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Shakeri F, Mohamadynejad P, Moghanibashi M. Identification of ASMTL-AS1 and LINC02604 lncRNAs as novel biomarkers for diagnosis of colorectal cancer. Int J Colorectal Dis 2024; 39:112. [PMID: 39028420 DOI: 10.1007/s00384-024-04692-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
PURPOSE Colorectal cancer is one of the major leading causes of death worldwide, and available treatments for advanced colorectal cancer are not successful. Therefore, early detection of colorectal cancer is essential to improve patient survival, and biomarkers are potential tools to achieve this goal. Considering the key role of lncRNAs in cancers, the aim of this study is to identify lncRNAs involved in colorectal cancer as new potential prognosis biomarkers for CRC. METHODS In this observational study, gene expression data obtained from the TCGA database were analyzed, Identification of differentially expressed mRNAs, miRNAs, and lncRNAs was performed, and ceRNA network was drawn. Also, survival analysis of patients was performed in order to identify potential biomarkers related to the diagnosis and prognosis of colon cancer. After confirming the results using the GSE39582 dataset, the expression of target lncRNAs in colorectal tumor tissues was also investigated to confirm the bioinformatic data. RESULTS Analysis of the TCGA data showed that the expression of three lncRNAs-SNHG7, ASMTL-AS1, and LINC02604-that had the highest interaction with other miRNAs and mRNAs identified based on the ceRNA network was increased in colorectal cancer. Also, based on the ceRNA network, three microRNAs, hsa-let-7d-5p, hsa-mir-92a-3p, and hsa-mir-423-5p, and eight mRNAs, including CPA4, MSI2, RRM2, IGF2BP1, ONECUT2, HMGA1, SOX4, and SRM, were associated with all three mentioned lncRNAs, the expression of microRNAs was decreased and the expression of mRNAs was increased. By enrichment analysis, it was found that the target lncRNAs are involved in the processes of cell proliferation, apoptosis, and metastasis, indicating their importance in the development and malignancy of colorectal cancer. Furthermore, Kaplan-Meier analysis showed a significant increase in mortality in patients with higher expression levels of these lncRNAs. Analysis of the GSE39582 dataset, and real-time RT-PCR analysis, confirmed our bioinformatic results. Also, ROC analysis showed that SNHG7 was a relatively good promising biomarker (AUC = 0.73, p value = 0.02), while ASMTL-AS1 (AUC = 0.92, p value < 0.0001) and LINC02604 (AUC = 1.00, p value < 0.0001) emerged as excellent diagnostic biomarkers in colorectal cancer. CONCLUSION It seems that increased expression of lncRNAs ASMTL-AS1 and LINC02604 can serve as molecular biomarkers for CRC, possibly through the sponge hsa-let-7d-5p, hsa-mir-92a-3p, and hsa-mir-423 5p, which increases target mRNAs, which are effective in the carcinogenesis process.
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Affiliation(s)
- Fariba Shakeri
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Parisa Mohamadynejad
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Mehdi Moghanibashi
- Department of Genetics, Faculty of Medicine, Kazerun Branch, Islamic Azad University, Kazerun, Iran
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Biyu H, Mengshan L, Yuxin H, Ming Z, Nan W, Lixin G. A miRNA-disease association prediction model based on tree-path global feature extraction and fully connected artificial neural network with multi-head self-attention mechanism. BMC Cancer 2024; 24:683. [PMID: 38840078 PMCID: PMC11151537 DOI: 10.1186/s12885-024-12420-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 05/23/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) emerge in various organisms, ranging from viruses to humans, and play crucial regulatory roles within cells, participating in a variety of biological processes. In numerous prediction methods for miRNA-disease associations, the issue of over-dependence on both similarity measurement data and the association matrix still hasn't been improved. In this paper, a miRNA-Disease association prediction model (called TP-MDA) based on tree path global feature extraction and fully connected artificial neural network (FANN) with multi-head self-attention mechanism is proposed. The TP-MDA model utilizes an association tree structure to represent the data relationships, multi-head self-attention mechanism for extracting feature vectors, and fully connected artificial neural network with 5-fold cross-validation for model training. RESULTS The experimental results indicate that the TP-MDA model outperforms the other comparative models, AUC is 0.9714. In the case studies of miRNAs associated with colorectal cancer and lung cancer, among the top 15 miRNAs predicted by the model, 12 in colorectal cancer and 15 in lung cancer were validated respectively, the accuracy is as high as 0.9227. CONCLUSIONS The model proposed in this paper can accurately predict the miRNA-disease association, and can serve as a valuable reference for data mining and association prediction in the fields of life sciences, biology, and disease genetics, among others.
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Affiliation(s)
- Hou Biyu
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Li Mengshan
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China.
| | - Hou Yuxin
- College of Computer Science and Engineering, Shanxi Datong University, Datong, Shanxi, 037000, China
| | - Zeng Ming
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Wang Nan
- College of Life Sciences, Jiaying University, Meizhou, Guangdong, 514000, China
| | - Guan Lixin
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
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Karabulut S, Şen S, Soydinç HO, Doğan İ, Taştekin D, Karabulut M, Duman M, Turan M. Investigation of the potential of miRNA candidates as non-invasive biomarkers for the diagnosis and follow-up of colorectal cancer. Pathol Res Pract 2024; 254:155094. [PMID: 38219497 DOI: 10.1016/j.prp.2024.155094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) is the third most common cancer worldwide, and despite advances in treatment, molecular biomarkers are needed for both early diagnosis and prognosis monitoring. It is known that microRNAs (miRNA), one of the epigenetic mechanisms, are effective in the initiation and development of cancer by regulating the activity of tumor suppressors and/or oncogenes. In this study, the potential of the molecules let-7, miRNA125b, and miRNA30a, which are known to play a role in cellular processes, as biomarkers for colorectal cancer and their molecular mechanisms were investigated in this model. The aim was to evaluate the diagnostic, prognostic, and predictive utility of the target miRNAs in colorectal cancer patients. MATERIAL AND METHODS The expression changes of miRNAs let-7, miRNA125b, and miRNA30a were investigated by miRNAs isolation and cDNA synthesis from the serum samples of 60 patients diagnosed with CRC or from the serum samples of 20 healthy individuals. The calculation was performed using the quantitative real-time polymerase chain reaction method to determine the expression level. The results were compared with clinical parameters. RESULT An 8-fold decrease in the expression of let-7 and miRNA125b and a 60-fold decrease in the expression of miRNA30a were found in the serum samples of patients diagnosed with colorectal cancer (CRC) compared to the healthy group. A decrease in let-7 was observed in 53.3%, miRNA125b in 58.3%, and miRNA30a in 55% of patients. A significant correlation was found between the reduced expression status and the stage, lymph nodes, local recurrence, and metastasis (p < 0.05). The ROC analysis showed that the miRNA30a level could be a diagnostic biomarker for CRC (p < 0.001). No significant impact of target miRNA expression changes on overall disease survival was observed. CONCLUSION It is thought that the target miRNA30a can be used for early diagnosis and screening and that the target miRNA let-7, miRNA125b, and miRNA30a can be used as non-invasive biomarkers for disease follow-up, with larger patient studies being conducted on CRC patients.
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Affiliation(s)
- Senem Karabulut
- Department of Clinic Oncology, Oncology Institute, Istanbul University, Istanbul, Turkiye; Department of Molecular Oncology, Hamidiye Health Sciences Institute, University of Health Sciences, Istanbul, Turkiye.
| | - Sena Şen
- Department of Basic Oncology, Oncology Institute, Istanbul University, Istanbul, Turkiye
| | - Hilal Oğuz Soydinç
- Department of Basic Oncology, Oncology Institute, Istanbul University, Istanbul, Turkiye
| | - İzzet Doğan
- Department of Clinic Oncology, Oncology Institute, Istanbul University, Istanbul, Turkiye
| | - Didem Taştekin
- Department of Clinic Oncology, Oncology Institute, Istanbul University, Istanbul, Turkiye
| | - Mehmet Karabulut
- Department of General Surgery, Dr. Sadi Konuk Education and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Mustafa Duman
- Department of Molecular Oncology, Hamidiye Health Sciences Institute, University of Health Sciences, Istanbul, Turkiye
| | - Mustafa Turan
- Department of Molecular Oncology, Hamidiye Health Sciences Institute, University of Health Sciences, Istanbul, Turkiye
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Ponomaryova AA, Rykova EY, Solovyova AI, Tarasova AS, Kostromitsky DN, Dobrodeev AY, Afanasiev SA, Cherdyntseva NV. Genomic and Transcriptomic Research in the Discovery and Application of Colorectal Cancer Circulating Markers. Int J Mol Sci 2023; 24:12407. [PMID: 37569782 PMCID: PMC10419249 DOI: 10.3390/ijms241512407] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/24/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Colorectal cancer (CRC) is the most frequently occurring malignancy in the world. However, the mortality from CRC can be reduced through early diagnostics, selection of the most effective treatment, observation of the therapy success, and the earliest possible diagnosis of recurrences. A comprehensive analysis of genetic and epigenetic factors contributing to the CRC development is needed to refine diagnostic, therapeutic, and preventive strategies and to ensure appropriate decision making in managing specific CRC cases. The liquid biopsy approach utilizing circulating markers has demonstrated its good performance as a tool to detect the changes in the molecular pathways associated with various cancers. In this review, we attempted to brief the main tendencies in the development of circulating DNA and RNA-based markers in CRC such as cancer-associated DNA mutations, DNA methylation changes, and non-coding RNA expression shifts. Attention is devoted to the existing circulating nucleic acid-based CRC markers, the possibility of their application in clinical practice today, and their future improvement. Approaches to the discovery and verification of new markers are described, and the existing problems and potential solutions for them are highlighted.
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Affiliation(s)
- Anastasia A. Ponomaryova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Elena Yu. Rykova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Engineering Problems of Ecology, Novosibirsk State Technical University, 630087 Novosibirsk, Russia
| | - Anastasia I. Solovyova
- Department of Biochemistry, Medico-Biological Faculty, Siberian State Medical University, 634050 Tomsk, Russia
| | - Anna S. Tarasova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Dmitry N. Kostromitsky
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Alexey Yu. Dobrodeev
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Sergey A. Afanasiev
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Nadezhda V. Cherdyntseva
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
- Faculty of Chemistry, National Research Tomsk State University, 634050 Tomsk, Russia
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Shaikh K, Iqbal Y, Abdel-Maksoud MA, Murad A, Badar N, Alarjani KM, Siddiqui K, Chandio K, Almanaa TN, Jamil M, Ali M, Jabeen N, Hussein AM. Characterization of ferroptosis driver gene signature in head and neck squamous cell carcinoma (HNSC). Am J Transl Res 2023; 15:4829-4850. [PMID: 37560204 PMCID: PMC10408515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/29/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSC), a prevalent malignant tumor with a low survival rate, is often accompanied by ferroptosis, which is a recently-described type ofprogrammed cell death. Investigating the significance of ferroptosis driver genes in HNSC, this study aimed to assess their diagnostic and prognostic values, as well as their impact on treatment and tumor immune function. The results of this investigation provide novel insight into using ferroptosis-related genes as molecular biomarkers as well as precise chemotherapeutic targets for the therapy of HNSC. METHODOLOGY A detailed in silico and in vitro experiment-based methodology was adopted to achieve the goals. RESULTS A total of 233 ferroptosis driver genes were downloaded from the FerrDB database. After comprehensively analyzing these 233 ferroptosis driver genes by various TCGA databases, RNA-sequencing (RNA-seq), and Reverse Transcription Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR) techniques, TP53 (tumor protein 53), PTEN (Phosphatase and TENsin homolog deleted on chromosome 10), KRAS (Ki-ras2 Kirsten rat sarcoma viral oncogene homolog), and HRAS (Harvey Rat sarcoma virus) were identified as differentially expressed hub genes. Interestingly, these hub genes were found to have significant (P < 0.05) variations in their mRNA and protein expressions and effects on overall survival of the HNSC patients. Moreover, targeted bisulfite-sequencing (bisulfite-seq) analysis revealed that promoter hypomethylation pattern was associated with up-regulation of hub genes (TP53, PTEN, KRAS, and HRAS). In addition to this, hub genes were involved in diverse oncogenic pathways. CONCLUSION Since HNSC pathogenesis is a complex process, using ferroptosis driver hub genes (TP53, PTEN, KRAS, and HRAS) as a diagnostic and prognostic tool, and therapeutically targeting those genes through appropriate drugs could bring a milestone change in the drug discovery and management and survival in HNSC.
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Affiliation(s)
- Khalida Shaikh
- Liaquat University of Medical and Health SciencesJamshoro, Pakistan
| | - Yusra Iqbal
- Continental Medical College LahoreLahore 54660, Pakistan
| | - Mostafa A Abdel-Maksoud
- Botany and Microbiology Department, College of Science, King Saud UniversityRiyadh 11451, Saudi Arabia
| | - Amina Murad
- Department of Bioscience, Comsats UniversityIslamabad, Pakistan
| | - Nadia Badar
- Department of Medical Oncology Allied HospitalFaisalabad, Pakistan
| | - Khaloud Mohammed Alarjani
- Botany and Microbiology Department, College of Science, King Saud UniversityRiyadh 11451, Saudi Arabia
| | - Komal Siddiqui
- Institute of Biotechnology and Genetic Engineering University of SindhJamshoro, Pakistan
| | | | | | - Muhammad Jamil
- PARC Arid Zone Research CentreDera Ismail Khan 29050, Pakistan
| | - Mubarik Ali
- Animal Science Institute, National Agricultural Research CenterIslamabad 54000, Pakistan
| | - Norina Jabeen
- Department of Rural Sociology, University of AgricultureFaisalabad 38000, Pakistan
| | - Ahmed M Hussein
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna1090 Vienna, Austria
- Programme for Proteomics, Paracelsus Medical UniversitySalzburg, Austria
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Tesolato SE, González-Gamo D, Barabash A, Claver P, de la Serna SC, Domínguez-Serrano I, Dziakova J, de Juan C, Torres AJ, Iniesta P. Expression Analysis of hsa-miR-181a-5p, hsa-miR-143-3p, hsa-miR-132-3p and hsa-miR-23a-3p as Biomarkers in Colorectal Cancer-Relationship to the Body Mass Index. Cancers (Basel) 2023; 15:3324. [PMID: 37444431 DOI: 10.3390/cancers15133324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/16/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
This work aims to investigate the expression levels of four preselected miRNAs previously linked to cancer and/or obesity, with the purpose of finding potential biomarkers in the clinical management of CRC developed by patients showing different BMI values. We analyzed samples from a total of 65 subjects: 43 affected by CRC and 22 without cancer. Serum and both subcutaneous and omental adipose tissues (SAT and OAT) were investigated, as well as tumor and non-tumor colorectal tissues in the case of the CRC patients. The relative expression (2-∆∆Ct) levels of 4 miRNAs (hsa-miR-181a-5p, hsa-miR-143-3p, has-miR-132-3p and hsa-miR-23a-3p) were measured by RT-qPCR. Serum, SAT and OAT expression levels of these miRNAs showed significant differences between subjects with and without CRC, especially in the group of overweight/obese subjects. In CRC, serum levels of hsa-miR-143-3p clearly correlated with their levels in both SAT and OAT, independently of the BMI group. Moreover, hsa-miR-181a-5p could be considered as a biomarker in CRC patients with BMI ≥ 25 Kg/m2 and emerges as a tumor location marker. We conclude that both adiposity and CRC induce changes in the expression of the miRNAs investigated, and hsa-miR-143-3p and hsa-miR-181a-5p expression analysis could be useful in the clinical management of CRC.
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Affiliation(s)
- Sofía Elena Tesolato
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University, 28040 Madrid, Spain
- Health Research Institute of the San Carlos Hospital (IdISSC), 28040 Madrid, Spain
| | - Daniel González-Gamo
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University, 28040 Madrid, Spain
| | - Ana Barabash
- Health Research Institute of the San Carlos Hospital (IdISSC), 28040 Madrid, Spain
- CIBERDEM (Network Biomedical Research Center for Diabetes and Associated Metabolic Diseases), Carlos III Institute of Health, 28029 Madrid, Spain
- Endocrinology & Nutrition Service, San Carlos Hospital, 28040 Madrid, Spain
- Department of Medicine, Faculty of Medicine, Complutense University, 28040 Madrid, Spain
| | - Paula Claver
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University, 28040 Madrid, Spain
| | - Sofía Cristina de la Serna
- Health Research Institute of the San Carlos Hospital (IdISSC), 28040 Madrid, Spain
- Digestive Surgery Service, San Carlos Hospital, 28040 Madrid, Spain
| | - Inmaculada Domínguez-Serrano
- Health Research Institute of the San Carlos Hospital (IdISSC), 28040 Madrid, Spain
- Digestive Surgery Service, San Carlos Hospital, 28040 Madrid, Spain
| | - Jana Dziakova
- Health Research Institute of the San Carlos Hospital (IdISSC), 28040 Madrid, Spain
- Digestive Surgery Service, San Carlos Hospital, 28040 Madrid, Spain
| | - Carmen de Juan
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University, 28040 Madrid, Spain
- Health Research Institute of the San Carlos Hospital (IdISSC), 28040 Madrid, Spain
| | - Antonio José Torres
- Health Research Institute of the San Carlos Hospital (IdISSC), 28040 Madrid, Spain
- Digestive Surgery Service, San Carlos Hospital, 28040 Madrid, Spain
| | - Pilar Iniesta
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University, 28040 Madrid, Spain
- Health Research Institute of the San Carlos Hospital (IdISSC), 28040 Madrid, Spain
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