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Jayarathna DK, Rentería ME, Batra J, Gandhi NS. Integrative competing endogenous RNA network analyses identify novel lncRNA and genes implicated in metastatic breast cancer. Sci Rep 2023; 13:2423. [PMID: 36765262 PMCID: PMC9918521 DOI: 10.1038/s41598-023-29585-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Competing endogenous RNAs (ceRNAs) have gained attention in cancer research owing to their involvement in microRNA-mediated gene regulation. Previous studies have identified ceRNA networks of individual cancers. Nevertheless, none of these studies has investigated different cancer stages. We identify stage-specific ceRNAs in breast cancer using the cancer genome atlas data. Moreover, we investigate the molecular functions and prognostic ability of ceRNAs involved in stage I-IV networks. We identified differentially expressed candidate ceRNAs using edgeR and limma R packages. A three-step analysis was used to identify statistically significant ceRNAs of each stage. Survival analysis and functional enrichment analysis were conducted to identify molecular functions and prognostic ability. We found five genes and one long non-coding RNA unique to the stage IV ceRNA network. These genes have been described in previous breast cancer studies. Genes acted as ceRNAs are enriched in cancer-associated pathways. Two, three, and three microRNAs from stages I, II, and III were prognostic from the Kaplan-Meier survival analysis. Our results reveal a set of unique ceRNAs in metastatic breast cancer. Further experimental work is required to evaluate their role in metastasis. Moreover, identifying stage-specific ceRNAs will improve the understanding of personalised therapeutics in breast cancer.
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Affiliation(s)
- Dulari K Jayarathna
- Centre for Genomics and Personalised Health, School of Chemistry and Physics, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Miguel E Rentería
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Kelvin Grove, Brisbane, QLD, 4059, Australia
| | - Jyotsna Batra
- Centre for Genomics and Personalised Health, School of Chemistry and Physics, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Kelvin Grove, Brisbane, QLD, 4059, Australia
- Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Neha S Gandhi
- Centre for Genomics and Personalised Health, School of Chemistry and Physics, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia.
- Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.
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Piechowska A, Kruszniewska-Rajs C, Kimsa-Dudek M, Kołomańska M, Strzałka-Mrozik B, Gola J, Głuszek S. The role of miR-370 and miR-138 in the regulation of BMP2 suppressor gene expression in colorectal cancer: preliminary studies. J Cancer Res Clin Oncol 2022; 148:1569-1582. [PMID: 35292840 DOI: 10.1007/s00432-022-03977-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/06/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE Colorectal cancer (CRC) is the fourth-most common cancer worldwide and the second most common cancer cause of death in the world. The components of the TGFβ-signalling pathway, which are often affected by miRNAs, are involved in the regulation of apoptosis and cell cycle. Therefore, in the current study, the expression of BMP2 gene in CRC tissues at different clinical stages compared to the non-tumour tissues has been assessed. Moreover, the plasma BMP2 protein concentration in the same group of CRC patients has been validated. Due to the constant necessity to conduct further research of the correlation between specific miRNAs and mRNAs in CRC, in silico analysis has been performed to select miRNAs that regulate BMP2 mRNA. METHODS The cDNA samples from tumor and non-tumor tissue were used in a qPCR reaction to determine the mRNA expression of the BMP2 gene and the expression of selected miRNAs. The concentration of BMP2 protein in plasma samples was also measured. RESULTS It was indicated that BMP2 was downregulated in CRC tissue. Moreover, miR-370 and miR-138 expression showed an upward trend. Decreased BMP2 with accompanied increasing miR-370 and miR-138 expression was relevant to the malignant clinicopathological features of CRC and consequently poor patient prognosis. CONCLUSION Our data suggest that miR-370 with its clear expression in plasma samples may be a potential diagnostic marker to determine the severity of the disease in patients at a later stage of colorectal cancer.
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Affiliation(s)
- Agnieszka Piechowska
- Department of Surgical Medicine With the Laboratory of Medical Genetics, Institute of Medical Sciences, Collegium Medicum, Jan Kochanowski University, Kielce, Poland
| | - Celina Kruszniewska-Rajs
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, Jednosci 8, 41-200, Sosnowiec, Poland
| | - Magdalena Kimsa-Dudek
- Department of Nutrigenomics and Bromatology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, Jednosci 8, 41-200, Sosnowiec, Poland
| | - Magdalena Kołomańska
- Department of Anatomy, Institute of Medical Sciences, Collegium Medicum, Jan Kochanowski University, Kielce, Poland
| | - Barbara Strzałka-Mrozik
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, Jednosci 8, 41-200, Sosnowiec, Poland.
| | - Joanna Gola
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, Jednosci 8, 41-200, Sosnowiec, Poland
| | - Stanisław Głuszek
- Department of Surgical Medicine With the Laboratory of Medical Genetics, Institute of Medical Sciences, Collegium Medicum, Jan Kochanowski University, Kielce, Poland.,Department of Clinic General Oncological and Endocrinological Surgery, Regional Hospital, Kielce, Poland
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Gray PC, Choe S. Design-augmented (DA) biologics: BMP chimeras for bone and cartilage regeneration. Osteoarthritis Cartilage 2020; 28:123-125. [PMID: 31606451 DOI: 10.1016/j.joca.2019.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 09/20/2019] [Accepted: 09/28/2019] [Indexed: 02/02/2023]
Affiliation(s)
- P C Gray
- Qualcomm Institute, University of California San Diego, Atkinson Hall - Fifth Floor, 9500 Gilman Drive #0436, La Jolla, CA 92093-0436, USA.
| | - S Choe
- Qualcomm Institute, University of California San Diego, Atkinson Hall - Fifth Floor, 9500 Gilman Drive #0436, La Jolla, CA 92093-0436, USA; Protein Engineering Laboratory, Joint Center for Biosciences, Songdo Smart Valley, Yeonsu-gu, Incheon, 406-840, USA.
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Zhang L, Hao C, Wu Y, Zhu Y, Ren Y, Tong Z. Microcalcification and BMP-2 in breast cancer: correlation with clinicopathological features and outcomes. Onco Targets Ther 2019; 12:2023-2033. [PMID: 30936719 PMCID: PMC6421899 DOI: 10.2147/ott.s187835] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Microcalcification is a very important diagnostic information in breast cancer. The purpose of this study was to determine the relationship of clinicopathological features and prognosis of breast cancer with microcalcification and to detect biomarkers related to the possible mechanisms of microcalcifications. Patients and methods All 529 subjects with microcalcifications were selected from patients who had been examined using breast mammography. The control group did not have detectable microcalcifications, and was matched in a ratio of 1:3. The clinicopathological factors, progression-free survival (PFS), and overall survival were evaluated by SPSS. Results There was a significant difference in tumor size between the two groups, with larger tumors in the calcification group than the control group, and the proportion of patients in the calcification group with tumors of >5 cm was 20.4% vs 17.2% in the control group (P=0.041). The proportion of patients with lymph node metastasis in the calcification group was higher than that of the control group (35% vs 27.9%, P=0.027). The recurrence rate in ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC) patients with microcalcification was higher than that in the control group (P=0.035 and 0.044). BMP-2 expression was higher in breast cancer tissues, especially in breast cancer tissues with microcalcifications. The recurrence rate in the BMP-2(+) group was higher than that in the BMP-2(-) group both in DCIS and IDC (P=0.044 and 0.049). Microcalcifications and the positive expression of BMP-2 were independent factors affecting the PFS of the breast cancer patients. Conclusion Through the analysis of this study, it was found that the prognosis of the patients with microcalcification was relatively poor. BMP-2 was highly expressed in the breast cancer with microcalcification and was associated with poor prognosis.
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Affiliation(s)
- Li Zhang
- Department of Breast Oncology, Key Laboratory of Breast Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China,
| | - Chunfang Hao
- Department of Breast Oncology, Key Laboratory of Breast Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China,
| | - Yansheng Wu
- Department of Maxillofacial and Otorhinolaryngology Head and Neck Surgery, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Yuying Zhu
- Department of Breast Oncology, Key Laboratory of Breast Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China,
| | - Yulin Ren
- Department of Breast Oncology, Key Laboratory of Breast Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China,
| | - Zhongsheng Tong
- Department of Breast Oncology, Key Laboratory of Breast Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China,
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Engineering TGF-β superfamily ligands for clinical applications. Trends Pharmacol Sci 2014; 35:648-57. [PMID: 25458539 DOI: 10.1016/j.tips.2014.10.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/14/2014] [Accepted: 10/14/2014] [Indexed: 12/11/2022]
Abstract
TGF-β superfamily ligands govern normal tissue development and homeostasis, and their dysfunction is a hallmark of many diseases. These ligands are also well defined both structurally and functionally. This review focuses on TGF-β superfamily ligand engineering for therapeutic purposes, in particular for regenerative medicine and musculoskeletal disorders. We describe the key discovery that structure-guided mutation of receptor-binding epitopes, especially swapping of these epitopes between ligands, results in new ligands with unique functional properties that can be harnessed clinically. Given the promising results with prototypical engineered TGF-β superfamily ligands, and the vast number of such molecules that remain to be produced and tested, this strategy is likely to hold great promise for the development of new biologics.
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