Non-coding transcripts of protein-coding genes as novel biomarkers for colorectal cancer diagnosis
Autori
Despotović, JovanaDragičević, Sandra
Babić, Tamara
Pavlović, Dunja
Karanović, Jelena
Nikolić, Aleksandra
Ostala autorstva
Morić, IvanaĐorđević, Valentina
Konferencijski prilog (Objavljena verzija)
Metapodaci
Prikaz svih podataka o dokumentuApstrakt
Recent research shows that non-coding RNA transcripts of protein-coding genes could
be an emerging novel class of diagnostic biomarkers. This study aimed to identify the
most promising biomarkers for colorectal cancer (CRC) screening among upregulated
non-coding transcripts of protein-coding genes in malignant CRC cells in comparison to
non-malignant cells grown in 3D. Malignant CRC cell lines HCT116, DLD-1 and SW620,
and a non-malignant human colon epithelial cell line HCEC-1CT, were cultivated in 3D
as spheroids in 24-well plates with low attachment surface for 7 days. RNA sequencing
was performed on ribosomal-depleted total RNA using Illumina’s NovaSeq6000 platform
that generated paired-end 150bp reads. Highly upregulated transcripts (>10 FPKM)
present in all malignant cell lines and absent in non-malignant cell line were filtered
and analyzed by a set of in silico tools to filter the best candidates for further validation
studies. The publicly available GSE164541 set con...sisting of triplicate tissue samples of
normal, adenoma and primary CRC tissues collected from five patients with CRC was
used for validation. As a result, 5 transcripts with retained introns ANXA3-204, LLGL2-
207, KRT19-204, KRT18-206 and KRT8-213 were analyzed by in silico tools. Only
ANXA3-204 was classified as non-coding according to both CPC2 and LGC online coding
potential prediction tools. Nucleus was predicted as subcellular localization for ANXA3-
204 by AnnoLnc2. Additionally, ANXA3-204 expression was upregulated in adenoma
(p=0.04) and CRC tissue samples, although statistical significance was not reached for
CRC, in comparison to normal tissue samples in the validation set. Transcriptomic analysis
revealed that non-coding ANXA3-204 transcript was highly upregulated in malignant CRC
cell lines and adenomas compared to control samples, making ANXA3-204 a potential
candidate for early CRC screening. Further studies are needed to confirm diagnostic
potential and regulatory role of ANXA3-204.
Ključne reči:
non-coding RNA / colorectal cancer / biomarker / ANXA3 / retained intronIzvor:
5th Belgrade Bioinformatics Conference, 2024, 110-110Izdavač:
- Belgrade : Institute of molecular genetics and genetic engineering
Finansiranje / projekti:
- Ministarstvo nauke, tehnološkog razvoja i inovacija Republike Srbije, institucionalno finansiranje - 200042 (Univerzitet u Beogradu, Institut za molekularnu genetiku i genetičko inženjerstvo) (RS-MESTD-inst-2020-200042)
- SENSOGENE - Cancer Biosensors Based on Gene Regulatory Elements (RS-ScienceFundRS-Promis-6052315)
Napomena:
- Book of abstracts: 5th Belgrade Bioinformatics Conference, Serbia, Belgrade,17-20 june 2024.
Kolekcije
Institucija/grupa
Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Despotović, Jovana AU - Dragičević, Sandra AU - Babić, Tamara AU - Pavlović, Dunja AU - Karanović, Jelena AU - Nikolić, Aleksandra PY - 2024 UR - www.belbi.bg.ac.rs UR - https://imagine.imgge.bg.ac.rs/handle/123456789/2473 AB - Recent research shows that non-coding RNA transcripts of protein-coding genes could be an emerging novel class of diagnostic biomarkers. This study aimed to identify the most promising biomarkers for colorectal cancer (CRC) screening among upregulated non-coding transcripts of protein-coding genes in malignant CRC cells in comparison to non-malignant cells grown in 3D. Malignant CRC cell lines HCT116, DLD-1 and SW620, and a non-malignant human colon epithelial cell line HCEC-1CT, were cultivated in 3D as spheroids in 24-well plates with low attachment surface for 7 days. RNA sequencing was performed on ribosomal-depleted total RNA using Illumina’s NovaSeq6000 platform that generated paired-end 150bp reads. Highly upregulated transcripts (>10 FPKM) present in all malignant cell lines and absent in non-malignant cell line were filtered and analyzed by a set of in silico tools to filter the best candidates for further validation studies. The publicly available GSE164541 set consisting of triplicate tissue samples of normal, adenoma and primary CRC tissues collected from five patients with CRC was used for validation. As a result, 5 transcripts with retained introns ANXA3-204, LLGL2- 207, KRT19-204, KRT18-206 and KRT8-213 were analyzed by in silico tools. Only ANXA3-204 was classified as non-coding according to both CPC2 and LGC online coding potential prediction tools. Nucleus was predicted as subcellular localization for ANXA3- 204 by AnnoLnc2. Additionally, ANXA3-204 expression was upregulated in adenoma (p=0.04) and CRC tissue samples, although statistical significance was not reached for CRC, in comparison to normal tissue samples in the validation set. Transcriptomic analysis revealed that non-coding ANXA3-204 transcript was highly upregulated in malignant CRC cell lines and adenomas compared to control samples, making ANXA3-204 a potential candidate for early CRC screening. Further studies are needed to confirm diagnostic potential and regulatory role of ANXA3-204. PB - Belgrade : Institute of molecular genetics and genetic engineering C3 - 5th Belgrade Bioinformatics Conference T1 - Non-coding transcripts of protein-coding genes as novel biomarkers for colorectal cancer diagnosis EP - 110 SP - 110 UR - https://hdl.handle.net/21.15107/rcub_imagine_2473 ER -
@conference{ author = "Despotović, Jovana and Dragičević, Sandra and Babić, Tamara and Pavlović, Dunja and Karanović, Jelena and Nikolić, Aleksandra", year = "2024", abstract = "Recent research shows that non-coding RNA transcripts of protein-coding genes could be an emerging novel class of diagnostic biomarkers. This study aimed to identify the most promising biomarkers for colorectal cancer (CRC) screening among upregulated non-coding transcripts of protein-coding genes in malignant CRC cells in comparison to non-malignant cells grown in 3D. Malignant CRC cell lines HCT116, DLD-1 and SW620, and a non-malignant human colon epithelial cell line HCEC-1CT, were cultivated in 3D as spheroids in 24-well plates with low attachment surface for 7 days. RNA sequencing was performed on ribosomal-depleted total RNA using Illumina’s NovaSeq6000 platform that generated paired-end 150bp reads. Highly upregulated transcripts (>10 FPKM) present in all malignant cell lines and absent in non-malignant cell line were filtered and analyzed by a set of in silico tools to filter the best candidates for further validation studies. The publicly available GSE164541 set consisting of triplicate tissue samples of normal, adenoma and primary CRC tissues collected from five patients with CRC was used for validation. As a result, 5 transcripts with retained introns ANXA3-204, LLGL2- 207, KRT19-204, KRT18-206 and KRT8-213 were analyzed by in silico tools. Only ANXA3-204 was classified as non-coding according to both CPC2 and LGC online coding potential prediction tools. Nucleus was predicted as subcellular localization for ANXA3- 204 by AnnoLnc2. Additionally, ANXA3-204 expression was upregulated in adenoma (p=0.04) and CRC tissue samples, although statistical significance was not reached for CRC, in comparison to normal tissue samples in the validation set. Transcriptomic analysis revealed that non-coding ANXA3-204 transcript was highly upregulated in malignant CRC cell lines and adenomas compared to control samples, making ANXA3-204 a potential candidate for early CRC screening. Further studies are needed to confirm diagnostic potential and regulatory role of ANXA3-204.", publisher = "Belgrade : Institute of molecular genetics and genetic engineering", journal = "5th Belgrade Bioinformatics Conference", title = "Non-coding transcripts of protein-coding genes as novel biomarkers for colorectal cancer diagnosis", pages = "110-110", url = "https://hdl.handle.net/21.15107/rcub_imagine_2473" }
Despotović, J., Dragičević, S., Babić, T., Pavlović, D., Karanović, J.,& Nikolić, A.. (2024). Non-coding transcripts of protein-coding genes as novel biomarkers for colorectal cancer diagnosis. in 5th Belgrade Bioinformatics Conference Belgrade : Institute of molecular genetics and genetic engineering., 110-110. https://hdl.handle.net/21.15107/rcub_imagine_2473
Despotović J, Dragičević S, Babić T, Pavlović D, Karanović J, Nikolić A. Non-coding transcripts of protein-coding genes as novel biomarkers for colorectal cancer diagnosis. in 5th Belgrade Bioinformatics Conference. 2024;:110-110. https://hdl.handle.net/21.15107/rcub_imagine_2473 .
Despotović, Jovana, Dragičević, Sandra, Babić, Tamara, Pavlović, Dunja, Karanović, Jelena, Nikolić, Aleksandra, "Non-coding transcripts of protein-coding genes as novel biomarkers for colorectal cancer diagnosis" in 5th Belgrade Bioinformatics Conference (2024):110-110, https://hdl.handle.net/21.15107/rcub_imagine_2473 .