A network-based analysis to identify a piRNA-target signature related to colorectal cancer prognosis: in silico and in vitro study
Abstract Purpose Patients with colorectal cancer (CRC) are diagnosed in advanced stages and have worse overall survival. Also, this cancer incidence is rising in many countries. The aim of this study is to find piwi-interacting RNAs (piRNA) predicting the prognosis of patients with colorectal cancer...
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| Format: | Article |
| Language: | English |
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Springer
2025-04-01
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| Series: | Discover Oncology |
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| Online Access: | https://doi.org/10.1007/s12672-025-02373-x |
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| author | Fatemeh Khavari Rezvan Najafi Saeed Afshar Akram Jalali Mehrdad Hashemi Alireza Soltanian Fatemeh Nouri |
| author_facet | Fatemeh Khavari Rezvan Najafi Saeed Afshar Akram Jalali Mehrdad Hashemi Alireza Soltanian Fatemeh Nouri |
| author_sort | Fatemeh Khavari |
| collection | DOAJ |
| description | Abstract Purpose Patients with colorectal cancer (CRC) are diagnosed in advanced stages and have worse overall survival. Also, this cancer incidence is rising in many countries. The aim of this study is to find piwi-interacting RNAs (piRNA) predicting the prognosis of patients with colorectal cancer, using bioinformatics and evaluating these results through RT-qPCR method. Methods The target genes of piRNAs were predicted using miRDB and TargetRank databases. Protein–protein interaction (PPI) networks were constructed by STRING and were analyzed with Cytoscape software and the MCODE tool used for module construction. Expression levels of final selected piRNAs in 18 pairs of CRC tissue and adjacent normal tissue were measured by quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR). Results Twenty CRC-related piRNAs and 980 target genes were included in this study. After PPI analysis 19 hub genes were identified. Then, the prognostic value of these hub genes was assessed via Kaplan–Meier survival analyses. This survival analysis indicated that the expression of six genes was significantly associated with overall survival of patients with CRC. These genes are targets of hsa-piR-487, hsa-piR-28944 and piR-hsa-8401. Also, the pathway analysis revealed the potential signal pathways of these piRNAs targets involved in CRC. RT-qPCR showed that hsa-piR-487 and hsa-piR-28944 expression significantly were down-regulated in CRC tumor tissues compared with the adjacent normal tissues (P < 0.05, P < 0.01). Conclusion It seems that hsa-piR-487 and hsa-piR-28944 can be considered as a potential biomarker for the diagnosis of CRC. However, it is still necessary to conduct studies with a higher statistical population and measure them in the serum of patients to confirm these results. |
| format | Article |
| id | doaj-art-9bed7437b7ee4619b53127da8ae5292f |
| institution | OA Journals |
| issn | 2730-6011 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Springer |
| record_format | Article |
| series | Discover Oncology |
| spelling | doaj-art-9bed7437b7ee4619b53127da8ae5292f2025-08-20T02:28:41ZengSpringerDiscover Oncology2730-60112025-04-0116111510.1007/s12672-025-02373-xA network-based analysis to identify a piRNA-target signature related to colorectal cancer prognosis: in silico and in vitro studyFatemeh Khavari0Rezvan Najafi1Saeed Afshar2Akram Jalali3Mehrdad Hashemi4Alireza Soltanian5Fatemeh Nouri6Research Center for Molecular Medicine, Institute of Cancer, Avicenna Health Research Institute, Hamadan University of Medical SciencesResearch Center for Molecular Medicine, Institute of Cancer, Avicenna Health Research Institute, Hamadan University of Medical SciencesResearch Center for Molecular Medicine, Institute of Cancer, Avicenna Health Research Institute, Hamadan University of Medical SciencesResearch Center for Molecular Medicine, Institute of Cancer, Avicenna Health Research Institute, Hamadan University of Medical SciencesDepartment of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad UniversityModeling of Noncommunicable Diseases Research Center, Institute of Health Sciences and Technologies, Avicenna Health Research Institute, Hamadan University of Medical SciencesResearch Center for Molecular Medicine, Institute of Cancer, Avicenna Health Research Institute, Hamadan University of Medical SciencesAbstract Purpose Patients with colorectal cancer (CRC) are diagnosed in advanced stages and have worse overall survival. Also, this cancer incidence is rising in many countries. The aim of this study is to find piwi-interacting RNAs (piRNA) predicting the prognosis of patients with colorectal cancer, using bioinformatics and evaluating these results through RT-qPCR method. Methods The target genes of piRNAs were predicted using miRDB and TargetRank databases. Protein–protein interaction (PPI) networks were constructed by STRING and were analyzed with Cytoscape software and the MCODE tool used for module construction. Expression levels of final selected piRNAs in 18 pairs of CRC tissue and adjacent normal tissue were measured by quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR). Results Twenty CRC-related piRNAs and 980 target genes were included in this study. After PPI analysis 19 hub genes were identified. Then, the prognostic value of these hub genes was assessed via Kaplan–Meier survival analyses. This survival analysis indicated that the expression of six genes was significantly associated with overall survival of patients with CRC. These genes are targets of hsa-piR-487, hsa-piR-28944 and piR-hsa-8401. Also, the pathway analysis revealed the potential signal pathways of these piRNAs targets involved in CRC. RT-qPCR showed that hsa-piR-487 and hsa-piR-28944 expression significantly were down-regulated in CRC tumor tissues compared with the adjacent normal tissues (P < 0.05, P < 0.01). Conclusion It seems that hsa-piR-487 and hsa-piR-28944 can be considered as a potential biomarker for the diagnosis of CRC. However, it is still necessary to conduct studies with a higher statistical population and measure them in the serum of patients to confirm these results.https://doi.org/10.1007/s12672-025-02373-xColorectal neoplasmsPiwi-interacting RNABiomarkersPrognosis |
| spellingShingle | Fatemeh Khavari Rezvan Najafi Saeed Afshar Akram Jalali Mehrdad Hashemi Alireza Soltanian Fatemeh Nouri A network-based analysis to identify a piRNA-target signature related to colorectal cancer prognosis: in silico and in vitro study Discover Oncology Colorectal neoplasms Piwi-interacting RNA Biomarkers Prognosis |
| title | A network-based analysis to identify a piRNA-target signature related to colorectal cancer prognosis: in silico and in vitro study |
| title_full | A network-based analysis to identify a piRNA-target signature related to colorectal cancer prognosis: in silico and in vitro study |
| title_fullStr | A network-based analysis to identify a piRNA-target signature related to colorectal cancer prognosis: in silico and in vitro study |
| title_full_unstemmed | A network-based analysis to identify a piRNA-target signature related to colorectal cancer prognosis: in silico and in vitro study |
| title_short | A network-based analysis to identify a piRNA-target signature related to colorectal cancer prognosis: in silico and in vitro study |
| title_sort | network based analysis to identify a pirna target signature related to colorectal cancer prognosis in silico and in vitro study |
| topic | Colorectal neoplasms Piwi-interacting RNA Biomarkers Prognosis |
| url | https://doi.org/10.1007/s12672-025-02373-x |
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