Transcriptional profiling of PHF19 gene in colon cancer cell lines cultivated in 3D
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 c...omparison 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.
Keywords:
PHF19 / colorectal cancer / transcript / biomarkerSource:
CoMBoS2 – the Second Congress of Molecular Biologists of Serbia, Abstract Book – Trends in Molecular Biology, Special issue 06-08 October 2023, Belgrade, Serbia, 2023, 178-178Publisher:
- Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade
Funding / projects:
- SENSOGENE - Cancer Biosensors Based on Gene Regulatory Elements (RS-ScienceFundRS-Promis-6052315)
Collections
Institution/Community
Institut za molekularnu genetiku i genetičko inženjerstvoTY - 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 .