serbia
Belgrade: Institute of Molecular Genetics and Genetic Engineering, University of Belgrade., 151-151.
https://hdl.handle.net/21.15107/rcub_ibiss_6307

Đorđević M, Feuerstein-Akgoz C, Arambašić Jovanović J, Tolić A, Rajić J, Sarić A, Grdović N, Dinić S, Uskoković A, Mihailović M, Gerhauser C, Jurkowski T, Vidaković M. Changes in up and down regulated gene expression after transient suppression of Arx gene in pancreatic alphaTC1-6 cell line. in Abstract Book: CoMBoS2 - the Second Congress of Molecular Biologists of Serbia; 2023 Oct 6-8; Belgrade, Serbia. 2023;:151-151.
https://hdl.handle.net/21.15107/rcub_ibiss_6307 .

Đorđević, Marija, Feuerstein-Akgoz, Clarissa, Arambašić Jovanović, Jelena, Tolić, Anja, Rajić, Jovana, Sarić, Ana, Grdović, Nevena, Dinić, Svetlana, Uskoković, Aleksandra, Mihailović, Mirjana, Gerhauser, Clarissa, Jurkowski, Tomasz, Vidaković, Melita, "Changes in up and down regulated gene expression after transient suppression of Arx gene in pancreatic alphaTC1-6 cell line" in Abstract Book: CoMBoS2 - the Second Congress of Molecular Biologists of Serbia; 2023 Oct 6-8; Belgrade, Serbia (2023):151-151,
https://hdl.handle.net/21.15107/rcub_ibiss_6307 .

TY  - CONF
AU  - Sarić, Ana
AU  - Rajić, Jovana
AU  - Tolić, Anja
AU  - Đorđević, Marija
AU  - Grdović, Nevena
AU  - Uskoković, Aleksandra
AU  - Dinić, Svetlana
AU  - Arambašić Jovanović, Jelena
AU  - Mihailović, Mirjana
AU  - Vidaković, Melita
AU  - Dučić, Tanja
PY  - 2023
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/6304
AB  - Introduction: DNA methylation is a major regulator of transcriptional activity and alongside other epigenetic modifications it introduces specific level of chromatin complexity. Fourier transform infrared (FTIR) spectroscopy is a rapid, non-destructive, and label-free technique for identifying subtle changes in all bio-macromolecules, and it has been used as a method of choice for studying DNA conformation. The present study was designed to explore the use of synchrotron-based FTIR spectroscopy to monitor the subtle changes on molecular level regarding the DNA methylation status of cytosine in the whole genome.
Methods: For FTIR-based DNA methylation analysis in situ, DNA-HALO samples were prepared using slightly modified methodology for nuclear HALO preparations where DNA-HALOs are liberated of any protein residues but preserve higher order chromatin structure.
Results: Using FTIR spectroscopy we analysed and compared methylation profiles of isolated genomic DNA and DNA-HALO samples. DNA-HALO structure shows more distinct peaks in fingerprint region of spectra. DNA-HALO structure is more accurate for detecting bonds in unmemthylated cytosine as specific infrared peaks are defined as vibrations of bonds in unmethylated cytosine at 1151 cm-1 and 1357 cm-1. The ratio of integrated area under the peak 1151 cm-1 over integrated area under the peak that represents PO2-backbone vibrations can be used to assess level of unmethylated cytosine and thus methylation rate in the DNA-HALO samples.
Conclusion: This study demonstrates potential of FTIR spectroscopy to detect DNA methylation in DNA-HALO samples more precisely compared to classical DNA extraction procedure that yield unstructured whole genomic DNA.
PB  - Belgrade: Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
C3  - Abstract Book: CoMBoS2 - the Second Congress of Molecular Biologists of Serbia; 2023 Oct 6-8; Belgrade, Serbia
T1  - Methylation profile analysis of Of DNA-HALO structure by synchrotron-based FTIR spectroscopy
SP  - 68
EP  - 68
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_6304
ER  - 

@conference{
author = "Sarić, Ana and Rajić, Jovana and Tolić, Anja and Đorđević, Marija and Grdović, Nevena and Uskoković, Aleksandra and Dinić, Svetlana and Arambašić Jovanović, Jelena and Mihailović, Mirjana and Vidaković, Melita and Dučić, Tanja",
year = "2023",
abstract = "Introduction: DNA methylation is a major regulator of transcriptional activity and alongside other epigenetic modifications it introduces specific level of chromatin complexity. Fourier transform infrared (FTIR) spectroscopy is a rapid, non-destructive, and label-free technique for identifying subtle changes in all bio-macromolecules, and it has been used as a method of choice for studying DNA conformation. The present study was designed to explore the use of synchrotron-based FTIR spectroscopy to monitor the subtle changes on molecular level regarding the DNA methylation status of cytosine in the whole genome.
Methods: For FTIR-based DNA methylation analysis in situ, DNA-HALO samples were prepared using slightly modified methodology for nuclear HALO preparations where DNA-HALOs are liberated of any protein residues but preserve higher order chromatin structure.
Results: Using FTIR spectroscopy we analysed and compared methylation profiles of isolated genomic DNA and DNA-HALO samples. DNA-HALO structure shows more distinct peaks in fingerprint region of spectra. DNA-HALO structure is more accurate for detecting bonds in unmemthylated cytosine as specific infrared peaks are defined as vibrations of bonds in unmethylated cytosine at 1151 cm-1 and 1357 cm-1. The ratio of integrated area under the peak 1151 cm-1 over integrated area under the peak that represents PO2-backbone vibrations can be used to assess level of unmethylated cytosine and thus methylation rate in the DNA-HALO samples.
Conclusion: This study demonstrates potential of FTIR spectroscopy to detect DNA methylation in DNA-HALO samples more precisely compared to classical DNA extraction procedure that yield unstructured whole genomic DNA.",
publisher = "Belgrade: Institute of Molecular Genetics and Genetic Engineering, University of Belgrade",
journal = "Abstract Book: CoMBoS2 - the Second Congress of Molecular Biologists of Serbia; 2023 Oct 6-8; Belgrade, Serbia",
title = "Methylation profile analysis of Of DNA-HALO structure by synchrotron-based FTIR spectroscopy",
pages = "68-68",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_6304"
}

Sarić, A., Rajić, J., Tolić, A., Đorđević, M., Grdović, N., Uskoković, A., Dinić, S., Arambašić Jovanović, J., Mihailović, M., Vidaković, M.,& Dučić, T.. (2023). Methylation profile analysis of Of DNA-HALO structure by synchrotron-based FTIR spectroscopy. in Abstract Book: CoMBoS2 - the Second Congress of Molecular Biologists of Serbia; 2023 Oct 6-8; Belgrade, Serbia
Belgrade: Institute of Molecular Genetics and Genetic Engineering, University of Belgrade., 68-68.
https://hdl.handle.net/21.15107/rcub_ibiss_6304

Sarić A, Rajić J, Tolić A, Đorđević M, Grdović N, Uskoković A, Dinić S, Arambašić Jovanović J, Mihailović M, Vidaković M, Dučić T. Methylation profile analysis of Of DNA-HALO structure by synchrotron-based FTIR spectroscopy. in Abstract Book: CoMBoS2 - the Second Congress of Molecular Biologists of Serbia; 2023 Oct 6-8; Belgrade, Serbia. 2023;:68-68.
https://hdl.handle.net/21.15107/rcub_ibiss_6304 .

Sarić, Ana, Rajić, Jovana, Tolić, Anja, Đorđević, Marija, Grdović, Nevena, Uskoković, Aleksandra, Dinić, Svetlana, Arambašić Jovanović, Jelena, Mihailović, Mirjana, Vidaković, Melita, Dučić, Tanja, "Methylation profile analysis of Of DNA-HALO structure by synchrotron-based FTIR spectroscopy" in Abstract Book: CoMBoS2 - the Second Congress of Molecular Biologists of Serbia; 2023 Oct 6-8; Belgrade, Serbia (2023):68-68,
https://hdl.handle.net/21.15107/rcub_ibiss_6304 .

TY  - JOUR
AU  - Sarić, Ana
AU  - Rajić, Jovana
AU  - Tolić, Anja
AU  - Dučić, Tanja
AU  - Vidaković, Melita
PY  - 2023
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5948
AB  - Fourier transform infrared (FTIR) spectroscopy is a rapid, non-destructive and label-free technique for identifying subtle changes in all bio-macromolecules, and has been used as a method of choice for studying DNA conformation, secondary DNA structure transition and DNA damage. In addition, the specific level of chromatin complexity is introduced via epigenetic modifications forcing the technological upgrade in the analysis of such an intricacy. As the most studied epigenetic mechanism, DNA methylation is a major regulator of transcriptional activity, involved in the suppression of a broad spectrum of genes and its deregulation is involved in all non-communicable diseases. The present study was designed to explore the use of synchrotron-based FTIR analysis to monitor the subtle changes in molecule bases regarding the DNA methylation status of cytosine in the whole genome. In order to reveal the conformation-related best sample for FTIR-based DNA methylation analysis in situ, we used methodology for nuclear HALO preparations and slightly modified it to isolated DNA in HALO formations. Nuclear DNA-HALOs represent samples with preserved higher-order chromatin structure liberated of any protein residues that are closer to native DNA conformation than genomic DNA (gDNA) isolated by the standard batch procedure. Using FTIR spectroscopy we analyzed the DNA methylation profile of isolated gDNA and compared it with the DNA-HALOs. This study demonstrated the potential of FTIR microspectroscopy to detect DNA methylation marks in analyzed DNA-HALO specimens more precisely in comparison with classical DNA extraction procedures that yield unstructured whole genomic DNA. In addition, we used different cell types to assess their global DNA methylation profile, as well as defined specific infrared peaks that can be used for screening DNA methylation.
PB  - Elsevier
T2  - Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
T1  - Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure
IS  - 123090
VL  - 302
DO  - 10.1016/j.saa.2023.123090
ER  - 

@article{
author = "Sarić, Ana and Rajić, Jovana and Tolić, Anja and Dučić, Tanja and Vidaković, Melita",
year = "2023",
abstract = "Fourier transform infrared (FTIR) spectroscopy is a rapid, non-destructive and label-free technique for identifying subtle changes in all bio-macromolecules, and has been used as a method of choice for studying DNA conformation, secondary DNA structure transition and DNA damage. In addition, the specific level of chromatin complexity is introduced via epigenetic modifications forcing the technological upgrade in the analysis of such an intricacy. As the most studied epigenetic mechanism, DNA methylation is a major regulator of transcriptional activity, involved in the suppression of a broad spectrum of genes and its deregulation is involved in all non-communicable diseases. The present study was designed to explore the use of synchrotron-based FTIR analysis to monitor the subtle changes in molecule bases regarding the DNA methylation status of cytosine in the whole genome. In order to reveal the conformation-related best sample for FTIR-based DNA methylation analysis in situ, we used methodology for nuclear HALO preparations and slightly modified it to isolated DNA in HALO formations. Nuclear DNA-HALOs represent samples with preserved higher-order chromatin structure liberated of any protein residues that are closer to native DNA conformation than genomic DNA (gDNA) isolated by the standard batch procedure. Using FTIR spectroscopy we analyzed the DNA methylation profile of isolated gDNA and compared it with the DNA-HALOs. This study demonstrated the potential of FTIR microspectroscopy to detect DNA methylation marks in analyzed DNA-HALO specimens more precisely in comparison with classical DNA extraction procedures that yield unstructured whole genomic DNA. In addition, we used different cell types to assess their global DNA methylation profile, as well as defined specific infrared peaks that can be used for screening DNA methylation.",
publisher = "Elsevier",
journal = "Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy",
title = "Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure",
number = "123090",
volume = "302",
doi = "10.1016/j.saa.2023.123090"
}

Sarić, A., Rajić, J., Tolić, A., Dučić, T.,& Vidaković, M.. (2023). Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure. in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
Elsevier., 302(123090).
https://doi.org/10.1016/j.saa.2023.123090

Sarić A, Rajić J, Tolić A, Dučić T, Vidaković M. Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure. in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2023;302(123090).
doi:10.1016/j.saa.2023.123090 .

Sarić, Ana, Rajić, Jovana, Tolić, Anja, Dučić, Tanja, Vidaković, Melita, "Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure" in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 302, no. 123090 (2023),
https://doi.org/10.1016/j.saa.2023.123090 . .

TY  - JOUR
AU  - Sarić, Ana
AU  - Rajić, Jovana
AU  - Tolić, Anja
AU  - Dučić, Tanja
AU  - Vidaković, Melita
PY  - 2023
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5947
AB  - Fourier transform infrared (FTIR) spectroscopy is a rapid, non-destructive and label-free technique for identifying subtle changes in all bio-macromolecules, and has been used as a method of choice for studying DNA conformation, secondary DNA structure transition and DNA damage. In addition, the specific level of chromatin complexity is introduced via epigenetic modifications forcing the technological upgrade in the analysis of such an intricacy. As the most studied epigenetic mechanism, DNA methylation is a major regulator of transcriptional activity, involved in the suppression of a broad spectrum of genes and its deregulation is involved in all non-communicable diseases. The present study was designed to explore the use of synchrotron-based FTIR analysis to monitor the subtle changes in molecule bases regarding the DNA methylation status of cytosine in the whole genome. In order to reveal the conformation-related best sample for FTIR-based DNA methylation analysis in situ, we used methodology for nuclear HALO preparations and slightly modified it to isolated DNA in HALO formations. Nuclear DNA-HALOs represent samples with preserved higher-order chromatin structure liberated of any protein residues that are closer to native DNA conformation than genomic DNA (gDNA) isolated by the standard batch procedure. Using FTIR spectroscopy we analyzed the DNA methylation profile of isolated gDNA and compared it with the DNA-HALOs. This study demonstrated the potential of FTIR microspectroscopy to detect DNA methylation marks in analyzed DNA-HALO specimens more precisely in comparison with classical DNA extraction procedures that yield unstructured whole genomic DNA. In addition, we used different cell types to assess their global DNA methylation profile, as well as defined specific infrared peaks that can be used for screening DNA methylation.
PB  - Elsevier
T2  - Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
T1  - Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure
IS  - 123090
VL  - 302
DO  - 10.1016/j.saa.2023.123090
ER  - 

@article{
author = "Sarić, Ana and Rajić, Jovana and Tolić, Anja and Dučić, Tanja and Vidaković, Melita",
year = "2023",
abstract = "Fourier transform infrared (FTIR) spectroscopy is a rapid, non-destructive and label-free technique for identifying subtle changes in all bio-macromolecules, and has been used as a method of choice for studying DNA conformation, secondary DNA structure transition and DNA damage. In addition, the specific level of chromatin complexity is introduced via epigenetic modifications forcing the technological upgrade in the analysis of such an intricacy. As the most studied epigenetic mechanism, DNA methylation is a major regulator of transcriptional activity, involved in the suppression of a broad spectrum of genes and its deregulation is involved in all non-communicable diseases. The present study was designed to explore the use of synchrotron-based FTIR analysis to monitor the subtle changes in molecule bases regarding the DNA methylation status of cytosine in the whole genome. In order to reveal the conformation-related best sample for FTIR-based DNA methylation analysis in situ, we used methodology for nuclear HALO preparations and slightly modified it to isolated DNA in HALO formations. Nuclear DNA-HALOs represent samples with preserved higher-order chromatin structure liberated of any protein residues that are closer to native DNA conformation than genomic DNA (gDNA) isolated by the standard batch procedure. Using FTIR spectroscopy we analyzed the DNA methylation profile of isolated gDNA and compared it with the DNA-HALOs. This study demonstrated the potential of FTIR microspectroscopy to detect DNA methylation marks in analyzed DNA-HALO specimens more precisely in comparison with classical DNA extraction procedures that yield unstructured whole genomic DNA. In addition, we used different cell types to assess their global DNA methylation profile, as well as defined specific infrared peaks that can be used for screening DNA methylation.",
publisher = "Elsevier",
journal = "Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy",
title = "Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure",
number = "123090",
volume = "302",
doi = "10.1016/j.saa.2023.123090"
}

Sarić, A., Rajić, J., Tolić, A., Dučić, T.,& Vidaković, M.. (2023). Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure. in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
Elsevier., 302(123090).
https://doi.org/10.1016/j.saa.2023.123090

Sarić A, Rajić J, Tolić A, Dučić T, Vidaković M. Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure. in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2023;302(123090).
doi:10.1016/j.saa.2023.123090 .

Sarić, Ana, Rajić, Jovana, Tolić, Anja, Dučić, Tanja, Vidaković, Melita, "Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure" in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 302, no. 123090 (2023),
https://doi.org/10.1016/j.saa.2023.123090 . .

TY  - DATA
AU  - Sarić, Ana
AU  - Rajić, Jovana
AU  - Tolić, Anja
AU  - Dučić, Tanja
AU  - Vidaković, Melita
PY  - 2023
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5960
AB  - Supplementary Figure 1:
Curve fitting of FTIR spectra for analyzing differences in DNA regions.
PB  - Elsevier
T2  - Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
T1  - Supplementary material for the article: Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure
IS  - 123090
VL  - 302
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_5960
ER  - 

@misc{
author = "Sarić, Ana and Rajić, Jovana and Tolić, Anja and Dučić, Tanja and Vidaković, Melita",
year = "2023",
abstract = "Supplementary Figure 1:
Curve fitting of FTIR spectra for analyzing differences in DNA regions.",
publisher = "Elsevier",
journal = "Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy",
title = "Supplementary material for the article: Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure",
number = "123090",
volume = "302",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_5960"
}

Sarić, A., Rajić, J., Tolić, A., Dučić, T.,& Vidaković, M.. (2023). Supplementary material for the article: Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure. in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
Elsevier., 302(123090).
https://hdl.handle.net/21.15107/rcub_ibiss_5960

Sarić A, Rajić J, Tolić A, Dučić T, Vidaković M. Supplementary material for the article: Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure. in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2023;302(123090).
https://hdl.handle.net/21.15107/rcub_ibiss_5960 .

Sarić, Ana, Rajić, Jovana, Tolić, Anja, Dučić, Tanja, Vidaković, Melita, "Supplementary material for the article: Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure" in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 302, no. 123090 (2023),
https://hdl.handle.net/21.15107/rcub_ibiss_5960 .

TY  - CONF
AU  - Sarić, Ana
AU  - Rajić, Jovana
AU  - Đorđević, Marija
AU  - Jovanović, Mirna
AU  - Podolski-Renić, Ana
AU  - Pešić, Milica
AU  - Uskoković, Aleksandra
AU  - Tolić, Anja
PY  - 2022
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5918
AB  - 5-hydroxymethylcytosine (5-hmC) is formed through the oxidation of 5-methylcytosine (5-mC) by the catalytic activity of TET enzymes. It has been proposed to have regulatory functions as an independent epigenetic mark and it might have diagnostic potential as global loss of 5hmC level is commonly observed in cancers.
We have recently shown the inhibitory influence of PARP-1 dependent PARylation on TET1 hydroxylase activity in DNA demethylation. These findings could provide the rationale for using PARP inhibitors in cancers that are characterised by the 5hmC loss, other than cancer where treatment with PARP inhibitors exploited homologues repair (HR) defects on the basis of the synthetic lethality phenomenon. The activating effects of PARP inhibition on TET activity could provide the additional mechanism of action of PARP inhibitors (which are less cytotoxic than standard chemotherapeutic agents) in the treatment of cancers characterised by diminishing levels of 5hmC.
In our study, we have tested the effects of PARP inhibition on 5-hmC levels in non-small cell lung cancer. First, we analysed global levels of 5-hmC in several non-small cell lung cancer cell lines (NCI-H460 sensitive and resistant to doxorubicin, A549, NCI-H661) in comparison to normal fetal lung fibroblast cells MRC-5. Since both slot-blot and confocal microscopy analyses have shown that the A549 cell line has the lowest level of 5-hmC this cell line was selected for further experiments in which we set out to raise DNA hydroxymethylation levels by inhibiting PARP activity. After 72h treatment of A549 cells with PARylation inhibitor niraparib (IC50= 10 μM), we indeed observed an increase in 5-hmC level while 5-mC level did not change. This is a promising start to our investigation of alternative mechanisms of action of PARP inhibition in the treatment of cancers. Through this research, we hope to expand the range of cancer types that would be treated with PARP inhibitors, regardless of the HR status.
PB  - Josep Carreras Leukaemia Research Institute (IJC)
PB  - Innovative Training Network (ITN) INTERCEPT-MDS
C3  - Spetses summer school: Cancer epigenetics: Principles, Applications and Single-cell resolution; 2022 Aug 28 - Sep 3; Spteses Island, Greece
T1  - Influence of PARP inhibition on 5-hmC level in NSCLC
SP  - 116
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_5918
ER  - 

@conference{
author = "Sarić, Ana and Rajić, Jovana and Đorđević, Marija and Jovanović, Mirna and Podolski-Renić, Ana and Pešić, Milica and Uskoković, Aleksandra and Tolić, Anja",
year = "2022",
abstract = "5-hydroxymethylcytosine (5-hmC) is formed through the oxidation of 5-methylcytosine (5-mC) by the catalytic activity of TET enzymes. It has been proposed to have regulatory functions as an independent epigenetic mark and it might have diagnostic potential as global loss of 5hmC level is commonly observed in cancers.
We have recently shown the inhibitory influence of PARP-1 dependent PARylation on TET1 hydroxylase activity in DNA demethylation. These findings could provide the rationale for using PARP inhibitors in cancers that are characterised by the 5hmC loss, other than cancer where treatment with PARP inhibitors exploited homologues repair (HR) defects on the basis of the synthetic lethality phenomenon. The activating effects of PARP inhibition on TET activity could provide the additional mechanism of action of PARP inhibitors (which are less cytotoxic than standard chemotherapeutic agents) in the treatment of cancers characterised by diminishing levels of 5hmC.
In our study, we have tested the effects of PARP inhibition on 5-hmC levels in non-small cell lung cancer. First, we analysed global levels of 5-hmC in several non-small cell lung cancer cell lines (NCI-H460 sensitive and resistant to doxorubicin, A549, NCI-H661) in comparison to normal fetal lung fibroblast cells MRC-5. Since both slot-blot and confocal microscopy analyses have shown that the A549 cell line has the lowest level of 5-hmC this cell line was selected for further experiments in which we set out to raise DNA hydroxymethylation levels by inhibiting PARP activity. After 72h treatment of A549 cells with PARylation inhibitor niraparib (IC50= 10 μM), we indeed observed an increase in 5-hmC level while 5-mC level did not change. This is a promising start to our investigation of alternative mechanisms of action of PARP inhibition in the treatment of cancers. Through this research, we hope to expand the range of cancer types that would be treated with PARP inhibitors, regardless of the HR status.",
publisher = "Josep Carreras Leukaemia Research Institute (IJC), Innovative Training Network (ITN) INTERCEPT-MDS",
journal = "Spetses summer school: Cancer epigenetics: Principles, Applications and Single-cell resolution; 2022 Aug 28 - Sep 3; Spteses Island, Greece",
title = "Influence of PARP inhibition on 5-hmC level in NSCLC",
pages = "116",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_5918"
}

Sarić, A., Rajić, J., Đorđević, M., Jovanović, M., Podolski-Renić, A., Pešić, M., Uskoković, A.,& Tolić, A.. (2022). Influence of PARP inhibition on 5-hmC level in NSCLC. in Spetses summer school: Cancer epigenetics: Principles, Applications and Single-cell resolution; 2022 Aug 28 - Sep 3; Spteses Island, Greece
Josep Carreras Leukaemia Research Institute (IJC)., 116.
https://hdl.handle.net/21.15107/rcub_ibiss_5918

Sarić A, Rajić J, Đorđević M, Jovanović M, Podolski-Renić A, Pešić M, Uskoković A, Tolić A. Influence of PARP inhibition on 5-hmC level in NSCLC. in Spetses summer school: Cancer epigenetics: Principles, Applications and Single-cell resolution; 2022 Aug 28 - Sep 3; Spteses Island, Greece. 2022;:116.
https://hdl.handle.net/21.15107/rcub_ibiss_5918 .

Sarić, Ana, Rajić, Jovana, Đorđević, Marija, Jovanović, Mirna, Podolski-Renić, Ana, Pešić, Milica, Uskoković, Aleksandra, Tolić, Anja, "Influence of PARP inhibition on 5-hmC level in NSCLC" in Spetses summer school: Cancer epigenetics: Principles, Applications and Single-cell resolution; 2022 Aug 28 - Sep 3; Spteses Island, Greece (2022):116,
https://hdl.handle.net/21.15107/rcub_ibiss_5918 .

TY  - CONF
AU  - Sarić, Ana
AU  - Tolić, Anja
AU  - Grdović, Nevena
AU  - Dinić, Svetlana
AU  - Rajić, Jovana
AU  - Đorđević, Miloš
AU  - Đorđević, Marija
AU  - Arambašić Jovanović, Jelena
AU  - Mihailović, Mirjana
AU  - Uskoković, Aleksandra
AU  - Dučić, Tanja
AU  - Vidaković, Melita
PY  - 2019
UR  - https://www.cost.eu/cost-events/the-extracellular-vesicles-paradigm-of-intra-intercellular-communication/
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5920
AB  - Double-strand deoxyribonucleic acid (dsDNA) carries the genetic information needed for normal development, growth, survival and reproduction of all living beings (except RNA viruses and other potential DNA-less microorganisms). On top of it, epigenetic processes orchestrate the cell type-specific use of the genetic information essential for normal development and for maintaining the overall integrity of the genome. The alteration of epigenetic marks (e.g. DNA methylation patterns) by hyperglycaemia, oxidative stress and inflammation may have potential epigenetic impacts on gene regulation in diabetic individuals. We used the Fourier transform-infrared (FTIR) spectroscopy (ALBA synchrotron, Cerdanyola del valles, Spain) for qualitative spectral analysis of DNA from mouse fibroblast cells (NIH3T3) and the same cells treated with demetilating agent 5-azacytidine (5-aza). FTIR spectroscopy has the advantage of generating structural information of the entire DNA molecule in a single spectrum, including possible conformational sub-states, present in the sample (methylated/nonmethylated cytosine). The technique is ideal for systematic studies of DNA/RNA sequence variations and covalent modifications, since it is non-destructive and requires only small sample amounts. The FTIR region of interest when studying nucleic acids is 1800–900 cm-1.We obtained the global information regarding the DNA profiles in NIH3T3 with and without 5-aza treatment by FTIR spectroscopy. Some differences in DNA methylation profiles between examined cell lines were qualitatively described by FTIR spectroscopy and compared with restriction analysis method. Using FTIR spectroscopy the most interesting picks were observed approximately at wavelength: 2960-2850 cm-1, 1400-900 cm-1 and 1150 cm-1. These results are in the same time a verification of the proof of principle for synchrotron-based FTIR micro-spectroscopic detection of the differences in the DNA methylation profiles in cells.
PB  - COST Action CellFit
C3  - 3rd CellFit annual meeting: The extracellular vesicles paradigm of intracellular communication; 2019 Oct 10-12; Athens, Greece
T1  - The FTIR spectroscopy as a method of choice for detecting changes in DNA profiles of the mouse embryonic fibroblasts after the treatment with 5-aza
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_5920
ER  - 

@conference{
author = "Sarić, Ana and Tolić, Anja and Grdović, Nevena and Dinić, Svetlana and Rajić, Jovana and Đorđević, Miloš and Đorđević, Marija and Arambašić Jovanović, Jelena and Mihailović, Mirjana and Uskoković, Aleksandra and Dučić, Tanja and Vidaković, Melita",
year = "2019",
abstract = "Double-strand deoxyribonucleic acid (dsDNA) carries the genetic information needed for normal development, growth, survival and reproduction of all living beings (except RNA viruses and other potential DNA-less microorganisms). On top of it, epigenetic processes orchestrate the cell type-specific use of the genetic information essential for normal development and for maintaining the overall integrity of the genome. The alteration of epigenetic marks (e.g. DNA methylation patterns) by hyperglycaemia, oxidative stress and inflammation may have potential epigenetic impacts on gene regulation in diabetic individuals. We used the Fourier transform-infrared (FTIR) spectroscopy (ALBA synchrotron, Cerdanyola del valles, Spain) for qualitative spectral analysis of DNA from mouse fibroblast cells (NIH3T3) and the same cells treated with demetilating agent 5-azacytidine (5-aza). FTIR spectroscopy has the advantage of generating structural information of the entire DNA molecule in a single spectrum, including possible conformational sub-states, present in the sample (methylated/nonmethylated cytosine). The technique is ideal for systematic studies of DNA/RNA sequence variations and covalent modifications, since it is non-destructive and requires only small sample amounts. The FTIR region of interest when studying nucleic acids is 1800–900 cm-1.We obtained the global information regarding the DNA profiles in NIH3T3 with and without 5-aza treatment by FTIR spectroscopy. Some differences in DNA methylation profiles between examined cell lines were qualitatively described by FTIR spectroscopy and compared with restriction analysis method. Using FTIR spectroscopy the most interesting picks were observed approximately at wavelength: 2960-2850 cm-1, 1400-900 cm-1 and 1150 cm-1. These results are in the same time a verification of the proof of principle for synchrotron-based FTIR micro-spectroscopic detection of the differences in the DNA methylation profiles in cells.",
publisher = "COST Action CellFit",
journal = "3rd CellFit annual meeting: The extracellular vesicles paradigm of intracellular communication; 2019 Oct 10-12; Athens, Greece",
title = "The FTIR spectroscopy as a method of choice for detecting changes in DNA profiles of the mouse embryonic fibroblasts after the treatment with 5-aza",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_5920"
}

Sarić, A., Tolić, A., Grdović, N., Dinić, S., Rajić, J., Đorđević, M., Đorđević, M., Arambašić Jovanović, J., Mihailović, M., Uskoković, A., Dučić, T.,& Vidaković, M.. (2019). The FTIR spectroscopy as a method of choice for detecting changes in DNA profiles of the mouse embryonic fibroblasts after the treatment with 5-aza. in 3rd CellFit annual meeting: The extracellular vesicles paradigm of intracellular communication; 2019 Oct 10-12; Athens, Greece
COST Action CellFit..
https://hdl.handle.net/21.15107/rcub_ibiss_5920

Sarić A, Tolić A, Grdović N, Dinić S, Rajić J, Đorđević M, Đorđević M, Arambašić Jovanović J, Mihailović M, Uskoković A, Dučić T, Vidaković M. The FTIR spectroscopy as a method of choice for detecting changes in DNA profiles of the mouse embryonic fibroblasts after the treatment with 5-aza. in 3rd CellFit annual meeting: The extracellular vesicles paradigm of intracellular communication; 2019 Oct 10-12; Athens, Greece. 2019;.
https://hdl.handle.net/21.15107/rcub_ibiss_5920 .

Sarić, Ana, Tolić, Anja, Grdović, Nevena, Dinić, Svetlana, Rajić, Jovana, Đorđević, Miloš, Đorđević, Marija, Arambašić Jovanović, Jelena, Mihailović, Mirjana, Uskoković, Aleksandra, Dučić, Tanja, Vidaković, Melita, "The FTIR spectroscopy as a method of choice for detecting changes in DNA profiles of the mouse embryonic fibroblasts after the treatment with 5-aza" in 3rd CellFit annual meeting: The extracellular vesicles paradigm of intracellular communication; 2019 Oct 10-12; Athens, Greece (2019),
https://hdl.handle.net/21.15107/rcub_ibiss_5920 .

TY  - CONF
AU  - Sarić, Ana
AU  - Tolić, Anja
AU  - Grdović, Nevena
AU  - Dinić, Svetlana
AU  - Rajić, Jovana
AU  - Đorđević, Miloš
AU  - Đorđević, Marija
AU  - Arambašić Jovanović, Jelena
AU  - Mihailović, Mirjana
AU  - Poznanović, Goran
AU  - Uskoković, Aleksandra
AU  - Vidaković, Melita
AU  - Dučić, Tanja
PY  - 2019
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5694
AB  - Epigenetic processes orchestrate the cell type-specific use of the genetic information
essential for normal development and for maintaining the overall integrity of the genome.
DNA methylation is probably the most extensively studied epigenetic mark and represents
the covalent attachment of a methyl group to cytosine that is located next to guanine within
the genomic DNA. The alteration of DNA methylation patterns by hyperglycaemia, oxidative
stress and inflammation may have potential epigenetic impacts on gene regulation in diabetic
individuals. Further research devoted to improve the steps that could be undertaken in the
early diagnosis, prevention and treatment of diabetes and its complications is a scientifically
and socially significant task. We used the Fourier transform-infrared (FTIR) spectroscopy
(ALBA synchrotron, Cerdanyola del valles, Spain) for qualitative spectral analysis of
normomethylated DNA from mouse fibroblast cells (NIH3T3) and hypomethylated DNA
from PARP-1 knockout mouse fibroblast cells (PARP-/-). We obtained the global information
regarding the DNA methylation profiles in mouse fibroblast cells by FTIR spectroscopy that
was visualised by immune-fluorescent staining using anti-methyl cytosine (5mC) antibody.
Some differences in DNA methylation profiles between examined cell lines were observed
in spectral region significant for cytosine (990-1250 nm). The most interesting picks were
observed approximately at wavelength: 1240 nm, 1150 nm, 1110 nm and 1010 nm. These
results are in the same time a verification of the proof of principle for FTIR based analysis of
the differences between normomethylated and hypomethylated genomic DNA which could
be set as a potential predictive and diagnostic tool in future. To our knowledge this is a first
time that synchrotron-based FTIR micro-spectroscopy is used for detection of the presence
of 5mC and changes in the DNA methylation profile in cells.
PB  - Belgrade: Serbian Genetic Society
C3  - 6th Congress of the Serbian genetic society: Book of abstracts; 2019 Oct 13-17; Vrnjačka Banja, Serbia
T1  - Detection of DNA methylation profiles in mouse embryonic fibroblasts using Fourier transform-infrared spectroscopy
SP  - 75
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_5694
ER  - 

@conference{
author = "Sarić, Ana and Tolić, Anja and Grdović, Nevena and Dinić, Svetlana and Rajić, Jovana and Đorđević, Miloš and Đorđević, Marija and Arambašić Jovanović, Jelena and Mihailović, Mirjana and Poznanović, Goran and Uskoković, Aleksandra and Vidaković, Melita and Dučić, Tanja",
year = "2019",
abstract = "Epigenetic processes orchestrate the cell type-specific use of the genetic information
essential for normal development and for maintaining the overall integrity of the genome.
DNA methylation is probably the most extensively studied epigenetic mark and represents
the covalent attachment of a methyl group to cytosine that is located next to guanine within
the genomic DNA. The alteration of DNA methylation patterns by hyperglycaemia, oxidative
stress and inflammation may have potential epigenetic impacts on gene regulation in diabetic
individuals. Further research devoted to improve the steps that could be undertaken in the
early diagnosis, prevention and treatment of diabetes and its complications is a scientifically
and socially significant task. We used the Fourier transform-infrared (FTIR) spectroscopy
(ALBA synchrotron, Cerdanyola del valles, Spain) for qualitative spectral analysis of
normomethylated DNA from mouse fibroblast cells (NIH3T3) and hypomethylated DNA
from PARP-1 knockout mouse fibroblast cells (PARP-/-). We obtained the global information
regarding the DNA methylation profiles in mouse fibroblast cells by FTIR spectroscopy that
was visualised by immune-fluorescent staining using anti-methyl cytosine (5mC) antibody.
Some differences in DNA methylation profiles between examined cell lines were observed
in spectral region significant for cytosine (990-1250 nm). The most interesting picks were
observed approximately at wavelength: 1240 nm, 1150 nm, 1110 nm and 1010 nm. These
results are in the same time a verification of the proof of principle for FTIR based analysis of
the differences between normomethylated and hypomethylated genomic DNA which could
be set as a potential predictive and diagnostic tool in future. To our knowledge this is a first
time that synchrotron-based FTIR micro-spectroscopy is used for detection of the presence
of 5mC and changes in the DNA methylation profile in cells.",
publisher = "Belgrade: Serbian Genetic Society",
journal = "6th Congress of the Serbian genetic society: Book of abstracts; 2019 Oct 13-17; Vrnjačka Banja, Serbia",
title = "Detection of DNA methylation profiles in mouse embryonic fibroblasts using Fourier transform-infrared spectroscopy",
pages = "75",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_5694"
}

Sarić, A., Tolić, A., Grdović, N., Dinić, S., Rajić, J., Đorđević, M., Đorđević, M., Arambašić Jovanović, J., Mihailović, M., Poznanović, G., Uskoković, A., Vidaković, M.,& Dučić, T.. (2019). Detection of DNA methylation profiles in mouse embryonic fibroblasts using Fourier transform-infrared spectroscopy. in 6th Congress of the Serbian genetic society: Book of abstracts; 2019 Oct 13-17; Vrnjačka Banja, Serbia
Belgrade: Serbian Genetic Society., 75.
https://hdl.handle.net/21.15107/rcub_ibiss_5694

Sarić A, Tolić A, Grdović N, Dinić S, Rajić J, Đorđević M, Đorđević M, Arambašić Jovanović J, Mihailović M, Poznanović G, Uskoković A, Vidaković M, Dučić T. Detection of DNA methylation profiles in mouse embryonic fibroblasts using Fourier transform-infrared spectroscopy. in 6th Congress of the Serbian genetic society: Book of abstracts; 2019 Oct 13-17; Vrnjačka Banja, Serbia. 2019;:75.
https://hdl.handle.net/21.15107/rcub_ibiss_5694 .

Sarić, Ana, Tolić, Anja, Grdović, Nevena, Dinić, Svetlana, Rajić, Jovana, Đorđević, Miloš, Đorđević, Marija, Arambašić Jovanović, Jelena, Mihailović, Mirjana, Poznanović, Goran, Uskoković, Aleksandra, Vidaković, Melita, Dučić, Tanja, "Detection of DNA methylation profiles in mouse embryonic fibroblasts using Fourier transform-infrared spectroscopy" in 6th Congress of the Serbian genetic society: Book of abstracts; 2019 Oct 13-17; Vrnjačka Banja, Serbia (2019):75,
https://hdl.handle.net/21.15107/rcub_ibiss_5694 .