Transcriptomic Profiling for the Autophagy Pathway in Colorectal Cancer
The role of autophagy in colorectal cancer (CRC) pathogenesis appears to be crucial. Autophagy acts both as a tumor suppressor, by removing redundant cellular material, and a tumor-promoting factor, by providing access to components necessary for growth, metabolism, and proliferation. To date, littl...
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doaj-c37e7ea4b76c4807a6cebb07879e56772020-11-25T03:55:39ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-09-01217101710110.3390/ijms21197101Transcriptomic Profiling for the Autophagy Pathway in Colorectal CancerJustyna Gil0Paweł Karpiński1Maria M. Sąsiadek2Department of Genetics, Wroclaw Medical University, Marcinkowskiego 1, 50-368 Wroclaw, PolandDepartment of Genetics, Wroclaw Medical University, Marcinkowskiego 1, 50-368 Wroclaw, PolandDepartment of Genetics, Wroclaw Medical University, Marcinkowskiego 1, 50-368 Wroclaw, PolandThe role of autophagy in colorectal cancer (CRC) pathogenesis appears to be crucial. Autophagy acts both as a tumor suppressor, by removing redundant cellular material, and a tumor-promoting factor, by providing access to components necessary for growth, metabolism, and proliferation. To date, little is known about the expression of genes that play a basal role in the autophagy in CRC. In this study, we aimed to compare the expression levels of 46 genes involved in the autophagy pathway between tumor-adjacent and tumor tissue, employing large RNA sequencing (RNA-seq) and microarray datasets. Additionally, we verified our results using data on 38 CRC cell lines. Gene set enrichment analysis revealed a significant deregulation of autophagy-related gene sets in CRC. The unsupervised clustering of tumors using the mRNA levels of autophagy-related genes revealed the existence of two major clusters: microsatellite instability (MSI)-enriched and -depleted. In cluster 1 (MSI-depleted), <i>ATG9B</i> and <i>LAMP1</i> genes were the most prominently expressed, whereas cluster 2 (MSI-enriched) was characterized by <i>DRAM1</i> upregulation. CRC cell lines were also clustered according to MSI-enriched/-depleted subgroups. The moderate deregulation of autophagy-related genes in cancer tissue, as compared to adjacent tissue, suggests a prominent field cancerization or early disruption of autophagy. Genes differentiating these clusters are promising candidates for CRC targeting therapy worthy of further investigation.https://www.mdpi.com/1422-0067/21/19/7101autophagygene expressioncolorectal cancer |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Justyna Gil Paweł Karpiński Maria M. Sąsiadek |
spellingShingle |
Justyna Gil Paweł Karpiński Maria M. Sąsiadek Transcriptomic Profiling for the Autophagy Pathway in Colorectal Cancer International Journal of Molecular Sciences autophagy gene expression colorectal cancer |
author_facet |
Justyna Gil Paweł Karpiński Maria M. Sąsiadek |
author_sort |
Justyna Gil |
title |
Transcriptomic Profiling for the Autophagy Pathway in Colorectal Cancer |
title_short |
Transcriptomic Profiling for the Autophagy Pathway in Colorectal Cancer |
title_full |
Transcriptomic Profiling for the Autophagy Pathway in Colorectal Cancer |
title_fullStr |
Transcriptomic Profiling for the Autophagy Pathway in Colorectal Cancer |
title_full_unstemmed |
Transcriptomic Profiling for the Autophagy Pathway in Colorectal Cancer |
title_sort |
transcriptomic profiling for the autophagy pathway in colorectal cancer |
publisher |
MDPI AG |
series |
International Journal of Molecular Sciences |
issn |
1661-6596 1422-0067 |
publishDate |
2020-09-01 |
description |
The role of autophagy in colorectal cancer (CRC) pathogenesis appears to be crucial. Autophagy acts both as a tumor suppressor, by removing redundant cellular material, and a tumor-promoting factor, by providing access to components necessary for growth, metabolism, and proliferation. To date, little is known about the expression of genes that play a basal role in the autophagy in CRC. In this study, we aimed to compare the expression levels of 46 genes involved in the autophagy pathway between tumor-adjacent and tumor tissue, employing large RNA sequencing (RNA-seq) and microarray datasets. Additionally, we verified our results using data on 38 CRC cell lines. Gene set enrichment analysis revealed a significant deregulation of autophagy-related gene sets in CRC. The unsupervised clustering of tumors using the mRNA levels of autophagy-related genes revealed the existence of two major clusters: microsatellite instability (MSI)-enriched and -depleted. In cluster 1 (MSI-depleted), <i>ATG9B</i> and <i>LAMP1</i> genes were the most prominently expressed, whereas cluster 2 (MSI-enriched) was characterized by <i>DRAM1</i> upregulation. CRC cell lines were also clustered according to MSI-enriched/-depleted subgroups. The moderate deregulation of autophagy-related genes in cancer tissue, as compared to adjacent tissue, suggests a prominent field cancerization or early disruption of autophagy. Genes differentiating these clusters are promising candidates for CRC targeting therapy worthy of further investigation. |
topic |
autophagy gene expression colorectal cancer |
url |
https://www.mdpi.com/1422-0067/21/19/7101 |
work_keys_str_mv |
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