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Fotopoulos I, Nguyen OTD, Nøst TH, Markaki M, Lagani V, Mjelle R, Sandanger TM, Sætrom P, Tsamardinos I, Røe OD. Promising microRNAs in pre-diagnostic serum associated with lung cancer up to eight years before diagnosis: a HUNT study. J Cancer Res Clin Oncol 2024; 150:355. [PMID: 39031255 PMCID: PMC11271336 DOI: 10.1007/s00432-024-05882-4] [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: 05/25/2024] [Accepted: 07/04/2024] [Indexed: 07/22/2024]
Abstract
INTRODUCTION Blood biomarkers for early detection of lung cancer (LC) are in demand. There are few studies of the full microRNome in serum of asymptomatic subjects that later develop LC. Here we searched for novel microRNA biomarkers in blood from non-cancer, ever-smokers populations up to eight years before diagnosis. METHODS Serum samples from 98,737 subjects from two prospective population studies, HUNT2 and HUNT3, were considered initially. Inclusion criteria for cases were: ever-smokers; no known cancer at study entrance; 0-8 years from blood sampling to LC diagnosis. Each future LC case had one control matched to sex, age at study entrance, pack-years, smoking cessation time, and similar HUNT Lung Cancer Model risk score. A total of 240 and 72 serum samples were included in the discovery (HUNT2) and validation (HUNT3) datasets, respectively, and analysed by next-generation sequencing. The validated serum microRNAs were also tested in two pre-diagnostic plasma datasets from the prospective population studies NOWAC (n = 266) and NSHDS (n = 258). A new model adding clinical variables was also developed and validated. RESULTS Fifteen unique microRNAs were discovered and validated in the pre-diagnostic serum datasets when all cases were contrasted against all controls, all with AUC > 0.60. In combination as a 15-microRNAs signature, the AUC reached 0.708 (discovery) and 0.703 (validation). A non-small cell lung cancer signature of six microRNAs showed AUC 0.777 (discovery) and 0.806 (validation). Combined with clinical variables of the HUNT Lung Cancer Model (age, gender, pack-years, daily cough parts of the year, hours of indoor smoke exposure, quit time in years, number of cigarettes daily, body mass index (BMI)) the AUC reached 0.790 (discovery) and 0.833 (validation). These results could not be validated in the plasma samples. CONCLUSION There were a few significantly differential expressed microRNAs in serum up to eight years before diagnosis. These promising microRNAs alone, in concert, or combined with clinical variables have the potential to serve as early diagnostic LC biomarkers. Plasma is not suitable for this analysis. Further validation in larger prospective serum datasets is needed.
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Affiliation(s)
- Ioannis Fotopoulos
- Department of Computer Science, University of Crete, 700 13, Heraklion, Crete, Greece
| | - Olav Toai Duc Nguyen
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Prinsesse Kristinas Gate 1, 7030, Trondheim, Norway
- Cancer Clinic, Levanger Hospital, Nord-Trøndelag Health Trust, Kirkegata 2, 7600, Levanger, Norway
| | - Therese Haugdahl Nøst
- Department of Community Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, 9037, Tromsø, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU-Norwegian University of Science and Technology, Postboks 8905, 7491, Trondheim, Norway
| | - Maria Markaki
- Institute of Applied and Computational Mathematics, FORTH, 700 13, Heraklion, Crete, Greece
| | - Vincenzo Lagani
- Institute of Chemical Biology, Ilia State University, 3/5, Kakuca Cholokashvili Ave, Tbilisi, Georgia
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
- SDAIA-KAUST Center of Excellence in Data Science and Artificial Intelligence, 23952, Thuwal, Saudi Arabia
| | - Robin Mjelle
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Prinsesse Kristinas Gate 1, 7030, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU-Norwegian University of Science and Technology, Postboks 8905, 7491, Trondheim, Norway
- Bioinformatics Core Facility, NTNU-Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Torkjel Manning Sandanger
- Department of Community Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, 9037, Tromsø, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Prinsesse Kristinas Gate 1, 7030, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU-Norwegian University of Science and Technology, Postboks 8905, 7491, Trondheim, Norway
- Bioinformatics Core Facility, NTNU-Norwegian University of Science and Technology, 7491, Trondheim, Norway
- Department of Computer Science, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Ioannis Tsamardinos
- Department of Computer Science, University of Crete, 700 13, Heraklion, Crete, Greece
- Institute of Applied and Computational Mathematics, FORTH, 700 13, Heraklion, Crete, Greece
- JADBio Gnosis DA S.A., STEP-C, N. Plastira 100, 700-13, Heraklion, Greece
| | - Oluf Dimitri Røe
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Prinsesse Kristinas Gate 1, 7030, Trondheim, Norway.
- Cancer Clinic, Levanger Hospital, Nord-Trøndelag Health Trust, Kirkegata 2, 7600, Levanger, Norway.
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, 9000, Aalborg, Denmark.
- Department of Clinical Medicine, Aalborg University Hospital, 9000, Aalborg, Denmark.
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Mjelle R, Kristensen AK, Tora S Solheim, Westvik GS, Elvebakken H, Hofsli E. Serum small RNAs in metastatic colorectal cancer predict response to chemotherapy and characterize high-risk patients. Mol Cancer 2024; 23:133. [PMID: 38937787 PMCID: PMC11209991 DOI: 10.1186/s12943-024-02042-7] [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: 04/08/2024] [Accepted: 06/12/2024] [Indexed: 06/29/2024] Open
Abstract
Metastatic colorectal cancer (mCRC) presents significant challenges in clinical management due to its heterogeneity and variable response to treatment. In this study, we conducted comprehensive small RNA (sRNA) sequencing analyses to identify sRNA biomarkers associated with survival and treatment response in mCRC patients. We measured serum sRNAs before and after chemotherapy treatment in a discovery cohort of 189 mCRC patients. Our analysis revealed 25 microRNAs (miRNA) as significantly associated with overall survival at baseline. We found that 11 of the 25 significant miRNAs were also significant in an independent validation cohort of 20 mCRC patients, including the top five miRNAs from the discovery cohort. Importantly, all but four of the 25 significant miRNAs from the discovery cohort had hazard ratios in the same direction in the validation cohort. Among the 25 significant miRNAs, we identified the miR-320 family of miRNAs as the strongest independent prognostic marker, with high baseline levels correlating with poor survival outcomes. Furthermore, post-treatment levels of the same miRNAs were even more predictive of overall survival, emphasizing the prognostic value of serum changes in miRNA levels before and after treatment. Moreover, we observed significant changes in serum miRNAs and other sRNAs when comparing samples before and after chemotherapy, with distinct expression patterns between responders and non-responders. Leveraging these differential expression patterns, we established a serum sRNA signature that accurately predicts response to chemotherapy with an area under the curve (AUC) of 0.8. In summary, our study highlights the prognostic and predictive potential of sRNA biomarkers in mCRC, offering valuable insights into patient stratification and personalized treatment approaches.
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Affiliation(s)
- Robin Mjelle
- Department of Cancer and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Laboratoriesenteret 4. Etg Erling Skjalgssons Gate 1 7030, Trondheim, Norway.
- Department of Pathology, St.Olav's Hospital, Trondheim, Norway.
| | - Are K Kristensen
- Department of Oncology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Tora S Solheim
- Department of Cancer and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Laboratoriesenteret 4. Etg Erling Skjalgssons Gate 1 7030, Trondheim, Norway
- Department of Oncology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Ganna S Westvik
- Cancer Clinic, Levanger Hospital, Nord-Trøndelag Health Trust, Trondheim, Norway
| | - Hege Elvebakken
- Department of Oncology, Møre Og Romsdal Hospital Trust, Åsehaugen 5, 6017, Ålesund, Norway
| | - Eva Hofsli
- Department of Cancer and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Laboratoriesenteret 4. Etg Erling Skjalgssons Gate 1 7030, Trondheim, Norway
- Department of Oncology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
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The Impact of YRNAs on HNSCC and HPV Infection. Biomedicines 2023; 11:biomedicines11030681. [PMID: 36979661 PMCID: PMC10045647 DOI: 10.3390/biomedicines11030681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/20/2023] [Accepted: 02/17/2023] [Indexed: 02/27/2023] Open
Abstract
HPV infection is one of the most important risk factors for head and neck squamous cell carcinoma among younger patients. YRNAs are short non-coding RNAs involved in DNA replication. YRNAs have been found to be dysregulated in many cancers, including head and neck squamous cell carcinoma (HNSCC). In this study, we investigated the role of YRNAs in HPV-positive HNSCC using publicly available gene expression datasets from HNSCC tissue, where expression patterns of YRNAs in HPV(+) and HPV(−) HNSCC samples significantly differed. Additionally, HNSCC cell lines were treated with YRNA1-overexpressing plasmid and RNA derived from these cell lines was used to perform a NGS analysis. Additionally, a deconvolution analysis was performed to determine YRNA1’s impact on immune cells. YRNA expression levels varied according to cancer pathological and clinical stages, and correlated with more aggressive subtypes. YRNAs were mostly associated with more advanced cancer stages in the HPV(+) group, and YRNA3 and YRNA1 expression levels were found to be correlated with more advanced clinical stages despite HPV infection status, showing that they may function as potential biomarkers of more advanced stages of the disease. YRNA5 was associated with less-advanced cancer stages in the HPV(−) group. Overall survival and progression-free survival analyses showed opposite results between the HPV groups. The expression of YRNAs, especially YRNA1, correlated with a vast number of proteins and cellular processes associated with viral infections and immunologic responses to viruses. HNSCC-derived cell lines overexpressing YRNA1 were then used to determine the correlation of YRNA1 and the expression of genes associated with HPV infections. Taken together, our results highlight the potential of YRNAs as possible HNSCC biomarkers and new molecular targets.
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Roseth Aass K, Nedal TMV, Anshushaug Bouma S, Tryggestad SS, Haukås E, Slørdahl TS, Waage A, Standal T, Mjelle R. Comprehensive small RNA-sequencing of primary myeloma cells identifies miR-105-5p as a predictor of patient survival. Br J Cancer 2023; 128:656-664. [PMID: 36446884 PMCID: PMC9938247 DOI: 10.1038/s41416-022-02065-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Small RNAs (sRNAs), a heterogenous group of non-coding RNAs, are emerging as promising molecules for cancer patient risk stratification and as players in tumour pathogenesis. Here, we have studied microRNAs (miRNAs) and other sRNAs in relation to survival and disease severity in multiple myeloma. METHODS We comprehensively characterised sRNA expression in multiple myeloma patients by performing sRNA-sequencing on myeloma cells isolated from bone marrow aspirates of 86 myeloma patients. The sRNA expression profiles were correlated with the patients' clinical data to investigate associations with survival and disease subgroups, by using cox proportional hazards (coxph) -models and limma-voom, respectively. A publicly available sRNA dataset was used as external validation (n = 151). RESULTS We show that multiple miRNAs are differentially expressed between ISS Stage I and III. Interestingly, we observed the downregulation of seven different U2 spliceosomal RNAs, a type of small nuclear RNAs in severe disease stages. Further, by a discovery-based approach, we identified miRNA miR-105-5p as a predictor of poor overall survival (OS) in multiple myeloma. Multivariate analysis showed that miR-105-5p predict OS independently of established disease markers. CONCLUSIONS Overexpression of miR-105-5p in myeloma cells correlates with reduced OS, potentially improving prognostic risk stratification in multiple myeloma.
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Affiliation(s)
- Kristin Roseth Aass
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Tonje Marie Vikene Nedal
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Siri Anshushaug Bouma
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Synne Stokke Tryggestad
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Einar Haukås
- Department of Hematology, Stavanger University Hospital, 4011, Stavanger, Norway
| | - Tobias Schmidt Slørdahl
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway
- Department of Hematology, St. Olavs University Hospital, 7030, Trondheim, Norway
| | - Anders Waage
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway
- Department of Hematology, St. Olavs University Hospital, 7030, Trondheim, Norway
| | - Therese Standal
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway.
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway.
- Department of Hematology, St. Olavs University Hospital, 7030, Trondheim, Norway.
| | - Robin Mjelle
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway.
- Bioinformatics Core Facility-BioCore, Norwegian University of Science and Technology NTNU, 7491, Trondheim, Norway.
- Department of Pathology, St. Olavs University Hospital, 7030, Trondheim, Norway.
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5
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Nøst TH, Skogholt AH, Urbarova I, Mjelle R, Paulsen E, Dønnem T, Andersen S, Markaki M, Røe OD, Johansson M, Johansson M, Grønberg BH, Sandanger TM, Sætrom P. Increased levels of microRNA-320 in blood serum and plasma is associated with imminent and advanced lung cancer. Mol Oncol 2023; 17:312-327. [PMID: 36337027 PMCID: PMC9892825 DOI: 10.1002/1878-0261.13336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/04/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Lung cancer (LC) incidence is increasing globally and altered levels of microRNAs (miRNAs) in blood may contribute to identification of individuals with LC. We identified miRNAs differentially expressed in peripheral blood at LC diagnosis and evaluated, in pre-diagnostic blood specimens, how long before diagnosis expression changes in such candidate miRNAs could be detected. We identified upregulated candidate miRNAs in plasma specimens from a hospital-based study sample of 128 patients with confirmed LC and 62 individuals with suspected but confirmed negative LC (FalsePos). We then evaluated the expression of candidate miRNAs in pre-diagnostic plasma or serum specimens of 360 future LC cases and 375 matched controls. There were 1663 miRNAs detected in diagnostic specimens, nine of which met our criteria for candidate miRNAs. Higher expression of three candidates, miR-320b, 320c, and 320d, was associated with poor survival, independent of LC stage and subtype. Moreover, miR-320c and miR-320d expression was higher in pre-diagnostic specimens collected within 2 years of LC diagnosis. Our results indicated that elevated levels of miR-320c and miR-320d may be early indications of imminent and advanced LC.
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Affiliation(s)
- Therese Haugdahl Nøst
- Department of Community Medicine, Faculty of Health SciencesUiT The Arctic University of NorwayTromsøNorway
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic EpidemiologyNTNU – Norwegian University of Science and TechnologyTrondheimNorway
| | - Anne Heidi Skogholt
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic EpidemiologyNTNU – Norwegian University of Science and TechnologyTrondheimNorway
| | - Ilona Urbarova
- Department of Community Medicine, Faculty of Health SciencesUiT The Arctic University of NorwayTromsøNorway
| | - Robin Mjelle
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic EpidemiologyNTNU – Norwegian University of Science and TechnologyTrondheimNorway
- Department of Clinical and Molecular MedicineNTNU – Norwegian University of Science and TechnologyTrondheimNorway
- Bioinformatics Core FacilityNTNU – Norwegian University of Science and TechnologyTrondheimNorway
| | - Erna‐Elise Paulsen
- Department of Clinical Medicine, Faculty of Health SciencesUiT The Arctic University of NorwayTromsøNorway
- Department of PulmonologyUniversity Hospital of North NorwayTromsøNorway
| | - Tom Dønnem
- Department of Clinical Medicine, Faculty of Health SciencesUiT The Arctic University of NorwayTromsøNorway
- Department of OncologyUniversity Hospital of North NorwayTromsøNorway
| | - Sigve Andersen
- Department of Clinical Medicine, Faculty of Health SciencesUiT The Arctic University of NorwayTromsøNorway
- Department of OncologyUniversity Hospital of North NorwayTromsøNorway
| | | | - Oluf Dimitri Røe
- Department of Clinical and Molecular MedicineNTNU – Norwegian University of Science and TechnologyTrondheimNorway
- Cancer Clinic, Levanger HospitalNord‐Trøndelag Health TrustLevangerNorway
| | | | | | - Bjørn Henning Grønberg
- Department of Clinical and Molecular MedicineNTNU – Norwegian University of Science and TechnologyTrondheimNorway
- Department of Oncology, St. Olavs HospitalTrondheim University HospitalNorway
| | - Torkjel Manning Sandanger
- Department of Community Medicine, Faculty of Health SciencesUiT The Arctic University of NorwayTromsøNorway
| | - Pål Sætrom
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic EpidemiologyNTNU – Norwegian University of Science and TechnologyTrondheimNorway
- Department of Clinical and Molecular MedicineNTNU – Norwegian University of Science and TechnologyTrondheimNorway
- Bioinformatics Core FacilityNTNU – Norwegian University of Science and TechnologyTrondheimNorway
- Department of Computer ScienceNorwegian University of Science and TechnologyTrondheimNorway
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6
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Yang CK, Hsu HC, Liu YH, Tsai WS, Ma CP, Chen YT, Tan BCM, Lai YY, Chang IYF, Yang C, Yang CY, Yu JS, Liu H. EV-miRome-wide profiling uncovers miR-320c for detecting metastatic colorectal cancer and monitoring the therapeutic response. Cell Oncol (Dordr) 2022; 45:621-638. [PMID: 35849310 PMCID: PMC9424175 DOI: 10.1007/s13402-022-00688-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2022] [Indexed: 11/28/2022] Open
Abstract
PURPOSE Molecular composition of circulating small extracellular vesicles (EVs) does not merely reflect the cells of origin, but also is enriched in specific biomolecules directly associated with the cellular transformation. However, while most of the currently identified EV-miRs are only geared towards one-dimensional disease detection, their application for long-term tracking and treatment response monitoring has been largely elusive. METHODS We established and optimized a rapid, sensitive and robust liquid biopsy sampling method, and further used small RNA sequencing to comprehensively catalogue EV-miRomes in association with the progression and outcome of metastatic colorectal cancer (mCRC). RESULTS By cross-comparison of EV-miRomes (n = 290) from multi-stage and longitudinal cohorts, we uncovered a 15-EV-miR signature with dual detection and long-term monitoring of tumor size progression for mCRC. From this panel, EV-miR-320c was uncovered as a strong clinical marker - aside from its diagnostic power and a therapeutic monitoring performance superior to carcinoembryonic antigen (CEA), its high expression has also been linked to lower overall survival and a greater likelihood of disease recurrence. Further, integrative analyses of tissue transcriptomic and liquid biopsy implicated this 15-EV-miR signature in programming the mesenchymal-epithelial transition (MET) for distant localization of the metastasized cells and also in creating a tumor-favoring metastatic niche. CONCLUSION Our clinically-oriented delineation of the mCRC-associated circulating EV-miRomes systematically revealed the functional significance of these liquid biopsy markers and further strengthen their translational potential in mCRC therapeutic monitoring.
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Affiliation(s)
- Chan-Keng Yang
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hung-Chih Hsu
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Hao Liu
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wen-Sy Tsai
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Chung-Pei Ma
- Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Yi-Tung Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Bertrand Chin-Ming Tan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
- Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ying-Yu Lai
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ian Yi-Feng Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chi Yang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Yu Yang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Jau-Song Yu
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Hsuan Liu
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan.
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.
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7
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Aass KR, Nedal TMV, Tryggestad SS, Haukås E, Slørdahl TS, Waage A, Standal T, Mjelle R. Paired miRNA- and messenger RNA-sequencing identifies novel miRNA-mRNA interactions in multiple myeloma. Sci Rep 2022; 12:12147. [PMID: 35840794 PMCID: PMC9287335 DOI: 10.1038/s41598-022-16448-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/11/2022] [Indexed: 01/15/2023] Open
Abstract
Multiple myeloma (MM) is an incurable cancer of terminally differentiated plasma cells that proliferate in the bone marrow. miRNAs are promising biomarkers for risk stratification in MM and several miRNAs are shown to have a function in disease pathogenesis. However, to date, surprisingly few miRNA-mRNA interactions have been described for and functionally validated in MM. In this study, we performed miRNA-seq and mRNA-seq on CD138 + cells isolated from bone marrow aspirates of 86 MM patients to identify novel interactions between sRNAs and mRNAs. We detected 9.8% significantly correlated miRNA-mRNA pairs of which 5.17% were positively correlated and 4.65% were negatively correlated. We found that miRNA-mRNA pairs that were predicted by in silico target-prediction algorithms were more negatively correlated than non-target pairs, indicating functional miRNA targeting and that correlation between miRNAs and mRNAs from patients can be used to identify miRNA-targets. mRNAs for negatively correlated miRNA-mRNA target pairs were associated with gene ontology terms such as autophagy, protein degradation and endoplasmic stress response, reflecting important processes in MM. Targets for two specific miRNAs, miR-125b-5p and miR-365b-3p, were functionally validated in MM cell line transfection experiments followed by RNA-sequencing and qPCR. In summary, we identified functional miRNA-mRNA target pairs by correlating miRNA and mRNA data from primary MM cells. We identified several target pairs that are of potential interest for further studies. The data presented here may serve as a hypothesis-generating knowledge base for other researchers in the miRNA/MM field. We also provide an interactive web application that can be used to exploit the miRNA-target interactions as well as clinical parameters associated to these target-pairs.
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Affiliation(s)
- Kristin Roseth Aass
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Gastrosenteret, Prinsesse Kristinas gt. 1, 7491 Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway
| | - Tonje Marie Vikene Nedal
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Gastrosenteret, Prinsesse Kristinas gt. 1, 7491 Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway
| | - Synne Stokke Tryggestad
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Gastrosenteret, Prinsesse Kristinas gt. 1, 7491 Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway
| | - Einar Haukås
- grid.412835.90000 0004 0627 2891Department of Hematology, Stavanger University Hospital, 4011 Stavanger, Norway
| | - Tobias S. Slørdahl
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway ,grid.52522.320000 0004 0627 3560Department of Hematology, St. Olavs University Hospital, 7030 Trondheim, Norway
| | - Anders Waage
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway ,grid.52522.320000 0004 0627 3560Department of Hematology, St. Olavs University Hospital, 7030 Trondheim, Norway
| | - Therese Standal
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Gastrosenteret, Prinsesse Kristinas gt. 1, 7491 Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway ,grid.52522.320000 0004 0627 3560Department of Hematology, St. Olavs University Hospital, 7030 Trondheim, Norway
| | - Robin Mjelle
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Bioinformatics Core Facility - BioCore, Norwegian University of Science and Technology NTNU, 7491 Trondheim, Norway
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8
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Sørgjerd EP, Mjelle R, Beisvåg V, Flatberg A, Grill V, Åsvold BO. Small RNAs are differentially expressed in autoimmune and non-autoimmune diabetes and controls. Eur J Endocrinol 2022; 187:231-240. [PMID: 35616612 PMCID: PMC9254298 DOI: 10.1530/eje-22-0083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/26/2022] [Indexed: 12/02/2022]
Abstract
OBJECTIVE Diabetes is a heterogeneous disease and a precise diagnosis of diabetes subgroups is necessary to initiate proper early treatment and clinical management of the disease. Circulating small RNAs (sRNAs) are potentially diagnostic biomarkers in diseases, including diabetes. Here we aimed to examine whether profiles of circulating sRNAs differed between patients with autoimmune and non-autoimmune diabetes and non-diabetic controls. DESIGN This cross-sectional case-control study included participants from the third survey of the HUNT study. METHODS We performed sRNA sequencing in serum from adult-onset type 1 diabetes (n = 51), type 2 diabetes (n = 50) and latent autoimmune diabetes in adult (LADA, n = 51), as well as non-diabetic HUNT3 participants as control group (n = 51). Differential expression analysis of the sRNAs was performed in R using limma-voom. RESULTS We identified differences in sRNA expression between autoimmune (type 1 diabetes and LADA) and non-autoimmune diabetes (type 2 diabetes) and between patients with diabetes and non-diabetic controls. Focusing on miRNA, we identified 10 differentially expressed mature miRNAs and 30 differentially expressed miRNA variants (isomiRs). We also identified significant changes within other sRNA classes, including a pronounced downregulation of a tRNA fragment in patients with diabetes compared to non-diabetic controls. We created cross-validated sRNA signatures based on the significant sRNAs that distinguished patients with diabetes from non-diabetic controls, and autoimmune from non-autoimmune diabetes, with high specificity and sensitivity. sRNA profiles did not distinguish between type 1 diabetes and LADA. CONCLUSIONS Circulating sRNAs are differentially expressed between patients with diabetes and non-diabetic controls and between autoimmune and non-autoimmune diabetes.
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Affiliation(s)
- Elin Pettersen Sørgjerd
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Correspondence should be addressed to E P Sørgjerd;
| | - Robin Mjelle
- Bioinformatics Core Facility – BioCore, Norwegian University of Science and Technology NTNU, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Vidar Beisvåg
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Central Administration, St. Olav’s Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Arnar Flatberg
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Central Administration, St. Olav’s Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Valdemar Grill
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Bjørn O Åsvold
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
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9
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Yufeng Z, Ming Q, Dandan W. MiR-320d Inhibits Progression of EGFR-Positive Colorectal Cancer by Targeting TUSC3. Front Genet 2021; 12:738559. [PMID: 34733314 PMCID: PMC8558375 DOI: 10.3389/fgene.2021.738559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/24/2021] [Indexed: 12/24/2022] Open
Abstract
Background: The mechanism of miR-320d in EGFR-positive colorectal cancer (CRC) has not been fully elucidated. The aim of the present study was to explore the molecular mechanism of miR-320d in CRC. Methods: The miRNA microarray analysis was conducted to identify differential expressed miRNAs. The expression of miR-320d was validated using quantitative real-time PCR. EGFR-positive CRC cells were transfected with miR-320d mimic and inhibitor, after which cell proliferation, migration, and invasion were assayed. The relationship between miR-320d and TUSC3 was confirmed using bioinformatics and dual-luciferase reporter gene assays. Proteins involved in signaling pathways and the epithelial–mesenchymal transition were detected with Western blot. Results: We found that the miR-320d expression is associated with tumor size and distant metastasis in colorectal cancer. Overexpression of miR-320d in EGFR-positive HCT-116 and SW480 cells decreased not only the proliferation ability but also the invasion and migration ability. In addition, miR-320d had the ability to inhibit epithelial-to-mesenchymal transition. Luciferase assays revealed that miR-320d directly targets the 3′-UTR of TUSC3. TUSC3 was downregulated by miR-320d at both the protein and mRNA levels in EGFR-positive CRC cell lines. Conclusion: Generally, our results demonstrated that miR-320d could inhibit the malignant phenotype of EGFR-positive CRC through targeting TUSC3. The miR-320d might be a potential therapeutic target for EGFR-positive CRC.
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Affiliation(s)
- Zhu Yufeng
- Department of General Surgery, The First Affiliated Hospital of JinZhou Medical University, JinZhou, China
| | - Qi Ming
- Department of Ultrasound, The First Affiliated Hospital of JinZhou Medical University, JinZhou, China
| | - Wu Dandan
- Department of Gastroenterology, The First Affiliated Hospital of JinZhou Medical University, JinZhou, China
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10
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Identification of miR-320 family members as potential diagnostic and prognostic biomarkers in myelodysplastic syndromes. Sci Rep 2021; 11:183. [PMID: 33420276 PMCID: PMC7794569 DOI: 10.1038/s41598-020-80571-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/23/2020] [Indexed: 12/15/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are characterized by ineffective hematopoiesis and the abnormal differentiation of hematopoietic stem cells. An increasing number of researches have demonstrated that microRNAs play crucial roles in the pathogenesis of myelodysplastic syndromes. Herein, we aimed to identify novel potential microRNAs bound up with the diagnosis and prognosis of MDS. MiRNA microarray analysis was used to screen deregulated microRNAs in the bone marrow of MDS patients. qRT-PCR was employed to confirm the microarray results. All members of miR-320 family (miR-320a, miR-320b, miR-320c, miR-320d, and miR-320e) were significantly increased in MDS patients compared to normal control. Although we found no correlation between miR-320 family and most clinical characteristics, high miR-320c and miR-320d expression seemed to be associated with high numbers of bone marrow (BM) blasts and worse karyotype. High expression of all the members of the miR-320 family seemed to be associated with a high prognostic score based on International Prognostic Scoring System (IPSS). The areas under the miR-320 family member ROC curves were 0.9037 (P < 0.0001), 0.7515 (P = 0.0002), 0.9647 (P < 0.0001), 0.8064 (P < 0.0001) and 0.9019 (P < 0.0001). Regarding Kaplan-Meier analysis, high miR-320c and miR-320d expression were related to shorter overall survival (OS). Moreover, multivariate analysis revealed the independent prognostic value of miR-320d for OS in MDS. The expression of miR-320 family members was up-regulated in MDS, and miR-320 family members could serve as candidate diagnostic biomarkers for MDS. High expression of miR-320d was an independent prognostic factor for OS in MDS.
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11
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De Palma FDE, Luglio G, Tropeano FP, Pagano G, D’Armiento M, Kroemer G, Maiuri MC, De Palma GD. The Role of Micro-RNAs and Circulating Tumor Markers as Predictors of Response to Neoadjuvant Therapy in Locally Advanced Rectal Cancer. Int J Mol Sci 2020; 21:E7040. [PMID: 32987896 PMCID: PMC7582560 DOI: 10.3390/ijms21197040] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 02/08/2023] Open
Abstract
The response to neoadjuvant chemoradiation (nCRT) is a critical step in the management of locally advanced rectal cancer (LARC) patients. Only a minority of LARC patients responds completely to neoadjuvant treatments, thus avoiding invasive radical surgical resection. Moreover, toxic side effects can adversely affect patients' survival. The difficulty in separating in advances responder from non-responder patients affected by LARC highlights the need for valid biomarkers that guide clinical decision-making. In this context, microRNAs (miRNAs) seem to be promising candidates for predicting LARC prognosis and/or therapy response, particularly due to their stability, facile detection, and disease-specific expression in human tissues, blood, serum, or urine. Although a considerable number of studies involving potential miRNA predictors to nCRT have been conducted over the years, to date, the identification of the perfect miRNA signatures or single miRNA, as well as their use in the clinical practice, is still representing a challenge for the management of LARC patients. In this review, we will first introduce LARC and its difficult management. Then, we will trace the scientific history and the key obstacles for the identification of specific miRNAs that predict responsiveness to nCRT. There is a high potential to identify non-invasive biomarkers that circulate in the human bloodstream and that might indicate the LARC patients who benefit from the watch-and-wait approach. For this, we will critically evaluate recent advances dealing with cell-free nucleic acids including miRNAs and circulating tumor cells as prognostic or predictive biomarkers.
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Affiliation(s)
- Fatima Domenica Elisa De Palma
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université of Paris, 75005 Paris, France; (G.K.); (M.C.M.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, 94800 Villejuif, France
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy
| | - Gaetano Luglio
- Department of Public Health, University of Naples “Federico II”, 80138 Naples, Italy; (G.L.); (M.D.)
| | - Francesca Paola Tropeano
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, 80138 Naples, Italy; (F.P.T.); (G.P.)
| | - Gianluca Pagano
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, 80138 Naples, Italy; (F.P.T.); (G.P.)
| | - Maria D’Armiento
- Department of Public Health, University of Naples “Federico II”, 80138 Naples, Italy; (G.L.); (M.D.)
| | - Guido Kroemer
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université of Paris, 75005 Paris, France; (G.K.); (M.C.M.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, 94800 Villejuif, France
- Suzhou Institute for Systems Medicine, Chinese Academy of Sciences, Suzhou 100864, China
- Department of Women’s and Children’s Health, Karolinska Institutet, 171 77 Stockholm, Sweden
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
| | - Maria Chiara Maiuri
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université of Paris, 75005 Paris, France; (G.K.); (M.C.M.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, 94800 Villejuif, France
| | - Giovanni Domenico De Palma
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, 80138 Naples, Italy; (F.P.T.); (G.P.)
- Centro Interuniversitario di Studi per l’Innovazione Tecnologica in Chirurgia, University of Naples Federico II, 80138 Naples, Italy
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12
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Guglas K, Kołodziejczak I, Kolenda T, Kopczyńska M, Teresiak A, Sobocińska J, Bliźniak R, Lamperska K. YRNAs and YRNA-Derived Fragments as New Players in Cancer Research and Their Potential Role in Diagnostics. Int J Mol Sci 2020; 21:ijms21165682. [PMID: 32784396 PMCID: PMC7460810 DOI: 10.3390/ijms21165682] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/02/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023] Open
Abstract
YRNAs are a type of short, noncoding RNAs. A total of four different transcripts can be distinguished, which are YRNA1, YRNA3, YRNA4 and YRNA5. All YRNAs are relatively small, made up of about 100 nucleotides each. YRNAs are characterized by a stem-loop structure and each part of that structure carries a different function. YRNAs are transcribed in the nucleus by RNA polymerase III. Then, the YRNA molecule is bound to the polyuridine tail of the La protein responsible for both its nuclear retention and protection from degradation. They also bind to the Ro60 protein, making the molecule more stable. In turn, YRNA-derived small RNAs (YsRNAs) are a class of YRNAs produced in apoptotic cells as a result of YRNA degradation. This process is performed by caspase-3-dependent pathways that form two groups of YsRNAs, with lengths of either approximately 24 or 31 nucleotides. From all four YRNA transcripts, 75 well-described pseudogenes are generated as a result of the mutation. However, available data indicates the formation of up to 1000 pseudogenes. YRNAs and YRNA-derived small RNAs may play a role in carcinogenesis due to their altered expression in cancers and influence on cell proliferation and inflammation. Nevertheless, our knowledge is still limited, and more research is required. The main aim of this review is to describe the current state of knowledge about YRNAs, their function and contribution to carcinogenesis, as well as their potential role in cancer diagnostics. To confirm the promising potential of YRNAs and YRNA-derived fragments as biomarkers, their significant role in several tumor types was taken into consideration.
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Affiliation(s)
- Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Iga Kołodziejczak
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland
- International Institute for Molecular Oncology, 60-203 Poznań, Poland
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Magda Kopczyńska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
| | - Joanna Sobocińska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
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13
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Y RNA: An Overview of Their Role as Potential Biomarkers and Molecular Targets in Human Cancers. Cancers (Basel) 2020; 12:cancers12051238. [PMID: 32423154 PMCID: PMC7281143 DOI: 10.3390/cancers12051238] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 12/12/2022] Open
Abstract
Y RNA are a class of small non-coding RNA that are largely conserved. Although their discovery was almost 40 years ago, their function is still under investigation. This is evident in cancer biology, where their role was first studied just a dozen years ago. Since then, only a few contributions were published, mostly scattered across different tumor types and, in some cases, also suffering from methodological limitations. Nonetheless, these sparse data may be used to make some estimations and suggest routes to better understand the role of Y RNA in cancer formation and characterization. Here we summarize the current knowledge about Y RNA in multiple types of cancer, also including a paragraph about tumors that might be included in this list in the future, if more evidence becomes available. The picture arising indicates that Y RNA might be useful in tumor characterization, also relying on non-invasive methods, such as the analysis of the content of extracellular vesicles (EV) that are retrieved from blood plasma and other bodily fluids. Due to the established role of Y RNA in DNA replication, it is possible to hypothesize their therapeutic targeting to inhibit cell proliferation in oncological patients.
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14
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Ibuki Y, Nishiyama Y, Tsutani Y, Emi M, Hamai Y, Okada M, Tahara H. Circulating microRNA/isomiRs as novel biomarkers of esophageal squamous cell carcinoma. PLoS One 2020; 15:e0231116. [PMID: 32251457 PMCID: PMC7135252 DOI: 10.1371/journal.pone.0231116] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/16/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND MicroRNA (miR)s are promising diagnostic biomarkers of cancer. Recent next generation sequencer (NGS) studies have found that isoforms of micro RNA (isomiR) circulate in the bloodstream similarly to mature micro RNA (miR). We hypothesized that combination of circulating miR and isomiRs detected by NGS are potentially powerful cancer biomarker. The present study aimed to investigate their application in esophageal cancer. METHODS Serum samples from patients with esophageal squamous cell carcinoma (ESCC) and age and sex matched healthy control (HC) individuals were investigated for the expression of miR/isomiRs using NGS. Candidate miR/isomiRs which met the criteria in the 1st group (ESCC = 18 and HC = 12) were validated in the 2nd group (ESCC = 30 and HC = 30). A diagnostic panel was generated using miR/isomiRs that were consistently confirmed in the 1st and 2nd groups. Accuracy of the panel was tested then in the 3rd group (ESCC = 18 and HC = 18). Their use was also investigated in 22 paired samples obtained pre- and post-treatment, and in patients with esophageal adenocarcinoma (EAD) and high-grade dysplasia (HGD). RESULTS Twenty-four miR/isomiRs met the criteria for diagnostic biomarker in the 1st and 2nd group. A multiple regression model selected one mature miR (miR-30a-5p) and two isomiRs (isoform of miR-574-3p and miR-205-5p). The index calculated from the diagnostic panel was significantly higher in ESCC patients than in the HCs (13.3±8.9 vs. 3.1±1.3, p<0.001). The area under the receiver operating characteristics (ROC) curves of the panel index was 0.95. Sensitivity and specificity were 93.8%, and 81% in the 1st and 2nd groups, and 88.9% and 72.3% in the 3rd group, respectively. The panel index was significantly lower in patients with EAD (6.2±4.5) and HGD (4.2±1.7) than in those with ESCC and was significantly decreased at post-treatment compared with pre-treatment (6.2±5.6 vs 11.6±11.5, p = 0.03). CONCLUSION Our diagnostic panel had high accuracy in the diagnosis of ESCC. MiR/isomiRs detected by NGS could serve as novel biomarkers of ESCC.
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Affiliation(s)
- Yuta Ibuki
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yukie Nishiyama
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan
| | - Yasuhiro Tsutani
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Manabu Emi
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yoichi Hamai
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Morihito Okada
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan
- Collaborative laboratory of Liquid Biopsy, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- The Research Center for Drug Development and Biomarker Discovery, Hiroshima University, Hiroshima, Japan
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15
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Kirchner B, Buschmann D, Paul V, Pfaffl MW. Postprandial transfer of colostral extracellular vesicles and their protein and miRNA cargo in neonatal calves. PLoS One 2020; 15:e0229606. [PMID: 32109241 PMCID: PMC7048281 DOI: 10.1371/journal.pone.0229606] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/10/2020] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs) such as exosomes are key regulators of intercellular communication that can be found in almost all bio fluids. Although studies in the last decade have made great headway in discerning the role of EVs in many physiological and pathophysiological processes, the bioavailability and impact of dietary EVs and their cargo still remain to be elucidated. Due to its widespread consumption and high content of EV-associated microRNAs and proteins, a major focus in this field has been set on EVs in bovine milk and colostrum. Despite promising in vitro studies in recent years that show high resiliency of milk EVs to degradation and uptake of milk EV cargo in a variety of intestinal and blood cell types, in vivo experiments continue to be inconclusive and sometimes outright contradictive. To resolve this discrepancy, we assessed the potential postprandial transfer of colostral EVs to the circulation of newborn calves by analysing colostrum-specific protein and miRNAs, including specific isoforms (isomiRs) in cells, EV isolations and unfractionated samples from blood and colostrum. Our findings reveal distinct populations of EVs in colostrum and blood from cows that can be clearly separated by density, particle concentration and protein content (BTN1A1, MFGE8). Postprandial blood samples of calves show a time-dependent increase in EVs that share morphological and protein characteristics of colostral EVs. Analysis of miRNA expression profiles by Next-Generation Sequencing gave a different picture however. Although significant postprandial expression changes could only be detected for calf EV samples, expression profiles show very limited overlap with highly expressed miRNAs in colostral EVs or colostrum in general. Taken together our results indicate a selective uptake of membrane-associated protein cargo but not luminal miRNAs from colostral EVs into the circulation of neonatal calves.
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Affiliation(s)
- Benedikt Kirchner
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
- * E-mail:
| | - Dominik Buschmann
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
- Institute of Human Genetics, University Hospital, LMU Munich, Munich, Germany
| | - Vijay Paul
- National Research Centre on Yak, ICAR, Dirang, India
| | - Michael W. Pfaffl
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
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16
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Mjelle R, Dima SO, Bacalbasa N, Chawla K, Sorop A, Cucu D, Herlea V, Sætrom P, Popescu I. Comprehensive transcriptomic analyses of tissue, serum, and serum exosomes from hepatocellular carcinoma patients. BMC Cancer 2019; 19:1007. [PMID: 31660891 PMCID: PMC6816220 DOI: 10.1186/s12885-019-6249-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/10/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The expression of microRNAs (miRNAs) is a promising prognostic and diagnostic tool in hepatocellular carcinoma (HCC). Here we performed small RNA sequencing (sRNA-seq) of tissue, serum and serum exosomes to investigate changes in miRNA expression between the different sample types and correlated the expression with clinical parameters. We also performed gene expression arrays on tumor and normal tissue. RESULTS Paired tissue, serum and serum exosomes sequencing revealed consistent positive correlation of miR-21 between serum exosomes and tumor tissue, indicating that miR-21 could be exported from tissue to circulation via exosomes. We found that let-7 miRNAs are generally upregulated in serum exosomes compared to whole serum, indicating that these miRNAs could be preferentially loaded into exosomes. Comparing serum from HCC patients with serum from healthy individuals revealed a global increase of miRNAs in serum from HCC patients, including an almost 4-fold increase of several miRNAs, including the liver-specific miR-122. When correlating miRNA expression with clinical parameters we detected significant association between hepatitis B virus (HBV) infection and miR-122 in serum as well as several serum and tissue-miRNAs that correlated with surgery type. We found that miR-141 and miR-146 correlated with cirrhosis in tumor tissue and normal tissue, respectively. Finally, high expression of miR-21 in tumors were associated with poor survival. Focusing on gene expression we found several significant messenger RNAs (mRNAs) between tumor and normal tissue and a Gene Ontology (GO) analysis revealed that these changes were mainly related to cell cycle and metabolism. Further, we detected mRNAs that correlated with cirrhosis and HBV infection in tissue. Finally, GO analysis of predicted targets for miRNAs down-regulated in tumor found that these were enriched for functions related to collagen synthesis. CONCLUSIONS Our combined data point to altered miRNA and mRNA expression contributing to both generally impaired lipid metabolism and increased cell proliferation and a miRNA-driven increase in collagen synthesis in HCC. Our results further indicate a correlation in miRNA expression between exosomes, serum, and tissue samples suggesting export from tumors via exosomes. This correlation could provide a basis for a more tumor-specific miRNA profile in serum.
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Affiliation(s)
- Robin Mjelle
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway. .,Department of Computer Science, Norwegian University of Science and Technology, NTNU, Trondheim, Norway.
| | - Simona O Dima
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania.,Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Nicolae Bacalbasa
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania.,Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Konika Chawla
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.,Bioinformatics Core Facility-BioCore, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - Andrei Sorop
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Dana Cucu
- Department of Anatomy, Physiology, and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Vlad Herlea
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania.,K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.,Department of Computer Science, Norwegian University of Science and Technology, NTNU, Trondheim, Norway.,Bioinformatics Core Facility-BioCore, Norwegian University of Science and Technology, NTNU, Trondheim, Norway.,K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - Irinel Popescu
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania.,Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania.,Acad. Nicolae Cajal Institute of Medical Scientific Research, Titu Maiorescu University, Bucharest, Romania
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17
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Machackova T, Prochazka V, Kala Z, Slaby O. Translational Potential of MicroRNAs for Preoperative Staging and Prediction of Chemoradiotherapy Response in Rectal Cancer. Cancers (Basel) 2019; 11:cancers11101545. [PMID: 31614848 PMCID: PMC6827048 DOI: 10.3390/cancers11101545] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer is the third most common cancer and the second cause of cancer-related deaths. Rectal cancer presents roughly one-third of all colorectal cancer cases and differs from it on both anatomical and molecular levels. While standard treatment of colon cancer patients is radical surgery, rectal cancer is usually treated with pre-operative chemoradiotherapy followed by total mesorectal excision, which requires precise estimation of TNM staging. Unfortunately, stage evaluation is based solely on imaging modalities, and they often do not correlate with postoperative pathological findings. Moreover, approximately half of rectal cancer patients do not respond to such pre-operative therapy, so they are exposed to its toxic effects without any clinical benefit. Thus, biomarkers that could precisely predict pre-operative TNM staging, and especially response to therapy, would significantly advance rectal cancer treatment—but till now, no such biomarker has been identified. In cancer research, microRNAs are emerging biomarkers due to their connection with carcinogenesis and exceptional stability. Circulating miRNAs are promising non-invasive biomarkers that could allow monitoring of a patient throughout the whole therapeutic process. This mini-review aims to summarize the current knowledge on miRNAs and circulating miRNAs involved in the prediction of response to treatment and pre-operative staging in rectal cancer patients.
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Affiliation(s)
- Tana Machackova
- Department of Molecular Medicine, European Institute of Technology, 625 00 Brno, Czech Republic.
| | - Vladimir Prochazka
- Department of Surgery, University Hospital Brno, 625 00 Brno, Czech Republic.
| | - Zdenek Kala
- Department of Surgery, University Hospital Brno, 625 00 Brno, Czech Republic.
| | - Ondrej Slaby
- Department of Molecular Medicine, European Institute of Technology, 625 00 Brno, Czech Republic.
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18
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Larose TL, Sætrom P, Martinussen MP, Skogseth H, Sandanger TM, Scélo G, McHale CM, Jacobsen GW, Smith MT. In utero exposure to endocrine disrupting chemicals, micro-RNA profiles, and fetal growth: a pilot study protocol. J Public Health Res 2019; 8:1550. [PMID: 31572695 PMCID: PMC6747021 DOI: 10.4081/jphr.2019.1550] [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: 01/11/2019] [Accepted: 05/15/2019] [Indexed: 11/22/2022] Open
Abstract
Background: The developing fetus is particularly vulnerable to the effects of endocrine disrupting chemicals (EDCs). Molecular fingerprints of EDCs can be identified via microRNA (miRNA) expression profiles and may be etiologically implicated in the developmental origin of disease (DOHaD). Methods/design: This pilot study includes pregnant women at high risk (smoking at conception), and low risk (non-smoking at conception) for SGA birth (birthweight<10th percentile for gestational age). We have randomly selected 12 mothers (3 high-risk SGA birth, 3 low-risk SGA birth, 3 high-risk non-SGA birth, 3 low-risk non-SGA birth), with EDC measurements from gestational week 17. All offspring are female. We aim to test the stability of our samples (maternal serum, cord blood, placenta tissue), observe the differential expression of miRNA profiles over time (gestational weeks 17, 25, 33, 37, birth), and study the consistency between maternal EDC measures and miRNA expression profiles across our repeated measures. Expected impact of the study for Public Health: Results from this pilot study will inform the development of a larger cohort wide analysis, and will impact the current state of knowledge in the fields of public health, epigenetics, and the DOHaD. Significance for public health This research focuses on the developmental origin of disease with particular emphasis on maternal exposure to endocrine disrupting chemicals during pregnancy and fetal growth by examining microRNA profiles in maternal serum, placenta tissue, and cord blood. Pregnant mothers and offspring are the most vulnerable populations affected by environmental exposures including exposure to pesticides, metals, and contaminants in food. Results from our pilot study will inform a larger project proposal that will look not only at epigenetic modifications and fetal development, but also the epigenetic effects on longer term neurodevelopmental and metabolic outcomes in childhood and early adulthood.
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Affiliation(s)
- Tricia L Larose
- K.G. Jebsen Center for Genetic Epidemiology, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Pål Sætrom
- K.G. Jebsen Center for Genetic Epidemiology, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Computer Science, Faculty of Information Technology and Electrical Engineering, Norwegian University of Science and Technology, Trondheim, Norway.,Bioinformatics core facility - BioCore, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Marit P Martinussen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Håkon Skogseth
- Biobank 1, St. Olavs University Hospital, Trondheim, Norway
| | - Torkjel M Sandanger
- Department of Community Medicine, Faculty of Health Sciences, UiT-the Arctic University of Norway, Tromsø, Norway
| | - Ghislaine Scélo
- Genetic Epidemiology Group, Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Cliona M McHale
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Geir W Jacobsen
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Martyn T Smith
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
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19
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Long JP, Dong LF, Chen FF, Fan YF. miR-146a-5p targets interleukin-1 receptor-associated kinase 1 to inhibit the growth, migration, and invasion of breast cancer cells. Oncol Lett 2018; 17:1573-1580. [PMID: 30675215 PMCID: PMC6341734 DOI: 10.3892/ol.2018.9769] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 11/16/2018] [Indexed: 01/11/2023] Open
Abstract
MicroRNAs (miRNAs) are associated with the formation and progression of many types of cancers. In the present study, the aim was to elucidate the involvement of miR-146a-5p in the regulation of human breast cancer (BC) cell growth and invasion, as well as the mechanisms underlying its effects. Reverse transcription-quantitative polymerase chain reaction results revealed that miR-146a-5p was markedly downregulated in BC tissues relative to those of adjacent normal tissues. miR-146a-5p expression was also markedly downregulated in BC cells. Overexpression of miR-146a-5p significantly suppressed the proliferation, invasion and migration of BC MDA-MB-453 and MCF7 cells. Furthermore, the results indicated that miR-146a-5p downregulated the expression of interleukin-1 receptor-associated kinase 1 (IRAK1) by directly binding to its 3′-untranslated region in BC cells. Furthermore, IRAK1 expression was observed to be markedly upregulated and inversely correlated with miR-146a-5p expression in BC tissues. Mechanical studies indicated that restoring IRAK1 expression reversed the miR-146a-5p-induced inhibitory effects on proliferation and invasion of BC cells. In conclusion, miR-146a-5p may act as a tumor suppressor in BC by directly targeting IRAK1. These results highlighted the potential of miR-146a-5p as a novel therapeutic target for the treatment of BC.
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Affiliation(s)
- Jing-Pei Long
- Department of Breast, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Li-Feng Dong
- Department of Breast, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Fang-Fang Chen
- Department of Breast, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Yang-Fan Fan
- Department of Breast, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
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