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Huang G, Wu X, Ji X, Peng Y, Wang J, Cai X, Wang Y, Yang E, Zhu L, Wu Y, Sun Q, Shen L, Sha W, Shen H, Wang F. LncRNA SNHG16 Inhibits Intracellular M. tuberculosis Growth Involving Cathelicidin Pathway, Autophagy, and Effector Cytokines Production. ACS OMEGA 2024; 9:43115-43128. [PMID: 39464459 PMCID: PMC11500371 DOI: 10.1021/acsomega.4c07053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 09/29/2024] [Accepted: 10/02/2024] [Indexed: 10/29/2024]
Abstract
Long noncoding small nucleolar RNA (LncRNA) host gene 16 (SNHG16) is associated with certain diseases, including cancers. However, its role and mechanism in Mycobacterium tuberculosis (Mtb) infection remain unclear. Here, we demonstrated that SNHG16 expression levels were suppressed in peripheral blood mononuclear cells (PBMCs) and CD14+ monocytes of tuberculosis (TB) patients. SNHG16 was up-regulated by acute Mtb infection of PBMCs from healthy control (HC) subjects. Such TB suppression of SNHG16 was consistent with an immunosuppressive-like state driven by IL-10 signaling as seen in TB patients. Notably, SNHG16 limited Mtb growth in macrophages/monocytes through autophagy and vitamin D receptor (VDR)-dependent cathelicidin (CAMP) antimicrobial pathways. Concurrently, SNHG16 was highly expressed in lymphocytes, including CD8+ and Vγ2 Vδ2 T-cell subsets in HCs. SNHG16 overexpression in lymphocytes allowed them to control Mtb infection in macrophages, and SNHG16 epigenetically increased the expression of anti-Mtb effector cytokines in lymphocytes by developing more accessible chromatin states in gene loci encoding IFN-γ, TNF-α, and Granzyme B. Furthermore, the adoptive transfer of SNHG16-overexpressing human PBMCs into Mtb-infected SCID mice conferred protective immunity against Mtb infection. Thus, SNHG16 drove the induction of pleiotropic effector functions that inhibited intracellular Mtb growth in vitro and in vivo, serving as an immunotherapy target in TB.
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Affiliation(s)
- Guixian Huang
- Shanghai
Clinical Research Center for Infectious Disease (tuberculosis), Shanghai
Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Institute
for Advanced Study, Tongji University School
of Medicine, Shanghai 200433, China
| | - Xiaocui Wu
- Department
of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Xuejiao Ji
- Shanghai
Clinical Research Center for Infectious Disease (tuberculosis), Shanghai
Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Institute
for Advanced Study, Tongji University School
of Medicine, Shanghai 200433, China
| | - Ying Peng
- Shanghai
Clinical Research Center for Infectious Disease (tuberculosis), Shanghai
Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Institute
for Advanced Study, Tongji University School
of Medicine, Shanghai 200433, China
| | - Juechu Wang
- Shanghai
Clinical Research Center for Infectious Disease (tuberculosis), Shanghai
Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Institute
for Advanced Study, Tongji University School
of Medicine, Shanghai 200433, China
| | - Xia Cai
- Key
Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Biosafety
Level 3 Laboratory, Shanghai Institute of Infectious Disease and Biosecurity,
Department of Medical Microbiology and Parasitology, School of Basic
Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yihui Wang
- Haide
College, Ocean University of China, Qingdao 266100, China
| | - Enzhuo Yang
- Shanghai
Clinical Research Center for Infectious Disease (tuberculosis), Shanghai
Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Institute
for Advanced Study, Tongji University School
of Medicine, Shanghai 200433, China
| | - Liying Zhu
- Key
Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Biosafety
Level 3 Laboratory, Shanghai Institute of Infectious Disease and Biosecurity,
Department of Medical Microbiology and Parasitology, School of Basic
Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yuan Wu
- Key
Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Biosafety
Level 3 Laboratory, Shanghai Institute of Infectious Disease and Biosecurity,
Department of Medical Microbiology and Parasitology, School of Basic
Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qin Sun
- Shanghai
Clinical Research Center for Infectious Disease (tuberculosis), Shanghai
Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Institute
for Advanced Study, Tongji University School
of Medicine, Shanghai 200433, China
| | - Ling Shen
- Department
of Microbiology & Immunology and Center for Primate Biomedical
Research, University of Illinois College
of Medicine, Chicago, Illinois 60607, United States
| | - Wei Sha
- Shanghai
Clinical Research Center for Infectious Disease (tuberculosis), Shanghai
Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Institute
for Advanced Study, Tongji University School
of Medicine, Shanghai 200433, China
| | - Hongbo Shen
- Shanghai
Clinical Research Center for Infectious Disease (tuberculosis), Shanghai
Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Institute
for Advanced Study, Tongji University School
of Medicine, Shanghai 200433, China
| | - Feifei Wang
- Key
Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Biosafety
Level 3 Laboratory, Shanghai Institute of Infectious Disease and Biosecurity,
Department of Medical Microbiology and Parasitology, School of Basic
Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
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Lietz CE, Newman ET, Kelly AD, Xiang DH, Zhang Z, Ramavenkat N, Bowers JJ, Lozano-Calderon SA, Ebb DH, Raskin KA, Cote GM, Choy E, Nielsen GP, Vlachos IS, Haibe-Kains B, Spentzos D. A dynamic microRNA profile that tracks a chemotherapy resistance phenotype in osteosarcoma. Implications for novel therapeutics. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.19.24309087. [PMID: 38946948 PMCID: PMC11213079 DOI: 10.1101/2024.06.19.24309087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Osteosarcoma is a rare primary bone tumor for which no significant therapeutic advancement has been made since the late 1980s despite ongoing efforts. Overall, the five-year survival rate remains about 65%, and is much lower in patients with tumors unresponsive to methotrexate, doxorubicin, and cisplatin therapy. Genetic studies have not revealed actionable drug targets, but our group, and others, have reported that epigenomic biomarkers, including regulatory RNAs, may be useful prognostic tools for osteosarcoma. We tested if microRNA (miRNA) transcriptional patterns mark the transition from a chemotherapy sensitive to resistant tumor phenotype. Small RNA sequencing was performed using 14 patient matched pre-chemotherapy biopsy and post-chemotherapy resection high-grade osteosarcoma frozen tumor samples. Independently, small RNA sequencing was performed using 14 patient matched biopsy and resection samples from untreated tumors. Separately, miRNA specific Illumina DASL arrays were used to assay an independent cohort of 65 pre-chemotherapy biopsy and 26 patient matched post-chemotherapy resection formalin fixed paraffin embedded (FFPE) tumor samples. mRNA specific Illumina DASL arrays were used to profile 37 pre-chemotherapy biopsy and five post-chemotherapy resection FFPE samples, all of which were also used for Illumina DASL miRNA profiling. The National Cancer Institute Therapeutically Applicable Research to Generate Effective Treatments dataset, including PCR based miRNA profiling and RNA-seq data for 86 and 93 pre-chemotherapy tumor samples, respectively, was also used. Paired differential expression testing revealed a profile of 17 miRNAs with significantly different transcriptional levels following chemotherapy. Genes targeted by the miRNAs were differentially expressed following chemotherapy, suggesting the miRNAs may regulate transcriptional networks. Finally, an in vitro pharmacogenomic screen using miRNAs and their target transcripts predicted response to a set of candidate small molecule therapeutics which potentially reverse the chemotherapy resistance phenotype and synergize with chemotherapy in otherwise treatment resistant tumors. Importantly, these novel therapeutic targets are distinct from targets identified by a similar pharmacogenomic analysis of previously published prognostic miRNA profiles from pre chemotherapy biopsy specimens.
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Affiliation(s)
- Christopher E Lietz
- Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedic Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Erik T Newman
- Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedic Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | | | - David H Xiang
- Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedic Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Ziying Zhang
- Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedic Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, USA
| | - Nikhil Ramavenkat
- Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedic Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Joshua J Bowers
- Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedic Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Santiago A Lozano-Calderon
- Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedic Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - David H Ebb
- Division of Pediatric Hematology/Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kevin A Raskin
- Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedic Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Gregory M Cote
- Division of Hematology/Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Edwin Choy
- Division of Hematology/Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - G Petur Nielsen
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ioannis S Vlachos
- Harvard Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 1L7, Ontario, Canada
- Medical Biophysics, University of Toronto, Toronto M5G 2M9, Ontario, Canada
- Vector Institute for Artificial Intelligence, Toronto M5G 1L7, Ontario, Canada
| | - Dimitrios Spentzos
- Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedic Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
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Torshizi Esfahani A, Mohammadpour S, Jalali P, Yaghoobi A, Karimpour R, Torkamani S, Pardakhtchi A, Salehi Z, Nazemalhosseini-Mojarad E. Differential expression of angiogenesis-related genes 'VEGF' and 'angiopoietin-1' in metastatic and EMAST-positive colorectal cancer patients. Sci Rep 2024; 14:10539. [PMID: 38719941 PMCID: PMC11079037 DOI: 10.1038/s41598-024-61000-x] [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: 11/11/2023] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
Abnormal angiogenesis leads to tumor progression and metastasis in colorectal cancer (CRC). This study aimed to elucidate the association between angiogenesis-related genes, including VEGF-A, ANGPT-1, and ANGPT-2 with both metastatic and microsatellite alterations at selected tetranucleotide repeats (EMAST) subtypes of CRC. We conducted a thorough assessment of the ANGPT-1, ANGPT-2, and VEGF-A gene expression utilizing publicly available RNA sequencing and microarray datasets. Then, the experimental validation was performed in 122 CRC patients, considering their disease metastasis and EMAST+/- profile by using reverse transcription polymerase chain reaction (RT-PCR). Subsequently, a competing endogenous RNA (ceRNA) network associated with these angiogenesis-related genes was constructed and analyzed. The expression level of VEGF-A and ANGPT-2 genes were significantly higher in tumor tissues as compared with normal adjacent tissues (P-value < 0.001). Nevertheless, ANGPT-1 had a significantly lower expression in tumor samples than in normal colon tissue (P-value < 0.01). We identified a significantly increased VEGF-A (P-value = 0.002) and decreased ANGPT-1 (P-value = 0.04) expression in EMAST+ colorectal tumors. Regarding metastasis, a significantly increased VEGF-A and ANGPT-2 expression (P-value = 0.001) and decreased ANGPT-1 expression (P-value < 0.05) were established in metastatic CRC patients. Remarkably, co-expression analysis also showed a strong correlation between ANGPT-2 and VEGF-A gene expressions. The ceRNA network was constructed by ANGPT-1, ANGPT-2, VEGF-A, and experimentally validated miRNAs (hsa-miR-190a-3p, hsa-miR-374c-5p, hsa-miR-452-5p, and hsa-miR-889-3p), lncRNAs (AFAP1-AS1, KCNQ1OT1 and MALAT1), and TFs (Sp1, E2F1, and STAT3). Network analysis revealed that colorectal cancer is amongst the 82 significant pathways. We demonstrated a significant differential expression of VEGF-A and ANGPT-1 in colorectal cancer patients exhibiting the EMAST+ phenotype. This finding provides novel insights into the molecular pathogenesis of colorectal cancer, specifically in EMAST subtypes. Yet, the generalization of in silico findings to EMAST+ colorectal cancer warrants future experimental investigations. In the end, this study proposes that the EMAST biomarker could serve as an additional perspective on CMS4 biology which is well-defined by activated angiogenesis and worse overall survival.
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Affiliation(s)
- Amir Torshizi Esfahani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Mohammadpour
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pooya Jalali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Yaghoobi
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Raana Karimpour
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Soha Torkamani
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ali Pardakhtchi
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Zahra Salehi
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
- Research Institute for Oncology, Hematology and Cell Therapy, Tehran University of Medical Sciences, Tehran, Iran.
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands.
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Li J, Li Y, Sun X, Wei L, Guan J, Fu L, Du J, Zhang X, Cheng M, Ma H, Jiang S, Zheng Q, Wang L. Silencing lncRNA-DARS-AS1 suppresses nonsmall cell lung cancer progression by stimulating miR-302a-3p to inhibit ACAT1 expression. Mol Carcinog 2024; 63:757-771. [PMID: 38289172 DOI: 10.1002/mc.23686] [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: 10/13/2023] [Revised: 11/17/2023] [Accepted: 01/13/2024] [Indexed: 03/16/2024]
Abstract
Long noncoding RNAs (LncRNAs) have been gaining attention as potential therapeutic targets for lung cancer. In this study, we investigated the expression and biological behavior of lncRNA DARS-AS1, its predicted interacting partner miR-302a-3p, and ACAT1 in nonsmall cell lung cancer (NSCLC). The transcript level of DARS-AS1, miR-302a-3p, and ACAT1 was analyzed using qRT-PCR. Endogenous expression of ACAT1 and the expression of-and changes in-AKT/ERK pathway-related proteins were determined using western blotting. MTS, Transwell, and apoptosis experiments were used to investigate the behavior of cells. The subcellular localization of DARS-AS1 was verified using FISH, and its binding site was verified using dual-luciferase reporter experiments. The binding of DARS-AS1 to miR-302a-3p was verified using RNA co-immunoprecipitation. In vivo experiments were performed using a xenograft model to determine the effect of DARS-AS1 knockout on ACAT1 and NSCLC. lncRNA DARS-AS1 was upregulated in NSCLC cell lines and tissues and the expression of lncRNA DARS-AS1 was negatively correlated with survival of patients with NSCLC. Knockdown of DARS-AS1 inhibited the malignant behaviors of NSCLC via upregulating miR-302a-3p. miR-302a-3p induced suppression of malignancy through regulating oncogene ACAT1. This study demonstrates that the DARS-AS1-miR-302a-3p-ACAT1 pathway plays a key role in NSCLC.
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Affiliation(s)
- Ji Li
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Yizhuo Li
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Xiaodan Sun
- Postdoctoral Research Workstation, Jilin Cancer Hospital, Changchun, China
| | - Lai Wei
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Jingqian Guan
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Lin Fu
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Jiang Du
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Xiupeng Zhang
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Ming Cheng
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Huan Ma
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
- Department of Gastroenterology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Siyu Jiang
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Qianqian Zheng
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Liang Wang
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
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circZC3HAV1 Regulates TBC1D9 to Affect the Biological Behavior of Colorectal Cancer Cells. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7386946. [PMID: 36164444 PMCID: PMC9508460 DOI: 10.1155/2022/7386946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/24/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022]
Abstract
Background Colorectal cancer (CRC) is one of the most frequently diagnosed cancers all over the world, which accounts for a large proportion of cancer-associated deaths. The regulatory function of circular RNAs (circRNAs) has been affirmed in diverse cancers. circ_0082628, named circRNA zinc finger CCCH-type containing antiviral 1 (circZC3HAV1), has been discovered to be significantly downregulated in CRC tissues. Nevertheless, the function and mechanism of circZC3HAV1 in CRC remain unclear. Purpose We targeted at studying the specific role and mechanism of circZC3HAV1 in CRC cells. Methods The expression of the genes was detected by quantitative real-time polymerase chain reaction (qPCR). The binding relationship among different genes was verified by mechanism assays. Functional assays were carried out to reveal the role of different RNAs in CRC cell malignant behaviors. Results circZC3HAV1 was significantly downregulated in CRC cells. circZC3HAV1 overexpression hampered CRC cell migratory and invasive abilities. As for the mechanism, circZC3HAV1 competitively bound with microRNA-146b-3p (miR-146b-3p) to enhance the expression of TBC1 domain family member 9 (TBC1D9). Rescue assays demonstrated circZC3HAV1 sponged miR-146b-3p and upregulated TBC1D9 to restrict migration and invasion of CRC cells. Conclusion circZC3HAV1 could upregulate TBC1D9 via absorbing miR-146b-3p, consequently inhibiting migratory and invasive capabilities of CRC cells.
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Gvaldin DY, Pushkin AA, Timoshkina NN, Rostorguev EE, Nalgiev AM, Kit OI. Integrative analysis of mRNA and miRNA sequencing data for gliomas of various grades. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-00119-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Abstract
Background
The purpose of this study was to characterize subtype-specific patterns of mRNA and miRNA expression of gliomas using The Cancer Genome Atlas (TCGA) data to search for genetic determinants that predict prognosis in terms of overall survival and to create interaction networks for grade 2 and 3 (G2 and G3) astrocytomas, oligodendrogliomas and grade 4 (G4) glioblastoma multiforme. Based on open-access TCGA data, 5 groups were formed: astrocytoma G2 (n = 58), astrocytoma G3 (n = 128), oligodendroglioma G2 (n = 102), oligodendroglioma G3 (n = 72) and glioblastoma G4 (n = 564); normal samples of brain tissue were also analysed (n = 15). Data of patient age, sex, survival and expression patterns of mRNA and miRNA were extracted for each sample. After stratification of the data into groups, a differential analysis of expression was carried out, genes and miRNAs that affect overall survival were identified and gene set enrichment analysis (GSEA) and interaction analysis were performed.
Results
A total of 939 samples of glial tumours were analysed, for which subtype-specific expression profiles of genes and miRNAs were identified and networks of mRNA-miRNA interactions were constructed. Genes whose aberrant expression level was associated with survival were determined, and pairwise correlations between differential gene expression (DEG) and differential miRNA expression (DE miRNA) were calculated.
Conclusions
The developed panel of genes and miRNAs allowed us to differentiate glioma subtypes and evaluate prognosis in terms of the overall survival of patients. The regulatory miRNA-mRNA pairs unique to the five glioma subtypes identified in this study can stimulate the development of new therapeutic approaches based on subtype-specific mechanisms of oncogenesis.
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Cimadomo D, Rienzi L, Giancani A, Alviggi E, Dusi L, Canipari R, Noli L, Ilic D, Khalaf Y, Ubaldi FM, Capalbo A. Definition and validation of a custom protocol to detect miRNAs in the spent media after blastocyst culture: searching for biomarkers of implantation. Hum Reprod 2020; 34:1746-1761. [PMID: 31419301 DOI: 10.1093/humrep/dez119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/09/2019] [Indexed: 12/18/2022] Open
Abstract
STUDY QUESTION Can miRNAs be reliably detected in the spent blastocyst media (SBM) after IVF as putative biomarkers of the implantation potential of euploid embryos? SUMMARY ANSWER Adjustment of the data for blastocyst quality and the day of full-expansion hinders the predictive power of a fast, inexpensive, reproducible and user-friendly protocol based on the detection of 10 selected miRNAs from SBM. WHAT IS KNOWN ALREADY Euploidy represents so far the strongest predictor of blastocyst competence. Nevertheless, ~50% of the euploid blastocysts fail to implant. Several studies across the years have suggested that a dialogue exists between the embryo and the endometrium aimed at the establishment of a pregnancy. MicroRNAs have been proposed as mediators of such a dialogue and investigated in this respect. Several expensive, time-consuming and complex protocols have been adopted and promising results have been produced, but conclusive evidence from large clinical studies is missing. STUDY DESIGN, SIZE, DURATION This study was conducted in two phases from September 2015 to December 2017. In Phase 1, the human blastocyst miRNome profile was defined from the inner cell mass (ICM) and the corresponding whole-trophectoderm (TE) of six donated blastocysts. Two different protocols were adopted to this end. In parallel, 6 pools of 10 SBM each were run (3 from only implanted euploid blastocysts, IEBs; and 3 from only not-implanted euploid blastocysts, not-IEBs). A fast, inexpensive and user-friendly custom protocol for miRNA SBM profiling was designed. In Phase 2, 239 SBM from IEB and not-IEB were collected at three IVF centres. After 18 SBM from poor-quality blastocysts were excluded from the analysis, data from 107 SBM from not-IEB and 114 from IEB were produced through the previously developed custom protocol and compared. The data were corrected through logistic regressions. PARTICIPANT/MATERIALS, SETTINGS, METHODS Donated blastocysts underwent ICM and whole-TE isolation. SBM were collected during IVF cycles characterized by ICSI, blastocyst culture in a continuous media, TE biopsy without zona pellucida opening in Day 3, quantitative PCR (qPCR)-based aneuploidy testing and vitrified-warmed single euploid embryo transfer. Not-IEB and IEB were clustered following a negative pregnancy test and a live birth, respectively. The Taqman Low Density Array (TLDA) cards and the Exiqon microRNA human panel I+II qPCR analysis protocols were adopted to analyse the ICM and whole-TE. The latter was used also for SBM pools. A custom protocol and plate was then designed based on the Exiqon workflow, validated and finally adopted for SBM analysis in study Phase 2. This custom protocol allows the analysis of 10 miRNAs from 10 SBM in 3 hours from sample collection to data inspection. MAIN RESULTS AND ROLE OF THE CHANCE The TLDA cards protocol involved a higher rate of false positive results (5.6% versus 2.8% with Exiqon). There were 44 miRNAs detected in the ICM and TE from both the protocols. One and 24 miRNAs were instead detected solely in the ICM and the TE, respectively. Overall, 29 miRNAs were detected in the pooled SBM: 8 only from not-IEB, 8 only from IEB and 13 from both. Most of them (N = 24/29, 82.7%) were also detected previously in both the ICM and TE with the Exiqon protocol; two miRNAs (N = 2/29, 6.9%) were previously detected only in the TE, and three (N = 3/29, 10.3%) were never detected previously. In study Phase 2, significant differences were shown between not-IEB and IEB in terms of both miRNA detection and relative quantitation. However, when the data were corrected for embryo morphology and day of full development (i.e. SBM collection), no significant association was confirmed. LIMITATIONS, REASONS FOR CAUTION This study did not evaluate specifically exosomal miRNAs, thereby reducing the chance of identifying the functional miRNAs. Ex-vivo experiments are required to confirm the role of miRNAs in mediating the dialogue with endometrial cells, and higher throughput technologies need to be further evaluated for miRNA profiling from clinical SBM samples. WIDER IMPLICATIONS OF THE FINDINGS Although no clinical predictive power was reported in this study, the absence of invasiveness related with SBM analysis and the evidence that embryonic genetic material can be reliably detected and analysed from SBM make this waste product of IVF an important source for further investigations aimed at improving embryo selection. STUDY FUNDING/COMPETING INTEREST(S) This project has been financially supported by Merck KgaA (Darmstadt, Germany) with a Grant for Fertility Innovation (GFI) 2015. The authors have no conflict of interest to declare related with this study. TRIAL REGISTRATION NUMBER None.
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Affiliation(s)
- Danilo Cimadomo
- Clinica Valle Giulia, G.en.e.r.a. center for reproductive medicine, Rome, Italy.,Clinica Ruesch, G.en.e.r.a. Center for Reproductive Medicine, Naples, Italy.,G.en.e.r.a. Veneto, G.en.e.r.a. Center for Reproductive Medicine, Marostica, Italy
| | - Laura Rienzi
- Clinica Valle Giulia, G.en.e.r.a. center for reproductive medicine, Rome, Italy.,Clinica Ruesch, G.en.e.r.a. Center for Reproductive Medicine, Naples, Italy.,G.en.e.r.a. Veneto, G.en.e.r.a. Center for Reproductive Medicine, Marostica, Italy
| | - Adriano Giancani
- Clinica Valle Giulia, G.en.e.r.a. center for reproductive medicine, Rome, Italy.,DAHFMO, Unit of Histology and Medical Embryology, Sapienza, University of Rome, Italy
| | - Erminia Alviggi
- Clinica Ruesch, G.en.e.r.a. Center for Reproductive Medicine, Naples, Italy
| | - Ludovica Dusi
- G.en.e.r.a. Veneto, G.en.e.r.a. Center for Reproductive Medicine, Marostica, Italy
| | - Rita Canipari
- DAHFMO, Unit of Histology and Medical Embryology, Sapienza, University of Rome, Italy
| | - Laila Noli
- Fakeeh College of Medical Sciences, Jeddah, Saudi Arabia.,Division of Women's Health and Assisted Conception Unit, King's College of London, Guy's Hospital, London, United Kingdom
| | - Dusko Ilic
- Division of Women's Health and Assisted Conception Unit, King's College of London, Guy's Hospital, London, United Kingdom
| | - Yacoub Khalaf
- Division of Women's Health and Assisted Conception Unit, King's College of London, Guy's Hospital, London, United Kingdom
| | - Filippo Maria Ubaldi
- Clinica Valle Giulia, G.en.e.r.a. center for reproductive medicine, Rome, Italy.,Clinica Ruesch, G.en.e.r.a. Center for Reproductive Medicine, Naples, Italy.,G.en.e.r.a. Veneto, G.en.e.r.a. Center for Reproductive Medicine, Marostica, Italy
| | - Antonio Capalbo
- DAHFMO, Unit of Histology and Medical Embryology, Sapienza, University of Rome, Italy.,Igenomix, Marostica, Italy
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8
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Pidíkova P, Reis R, Herichova I. miRNA Clusters with Down-Regulated Expression in Human Colorectal Cancer and Their Regulation. Int J Mol Sci 2020; 21:E4633. [PMID: 32610706 PMCID: PMC7369991 DOI: 10.3390/ijms21134633] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/24/2020] [Accepted: 06/27/2020] [Indexed: 02/07/2023] Open
Abstract
Regulation of microRNA (miRNA) expression has been extensively studied with respect to colorectal cancer (CRC), since CRC is one of the leading causes of cancer mortality worldwide. Transcriptional control of miRNAs creating clusters can be, to some extent, estimated from cluster position on a chromosome. Levels of miRNAs are also controlled by miRNAs "sponging" by long non-coding RNAs (ncRNAs). Both types of miRNA regulation strongly influence their function. We focused on clusters of miRNAs found to be down-regulated in CRC, containing miR-1, let-7, miR-15, miR-16, miR-99, miR-100, miR-125, miR-133, miR-143, miR-145, miR-192, miR-194, miR-195, miR-206, miR-215, miR-302, miR-367 and miR-497 and analysed their genome position, regulation and functions. Only evidence provided with the use of CRC in vivo and/or in vitro models was taken into consideration. Comprehensive research revealed that down-regulated miRNA clusters in CRC are mostly located in a gene intron and, in a majority of cases, miRNA clusters possess cluster-specific transcriptional regulation. For all selected clusters, regulation mediated by long ncRNA was experimentally demonstrated in CRC, at least in one cluster member. Oncostatic functions were predominantly linked with the reviewed miRNAs, and their high expression was usually associated with better survival. These findings implicate the potential of down-regulated clusters in CRC to become promising multi-targets for therapeutic manipulation.
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Affiliation(s)
- Paulína Pidíkova
- Department of Animal Physiology and Ethology, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovakia;
| | - Richard Reis
- First Surgery Department, University Hospital, Comenius University in Bratislava, 811 07 Bratislava, Slovakia;
| | - Iveta Herichova
- Department of Animal Physiology and Ethology, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovakia;
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9
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Rodrigues D, Souza T, Jennen DG, Lemmens L, Kleinjans JC, de Kok TM. Drug-induced gene expression profile changes in relation to intestinal toxicity: State-of-the-art and new approaches. Cancer Treat Rev 2019; 77:57-66. [DOI: 10.1016/j.ctrv.2019.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/22/2022]
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10
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Thankam FG, Boosani CS, Dilisio MF, Gross RM, Agrawal DK. Genes interconnecting AMPK and TREM-1 and associated microRNAs in rotator cuff tendon injury. Mol Cell Biochem 2019; 454:97-109. [PMID: 30306456 PMCID: PMC6438203 DOI: 10.1007/s11010-018-3456-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/05/2018] [Indexed: 12/14/2022]
Abstract
Fatty infiltration and inflammation delay the healing responses and raise major concerns in the therapeutic management of rotator cuff tendon injuries (RCTI). Our evaluations showed the upregulation of 'metabolic check point' AMPK and inflammatory molecule, TREM-1 from shoulder biceps tendons collected from RCTI subjects. However, the epigenetic regulation of these biomolecules by miRNAs is largely unknown and it is likely that a deeper understanding of the mechanism of action can have therapeutic potential for RCTI. Based on this background, we have evaluated the miRNAs from RCTI patients with fatty infiltration and inflammation (FI group) and compared with RCTI patients without fatty infiltration and inflammation (No-FI group). NetworkAnalyst was employed to evaluate the genes interconnecting AMPK and TREM-1 pathway, using PRKAA1 (AMPK), TREM-1, HIF1α, HMGB1, and AGER as input genes. The most relevant miRNAs were screened by considering the fold change below - 7.5 and the number of target genes 10 and more which showed 13 miRNAs and 216 target genes. The exact role of these miRNAs in the fatty infiltration and inflammation associated with RCTI is still unknown and the understanding of biological activity of these miRNAs can pave ways to develop miRNA-based therapeutics in the management of RCTI.
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Affiliation(s)
- Finosh G Thankam
- Departments of Clinical & Translational Science and Orthopedic Surgery, Creighton University School of Medicine, Omaha, NE, 68178, USA
| | - Chandra S Boosani
- Departments of Clinical & Translational Science and Orthopedic Surgery, Creighton University School of Medicine, Omaha, NE, 68178, USA
| | - Matthew F Dilisio
- Departments of Clinical & Translational Science and Orthopedic Surgery, Creighton University School of Medicine, Omaha, NE, 68178, USA
| | - R Michael Gross
- Departments of Clinical & Translational Science and Orthopedic Surgery, Creighton University School of Medicine, Omaha, NE, 68178, USA
| | - Devendra K Agrawal
- Departments of Clinical & Translational Science and Orthopedic Surgery, Creighton University School of Medicine, Omaha, NE, 68178, USA.
- Department of Clinical & Translational Science, The Peekie Nash Carpenter Endowed Chair in Medicine, CRISS II Room 510, 2500 California Plaza, Omaha, NE, 68178, USA.
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11
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Campayo M, Navarro A, Benítez JC, Santasusagna S, Ferrer C, Monzó M, Cirera L. miR-21, miR-99b and miR-375 combination as predictive response signature for preoperative chemoradiotherapy in rectal cancer. PLoS One 2018; 13:e0206542. [PMID: 30388154 PMCID: PMC6214543 DOI: 10.1371/journal.pone.0206542] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/15/2018] [Indexed: 12/29/2022] Open
Abstract
Introduction Preoperative chemoradiotherapy (CRT) is a standard treatment for locally advanced rectal cancer patients. Despite the benefits of CRT, its use in non-responder patients can be associated with increased toxicities and surgical resection delay. The identification of CRT response biomarkers, such as microRNAs, could improve the management of these patients. We have studied the microRNA expression in pretreatment endoscopy biopsies from rectal cancer patients treated with CRT to identify potential microRNAs able to predict CRT response and clinical outcome of these patients. Material and methods RNA from pretreatment endoscopy biopsies from 96 rectal cancer patients treated with preoperative CRT were studied. Pathological response was graded according to the tumor regression grade (TRG) Dworak classification. In the screening phase, 377 miRNAs were studied in 12 patients with extreme responses (TRG0-1 vs TRG4). The potential role as predictive biomarkers for CRT response, disease-free survival (DFS) and overall survival (OS) of the miRNAs identified in the screening phase were validated in the whole cohort. Results In the screening phase, an 8-miRNAs CRT-response signature was identified: let-7b, let-7e, miR-21, miR-99b, miR-183, miR-328, miR-375 and miR-483-5p. In the validation phase, miR-21, miR-99b and miR-375 emerged as CRT response-related miRNAs while miR-328 and let-7e emerged as prognostic markers for DFS and OS. Interestingly, ROC curve analysis showed that the combination of miR-21, miR-99b and miR-375 had the best capacity to distinguish patients with maximum response (TRG4) from others. Conclusions miR-21, miR-99b and miR-375 could add valuable information for individualizing treatment in locally advanced rectal cancer patients.
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Affiliation(s)
- Marc Campayo
- Department of Medical Oncology, Hospital Universitari Mutua Terrassa, University of Barcelona, Terrassa, Barcelona, Spain
- * E-mail:
| | - Alfons Navarro
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Jose Carlos Benítez
- Department of Medical Oncology, Hospital Universitari Mutua Terrassa, University of Barcelona, Terrassa, Barcelona, Spain
| | - Sandra Santasusagna
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Carme Ferrer
- Department of Pathology, Hospital Universitari Mutua Terrassa, University of Barcelona, Terrassa, Barcelona, Spain
| | - Mariano Monzó
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Luis Cirera
- Department of Medical Oncology, Hospital Universitari Mutua Terrassa, University of Barcelona, Terrassa, Barcelona, Spain
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12
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Neerincx M, Poel D, Sie DLS, van Grieken NCT, Shankaraiah RC, van der Wolf - de Lijster FSW, van Waesberghe JHTM, Burggraaf JD, Eijk PP, Verhoef C, Ylstra B, Meijer GA, van de Wiel MA, Buffart TE, Verheul HMW. Combination of a six microRNA expression profile with four clinicopathological factors for response prediction of systemic treatment in patients with advanced colorectal cancer. PLoS One 2018; 13:e0201809. [PMID: 30075027 PMCID: PMC6075783 DOI: 10.1371/journal.pone.0201809] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 07/22/2018] [Indexed: 12/19/2022] Open
Abstract
Background First line chemotherapy is effective in 75 to 80% of patients with metastatic colorectal cancer (mCRC). We studied whether microRNA (miR) expression profiles can predict treatment outcome for first line fluoropyrimidine containing systemic therapy in patients with mCRC. Methods MiR expression levels were determined by next generation sequencing from snap frozen tumor samples of 88 patients with mCRC. Predictive miRs were selected with penalized logistic regression and posterior forward selection. The prediction co-efficients of the miRs were re-estimated and validated by real-time quantitative PCR in an independent cohort of 81 patients with mCRC. Results Expression levels of miR-17-5p, miR-20a-5p, miR-30a-5p, miR-92a-3p, miR-92b-3p and miR-98-5p in combination with age, tumor differentiation, adjuvant therapy and type of systemic treatment, were predictive for clinical benefit in the training cohort with an AUC of 0.78. In the validation cohort the addition of the six miR signature to the four clinicopathological factors demonstrated a significant increased AUC for predicting treatment response versus those with stable disease (SD) from 0.79 to 0.90. The increase for predicting treatment response versus progressive disease (PD) and for patients with SD versus those with PD was not significant. in the validation cohort. MiR-17-5p, miR-20a-5p and miR-92a-3p were significantly upregulated in patients with treatment response in both the training and validation cohorts. Conclusion A six miR expression signature was identified that predicted treatment response to fluoropyrimidine containing first line systemic treatment in patients with mCRC when combined with four clinicopathological factors. Independent validation demonstrated added predictive value of this miR-signature for predicting treatment response versus SD. However, added predicted value for separating patients with PD could not be validated. The clinical relevance of the identified miRs for predicting treatment response has to be further explored.
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Affiliation(s)
- Maarten Neerincx
- Department of Medical Oncology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Dennis Poel
- Department of Medical Oncology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Daoud L. S. Sie
- Department of Pathology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Nicole C. T. van Grieken
- Department of Pathology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Ram C. Shankaraiah
- Department of Medical Oncology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | | | | | | | - Paul P. Eijk
- Department of Pathology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Cornelis Verhoef
- Department of Surgical Oncology, Erasmus Medical Center Cancer Institute, Rotterdam, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Gerrit A. Meijer
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mark A. van de Wiel
- Department of Epidemiology and Biostatistics, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
- Department of Mathematics, VU University, Amsterdam, The Netherlands
| | - Tineke E. Buffart
- Department of Medical Oncology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk M. W. Verheul
- Department of Medical Oncology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
- * E-mail:
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13
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Translational reprogramming of colorectal cancer cells induced by 5-fluorouracil through a miRNA-dependent mechanism. Oncotarget 2018; 8:46219-46233. [PMID: 28515355 PMCID: PMC5542262 DOI: 10.18632/oncotarget.17597] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/06/2017] [Indexed: 11/25/2022] Open
Abstract
5-Fluorouracil (5-FU) is a widely used chemotherapeutic drug in colorectal cancer. Previous studies showed that 5-FU modulates RNA metabolism and mRNA expression. In addition, it has been reported that 5-FU incorporates into the RNAs constituting the translational machinery and that 5-FU affects the amount of some mRNAs associated with ribosomes. However, the impact of 5-FU on translational regulation remains unclear. Using translatome profiling, we report that a clinically relevant dose of 5-FU induces a translational reprogramming in colorectal cancer cell lines. Comparison of mRNA distribution between polysomal and non-polysomal fractions in response to 5-FU treatment using microarray quantification identified 313 genes whose translation was selectively regulated. These regulations were mostly stimulatory (91%). Among these genes, we showed that 5-FU increases the mRNA translation of HIVEP2, which encodes a transcription factor whose translation in normal condition is known to be inhibited by mir-155. In response to 5-FU, the expression of mir-155 decreases thus stimulating the translation of HIVEP2 mRNA. Interestingly, the 5-FU-induced increase in specific mRNA translation was associated with reduction of global protein synthesis. Altogether, these findings indicate that 5-FU promotes a translational reprogramming leading to the increased translation of a subset of mRNAs that involves at least for some of them, miRNA-dependent mechanisms. This study supports a still poorly evaluated role of translational control in drug response.
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14
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Eldeib MG, Kandil YI, Abdelghany TM, Mansour OA, El-Zahabi MM. Alterations of microRNAs expression in response to 5-Fluorouracil, Oxaliplatin, and Irinotecan treatment of colorectal cancer cells. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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15
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Han J, Li J, Tang K, Zhang H, Guo B, Hou N, Huang C. miR-338-3p confers 5-fluorouracil resistance in p53 mutant colon cancer cells by targeting the mammalian target of rapamycin. Exp Cell Res 2017; 360:328-336. [PMID: 28928082 DOI: 10.1016/j.yexcr.2017.09.023] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/13/2017] [Accepted: 09/15/2017] [Indexed: 12/31/2022]
Abstract
Evidence demonstrate that p53 mutations and microRNAs (miRs) are important components of 5-FU resistance in colorectal cancer (CRC). miR-338-3p has been reported associated with cancer prognosis. However whether or not it influences chemotherapy sensitivity and the underlying mechanisms have not been elucidated. Here, three types of human colon cancer cell lines, HT29 (mutant p53), HCT116 (wild-type p53), and HCT116 p53-/- (deficient p53), were treated with 5-FU. We showed that expression of miR-338-3p was correlated with apoptosis and 5-FU resistance in colon cancer cells. Ectopic expression of miR-338-3p conferred resistance to 5-FU in HCT116 cells. Further experiments indicated that miR-338-3p mediated 5-FU resistance through down-regulation of mTOR expression. Moreover, inhibition of miR-338-3p in HT29 and HCT116 p53-/- cells increased their sensitivity to 5-FU treatment. Furthermore, we detected autophagy changes in our experiment because mTOR was known prominently regulating autophagy and the competition between autophagy and apoptosis in response to 5-FU was a mechanism influencing 5-FU sensitivity. Our results reveal a critical and novel role of miR-338-3p in the correlation of 5-FU resistance with p53 status. Moreover, the miR-338-3p inhibitor has the potential to overcome 5-FU resistance in p53 mutant colon cancer cells.
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Affiliation(s)
- Jia Han
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Jie Li
- Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Kaijie Tang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Huahua Zhang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China; Medical College, Yan'an University, Yan'an, China
| | - Bo Guo
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Ni Hou
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.
| | - Chen Huang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.
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16
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Yang D, Li Y, Zhao D. Curcumin induces apoptotic cell death in human pancreatic cancer cells via the miR-340/XIAP signaling pathway. Oncol Lett 2017; 14:1811-1816. [PMID: 28789415 DOI: 10.3892/ol.2017.6321] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 03/03/2017] [Indexed: 01/01/2023] Open
Abstract
The natural compound curcumin has previously been reported to inhibit pancreatic cancer cell growth. However, the underlying molecular mechanisms underlying this effect remain unclear. Results from the present study demonstrate that the miR-340/X-linked inhibitor of apoptosis (XIAP) signaling pathway mediates curcumin-induced pancreatic cancer cell apoptosis. miR-340 was identified to be significantly upregulated following curcumin treatment. In addition, treatment with curcumin or miR-340 induced pancreatic cancer cell apoptosis, whereas silencing endogenous miR-340 significantly inhibited the proapoptotic effect of curcumin. A luciferase reporter assay and western blot analysis identified that the oncogene XIAP is a direct target of miR-340. Furthermore, curcumin treatment significantly reduced XIAP expression, an effect that was rescued by treatment with anti-miR-340. The results of the present study suggest that the miR-340/XIAP signaling pathway is a downstream target of curcumin that mediates its proapoptotic effects on pancreatic cancer cells. This may provide the basis for novel treatment strategies for patients with pancreatic cancer.
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Affiliation(s)
- Deying Yang
- Department of Gastrointestinal Surgery, Linyi People's Hospital, Linyi, Shandong 276000, P.R. China
| | - Yutao Li
- Department of Gastrointestinal Surgery, Linyi People's Hospital, Linyi, Shandong 276000, P.R. China
| | - Deqin Zhao
- Department of Neurosurgery, Linyi Chinese Medicine Hospital, Linyi, Shandong 276000, P.R. China
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17
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Deng J, Wang Y, Lei J, Lei W, Xiong JP. Insights into the involvement of noncoding RNAs in 5-fluorouracil drug resistance. Tumour Biol 2017; 39:1010428317697553. [PMID: 28381160 DOI: 10.1177/1010428317697553] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
5-Fluorouracil is a classic chemotherapeutic drug that is widely used to treat various cancers. However, patients often exhibit primary or acquired drug resistance during treatment with 5-fluorouracil chemotherapy. 5-Fluorouracil resistance is a multifactorial event that involves abnormal enzyme metabolism, transport deregulation, cell cycle disorders, apoptosis resistance, and mismatch repair deficiency. Despite advancements in bioresearch technologies in the past several decades, the molecular mechanisms of 5-fluorouracil resistance have not been completely clarified. Recently, microarray analyses have shown that noncoding RNAs (i.e. microRNAs and long noncoding RNAs) play a vital role in 5-fluorouracil resistance in multiple cancer cell lines. These noncoding RNAs can function as oncogenes or tumor suppressors, contributing to 5-fluorouracil drug resistance. In this review, we discuss the effects of microRNAs on 5-fluorouracil sensitivity via targeting of metabolic enzymes, the cell cycle, apoptosis, autophagy, the epithelial–mesenchymal transition, and cancer stem cells. In particular, we focus on summarizing current knowledge on the molecular mechanisms through which long noncoding RNAs mediate 5-fluorouracil drug resistance. Moreover, we describe the specific microRNAs that may function as markers for prediction of chemotherapeutic response to 5-fluorouracil. This review will help to improve the current understanding of how to reverse 5-fluorouracil resistance and may facilitate the establishment of new strategies for alleviating drug resistance in the future.
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Affiliation(s)
- Jun Deng
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yi Wang
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jun Lei
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wan Lei
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jian Ping Xiong
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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18
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Zhou H, Yuan M, Yu Q, Zhou X, Min W, Gao D. Autophagy regulation and its role in gastric cancer and colorectal cancer. Cancer Biomark 2017; 17:1-10. [PMID: 27314289 DOI: 10.3233/cbm-160613] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Autophagy is associated with the occurrence, development, cellular adaptation, progression, treatment and prognosis of gastric cancer (GC) and colorectal cancer (CRC). The effect of autophagy in these two cancers has attracted our attention. OBJECTIVE The aim of this study was to describe the functional and regulatory mechanisms associated with autophagy in GC and CRC. METHODS We reviewed recent publications describing the role of autophagy in GC and CRC, including the functional characteristics, clinical significance and regulatory mechanisms. RESULTS Autophagy plays context-dependent dual roles in the development and progression of GC and CRC. It can either promote tumor growth and cell survival or can contribute to tumor suppression and promote cell death. Both of these effects employ complex regulatory networks, such as those mediated by p53, PI3K/Akt/mTOR, Ras and microRNA. Among the cellular process associated with these pathways, autophagy is a potential target for anti-tumor therapy. CONCLUSION Autophagy is associated with both tumorigenic and protective effects in cancer. However, the role of autophagy in GC and CRC remains unclear. Although the translation of the basic science of autophagy into clinical practice is a long process, the modulation of autophagy as a potential therapeutic approach in GC and CRC merits further investigation.
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Affiliation(s)
- Huangyan Zhou
- Department of Pathogen Biology and Immunology, Medical College of Nanchang University, Nanchang, Jiangxi, China.,Jiangxi Academy of Medical Sciences, Nanchang, Jiangxi, China.,Institute of Immunotherapy, Nanchang University, Nanchang, Jiangxi, China
| | - Min Yuan
- Department of Neurology, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Qiongfang Yu
- Department of Gastroenterology and Hepatology, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xiaoyan Zhou
- Department of Pathophysiology, Medical College of Nanchang University, Nanchang, Jiangxi, China
| | - Weiping Min
- Department of Pathogen Biology and Immunology, Medical College of Nanchang University, Nanchang, Jiangxi, China.,Jiangxi Academy of Medical Sciences, Nanchang, Jiangxi, China.,Institute of Immunotherapy, Nanchang University, Nanchang, Jiangxi, China
| | - Dian Gao
- Department of Pathogen Biology and Immunology, Medical College of Nanchang University, Nanchang, Jiangxi, China.,Jiangxi Academy of Medical Sciences, Nanchang, Jiangxi, China.,Institute of Immunotherapy, Nanchang University, Nanchang, Jiangxi, China
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19
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Piątek Ł, Grzymała-Busse JW. LEMRG: Decision Rule Generation Algorithm for Mining MicroRNA Expression Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1028:105-137. [DOI: 10.1007/978-981-10-6041-0_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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20
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MicroRNA-302a enhances 5-fluorouracil-induced cell death in human colon cancer cells. Oncol Rep 2016; 37:631-639. [PMID: 27840990 DOI: 10.3892/or.2016.5237] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 11/02/2016] [Indexed: 12/17/2022] Open
Abstract
New therapeutic strategies are needed for colorectal cancer (CRC) treatment. MicroRNAs are involved in cancer‑pertinent cellular processes, including chemoresistance. As miR‑302a is an embryonic stem cell‑specific microRNA, studies on miR‑302a have focused on its role in human stem cells. Studies analyzing miR‑302 function in cancer are limited. In this study, we used two human colon cancer cell lines, HCT116 and HT29, and evaluated the influence of miR‑302a on 5‑fluorouracil (5‑FU)‑induced cell death and viability inhibition. With bioinformatics tools, we hypothesized that insulin‑like growth factor‑1 receptor (IGF‑1R) is a novel target of miR‑302a, which we confirmed using a luciferase reporter assay and immunoblotting. Then, we designed siRNA against IGF‑1R and found that si‑IGF‑1R resembled the effect of miR‑302a on 5‑FU treatment. Both miR‑302a and si‑IGF‑1R inhibited Akt signaling. In conclusion, miR‑302a targeted IGF‑1R and enhanced 5‑FU‑induced cell death and viability inhibition in human colon cancer cells. Targeting miR‑302a may offer new therapeutic interventions in CRC.
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21
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Pathak S, Meng WJ, Nandy SK, Ping J, Bisgin A, Helmfors L, Waldmann P, Sun XF. Radiation and SN38 treatments modulate the expression of microRNAs, cytokines and chemokines in colon cancer cells in a p53-directed manner. Oncotarget 2016; 6:44758-80. [PMID: 26556872 PMCID: PMC4792590 DOI: 10.18632/oncotarget.5815] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 10/26/2015] [Indexed: 02/07/2023] Open
Abstract
Aberrant expression of miRNAs, cytokines and chemokines are involved in pathogenesis of colon cancer. However, the expression of p53 mediated miRNAs, cyto- and chemokines after radiation and SN38 treatment in colon cancer remains elusive. Here, human colon cancer cells, HCT116 with wild-type, heterozygous and a functionally null p53, were treated by radiation and SN38. The expression of 384 miRNAs was determined by using the TaqMan® miRNA array, and the expression of cyto- and chemokines was analyzed by Meso-Scale-Discovery instrument. Up- or down-regulations of miRNAs after radiation and SN38 treatments were largely dependent on p53 status of the cells. Cytokines, IL-6, TNF-α, IL-1β, Il-4, IL-10, VEGF, and chemokines, IL-8, MIP-1α were increased, and IFN-γ expression was decreased after radiation, whereas, IL-6, IFN-γ, TNF-α, IL-1β, Il-4, IL-10, IL-8 were decreased, and VEGF and MIP-1α were increased after SN38 treatment. Bioinformatic analysis pointed out that the highly up-regulated miRNAs, let-7f-5p, miR-455-3p, miR-98, miR-155-5p and the down-regulated miRNAs, miR-1, miR-127-5p, miR-142-5p, miR-202-5p were associated with colon cancer pathways and correlated with cyto- or chemokine expression. These miRNAs have the potential for use in colon cancer therapy as they are related to p53, pro- or anti-inflammatory cyto- or chemokines after the radiation and SN38 treatment.
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Affiliation(s)
- Surajit Pathak
- Department of Oncology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Wen-Jian Meng
- Department of Oncology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.,Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Suman Kumar Nandy
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, West Bengal, India
| | - Jie Ping
- Department of Oncology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Atil Bisgin
- Department of Oncology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Linda Helmfors
- Department of Molecular Biotechnology/IFM, Linköping University, Linköping, Sweden
| | - Patrik Waldmann
- Department of Computer and Information Science, Linköping University, Linköping, Sweden
| | - Xiao-Feng Sun
- Department of Oncology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
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Deregulation of miRNA-181c potentially contributes to the pathogenesis of AD by targeting collapsin response mediator protein 2 in mice. J Neurol Sci 2016; 367:3-10. [DOI: 10.1016/j.jns.2016.05.038] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/05/2016] [Accepted: 05/18/2016] [Indexed: 12/26/2022]
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23
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Yu X, Li Z, Yu J, Chan MTV, Wu WKK. MicroRNAs predict and modulate responses to chemotherapy in colorectal cancer. Cell Prolif 2015. [PMID: 26202377 DOI: 10.1111/cpr.12202] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the fourth leading cause of cancer-related death globally. Chemotherapy regimens consisting of 5-fluorouracil (5-FU) in combination with either oxaliplatin or irinotecan are the first-line options for treatment of metastatic CRC. However, primary or acquired resistance to these chemotherapeutics is a major clinical challenge. MicroRNAs (miRNAs) are a group of small non-coding RNAs that regulate gene expression post-transcriptionally. miRNAs play important roles in many cancer-related processes, including cell proliferation, apoptosis and invasion, and their dysregulation is implicated in colorectal tumourigenesis. Pertinent to chemotherapy, increasing evidence has revealed that miRNAs can be directly linked to chemosensitivity in CRC. In this review, we summarize current evidence concerning the role of miRNAs in prediction and modulation of cellular responses to 5-FU, oxaliplatin and irinotecan in CRC. We also discuss the possible targets and intracellular pathways involved in these processes.
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Affiliation(s)
- Xin Yu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100042, China
| | - Zheng Li
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100042, China
| | - Jun Yu
- State-Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Matthew T V Chan
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - William K K Wu
- State-Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, 999077, China.,Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, 999077, China
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