1
|
Gomes BC, Peixinho N, Pisco R, Gromicho M, Pronto-Laborinho AC, Rueff J, de Carvalho M, Rodrigues AS. Differential Expression of miRNAs in Amyotrophic Lateral Sclerosis Patients. Mol Neurobiol 2023; 60:7104-7117. [PMID: 37531027 PMCID: PMC10657797 DOI: 10.1007/s12035-023-03520-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/14/2023] [Indexed: 08/03/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease that affects nerve cells in the brain and spinal cord, causing loss of muscle control, muscle atrophy and in later stages, death. Diagnosis has an average delay of 1 year after symptoms onset, which impairs early management. The identification of a specific disease biomarker could help decrease the diagnostic delay. MicroRNA (miRNA) expression levels have been proposed as ALS biomarkers, and altered function has been reported in ALS pathogenesis. The aim of this study was to assess the differential expression of plasma miRNAs in ALS patients and two control populations (healthy controls and ALS-mimic disorders). For that, 16 samples from each group were pooled, and then 1008 miRNAs were assessed through reverse transcription-quantitative polymerase chain reaction (RT-qPCR). From these, ten candidate miRNAs were selected and validated in 35 ALS patients, 16 ALS-mimic disorders controls and 15 healthy controls. We also assessed the same miRNAs in two different time points of disease progression. Although we were unable to determine a miRNA signature to use as disease or condition marker, we found that miR-7-2-3p, miR-26a-1-3p, miR-224-5p and miR-206 are good study candidates to understand the pathophysiology of ALS.
Collapse
Affiliation(s)
- Bruno Costa Gomes
- Instituto de Fisiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
- ToxOmics, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa, Portugal.
| | - Nuno Peixinho
- ToxOmics, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Rita Pisco
- ToxOmics, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Marta Gromicho
- Instituto de Fisiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Catarina Pronto-Laborinho
- Instituto de Fisiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - José Rueff
- ToxOmics, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Mamede de Carvalho
- Instituto de Fisiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Department of Neurosciences and Mental Health, Hospital de Santa Maria CHULN, Lisboa, Portugal
| | - António Sebastião Rodrigues
- ToxOmics, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa, Portugal
| |
Collapse
|
2
|
Patel A, Patel P, Mandlik D, Patel K, Malaviya P, Johar K, Swamy KBS, Patel S, Tanavde V. A novel 3-miRNA network regulates tumour progression in oral squamous cell carcinoma. Biomark Res 2023; 11:64. [PMID: 37316916 PMCID: PMC10268489 DOI: 10.1186/s40364-023-00505-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Late diagnosis is one of the major confounders in oral squamous cell carcinoma (OSCC). Despite recent advances in molecular diagnostics, no disease-specific biomarkers are clinically available for early risk prediction of OSCC. Therefore, it is important to identify robust biomarkers that are detectable using non-invasive liquid biopsy techniques to facilitate the early diagnosis of oral cancer. This study identified potential salivary exosome-derived miRNA biomarkers and crucial miRNA-mRNA networks/underlying mechanisms responsible for OSCC progression. METHODS Small RNASeq (n = 23) was performed in order to identify potential miRNA biomarkers in both tissue and salivary exosomes derived from OSCC patients. Further, integrated analysis of The Cancer Genome Atlas (TCGA) datasets (n = 114), qPCR validation on larger patient cohorts (n = 70) and statistical analysis with various clinicopathological parameters was conducted to assess the effectiveness of the identified miRNA signature. miRNA-mRNA networks and pathway analysis was conducted by integrating the transcriptome sequencing and TCGA data. The OECM-1 cell line was transfected with the identified miRNA signature in order to observe its effect on various functional mechanisms such as cell proliferation, cell cycle, apoptosis, invasive as well as migratory potential and the downstream signaling pathways regulated by these miRNA-mRNA networks. RESULTS Small RNASeq and TCGA data identified 12 differentially expressed miRNAs in OSCC patients compared to controls. On validating these findings in a larger cohort of patients, miR-140-5p, miR-143-5p, and miR-145-5p were found to be significantly downregulated. This 3-miRNA signature demonstrated higher efficacy in predicting disease progression and clinically correlated with poor prognosis (p < 0.05). Transcriptome, TCGA, and miRNA-mRNA network analysis identified HIF1a, CDH1, CD44, EGFR, and CCND1 as hub genes regulated by the miRNA signature. Further, transfection-mediated upregulation of the 3-miRNA signature significantly decreased cell proliferation, induced apoptosis, resulted in G2/M phase cell cycle arrest and reduced the invasive and migratory potential by reversing the EMT process in the OECM-1 cell line. CONCLUSIONS Thus, this study identifies a 3-miRNA signature that can be utilized as a potential biomarker for predicting disease progression of OSCC and uncovers the underlying mechanisms responsible for converting a normal epithelial cell into a malignant phenotype.
Collapse
Affiliation(s)
- Aditi Patel
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, 380009, Gujarat, India
| | - Parina Patel
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, 380009, Gujarat, India
| | - Dushyant Mandlik
- Department of Head and Neck Oncology, HCG Cancer Centre, Ahmedabad, Gujarat, India
| | - Kaustubh Patel
- Department of Head and Neck Oncology, HCG Cancer Centre, Ahmedabad, Gujarat, India
| | - Pooja Malaviya
- Department of Cell and Molecular Biology, Iladevi Cataract and IOL Research Centre, Ahmedabad, Gujarat, India
| | - Kaid Johar
- Department of Zoology, BMTC and Human Genetics, School of Sciences, Gujarat University, Ahmedabad, India
| | - Krishna B S Swamy
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, 380009, Gujarat, India
| | - Shanaya Patel
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, 380009, Gujarat, India.
| | - Vivek Tanavde
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, 380009, Gujarat, India.
- Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), Singapore, Singapore.
| |
Collapse
|
3
|
Wang Y, Tian X, Zhu SX, Xu WH, Anwaier A, Su JQ, Gan HL, Qu YY, Zhao JY, Zhang HL, Ye DW. Identification of prognostic and therapeutic biomarkers in type 2 papillary renal cell carcinoma. World J Surg Oncol 2023; 21:98. [PMID: 36927438 PMCID: PMC10022194 DOI: 10.1186/s12957-022-02836-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/08/2022] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Papillary renal cell carcinoma (PRCC) can be divided into type 1 (PRCC1) and type 2 (PRCC2) and PRCC2 share a more invasive phenotype and worse prognosis. This study aims to identify potential prognostic and therapeutic biomarkers in PRCC2. METHODS A cohort from The Cancer Genome Atlas and two datasets from Gene Expression Omnibus were examined. Common differentially expressed genes (DEGs) were screened and potential biomarkers were explored by using Kaplan-Meier method and cox regression analysis. Functional enrichment analysis was utilized to evaluate the potential biological functions. Tumor infiltrating immune cells were estimated by CIBERSORT algorithm. Ninety-two PRCC2 samples from Fudan University Shanghai Cancer Center were obtained, and immunostaining was performed to validate prognostic and therapeutic significance of the potential biomarker. RESULTS PRCC2 has worse overall survival and shares distinct molecular characteristics from PRCC1. There was significant higher expression level of Targeting protein for Xklp2 (TPX2) in PRCC2 compared with normal tissues. Higher expression level of TPX2 was significantly associated with worse overall survival in PRCC2 and kinesin family genes expression were found significantly elevated in high risk PRCC2. Abundance of tumor infiltrating M1 macrophage was significantly higher in PRCC2 and it was also associated with worse overall survival. In the FUSCC cohort, higher TPX2 expression was significantly correlated with worse overall and progression-free survival. Retrospective analysis indicated that mTOR inhibitor (everolimus) had greater efficacy in the high-risk group than in the low-risk group (overall response rate: 28.6% vs. 16.7%) and that everolimus had greater efficacy than sunitinib in the high-risk group (overall response rate: 28.6% vs. 20%). CONCLUSIONS TPX2 was a prognostic and therapeutic biomarker in PRCC2. Higher abundance of tumor infiltrating M1 macrophage was significantly associated with worse overall survival in PRCC2. mTOR inhibitors may have good efficacy in patients with high-risk PRCC2.
Collapse
Affiliation(s)
- Yue Wang
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 20032, People's Republic of China
| | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 20032, People's Republic of China
| | - Shu-Xuan Zhu
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, 400016, China
| | - Wen-Hao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 20032, People's Republic of China
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 20032, People's Republic of China
| | - Jia-Qi Su
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 20032, People's Republic of China
| | - Hua-Lei Gan
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 20032, People's Republic of China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Yuan-Yuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 20032, People's Republic of China.
| | - Jian-Yuan Zhao
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.
| | - Hai-Liang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 20032, People's Republic of China.
| | - Ding-Wei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 20032, People's Republic of China.
| |
Collapse
|
4
|
Crosstalk of miRNAs with signaling networks in bladder cancer progression: Therapeutic, diagnostic and prognostic functions. Pharmacol Res 2022; 185:106475. [DOI: 10.1016/j.phrs.2022.106475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/17/2022] [Accepted: 09/27/2022] [Indexed: 12/24/2022]
|
5
|
Horak J, Dolnikova A, Cumaogullari O, Cumova A, Navvabi N, Vodickova L, Levy M, Schneiderova M, Liska V, Andera L, Vodicka P, Opattova A. MiR-140 leads to MRE11 downregulation and ameliorates oxaliplatin treatment and therapy response in colorectal cancer patients. Front Oncol 2022; 12:959407. [PMID: 36324569 PMCID: PMC9618941 DOI: 10.3389/fonc.2022.959407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/01/2022] [Indexed: 12/02/2022] Open
Abstract
Cancer therapy failure is a fundamental challenge in cancer treatment. One of the most common reasons for therapy failure is the development of acquired resistance of cancer cells. DNA-damaging agents are frequently used in first-line chemotherapy regimens and DNA damage response, and DNA repair pathways are significantly involved in the mechanisms of chemoresistance. MRE11, a part of the MRN complex involved in double-strand break (DSB) repair, is connected to colorectal cancer (CRC) patients’ prognosis. Our previous results showed that single-nucleotide polymorphisms (SNPs) in the 3′ untranslated region (3′UTR) microRNA (miRNA) binding sites of MRE11 gene are associated with decreased cancer risk but with shorter survival of CRC patients, which implies the role of miRNA regulation in CRC. The therapy of colorectal cancer utilizes oxaliplatin (oxalato(trans-l-1,2-diaminocyclohexane)platinum), which is often compromised by chemoresistance development. There is, therefore, a crucial clinical need to understand the cellular processes associated with drug resistance and improve treatment responses by applying efficient combination therapies. The main aim of this study was to investigate the effect of miRNAs on the oxaliplatin therapy response of CRC patients. By the in silico analysis, miR-140 was predicted to target MRE11 and modulate CRC prognosis. The lower expression of miR-140 was associated with the metastatic phenotype (p < 0.05) and poor progression-free survival (odds ratio (OR) = 0.4, p < 0.05). In the in vitro analysis, we used miRNA mimics to increase the level of miR-140 in the CRC cell line. This resulted in decreased proliferation of CRC cells (p < 0.05). Increased levels of miR-140 also led to increased sensitivity of cancer cells to oxaliplatin (p < 0.05) and to the accumulation of DNA damage. Our results, both in vitro and in vivo, suggest that miR-140 may act as a tumor suppressor and plays an important role in DSB DNA repair and, consequently, CRC therapy response.
Collapse
Affiliation(s)
- Josef Horak
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine Czech Academy of Sciences (CAS), Prague, Czechia
- Third Faculty of Medicine, Charles University, Prague, Czechia
| | - Alexandra Dolnikova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine Czech Academy of Sciences (CAS), Prague, Czechia
- First Faculty of Medicine, Charles University, Prague, Czechia
| | - Ozge Cumaogullari
- Eastern Mediterranean University, Dr. Fazıl Küçük Faculty of Medicine, North Cyprus, Turkey
- Gazimağusa State Hospital, Molecular Genetics Research Laboratory, North Cyprus, Turkey
| | - Andrea Cumova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine Czech Academy of Sciences (CAS), Prague, Czechia
- First Faculty of Medicine, Charles University, Prague, Czechia
| | - Nazila Navvabi
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine Czech Academy of Sciences (CAS), Prague, Czechia
- Biomedical Center in Pilsen, Charles University, Pilsen, Czechia
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine Czech Academy of Sciences (CAS), Prague, Czechia
- First Faculty of Medicine, Charles University, Prague, Czechia
- Biomedical Center in Pilsen, Charles University, Pilsen, Czechia
| | - Miroslav Levy
- Surgical Department, 1.st Medical Faculty, Charles University and Thomayer Hospital, Prague, Czechia
| | - Michaela Schneiderova
- Department of Surgery, University Hospital Kralovske Vinohrady and 3rd Faculty of Medicine, Charles University, Prague, Czechia
| | - Vaclav Liska
- Biomedical Center in Pilsen, Charles University, Pilsen, Czechia
- Department of Surgery, Medical Faculty in Pilsen, Charles University, Pilsen, Czechia
| | - Ladislav Andera
- Institute of Biotechnology, Czech Academy of Sciences (CAS), Vestec, Czechia
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine Czech Academy of Sciences (CAS), Prague, Czechia
- First Faculty of Medicine, Charles University, Prague, Czechia
- Biomedical Center in Pilsen, Charles University, Pilsen, Czechia
- *Correspondence: Alena Opattova, ; Pavel Vodicka,
| | - Alena Opattova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine Czech Academy of Sciences (CAS), Prague, Czechia
- First Faculty of Medicine, Charles University, Prague, Czechia
- Biomedical Center in Pilsen, Charles University, Pilsen, Czechia
- *Correspondence: Alena Opattova, ; Pavel Vodicka,
| |
Collapse
|
6
|
Zhou ZY, Yang JY, Shao CZ, Luo F, Du W. Positive regulation of ataxia-telangiectasia-mutated protein (ATM) by E2F transcription Factor 1 (E2F-1) in cisplatin-resistant nasopharyngeal carcinoma cells. World J Surg Oncol 2022; 20:88. [PMID: 35303867 PMCID: PMC8933998 DOI: 10.1186/s12957-022-02546-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 02/28/2022] [Indexed: 11/10/2022] Open
Abstract
Objective To explore the mechanism of E2F transcription Factor 1 (E2F-1)-mediated ataxia-telangiectasia-mutated protein (ATM) in cisplatin (DDP)-resistant nasopharyngeal carcinoma (NPC). Methods E2F-1 and ATM expression was assessed in DDP-resistant NPC cell lines (CNE2/DDP and HNE1/DDP) and parental cells. Then, DDP-resistant NPC cells were transfected with control shRNA (short hairpin RNA) or E2F-1 shRNAs with or without ATM lentiviral activation particles. The half maximal inhibitory concentration (IC50) was evaluated by 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assay, and the cell cycle and cell proliferation were measured by flow cytometry and EdU staining, respectively. In addition, the expression of genes and proteins was quantified by quantitative reverse-transcription polymerase chain reaction (qRT–PCR) and western blotting, respectively. Results Both E2F-1 and ATM expression in DDP-resistant NPC cells was much higher than that in parental cells. E2F-1 shRNA reduced ATM expression in DDP-resistant NPC cells, but ATM overexpression had no significant effect on E2F-1. ATM overexpression enhanced DDP resistance in DDP-resistant NPC cells with increased IC50 values, which was reversed by E2F-1 inhibition. Meanwhile, ATM overexpression resulted in upregulation of ABCA2 and ABCA5 in DDP-resistant NPC cells, induced elevations in the transition of the cells into S-phase, and increased cell proliferation with enhanced expression of cyclin E1, CDK2, and Ki67, which was reversed by E2F-1 shRNAs. Conclusion Downregulation of E2F-1, possibly by regulating ATM, could block the cell cycle in the G1 phase and reduce the proliferation of CNE2/DDP cells, thereby reversing the resistance of human NPC cells to DDP.
Collapse
Affiliation(s)
- Zun-Yan Zhou
- Department of Oncology, The First People's Hospital of Jingzhou, Jingzhou, 434000, China
| | - Ji-Yuan Yang
- Department of Oncology, The First People's Hospital of Jingzhou, Jingzhou, 434000, China
| | - Cheng-Ze Shao
- Department of Oncology, The First People's Hospital of Jingzhou, Jingzhou, 434000, China
| | - Fei Luo
- Department of Oncology, The First People's Hospital of Jingzhou, Jingzhou, 434000, China
| | - Wei Du
- Department of Oncology, The First People's Hospital of Jingzhou, Jingzhou, 434000, China.
| |
Collapse
|