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Arab I, Lim SG, Suk K, Lee WH. LINC01270 Regulates the NF-κB-Mediated Pro-Inflammatory Response via the miR-326/LDOC1 Axis in THP-1 Cells. Cells 2024; 13:2027. [PMID: 39682774 PMCID: PMC11640305 DOI: 10.3390/cells13232027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 11/28/2024] [Accepted: 12/06/2024] [Indexed: 12/18/2024] Open
Abstract
Long intergenic noncoding (LINC)01270 is a 2278 bp transcript belonging to the intergenic subset of long noncoding (lnc)RNAs. Despite increased reports of LINC01270's involvement in different diseases, evident research on its effects on inflammation is yet to be achieved. In the present study, we investigated the potential role of LINC01270 in modulating the inflammatory response in the human monocytic leukemia cell line THP-1. Lipopolysaccharide treatment upregulated LINC01270 expression, and siRNA-mediated suppression of LINC01270 enhanced NF-κB activity and the subsequent production of cytokines IL-6, IL-8, and MCP-1. Interestingly, the knockdown of LINC01270 downregulated expression of leucine zipper downregulated in cancer 1 (LDOC1), a novel NF-κB suppressor. An analysis of the LINC01270/micro-RNA (miRNA)/protein interactome profile identified miR-326 as a possible mediator. Synthetic RNA agents that perturb the interaction among LINC01270, miR-326, and LDOC1 mRNA mitigated the changes caused by LINC01270 knockdown in THP-1 cells. Additionally, a luciferase reporter assay in HEK293 cells further confirmed that LINC01270 knockdown enhances NF-κB activation, while its overexpression has the opposite effect. This study provides insight into LINC01270's role in modulating inflammatory responses to lipopolysaccharide stimulation in THP-1 cells via the miR-326/LDOC1 axis, which negatively regulates NF-κB activation.
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Affiliation(s)
- Imene Arab
- School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea; (I.A.); (S.-G.L.)
- BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Su-Geun Lim
- School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea; (I.A.); (S.-G.L.)
- BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyoungho Suk
- Brain Science & Engineering Institute, Kyungpook National University, Daegu 41944, Republic of Korea
- Department of Pharmacology, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
- BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Won-Ha Lee
- School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea; (I.A.); (S.-G.L.)
- BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- Brain Science & Engineering Institute, Kyungpook National University, Daegu 41944, Republic of Korea
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2
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Kasperczak M, Bromiński G, Kołodziejczak-Guglas I, Antczak A, Wiznerowicz M. Prognostic Significance of Elevated UCHL1, SNRNP200, and PAK4 Expression in High-Grade Clear Cell Renal Cell Carcinoma: Insights from LC-MS/MS Analysis and Immunohistochemical Validation. Cancers (Basel) 2024; 16:2844. [PMID: 39199615 PMCID: PMC11352290 DOI: 10.3390/cancers16162844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 08/07/2024] [Accepted: 08/10/2024] [Indexed: 09/01/2024] Open
Abstract
Recent advancements in proteomics have enhanced our understanding of clear cell renal cell carcinoma (CCRCC). Utilizing a combination of liquid chromatography-tandem mass spectrometry (LC-MS/MS) followed by immunohistochemical validation, we investigated the expression levels of UCHL1, PAK4, and SNRNP200 in high-grade CCRCC samples. Our analysis also integrated Reactome pathway enrichment to elucidate the roles of these proteins in cancer-related pathways. Our results revealed significant upregulation of UCHL1 and SNRNP200 and downregulation of PAK4 in high-grade CCRCC tissues compared to non-cancerous tissues. UCHL1, a member of the ubiquitin carboxy-terminal hydrolase family, showed variable expression across different tissues and was notably involved in the Akt signaling pathway, which plays a critical role in cellular survival in various cancers. SNRNP200, a key component of the RNA splicing machinery, was found to be essential for proper cell cycle progression and possibly linked to autosomal dominant retinitis pigmentosa. PAK4's role was noted as critical in RCC cell proliferation and invasion and its expression correlated significantly with poor progression-free survival in CCRCC. Additionally, the expression patterns of these proteins suggested potential as prognostic markers for aggressive disease phenotypes. This study confirms the upregulation of UCHL1, SNRNP200, and PAK4 as significant factors in the progression of high-grade CCRCC, linking their enhanced expression to poor clinical outcomes. These findings propose these proteins as potential prognostic markers and therapeutic targets in CCRCC, offering novel insights into the molecular landscape of this malignancy and highlighting the importance of targeted therapeutic interventions.
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Affiliation(s)
- Michał Kasperczak
- Department of Urology, Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | - Gabriel Bromiński
- Department of Urology, Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | | | - Andrzej Antczak
- Department of Urology, Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | - Maciej Wiznerowicz
- Department of Urology, Poznań University of Medical Sciences, 61-701 Poznań, Poland
- International Institute for Molecular Oncology, 60-203 Poznań, Poland
- University Hospital of Lord’s Transfiguration, 61-848 Poznań, Poland
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3
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Chen F, Zhang Y, Shen L, Creighton CJ. The DNA methylome of pediatric brain tumors appears shaped by structural variation and predicts survival. Nat Commun 2024; 15:6775. [PMID: 39117669 PMCID: PMC11310301 DOI: 10.1038/s41467-024-51276-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024] Open
Abstract
Structural variation heavily influences the molecular landscape of cancer, in part by impacting DNA methylation-mediated transcriptional regulation. Here, using multi-omic datasets involving >2400 pediatric brain and central nervous system tumors of diverse histologies from the Children's Brain Tumor Network, we report hundreds of genes and associated CpG islands (CGIs) for which the nearby presence of somatic structural variant (SV) breakpoints is recurrently associated with altered expression or DNA methylation, respectively, including tumor suppressor genes ATRX and CDKN2A. Altered DNA methylation near enhancers associates with nearby somatic SV breakpoints, including MYC and MYCN. A subset of genes with SV-CGI methylation associations also have expression associations with patient survival, including BCOR, TERT, RCOR2, and PDLIM4. DNA methylation changes in recurrent or progressive tumors compared to the initial tumor within the same patient can predict survival in pediatric and adult cancers. Our comprehensive and pan-histology genomic analyses reveal mechanisms of noncoding alterations impacting cancer genes.
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Affiliation(s)
- Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Lanlan Shen
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
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4
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Zhang Y, Chen F, Balic M, Creighton CJ. An essential gene signature of breast cancer metastasis reveals targetable pathways. Breast Cancer Res 2024; 26:98. [PMID: 38867323 PMCID: PMC11167932 DOI: 10.1186/s13058-024-01855-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND The differential gene expression profile of metastatic versus primary breast tumors represents an avenue for discovering new or underappreciated pathways underscoring processes of metastasis. However, as tumor biopsy samples are a mixture of cancer and non-cancer cells, most differentially expressed genes in metastases would represent confounders involving sample biopsy site rather than cancer cell biology. METHODS By paired analysis, we defined a top set of differentially expressed genes in breast cancer metastasis versus primary tumors using an RNA-sequencing dataset of 152 patients from The Breast International Group Aiming to Understand the Molecular Aberrations dataset (BIG-AURORA). To filter the genes higher in metastasis for genes essential for breast cancer proliferation, we incorporated CRISPR-based data from breast cancer cell lines. RESULTS A significant fraction of genes with higher expression in metastasis versus paired primary were essential by CRISPR. These 264 genes represented an essential signature of breast cancer metastasis. In contrast, nonessential metastasis genes largely involved tumor biopsy site. The essential signature predicted breast cancer patient outcome based on primary tumor expression patterns. Pathways underlying the essential signature included proteasome degradation, the electron transport chain, oxidative phosphorylation, and cancer metabolic reprogramming. Transcription factors MYC, MAX, HDAC3, and HCFC1 each bound significant fractions of essential genes. CONCLUSIONS Associations involving the essential gene signature of breast cancer metastasis indicate true biological changes intrinsic to cancer cells, with important implications for applying existing therapies or developing alternate therapeutic approaches.
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Affiliation(s)
- Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, MS305, Houston, TX, 77030, USA
| | - Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, MS305, Houston, TX, 77030, USA
| | - Marija Balic
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Unit for Translational Breast Cancer Research, Medical University of Graz, Graz, Austria
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, MS305, Houston, TX, 77030, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
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5
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Yadav P, Tamilselvan R, Mani H, Singh KK. MicroRNA-mediated regulation of nonsense-mediated mRNA decay factors: Insights into microRNA prediction tools and profiling techniques. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195022. [PMID: 38437914 DOI: 10.1016/j.bbagrm.2024.195022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) stands out as a prominent RNA surveillance mechanism within eukaryotes, meticulously overseeing both RNA abundance and integrity by eliminating aberrant transcripts. These defective transcripts are discerned through the concerted efforts of translating ribosomes, eukaryotic release factors (eRFs), and trans-acting NMD factors, with Up-Frameshift 3 (UPF3) serving as a noteworthy component. Remarkably, in humans, UPF3 exists in two paralogous forms, UPF3A (UPF3) and UPF3B (UPF3X). Beyond its role in quality control, UPF3 wields significant influence over critical cellular processes, including neural development, synaptic plasticity, and axon guidance. However, the precise regulatory mechanisms governing UPF3 remain elusive. MicroRNAs (miRNAs) emerge as pivotal post-transcriptional gene regulators, exerting substantial impact on diverse pathological and physiological pathways. This comprehensive review encapsulates our current understanding of the intricate regulatory nexus between NMD and miRNAs, with particular emphasis on the essential role played by UPF3B in neurodevelopment. Additionally, we bring out the significance of the 3'-untranslated region (3'-UTR) as the molecular bridge connecting NMD and miRNA-mediated gene regulation. Furthermore, we provide an in-depth exploration of diverse computational tools tailored for the prediction of potential miRNA targets. To complement these computational approaches, we delineate experimental techniques designed to validate predicted miRNA-mRNA interactions, empowering readers with the knowledge necessary to select the most appropriate methodology for their specific research objectives.
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Affiliation(s)
- Priyanka Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Raja Tamilselvan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Harita Mani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Kusum Kumari Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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6
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Bhadra M, Sachan M. An overview of challenges associated with exosomal miRNA isolation toward liquid biopsy-based ovarian cancer detection. Heliyon 2024; 10:e30328. [PMID: 38707279 PMCID: PMC11068823 DOI: 10.1016/j.heliyon.2024.e30328] [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: 10/30/2023] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/07/2024] Open
Abstract
As one of the deadliest gynaecological cancers, ovarian cancer has been on the list. With lesser-known symptoms and lack of an accurate detection method, it is still difficult to catch it early. In terms of both the diagnosis and outlook for cancer, liquid biopsy has come a long way with significant advancements. Exosomes, extracellular components commonly shed by cancerous cells, are nucleic acid-rich particles floating in almost all body fluids and hold enormous promise, leading to minimallyinvasive molecular diagnostics. They have been shown as potential biomarkers in liquid biopsy, being implicated in tumour growth and metastasis. In order to address the drawbacks of ovarian cancer tumor heterogeneity, a liquid biopsy-based approach is being investigated by detecting cell-free nucleic acids, particularly non-coding RNAs, having the advantage of being less invasive and more prominent in nature. microRNAs are known to actively contribute to cancer development and their existence inside exosomes has also been made quite apparent which can be leveraged to diagnose and treat the disease. Extraction of miRNAs and exosomes is an arduous execution, and while other approaches have been investigated, none have produced results that are as encouraging due to limits in time commitment, yield, and, most significantly, damage to the exosomal structure resulting discrepancies in miRNA-based expression profiling for disease diagnosis. We have briefly outlined and reviewed the difficulties with exosome isolation techniques and the need for their standardization. The several widely used procedures and their drawbacks in terms of the exosomal purity they may produce have also been outlined.
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Affiliation(s)
- Mridula Bhadra
- Department of Biotechnology, Motilal Nehru National Institute of Technology-Allahabad, Prayagraj, 211004, Uttar Pradesh, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology-Allahabad, Prayagraj, 211004, Uttar Pradesh, India
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7
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Monsivais D, Parks SE, Chandrashekar DS, Varambally S, Creighton CJ. Using cancer proteomics data to identify gene candidates for therapeutic targeting. Oncotarget 2023; 14:399-412. [PMID: 37141409 PMCID: PMC11623401 DOI: 10.18632/oncotarget.28420] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023] Open
Abstract
Gene-level associations obtained from mass-spectrometry-based cancer proteomics datasets represent a resource for identifying gene candidates for functional studies. When recently surveying proteomic correlates of tumor grade across multiple cancer types, we identified specific protein kinases having a functional impact on uterine endometrial cancer cells. This previously published study provides just one template for utilizing public molecular datasets to discover potential novel therapeutic targets and approaches for cancer patients. Proteomic profiling data combined with corresponding multi-omics data on human tumors and cell lines can be analyzed in various ways to prioritize genes of interest for interrogating biology. Across hundreds of cancer cell lines, CRISPR loss of function and drug sensitivity scoring can be readily integrated with protein data to predict any gene's functional impact before bench experiments are carried out. Public data portals make cancer proteomics data more accessible to the research community. Drug discovery platforms can screen hundreds of millions of small molecule inhibitors for those that target a gene or pathway of interest. Here, we discuss some of the available public genomic and proteomic resources while considering approaches to how these could be leveraged for molecular biology insights or drug discovery. We also demonstrate the inhibitory effect of BAY1217389, a TTK inhibitor recently tested in a Phase I clinical trial for the treatment of solid tumors, on uterine cancer cell line viability.
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Affiliation(s)
- Diana Monsivais
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sydney E. Parks
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Cancer and Cell Biology Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Darshan S. Chandrashekar
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35233, USA
- Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
- Genomic Diagnostics and Bioinformatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Sooryanarayana Varambally
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35233, USA
- Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
- The Informatics Institute, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Chad J. Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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8
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Toal TW, Estrada-Florez AP, Polanco-Echeverry GM, Sahasrabudhe RM, Lott PC, Suarez-Olaya JJ, Guevara-Tique AA, Rocha S, Morales-Arana A, Castro-Valencia F, Urayama S, Kirane A, Wei D, Rios-Sarabia N, Medrano R, Mantilla A, Echeverry de Polanco M, Torres J, Bohorquez-Lozano ME, Carvajal-Carmona LG. Multiregional Sequencing Analysis Reveals Extensive Genetic Heterogeneity in Gastric Tumors from Latinos. CANCER RESEARCH COMMUNICATIONS 2022; 2:1487-1496. [PMID: 36970058 PMCID: PMC10035402 DOI: 10.1158/2767-9764.crc-22-0149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/15/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
Gastric cancer is a leading cause of cancer mortality and health disparities in Latinos. We evaluated gastric intratumoral heterogeneity using multiregional sequencing of >700 cancer genes in 115 tumor biopsies from 32 patients, 29 who were Latinos. Analyses focused on comparisons with The Cancer Genome Atlas (TCGA) and on mutation clonality, druggability, and signatures. We found that only approximately 30% of all mutations were clonal and that only 61% of the known TCGA gastric cancer drivers harbored clonal mutations. Multiple clonal mutations were found in new candidate gastric cancer drivers such as EYS, FAT4, PCDHA1, RAD50, EXO1, RECQL4, and FSIP2. The genomically stable (GS) molecular subtype, which has the worse prognosis, was identified in 48% of our Latino patients, a fraction that was >2.3-fold higher than in TCGA Asian and White patients. Only a third of all tumors harbored clonal pathogenic mutations in druggable genes, with most (93%) GS tumors lacking actionable clonal mutations. Mutation signature analyses revealed that, in microsatellite-stable (MSS) tumors, DNA repair mutations were common for both tumor initiation and progression, while tobacco, POLE, and inflammation signatures likely initiate carcinogenesis. MSS tumor progression was likely driven by aging- and aflatoxin-associated mutations, as these latter changes were usually nonclonal. In microsatellite-unstable tumors, nonclonal tobacco-associated mutations were common. Our study, therefore, contributed to advancing gastric cancer molecular diagnostics and suggests clonal status is important to understanding gastric tumorigenesis. Our findings of a higher frequency of a poor prognosis associated molecular subtype in Latinos and a possible new aflatoxin gastric cancer etiology also advance cancer disparities research. Significance Our study contributes to advancing our knowledge of gastric carcinogenesis, diagnostics, and cancer health disparities.
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Affiliation(s)
- Ted W. Toal
- Genome Center, University of California, Davis, California
| | - Ana P. Estrada-Florez
- Genome Center, University of California, Davis, California
- Grupo de Citogenética, Filogenia y Evolución de las Poblaciones, Universidad del Tolima, Ibagué, Colombia
| | | | | | - Paul C. Lott
- Genome Center, University of California, Davis, California
| | - John J. Suarez-Olaya
- Grupo de Citogenética, Filogenia y Evolución de las Poblaciones, Universidad del Tolima, Ibagué, Colombia
| | - Alix A. Guevara-Tique
- Grupo de Citogenética, Filogenia y Evolución de las Poblaciones, Universidad del Tolima, Ibagué, Colombia
| | - Sienna Rocha
- Genome Center, University of California, Davis, California
| | | | - Fabian Castro-Valencia
- Grupo de Citogenética, Filogenia y Evolución de las Poblaciones, Universidad del Tolima, Ibagué, Colombia
| | - Shiro Urayama
- UC Davis Comprehensive Cancer Center, Sacramento, California
- Division of Gastroenterology & Hepatology, University of California, Davis, California
| | - Amanda Kirane
- UC Davis Comprehensive Cancer Center, Sacramento, California
| | - Dongguang Wei
- Department of Pathology and Laboratory Medicine, University of California, Davis, California
| | - Nora Rios-Sarabia
- Unidad de Investigación en Enfermedades Infecciosas y Parasitarias, Unidad Médica de Alta Especialidad en Pediatría, Instituto Mexicano del Seguro Social, México City, México
| | - Rafael Medrano
- Departamento de Sarcomas y Tubo Digestivo Alto, Unidad Medica de Alta Especialidad en Oncología Instituto Mexicano del Seguro Social (IMSS), México City, México
| | - Alejandra Mantilla
- Departamento de Patología, Unidad Medica de Alta Especialidad en Oncología, Instituto Mexicano del Seguro Social (IMSS), México City, México
| | | | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas y Parasitarias, Unidad Médica de Alta Especialidad en Pediatría, Instituto Mexicano del Seguro Social, México City, México
| | - Mabel E. Bohorquez-Lozano
- Grupo de Citogenética, Filogenia y Evolución de las Poblaciones, Universidad del Tolima, Ibagué, Colombia
| | - Luis G. Carvajal-Carmona
- Genome Center, University of California, Davis, California
- UC Davis Comprehensive Cancer Center, Sacramento, California
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, California
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9
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Epidemiology and Prevention of Renal Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14164059. [PMID: 36011051 PMCID: PMC9406474 DOI: 10.3390/cancers14164059] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
With 400,000 diagnosed and 180,000 deaths in 2020, renal cell carcinoma (RCC) accounts for 2.4% of all cancer diagnoses worldwide. The highest disease burden developed countries, primarily in Europe and North America. Incidence is projected to increase in the future as more countries shift to Western lifestyles. Risk factors for RCC include fixed factors such as gender, age, and hereditary diseases, as well as intervening factors such as smoking, obesity, hypertension, diabetes, diet and alcohol, and occupational exposure. Intervening factors in primary prevention, understanding of congenital risk factors and the establishment of early diagnostic tools are important for RCC. This review will discuss RCC epidemiology, risk factors, and biomarkers involved in reducing incidence and improving survival.
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10
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Wang H, Zhang X, Qiao L, Wang H. CircRNA circ_0000554 promotes ovarian cancer invasion and proliferation by regulating miR-567. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:19072-19080. [PMID: 34709546 DOI: 10.1007/s11356-021-13710-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/25/2021] [Indexed: 06/13/2023]
Abstract
Circular RNAs (circRNAs) indicated potential modulating effects in tumor development. However, the specific role of circ_0000554 in ovarian tumor remains unknown. We found that circ_0000554 was overexpressed in ovarian tumor specimens and cells. Forced expression of circ_0000554 promoted cell growth, invasion, and epithelial to mesenchymal transition (EMT). We illustrated that miR-567 was downregulated in ovarian tumor specimens and cells. circ_0000554 was negatively correlated with miR-567 in ovarian tumor specimens. circ_0000554 sponged miR-567 expression in ovarian tumor. RIP assay showed that elevated expression of miR-567 could be enriched with circ_0000554. Luciferase reporter assay indicated that luciferase intensity was inhibited after treated with miR-567 mimic; however, the luciferase value of mut type was not decreased. Elevated expression of circ_0000554 suppressed miR-567 expression in HO8910 cell. circ_0000554 promoted ovarian tumor cell growth, invasion, and EMT via sponging miR-567. It suggested that circ_0000554 represent a potential therapy target for ovarian tumor.
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Affiliation(s)
- Hui Wang
- Department of Gynaecology and Obstetrics, Shengli Oilfield Central Hospital, Dongying, 57000, Shandong, China
| | - Xuezhong Zhang
- Department of Laboratory Medicine, Zibo Central Hospital, Zibo, 255036, Shandong, China
| | - Lujun Qiao
- Intensive Care Unit, Shengli Oilfield Central Hospital, Dongying, 257000, Shandong, China
| | - Heng Wang
- Intensive Care Unit, Shengli Oilfield Central Hospital, Dongying, 257000, Shandong, China.
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11
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Kaunein N, Ramani RS, Koo K, Moore C, Celentano A, McCullough M, Yap T. A Systematic Review of MicroRNA Signatures Associated with the Progression of Leukoplakia with and without Epithelial Dysplasia. Biomolecules 2021; 11:biom11121879. [PMID: 34944523 PMCID: PMC8699326 DOI: 10.3390/biom11121879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 01/07/2023] Open
Abstract
Oral cancer is a significant public health issue, being the eighth most common cancer worldwide with over 300,000 cases diagnosed annually. Early diagnosis and adequate management of oral potentially malignant disorders (OPMDs) before transformation into oral squamous cell carcinoma (OSCC) is critical to reduce deaths, morbidity, and to improve overall prognosis. MicroRNAs (miRNAs) are small noncoding RNAs involved in the post-transcriptional regulation of protein expression and implicated in the control of numerous cellular pathways and impacting physiological, developmental, and pathological processes. Dysregulation of miRNAs has been reported in many cancers and has been demonstrated to play a critical role in cancer initiation, progression, apoptosis, invasion and metastasis. This systematic review provides a comprehensive summary of the prevailing literature on miRNA signatures in OPMDs, specifically leukoplakia with or without oral epithelial dysplasia, and their utility in predicting malignant transformation into OSCC. Eighteen articles describing 73 unique and differentially expressed microRNAs met the criteria for inclusion in this review. We reviewed the characteristics and methodology for each of these studies and assessed the sensitivity and specificity of the studied miRNAs in predicting malignant transformation. This systematic review highlights the significant interest in miRNAs and their tremendous potential as prognostic markers for predicting the malignant transformation of OPMDs into OSCC.
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Affiliation(s)
- Nadia Kaunein
- Melbourne Dental School, The University of Melbourne, 720 Swanston Street, Carlton, VIC 3053, Australia; (R.S.R.); (K.K.); (C.M.); (A.C.); (M.M.)
- Correspondence: (N.K.); (T.Y.); Tel.: +61-39-341-1485 (T.Y.)
| | - Rishi Sanjay Ramani
- Melbourne Dental School, The University of Melbourne, 720 Swanston Street, Carlton, VIC 3053, Australia; (R.S.R.); (K.K.); (C.M.); (A.C.); (M.M.)
| | - Kendrick Koo
- Melbourne Dental School, The University of Melbourne, 720 Swanston Street, Carlton, VIC 3053, Australia; (R.S.R.); (K.K.); (C.M.); (A.C.); (M.M.)
- Royal Melbourne Hospital, Victorian Comprehensive Cancer Centre, Parkville, VIC 3053, Australia
| | - Caroline Moore
- Melbourne Dental School, The University of Melbourne, 720 Swanston Street, Carlton, VIC 3053, Australia; (R.S.R.); (K.K.); (C.M.); (A.C.); (M.M.)
| | - Antonio Celentano
- Melbourne Dental School, The University of Melbourne, 720 Swanston Street, Carlton, VIC 3053, Australia; (R.S.R.); (K.K.); (C.M.); (A.C.); (M.M.)
| | - Michael McCullough
- Melbourne Dental School, The University of Melbourne, 720 Swanston Street, Carlton, VIC 3053, Australia; (R.S.R.); (K.K.); (C.M.); (A.C.); (M.M.)
| | - Tami Yap
- Melbourne Dental School, The University of Melbourne, 720 Swanston Street, Carlton, VIC 3053, Australia; (R.S.R.); (K.K.); (C.M.); (A.C.); (M.M.)
- Royal Melbourne Hospital, Victorian Comprehensive Cancer Centre, Parkville, VIC 3053, Australia
- Correspondence: (N.K.); (T.Y.); Tel.: +61-39-341-1485 (T.Y.)
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12
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Lopacinska-Jørgensen J, Oliveira DVNP, Wayne Novotny G, Høgdall CK, Høgdall EV. Integrated microRNA and mRNA signatures associated with overall survival in epithelial ovarian cancer. PLoS One 2021; 16:e0255142. [PMID: 34320033 PMCID: PMC8318284 DOI: 10.1371/journal.pone.0255142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 07/12/2021] [Indexed: 11/18/2022] Open
Abstract
Ovarian cancer (OC), the eighth-leading cause of cancer-related death among females worldwide, is mainly represented by epithelial OC (EOC) that can be further subdivided into four subtypes: serous (75%), endometrioid (10%), clear cell (10%), and mucinous (3%). Major reasons for high mortality are the poor biological understanding of the OC mechanisms and a lack of reliable markers defining each EOC subtype. MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression primarily by targeting messenger RNA (mRNA) transcripts. Their aberrant expression patterns have been associated with cancer development, including OC. However, the role of miRNAs in tumorigenesis is still to be determined, mainly due to the lack of consensus regarding optimal methodologies for identification and validation of miRNAs and their targets. Several tools for computational target prediction exist, but false interpretations remain a problem. The experimental validation of every potential miRNA-mRNA pair is not feasible, as it is laborious and expensive. In this study, we analyzed the correlation between global miRNA and mRNA expression patterns derived from microarray profiling of 197 EOC patients to identify the signatures of miRNA-mRNA interactions associated with overall survival (OS). The aim was to investigate whether these miRNA-mRNA signatures might have a prognostic value for OS in different subtypes of EOC. The content of our cohort (162 serous carcinomas, 15 endometrioid carcinomas, 11 mucinous carcinomas, and 9 clear cell carcinomas) reflects a real-world scenario of EOC. Several interaction pairs between 6 miRNAs (hsa-miR-126-3p, hsa-miR-223-3p, hsa-miR-23a-5p, hsa-miR-27a-5p, hsa-miR-486-5p, and hsa-miR-506-3p) and 8 mRNAs (ATF3, CH25H, EMP1, HBB, HBEGF, NAMPT, POSTN, and PROCR) were identified and the findings appear to be well supported by the literature. This indicates that our study has a potential to reveal miRNA-mRNA signatures relevant for EOC. Thus, the evaluation on independent cohorts will further evaluate the performance of such findings.
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MESH Headings
- Adenocarcinoma, Clear Cell/genetics
- Adenocarcinoma, Clear Cell/mortality
- Adenocarcinoma, Clear Cell/pathology
- Adenocarcinoma, Mucinous/genetics
- Adenocarcinoma, Mucinous/mortality
- Adenocarcinoma, Mucinous/pathology
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Carcinoma, Endometrioid/genetics
- Carcinoma, Endometrioid/mortality
- Carcinoma, Endometrioid/pathology
- Databases, Genetic
- Female
- Gene Regulatory Networks/genetics
- Humans
- MicroRNAs/metabolism
- Middle Aged
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/mortality
- Ovarian Neoplasms/pathology
- RNA, Messenger/metabolism
- Survival Rate
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Affiliation(s)
| | | | - Guy Wayne Novotny
- Department of Pathology, Herlev University Hospital, Herlev, Denmark
| | - Claus K. Høgdall
- Department of Gynaecology, Juliane Marie Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Estrid V. Høgdall
- Department of Pathology, Herlev University Hospital, Herlev, Denmark
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13
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Liu J, Yoo J, Ho JY, Jung Y, Lee S, Hur SY, Choi YJ. Plasma-derived exosomal miR-4732-5p is a promising noninvasive diagnostic biomarker for epithelial ovarian cancer. J Ovarian Res 2021; 14:59. [PMID: 33910598 PMCID: PMC8082916 DOI: 10.1186/s13048-021-00814-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/20/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Exosomal miRNAs regulate gene expression and play important roles in several diseases. We used exosomal miRNA profiling to investigate diagnostic biomarkers of epithelial ovarian cancer (EOC). METHODS In total, 55 individuals were enrolled, comprising healthy (n = 21) and EOC subjects (n = 34). Small mRNA (smRNA) sequencing and real-time PCR (RT-PCR) were performed to identify potential biomarkers. Receiver operating characteristic (ROC) curves were conducted to determine biomarker sensitivity and specificity. RESULTS Using smRNA sequencing, we identified seven up-regulated (miR-4732-5p, miR-877-5p, miR-574-3p, let-7a-5p, let-7b-5p, let-7c-5p, and let-7f-5p) and two down-regulated miRNAs (miR-1273f and miR-342-3p) in EOC patients when compared with healthy subjects. Of these, miR-4732-5p and miR-1273f were the most up-regulated and down-regulated respectively, therefore they were selected for RT-PCR analysis. Plasma derived exosomal miR-4732-5p had an area under the ROC curve of 0.889, with 85.7% sensitivity and 82.4% specificity in distinguishing EOC patients from healthy subjects (p<0.0001) and could be a potential biomarker for monitoring the EOC progression from early stage to late stage (p = 0.018). CONCLUSIONS Plasma derived exosomal miR-4732-5p may be a promising candidate biomarker for diagnosing EOC.
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Affiliation(s)
- Jingjing Liu
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Obstetrics and Gynecology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jigeun Yoo
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jung Yoon Ho
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yuyeon Jung
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sanha Lee
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Soo Young Hur
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Youn Jin Choi
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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14
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Mass-spectrometry-based proteomic correlates of grade and stage reveal pathways and kinases associated with aggressive human cancers. Oncogene 2021; 40:2081-2095. [PMID: 33627787 PMCID: PMC7981264 DOI: 10.1038/s41388-021-01681-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/11/2021] [Accepted: 01/25/2021] [Indexed: 01/30/2023]
Abstract
Proteomic signatures associated with clinical measures of more aggressive cancers could yield molecular clues as to disease drivers. Here, utilizing the Clinical Proteomic Tumor Analysis Consortium (CPTAC) mass-spectrometry-based proteomics datasets, we defined differentially expressed proteins and mRNAs associated with higher grade or higher stage, for each of seven cancer types (breast, colon, lung adenocarcinoma, clear cell renal, ovarian, uterine, and pediatric glioma), representing 794 patients. Widespread differential patterns of total proteins and phosphoproteins involved some common patterns shared between different cancer types. More proteins were associated with higher grade than higher stage. Most proteomic signatures predicted patient survival in independent transcriptomic datasets. The proteomic grade signatures, in particular, involved DNA copy number alterations. Pathways of interest were enriched within the grade-associated proteins across multiple cancer types, including pathways of altered metabolism, Warburg-like effects, and translation factors. Proteomic grade correlations identified protein kinases having functional impact in vitro in uterine endometrial cancer cells, including MAP3K2, MASTL, and TTK. The protein-level grade and stage associations for all proteins profiled-along with corresponding information on phosphorylation, pathways, mRNA expression, and copy alterations-represent a resource for identifying new potential targets. Proteomic analyses are often concordant with corresponding transcriptomic analyses, but with notable exceptions.
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15
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Pitman M, Oehler MK, Pitson SM. Sphingolipids as multifaceted mediators in ovarian cancer. Cell Signal 2021; 81:109949. [PMID: 33571664 DOI: 10.1016/j.cellsig.2021.109949] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/19/2022]
Abstract
Ovarian cancer is the most lethal gynaecological malignancy. It is commonly diagnosed at advanced stage when it has metastasised to the abdominal cavity and treatment becomes very challenging. While current standard therapy involving debulking surgery and platinum + taxane-based chemotherapy is associated with high response rates initially, the large majority of patients relapse and ultimately succumb to chemotherapy-resistant disease. In order to improve survival novel strategies for early detection and therapeutics against treatment-refractory disease are urgently needed. A promising new target against ovarian cancer is the sphingolipid pathway which is commonly hijacked in cancer to support cell proliferation and survival and has been shown to promote chemoresistance and metastasis in a wide range of malignant neoplasms. In particular, the sphingosine kinase 1-sphingosine 1-phosphate receptor 1 axis has been shown to be altered in ovarian cancer in multiple ways and therefore represents an attractive therapeutic target. Here we review the roles of sphingolipids in ovarian cancer progression, metastasis and chemoresistance, highlighting novel strategies to target this pathway that represent potential avenues to improve patient survival.
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Affiliation(s)
- MelissaR Pitman
- Centre for Cancer Biology, University of South Australia and SA Pathology, UniSA CRI Building, North Tce, Adelaide, SA 5000, Australia.
| | - Martin K Oehler
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia; School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, South Australia, Australia; Department of Gynaecological Oncology, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Stuart M Pitson
- Centre for Cancer Biology, University of South Australia and SA Pathology, UniSA CRI Building, North Tce, Adelaide, SA 5000, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia; School of Biological Sciences, University of Adelaide, Adelaide, Australia.
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16
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Chen F, Zhang Y, Sucgang R, Ramani S, Corry D, Kheradmand F, Creighton CJ. Meta-analysis of host transcriptional responses to SARS-CoV-2 infection reveals their manifestation in human tumors. Sci Rep 2021; 11:2459. [PMID: 33510359 PMCID: PMC7844278 DOI: 10.1038/s41598-021-82221-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
A deeper understanding of the molecular biology of SARS-CoV-2 infection, including the host response to the virus, is urgently needed. Commonalities exist between the host immune response to viral infections and cancer. Here, we defined transcriptional signatures of SARS-CoV-2 infection involving hundreds of genes common across lung adenocarcinoma cell lines (A549, Calu-3) and normal human bronchial epithelial cells (NHBE), with additional signatures being specific to one or both adenocarcinoma lines. Cross-examining eight transcriptomic databases, we found that host transcriptional responses of lung adenocarcinoma cells to SARS-CoV-2 infection shared broad similarities with host responses to multiple viruses across different model systems and patient samples. Furthermore, these SARS-CoV-2 transcriptional signatures were manifested within specific subsets of human cancer, involving ~ 20% of cases across a wide range of histopathological types. These cancer subsets show immune cell infiltration and inflammation and involve pathways linked to the SARS-CoV-2 response, such as immune checkpoint, IL-6, type II interferon signaling, and NF-κB. The cell line data represented immune responses activated specifically within the cancer cells of the tumor. Common genes and pathways implicated as part of the viral host response point to therapeutic strategies that may apply to both SARS-CoV-2 and cancer.
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Affiliation(s)
- Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard Sucgang
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David Corry
- Center for Translational Research in Inflammatory Diseases, Michael E. DeBakey VA, Houston, TX, 77030, USA
- Departments of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Biology of Inflammation Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Farrah Kheradmand
- Center for Translational Research in Inflammatory Diseases, Michael E. DeBakey VA, Houston, TX, 77030, USA
- Departments of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Biology of Inflammation Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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17
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Therapeutically Significant MicroRNAs in Primary and Metastatic Brain Malignancies. Cancers (Basel) 2020; 12:cancers12092534. [PMID: 32906592 PMCID: PMC7564168 DOI: 10.3390/cancers12092534] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 12/11/2022] Open
Abstract
Simple Summary The overall survival of brain cancer patients remains grim, with conventional therapies such as chemotherapy and radiotherapy only providing marginal benefits to patient survival. Cancers are complex, with multiple pathways being dysregulated simultaneously. Non-coding RNAs such as microRNA (miRNAs) are gaining importance due to their potential in regulating a variety of targets implicated in the pathology of cancers. This could be leveraged for the development of targeted and personalized therapies for cancers. Since miRNAs can upregulate and/or downregulate proteins, this review aims to understand the role of these miRNAs in primary and metastatic brain cancers. Here, we discuss the regulatory mechanisms of ten miRNAs that are highly dysregulated in glioblastoma and metastatic brain tumors. This will enable researchers to develop miRNA-based targeted cancer therapies and identify potential prognostic biomarkers. Abstract Brain cancer is one among the rare cancers with high mortality rate that affects both children and adults. The most aggressive form of primary brain tumor is glioblastoma. Secondary brain tumors most commonly metastasize from primary cancers of lung, breast, or melanoma. The five-year survival of primary and secondary brain tumors is 34% and 2.4%, respectively. Owing to poor prognosis, tumor heterogeneity, increased tumor relapse, and resistance to therapies, brain cancers have high mortality and poor survival rates compared to other cancers. Early diagnosis, effective targeted treatments, and improved prognosis have the potential to increase the survival rate of patients with primary and secondary brain malignancies. MicroRNAs (miRNAs) are short noncoding RNAs of approximately 18–22 nucleotides that play a significant role in the regulation of multiple genes. With growing interest in the development of miRNA-based therapeutics, it is crucial to understand the differential role of these miRNAs in the given cancer scenario. This review focuses on the differential expression of ten miRNAs (miR-145, miR-31, miR-451, miR-19a, miR-143, miR-125b, miR-328, miR-210, miR-146a, and miR-126) in glioblastoma and brain metastasis. These miRNAs are highly dysregulated in both primary and metastatic brain tumors, which necessitates a better understanding of their role in these cancers. In the context of the tumor microenvironment and the expression of different genes, these miRNAs possess both oncogenic and/or tumor-suppressive roles within the same cancer.
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18
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Kim D, Nguyen QT, Lee J, Lee SH, Janocha A, Kim S, Le HT, Dvorina N, Weiss K, Cameron MJ, Asosingh K, Erzurum SC, Baldwin WM, Lee JS, Min B. Anti-inflammatory Roles of Glucocorticoids Are Mediated by Foxp3 + Regulatory T Cells via a miR-342-Dependent Mechanism. Immunity 2020; 53:581-596.e5. [PMID: 32707034 DOI: 10.1016/j.immuni.2020.07.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 05/15/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023]
Abstract
Glucocorticoids (GC) are the mainstay treatment option for inflammatory conditions. Despite the broad usage of GC, the mechanisms by which GC exerts its effects remain elusive. Here, utilizing murine autoimmune and allergic inflammation models, we report that Foxp3+ regulatory T (Treg) cells are irreplaceable GC target cells in vivo. Dexamethasone (Dex) administered in the absence of Treg cells completely lost its ability to control inflammation, and the lack of glucocorticoid receptor in Treg cells alone resulted in the loss of therapeutic ability of Dex. Mechanistically, Dex induced miR-342-3p specifically in Treg cells and miR-342-3p directly targeted the mTORC2 component, Rictor. Altering miRNA-342-3p or Rictor expression in Treg cells dysregulated metabolic programming in Treg cells, controlling their regulatory functions in vivo. Our results uncover a previously unknown contribution of Treg cells during glucocorticoid-mediated treatment of inflammation and the underlying mechanisms operated via the Dex-miR-342-Rictor axis.
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Affiliation(s)
- Dongkyun Kim
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Quang Tam Nguyen
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Juyeun Lee
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Sung Hwan Lee
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230
| | - Allison Janocha
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Sohee Kim
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Hongnga T Le
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Nina Dvorina
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Kelly Weiss
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Mark J Cameron
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106
| | - Kewal Asosingh
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Serpil C Erzurum
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - William M Baldwin
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Ju-Seog Lee
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230
| | - Booki Min
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195.
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19
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Wang R, Du X, Zhi Y. Screening of Critical Genes Involved in Metastasis and Prognosis of High-Grade Serous Ovarian Cancer by Gene Expression Profile Data. J Comput Biol 2020; 27:1104-1114. [PMID: 31725318 DOI: 10.1089/cmb.2019.0235] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Ruike Wang
- Department of Traditional Chinese Medicine, Jining No. 1 People's Hospital, Jining City, China
- Affiliated Jining No. 1 People's Hospital of Jining Medical University, Jining City, China
| | - Xia Du
- Department of Dermatology, Jining No. 1 People's Hospital, Jining City, China
| | - Yaqin Zhi
- Affiliated Jining No. 1 People's Hospital of Jining Medical University, Jining City, China
- Department of Oncology, Jining No. 1 People's Hospital, Jining City, China
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20
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Yang T, Li S, Liu J, Yin D, Yang X, Tang Q, Wang S. Long non-coding RNA KRT16P2/miR-1294/EGFR axis regulates laryngeal squamous cell carcinoma cell aggressiveness. Am J Transl Res 2020; 12:2939-2955. [PMID: 32655821 PMCID: PMC7344088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Laryngeal squamous cell carcinoma (LSCC) is one of the most commonly seen head and neck malignancies. Identifying potent markers and/or targets for early diagnosis and individualized therapies for LSCC remains a considerable challenge. The present study analyzed online data and identified lncRNA KRT16P2 as a significantly upregulated long non-coding RNA (lncRNA) in LSCC. KRT16P2 knockdown in LSCC cells inhibited cancer cell proliferation, invasion, and migration. Similar to KRT16P2, EGFR expression was also significantly upregulated in LSCC. KRT16P2 and EGFR were positively correlated in LSCC tissue samples. EGFR knockdown also dramatically inhibited LSCC cell proliferation and aggressiveness (invasion and migration). Through online data and online tools, miR-1294 was predicted to target KRT16P2 and EGFR 3'UTR simultaneously. KRT16P2 inhibited miR-1294 expression, and miR-1294 inhibited EGFR expression through direct binding. miR-1294 overexpression repressed LSCC cell proliferation and aggressiveness. The effects of KRT16P2 silence on the expression of EGFR, LSCC cell proliferation, invasion, and migration, the protein levels of ki-67, PCNA, and cleaved-Caspase 3, as well as the phosphorylation of AKT, were all significantly reversed by miR-1294 inhibition. In conclusion, we demonstrated a lncRNA KRT16P2/miR-1294/EGFR axis that regulates LSCC cell proliferation, invasion, and migration. The clinical application of this axis needs further in vivo and clinical investigation.
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Affiliation(s)
- Tao Yang
- Department of Otolaryngology Head and Neck Surgery, The Second Xiangya Hospital, Central South University Changsha 410011, Hunan, PR China
| | - Shisheng Li
- Department of Otolaryngology Head and Neck Surgery, The Second Xiangya Hospital, Central South University Changsha 410011, Hunan, PR China
| | - Jiajia Liu
- Department of Otolaryngology Head and Neck Surgery, The Second Xiangya Hospital, Central South University Changsha 410011, Hunan, PR China
| | - Danhui Yin
- Department of Otolaryngology Head and Neck Surgery, The Second Xiangya Hospital, Central South University Changsha 410011, Hunan, PR China
| | - Xinming Yang
- Department of Otolaryngology Head and Neck Surgery, The Second Xiangya Hospital, Central South University Changsha 410011, Hunan, PR China
| | - Qinglai Tang
- Department of Otolaryngology Head and Neck Surgery, The Second Xiangya Hospital, Central South University Changsha 410011, Hunan, PR China
| | - Shuhui Wang
- Department of Otolaryngology Head and Neck Surgery, The Second Xiangya Hospital, Central South University Changsha 410011, Hunan, PR China
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21
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García-Guede Á, Vera O, Ibáñez-de-Caceres I. When Oxidative Stress Meets Epigenetics: Implications in Cancer Development. Antioxidants (Basel) 2020; 9:antiox9060468. [PMID: 32492865 PMCID: PMC7346131 DOI: 10.3390/antiox9060468] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 02/06/2023] Open
Abstract
Cancer is one of the leading causes of death worldwide and it can affect any part of the organism. It arises as a consequence of the genetic and epigenetic changes that lead to the uncontrolled growth of the cells. The epigenetic machinery can regulate gene expression without altering the DNA sequence, and it comprises methylation of the DNA, histones modifications, and non-coding RNAs. Alterations of these gene-expression regulatory elements can be produced by an imbalance of the intracellular environment, such as the one derived by oxidative stress, to promote cancer development, progression, and resistance to chemotherapeutic treatments. Here we review the current literature on the effect of oxidative stress in the epigenetic machinery, especially over the largely unknown ncRNAs and its consequences toward cancer development and progression.
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Affiliation(s)
- Álvaro García-Guede
- Epigenetics Laboratory, INGEMM, Hospital La PAZ. 28046 Madrid, Spain; (Á.G.-G.); (I.I.-d.-C.)
- Experimental Therapies and Novel Biomarkers in Cancer, Instituto de Investigación Sanitaria del Hospital La Paz. IdiPAZ, 28046 Madrid, Spain
| | - Olga Vera
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- Correspondence:
| | - Inmaculada Ibáñez-de-Caceres
- Epigenetics Laboratory, INGEMM, Hospital La PAZ. 28046 Madrid, Spain; (Á.G.-G.); (I.I.-d.-C.)
- Experimental Therapies and Novel Biomarkers in Cancer, Instituto de Investigación Sanitaria del Hospital La Paz. IdiPAZ, 28046 Madrid, Spain
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22
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Padala SA, Barsouk A, Thandra KC, Saginala K, Mohammed A, Vakiti A, Rawla P, Barsouk A. Epidemiology of Renal Cell Carcinoma. World J Oncol 2020; 11:79-87. [PMID: 32494314 PMCID: PMC7239575 DOI: 10.14740/wjon1279] [Citation(s) in RCA: 605] [Impact Index Per Article: 121.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/04/2020] [Indexed: 01/11/2023] Open
Abstract
Though renal cell carcinoma (RCC) accounts for 2% of global cancer diagnoses and deaths, it has more than doubled in incidence in the developed world over the past half-century, and today is the ninth most common neoplasm in the United States (US). While North America and Western Europe have the highest disease burden (with the Belarus highest in incidence), Latin America, Asia and Africa are projected to see an increase in incidence as nation’s transition to a Western lifestyle. Most cases of RCC are discovered incidentally on imaging, and survival is highly dependent on the stage at diagnosis, with the metastatic disease having only a 12% 5-year survival rate. Two-thirds of RCC diagnoses are made in men, and the average age of diagnosis in the US is 64. Those with genetic predispositions, namely von Hippel-Lindau disease, tend to be diagnosed 20 years earlier. RCC has a greater incidence among Hispanics and Native Americans, and a lower survival rate among African Americans in the US. Modifiable risk factors for RCC include smoking, obesity, poorly-controlled hypertension, diet and alcohol, and occupational exposures. Prevention strategies aimed at improving survival and reducing disparities include addressing lifestyle factors and access to regular healthcare among underserved populations and in developing nations, as well as more rigorous imaging guidelines to detect RCC at an earlier stage. A stronger understanding of global RCC epidemiology can facilitate prevention efforts, especially in developing nations and underserved communities where disease burden is predicted to rise in the coming decades.
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Affiliation(s)
- Sandeep Anand Padala
- Department of Medicine, Nephrology, Augusta University, Medical College of Georgia, Augusta, GA 30912, USA
| | - Adam Barsouk
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
| | - Krishna Chaitanya Thandra
- Department of Pulmonary and Critical Care Medicine, Sentara Virginia Beach General Hospital, Virginia Beach, VA, USA
| | - Kalyan Saginala
- Plains Regional Medical Group Internal Medicine, Clovis, NM 88101, USA
| | - Azeem Mohammed
- Department of Medicine, Nephrology, Augusta University, Medical College of Georgia, Augusta, GA 30912, USA
| | - Anusha Vakiti
- Department of Medicine, Hematology-Oncology, Augusta University, Medical College of Georgia, Augusta, GA 30912, USA
| | - Prashanth Rawla
- Department of Medicine, Sovah Health, Martinsville, VA 24112, USA
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Hu Y, Sun L, Zhang Y, Lang J, Rao J. Phosphoproteomics Reveals Key Regulatory Kinases and Modulated Pathways Associated with Ovarian Cancer Tumors. Onco Targets Ther 2020; 13:3595-3605. [PMID: 32425555 PMCID: PMC7196812 DOI: 10.2147/ott.s240164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/06/2020] [Indexed: 12/17/2022] Open
Abstract
Background Ovarian cancer (OC) is the seventh most common cancer worldwide for women. However, there are no sufficient diagnostic methods and few treatment options available due to poor understanding of its pathogenic mechanisms. Methods To comprehensively analyze the phosphoproteomic characterization for OC, we took advantage of a quantitative global phosphoproteomics method, titanium(IV) immobilized metal affinity chromatography (Ti4+-IMAC) coupled to nanoscale liquid chromatography and quadrupole time-of-flight tandem mass spectrometry (nanoLC/Q-TOF-MS/MS) on ovarian tissue samples obtained from five OC patients and five matched controls. Results A total of 722 phosphorylated sites corresponding to 534 proteins were significantly different (fold change ≥ 2, p < 0.01) between OC patients and the controls. Among them, 83 transcription factors mainly consisted of transcription cofactors, zf-C2H2, and chromatin remodeling factors and 29 kinases were included. Further functional analysis suggested significantly biological processes were highly enriched and involved in the pathogenesis of OC, especially fructose and mannose metabolism. Moreover, the regulatory roles of modulated pathways, including MAPK, ErbB, and GnRH signaling pathways were also identified as critical processes involved in OC. The results here highlighted key phosphorylated proteins, particularly kinases, and the corresponding cancer-related metabolic and signal pathways that played important roles in the development of OC. Additionally, the expression levels of two kinases, phosphorylated CDK (T14) and phosphorylated PRKCQ (S695), were validated by Western blot analysis in the other group of ovarian tissue samples. Conclusion Altogether, our data not only provided novel insights into the potential biomarkers and therapy options for OC but also extended our knowledge on its pathophysiological mechanism.
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Affiliation(s)
- Yingchao Hu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People's Republic of China
| | - Lejia Sun
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC & Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
| | - Yinglan Zhang
- Department of Obstetrics and Gynecology, Affiliated Beijing Chaoyang Hospital of Capital Medical University, Beijing 100020, People's Republic of China
| | - Jinghe Lang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People's Republic of China
| | - Jun Rao
- Jiangxi Provincial Key Laboratory of Translational Medicine and Oncology, Jiangxi Cancer Hospital, Jiangxi Cancer Center, Nanchang 330029, People's Republic of China
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24
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Xiao Y, Wang C, Zeng B, Tang X, Zhang Y, Xiang L, Mi L, Pan Y, Wang H, Yang Z. miR124-3p/FGFR2 axis inhibits human keratinocyte proliferation and migration and improve the inflammatory microenvironment in psoriasis. Mol Immunol 2020; 122:89-98. [PMID: 32330756 DOI: 10.1016/j.molimm.2020.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/24/2020] [Accepted: 04/06/2020] [Indexed: 01/07/2023]
Abstract
Keratinocyte hyperproliferation has been regarded as a central event in psoriasis pathogenesis. Investigating the mechanisms of keratinocyte hyperproliferation might provide novel strategies for psoriasis treatment. we demonstrated that fibroblast growth factor receptor 2 (FGFR2) expression was abnormally upregulated within psoriatic lesion tissues and HaCaT cells under rIL-22 stimulation. FGFR2 silence within HaCaT cells under rIL-22 stimulation significantly inhibited the capacity of cells to proliferate and to migrate, reduced IL-17A and TNFα mRNA expression, and decreased the protein levels of FGFR2, keratin 6, keratin 16, MMP1, MMP9, p-PI3K, p-AKT and p-ERK. In contrast to FGFR2, the expression of miR-124-3p showed to be remarkably downregulated within psoriasis lesion tissue samples and rIL-22-stimulated HaCaT cells. miR-124-3p inhibited the expression of FGFR2 via direct binding to its 3'UTR. Within HaCaT cells under rIL-22 stimulation, the overexpression of miR-124-3p also suppressed the capacity of cells to proliferate and to migrate, reduced IL-17A and TNFα mRNA expression, and decreased the protein levels of FGFR2, keratin 6, keratin 16, MMP1, MMP9 and p-PI3K, p-AKT and p-ERK. More importantly, when co-transfected to HaCaT cells, FGFR2-overexpressing vector significantly attenuated the effects of miR-124-3p mimics on HaCaT cells. In conclusion, we demonstrated an miR124-3p/FGFR2 axis that might inhibit human keratinocyte proliferation, migration, and improve the inflammatory microenvironment in psoriasis. miR124-3p/FGFR2 axis could be an underlying target for psoriasis therapy, which requires further in vivo and clinical investigation.
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Affiliation(s)
- Yueyuan Xiao
- Department of Dermatology, The Second Affiliated Hospital, The Domestic First-class Discipline Construction Project of Chinese Medicine of Hunan University of Chinese Medicine, Changsha, Hunan 410005, China; Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Chang Wang
- Department of Dermatology, The Second Affiliated Hospital, The Domestic First-class Discipline Construction Project of Chinese Medicine of Hunan University of Chinese Medicine, Changsha, Hunan 410005, China
| | - Bijun Zeng
- Department of Dermatology, The Second Affiliated Hospital, The Domestic First-class Discipline Construction Project of Chinese Medicine of Hunan University of Chinese Medicine, Changsha, Hunan 410005, China
| | - Xueyong Tang
- Department of Dermatology, The Second Affiliated Hospital, The Domestic First-class Discipline Construction Project of Chinese Medicine of Hunan University of Chinese Medicine, Changsha, Hunan 410005, China
| | - Yujin Zhang
- Department of Dermatology, The Second Affiliated Hospital, The Domestic First-class Discipline Construction Project of Chinese Medicine of Hunan University of Chinese Medicine, Changsha, Hunan 410005, China
| | - Liping Xiang
- Department of Dermatology, The Second Affiliated Hospital, The Domestic First-class Discipline Construction Project of Chinese Medicine of Hunan University of Chinese Medicine, Changsha, Hunan 410005, China
| | - Lan Mi
- Department of Dermatology, The Second Affiliated Hospital, The Domestic First-class Discipline Construction Project of Chinese Medicine of Hunan University of Chinese Medicine, Changsha, Hunan 410005, China
| | - Yi Pan
- Department of Dermatology, The Second Affiliated Hospital, The Domestic First-class Discipline Construction Project of Chinese Medicine of Hunan University of Chinese Medicine, Changsha, Hunan 410005, China
| | - Haizhen Wang
- Department of Dermatology, The Second Affiliated Hospital, The Domestic First-class Discipline Construction Project of Chinese Medicine of Hunan University of Chinese Medicine, Changsha, Hunan 410005, China.
| | - Zhibo Yang
- Department of Dermatology, The Second Affiliated Hospital, The Domestic First-class Discipline Construction Project of Chinese Medicine of Hunan University of Chinese Medicine, Changsha, Hunan 410005, China.
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25
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Yeung TL, Sheng J, Leung CS, Li F, Kim J, Ho SY, Matzuk MM, Lu KH, Wong STC, Mok SC. Systematic Identification of Druggable Epithelial-Stromal Crosstalk Signaling Networks in Ovarian Cancer. J Natl Cancer Inst 2020; 111:272-282. [PMID: 29860390 PMCID: PMC6410941 DOI: 10.1093/jnci/djy097] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 04/04/2018] [Accepted: 04/27/2018] [Indexed: 12/28/2022] Open
Abstract
Background Bulk tumor tissue samples are used for generating gene expression profiles in most research studies, making it difficult to decipher the stroma–cancer crosstalk networks. In the present study, we describe the use of microdissected transcriptome profiles for the identification of cancer–stroma crosstalk networks with prognostic value, which presents a unique opportunity for developing new treatment strategies for ovarian cancer. Methods Transcriptome profiles from microdissected ovarian cancer–associated fibroblasts (CAFs) and ovarian cancer cells from patients with high-grade serous ovarian cancer (n = 70) were used as input data for the computational systems biology program CCCExplorer to uncover crosstalk networks between various cell types within the tumor microenvironment. The crosstalk analysis results were subsequently used for discovery of new indications for old drugs in ovarian cancer by computational ranking of candidate agents. Survival analysis was performed on ovarian tumor–bearing Dicer/Pten double-knockout mice treated with calcitriol, a US Food and Drug Administration–approved agent that suppresses the Smad signaling cascade, or vehicle control (9–11 mice per group). All statistical tests were two-sided. Results Activation of TGF-β-dependent and TGF-β-independent Smad signaling was identified in a particular subtype of CAFs and was associated with poor patient survival (patients with higher levels of Smad-regulated gene expression by CAFs: median overall survival = 15 months, 95% confidence interval [CI] = 12.7 to 17.3 months; vs patients with lower levels of Smad-regulated gene expression: median overall survival = 26 months, 95% CI = 15.9 to 36.1 months, P = .02). In addition, the activated Smad signaling identified in CAFs was found to be targeted by repositioning calcitriol. Calcitriol suppressed Smad signaling in CAFs, inhibited tumor progression in mice, and prolonged the median survival duration of ovarian cancer–bearing mice from 36 to 48 weeks (P = .04). Conclusions Our findings suggest the feasibility of using novel multicellular systems biology modeling to identify and repurpose known drugs targeting cancer–stroma crosstalk networks, potentially leading to faster and more effective cures for cancers.
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Affiliation(s)
- Tsz-Lun Yeung
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianting Sheng
- Department of Systems Medicine and Bioengineering, Houston Methodist Cancer Center, Weill Cornell Medicine, Houston, TX.,Center for Modeling Cancer Development, Houston Methodist Cancer Center, Houston, TX
| | - Cecilia S Leung
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Fuhai Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH
| | - Jaeyeon Kim
- Department of Biochemistry and Molecular Biology, Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN
| | - Samuel Y Ho
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Martin M Matzuk
- Department of Pathology and Immunology and Center for Drug Discovery, Baylor College of Medicine, Houston, TX
| | - Karen H Lu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Stephen T C Wong
- Department of Systems Medicine and Bioengineering, Houston Methodist Cancer Center, Weill Cornell Medicine, Houston, TX.,Center for Modeling Cancer Development, Houston Methodist Cancer Center, Houston, TX
| | - Samuel C Mok
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX
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Görücü Yılmaz Ş, Bozkurt H, Ndadza A, Thomford NE, Karaoğlan M, Keskin M, Benlier N, Dandara C. Childhood Obesity Risk in Relationship to Perilipin 1 ( PLIN1) Gene Regulation by Circulating microRNAs. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 24:43-50. [PMID: 31851864 DOI: 10.1089/omi.2019.0150] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Childhood obesity is a growing public health burden in many countries. The lipid perilipin 1 (PLIN1) gene is involved in regulation of lipolysis, and thus represents a viable candidate mechanism for obesity genetics research in children. In addition, the regulation of candidate gene expression by circulating microRNAs (miRNAs) offers a new research venue for diagnostic innovation. We report new findings on associations among circulating miRNAs, regulation of the PLIN1 gene, and susceptibility to childhood obesity. In a sample of 135 unrelated subjects, 35 children with obesity (between ages 3 and 13) and 100 healthy controls (between ages 4 and 16), we examined the expression levels of four candidate miRNAs (hsa-miR-4777-3p, hsa-miR-642b-3p, hsa-miR-3671-1, and hsa-miR-551b-2) targeting the PLIN1 as measured by real-time polymerase chain reaction in whole blood samples. We found that the full genetic model, including the four candidate miRNAs and the PLIN1 gene, explained a statistically significant 12.7% of the variance in childhood obesity risk (p = 0.0034). The four miRNAs together explained 10.1% of the risk (p = 0.008). The percentage of variation in childhood obesity risk explained by hsa-miR-642b-3p and age was 19%. In accordance with biological polarity of the observed association, for example, hsa-miR-642b-3p was upregulated, while the PLIN1 expression decreased in obese participants compared to healthy controls. To the best of our knowledge, this is the first clinical association study of these candidate miRNAs targeting the PLIN1 in childhood obesity. These data offer new molecular leads for future clinical biomarker and diagnostic discovery for childhood obesity.
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Affiliation(s)
- Şenay Görücü Yılmaz
- Department of Nutrition and Dietetics, Gaziantep University, Gaziantep, Turkey
| | - Hakan Bozkurt
- Department of Neurology, Medical Park Hospital, Gaziantep, Turkey
| | - Arinao Ndadza
- Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Nicholas Ekow Thomford
- Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Murat Karaoğlan
- Department of Pediatric Endocrinology, Gaziantep University, Gaziantep, Turkey
| | - Mehmet Keskin
- Department of Pediatric Endocrinology, Gaziantep University, Gaziantep, Turkey
| | - Necla Benlier
- Department of Medical Pharmacology, Sanko University, Gaziantep, Turkey
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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27
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Oliveira DNP, Carlsen AL, Heegaard NHH, Prahm KP, Christensen IJ, Høgdall CK, Høgdall EV. Diagnostic plasma miRNA-profiles for ovarian cancer in patients with pelvic mass. PLoS One 2019; 14:e0225249. [PMID: 31738788 PMCID: PMC6860451 DOI: 10.1371/journal.pone.0225249] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/31/2019] [Indexed: 12/03/2022] Open
Abstract
Background Ovarian cancer is the fifth most common cancer in women worldwide. Moreover, there are no reliable minimal invasive tests to secure the diagnosis of malignant pelvic masses. Cell-free, circulating microRNAs have the potential as diagnostic biomarkers in cancer. Here, we performed and validated a miRNA panel with the potential to distinguish OC from benign pelvic masses. Methods The profile of plasma microRNA was determined with a panel of 46 candidates in a discovery group and a validation group, each consisting of 190 pre-surgery plasma samples from age-matched patients with malignant (n = 95) and benign pelvic mass (n = 95), by real time RT-qPCR. Results Four up-regulated (miR-200c-3p, miR-221-3p, miR-21-5p, and miR-484) and two down-regulated (miR-195-5p and miR-451a) microRNAs were discovered. From those, miR-200c-3p and miR-221-3p were further confirmed in a validation cohort. A combination of these 2 microRNAs together with CA-125 yielded an overall diagnostic accuracy of AUC = 0.96. Conclusions We showed consistent plasma microRNA profiles that provide independent diagnostic information of late stage OC.
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Affiliation(s)
| | - Anting Liu Carlsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark.,Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Niels H H Heegaard
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark
| | - Kira Philipsen Prahm
- Department of Pathology, Herlev Hospital, University of Copenhagen, Herlev, Denmark.,Department of Gynaecology, Juliane Marie Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Ib Jarle Christensen
- Department of Pathology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Claus K Høgdall
- Department of Gynaecology, Juliane Marie Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Estrid V Høgdall
- Department of Pathology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
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28
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Lee A, Kang J, Lee H, Lee YS, Choi YJ, Lee KH, Nistala GJ, Scafe CR, Choi J, Yoo J, Han M.D E, Kim Y, Kim M. BRCA1/2 somatic mutation detection in formalin-fixed paraffin embedded tissue by next-generation sequencing in Korean ovarian cancer patients. Pathol Res Pract 2019; 215:152595. [DOI: 10.1016/j.prp.2019.152595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/26/2019] [Accepted: 08/16/2019] [Indexed: 12/18/2022]
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29
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Zhang Y, Yang L, Kucherlapati M, Hadjipanayis A, Pantazi A, Bristow CA, Lee EA, Mahadeshwar HS, Tang J, Zhang J, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Park PJ, Kucherlapati R, Creighton CJ. Global impact of somatic structural variation on the DNA methylome of human cancers. Genome Biol 2019; 20:209. [PMID: 31610796 PMCID: PMC6792267 DOI: 10.1186/s13059-019-1818-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 09/09/2019] [Indexed: 12/21/2022] Open
Abstract
Background Genomic rearrangements exert a heavy influence on the molecular landscape of cancer. New analytical approaches integrating somatic structural variants (SSVs) with altered gene features represent a framework by which we can assign global significance to a core set of genes, analogous to established methods that identify genes non-randomly targeted by somatic mutation or copy number alteration. While recent studies have defined broad patterns of association involving gene transcription and nearby SSV breakpoints, global alterations in DNA methylation in the context of SSVs remain largely unexplored. Results By data integration of whole genome sequencing, RNA sequencing, and DNA methylation arrays from more than 1400 human cancers, we identify hundreds of genes and associated CpG islands (CGIs) for which the nearby presence of a somatic structural variant (SSV) breakpoint is recurrently associated with altered expression or DNA methylation, respectively, independently of copy number alterations. CGIs with SSV-associated increased methylation are predominantly promoter-associated, while CGIs with SSV-associated decreased methylation are enriched for gene body CGIs. Rearrangement of genomic regions normally having higher or lower methylation is often involved in SSV-associated CGI methylation alterations. Across cancers, the overall structural variation burden is associated with a global decrease in methylation, increased expression in methyltransferase genes and DNA damage response genes, and decreased immune cell infiltration. Conclusion Genomic rearrangement appears to have a major role in shaping the cancer DNA methylome, to be considered alongside commonly accepted mechanisms including histone modifications and disruption of DNA methyltransferases.
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Affiliation(s)
- Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lixing Yang
- Ben May Department for Cancer Research and Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Melanie Kucherlapati
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Angela Hadjipanayis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Angeliki Pantazi
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Christopher A Bristow
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Harshad S Mahadeshwar
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jiabin Tang
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sahil Seth
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Semin Lee
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Xiaojia Ren
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Xingzhi Song
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Huandong Sun
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jonathan Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lovelace J Luquette
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Ruibin Xi
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lynda Chin
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,The Eli and Edythe L. Broad Institute of Massachusetts Institute Of Technology and Harvard University, Cambridge, MA, 02142, USA
| | | | - Peter J Park
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Raju Kucherlapati
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA. .,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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Wilk G, Braun R. Integrative analysis reveals disrupted pathways regulated by microRNAs in cancer. Nucleic Acids Res 2019; 46:1089-1101. [PMID: 29294105 PMCID: PMC5814839 DOI: 10.1093/nar/gkx1250] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/01/2017] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small endogenous regulatory molecules that modulate gene expression post-transcriptionally. Although differential expression of miRNAs have been implicated in many diseases (including cancers), the underlying mechanisms of action remain unclear. Because each miRNA can target multiple genes, miRNAs may potentially have functional implications for the overall behavior of entire pathways. Here, we investigate the functional consequences of miRNA dysregulation through an integrative analysis of miRNA and mRNA expression data using a novel approach that incorporates pathway information a priori. By searching for miRNA-pathway associations that differ between healthy and tumor tissue, we identify specific relationships at the systems level which are disrupted in cancer. Our approach is motivated by the hypothesis that if an miRNA and pathway are associated, then the expression of the miRNA and the collective behavior of the genes in a pathway will be correlated. As such, we first obtain an expression-based summary of pathway activity using Isomap, a dimension reduction method which can articulate non-linear structure in high-dimensional data. We then search for miRNAs that exhibit differential correlations with the pathway summary between phenotypes as a means of finding aberrant miRNA-pathway coregulation in tumors. We apply our method to cancer data using gene and miRNA expression datasets from The Cancer Genome Atlas and compare ∼105 miRNA-pathway relationships between healthy and tumor samples from four tissues (breast, prostate, lung and liver). Many of the flagged pairs we identify have a biological basis for disruption in cancer.
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Affiliation(s)
- Gary Wilk
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Rosemary Braun
- Biostatistics Division, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.,Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
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31
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Alizadeh M, Safarzadeh A, Beyranvand F, Ahmadpour F, Hajiasgharzadeh K, Baghbanzadeh A, Baradaran B. The potential role of miR‐29 in health and cancer diagnosis, prognosis, and therapy. J Cell Physiol 2019; 234:19280-19297. [DOI: 10.1002/jcp.28607] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Mohsen Alizadeh
- Immunology Research Center Tabriz University of Medical Sciences Tabriz Iran
| | - Ali Safarzadeh
- Immunology Research Center Tabriz University of Medical Sciences Tabriz Iran
| | - Fatemeh Beyranvand
- Department of Pharmacology and Toxicology, Faculty of Pharmacy Lorestan University of Medical Sciences Khorramabad Iran
| | - Fatemeh Ahmadpour
- Department of Biochemistry, Faculty of Medicine Ahvaz Jundishapur University of Medical Sciences Ahvaz Iran
| | | | - Amir Baghbanzadeh
- Immunology Research Center Tabriz University of Medical Sciences Tabriz Iran
| | - Behzad Baradaran
- Immunology Research Center Tabriz University of Medical Sciences Tabriz Iran
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Valiollahi E, Ribera JM, Genescà E, Behravan J. Genome-wide identification of microRNA signatures associated with stem/progenitor cells in Philadelphia chromosome-positive acute lymphoblastic leukemia. Mol Biol Rep 2019; 46:1295-1306. [PMID: 30712246 DOI: 10.1007/s11033-019-04600-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 01/15/2019] [Indexed: 12/19/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is a malignant transformation with uncontrolled proliferation of lymphoid precursor cells within bone marrow including a dismal prognosis after relapse. Survival of a population of quiescent leukemia stem cells (LSCs, also termed leukemia-initiating cells (LICs)) after treatment is one of the relapse reasons in Ph+ ALL patient. MicroRNAs (miRNAs) are known as highly conserved 19-24 nucleotides non-protein-coding small RNAs that regulate the expression of human genes. miRNAs are often involved in the tuning of hematopoiesis. Therefore, the deregulation of miRNA expression and function in hematopoietic cells can cause cancer and promote its progression. This is the first comprehensive analysis of miRNA expression differences between CD34+CD38- LSCs and CD34+CD38+ leukemic progenitors (LPs) from the same Ph+ B-ALL bone marrow samples using high-throughput sequencing technologies. We identified multiple differentially expressed miRNAs including hsa-miR-3143, hsa-miR-6503-3p, hsa-miR-744-3p, hsa-miR-1226-3p, hsa-miR-10a-5p, hsa-miR-4658 and hsa-miR-493-3p related to LSC and LP populations which have regulatory functions in stem-cell associated biological processes. The deregulation of these miRNAs could affect leukemogenesis, clonogenic and stemness capacities in these subpopulations of Ph+ B-ALL. Therefore, identification of these LSC associated miRNAs may improve the diagnosis and management of B-ALL. These findings may also lead to future strategies to eliminate the presence of resistant LSCs, either by induction of apoptosis or by sensitizing these cells to chemotherapy.
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Affiliation(s)
- Ehsan Valiollahi
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Josep Maria Ribera
- Josep Carreras Research Institute (IJC), ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Eulàlia Genescà
- Josep Carreras Research Institute (IJC), ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.
| | - Javad Behravan
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- School of Pharmacy, University of Waterloo, 200 University Ave, Waterloo, N2L 3G1, Canada.
- Theraphage Inc, Waterloo, ON, Canada.
- Mediphage Bioceuticals, Inc, 661 University Avenue, Suite 1300, MaRS Centre, West Tower, Toronto, M5G0B7, Canada.
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Ushio N, Rahman MM, Maemura T, Lai YC, Iwanaga T, Kawaguchi H, Miyoshi N, Momoi Y, Miura N. Identification of dysregulated microRNAs in canine malignant melanoma. Oncol Lett 2018; 17:1080-1088. [PMID: 30655868 PMCID: PMC6313064 DOI: 10.3892/ol.2018.9692] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 09/27/2018] [Indexed: 12/29/2022] Open
Abstract
Inhibiting aberrantly upregulated microRNAs (miR/miRNAs) has emerged as a novel focus for therapeutic intervention in human melanoma. Thus, identifying upregulated miRNAs is essential for identifying additional melanoma-associated therapeutic targets. In the present study, microarray-based miRNA profiling of canine malignant melanoma (CMM) tissue obtained from the oral cavity was performed and differential expression was confirmed by a reverse transcription-quantitative polymerase chain reaction (RT-qPCR). An analysis of the microarray data revealed 17 dysregulated miRNAs; 5 were upregulated and 12 were downregulated. RT-qPCR analysis was performed for 2 upregulated (miR-204 and miR-383), 3 downregulated (miR-122, miR-143 and miR-205) and 6 additional oncogenic miRNAs (oncomiRs; miR-16, miR-21, miR-29b, miR-92a, miR-125b and miR-222). The expression levels of seven of the miRNAs, miR-16, miR-21, miR-29b, miR-122, miR-125b, miR-204 and miR-383 were significantly upregulated; however, the expression of miR-205 was downregulated in CMM tissues compared with normal oral tissues. The microarray and RT-qPCR analyses validated the upregulation of two potential oncomiRs miR-204 and miR-383. The present study additionally constructed a protein interaction network and a miRNA-target regulatory interaction network using STRING and Cytoscape. In the proposed network, cyclin dependent kinase 2 was a target for miR-383, sirtuin 1 and tumor protein p53 were targets for miR-204 and ATR serine/threonine kinase was a target for both. It was concluded that miR-383 and miR-204 were potential oncomiRs that may be involved in regulating melanoma development by evading DNA repair and apoptosis.
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Affiliation(s)
- Norio Ushio
- Department of Clinical Veterinary Science, United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi 753-8511, Japan
| | - Md Mahfuzur Rahman
- Department of Clinical Veterinary Science, United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi 753-8511, Japan
| | - Tadashi Maemura
- Kagoshima University Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan
| | - Yu-Chang Lai
- Department of Clinical Veterinary Science, United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi 753-8511, Japan.,Kagoshima University Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan
| | - Tomoko Iwanaga
- Kagoshima University Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan
| | - Hiroaki Kawaguchi
- Department of Hygiene and Health Promotion Medicine, Graduate School of Medicine and Dental Sciences, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan
| | - Noriaki Miyoshi
- Department of Veterinary Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan
| | - Yasuyuki Momoi
- Department of Veterinary Diagnostic Imaging, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan
| | - Naoki Miura
- Department of Clinical Veterinary Science, United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi 753-8511, Japan.,Kagoshima University Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan
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Chen F, Zhang Y, Varambally S, Creighton CJ. Molecular Correlates of Metastasis by Systematic Pan-Cancer Analysis Across The Cancer Genome Atlas. Mol Cancer Res 2018; 17:476-487. [PMID: 30401717 DOI: 10.1158/1541-7786.mcr-18-0601] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/19/2018] [Accepted: 10/26/2018] [Indexed: 12/19/2022]
Abstract
Tumor metastasis is a major contributor to mortality of cancer patients, but the process remains poorly understood. Molecular comparisons between primary tumors and metastases can provide insights into the pathways and processes involved. Here, we systematically analyzed and cataloged molecular correlates of metastasis using The Cancer Genome Atlas (TCGA) datasets across 11 different cancer types, these data involving 4,473 primary tumor samples and 395 tumor metastasis samples (including 369 from melanoma). For each cancer type, widespread differences in gene transcription between primary and metastasis samples were observed. For several cancer types, metastasis-associated genes from TCGA comparisons were found to overlap extensively with external results from independent profiling datasets of metastatic tumors. Although some differential expression patterns associated with metastasis were found to be shared across multiple cancer types, by and large each cancer type showed a metastasis signature that was distinctive from those of the other cancer types. Functional categories of genes enriched in multiple cancer type-specific metastatic overexpression signatures included cellular response to stress, DNA repair, oxidation-reduction process, protein deubiquitination, and receptor activity. The TCGA-derived prostate cancer metastasis signature in particular could define a subset of aggressive primary prostate cancer. Transglutaminase 2 protein and mRNA were both elevated in metastases from breast and melanoma cancers. Alterations in miRNAs and in DNA methylation were also identified. IMPLICATIONS: Our findings suggest that there are different molecular pathways to metastasis involved in different cancers. Our catalog of alterations provides a resource for future studies investigating the role of specific genes in metastasis.
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Affiliation(s)
- Fengju Chen
- Division of Biostatistics, Dan L. Duncan Comprehensive Cancer Center Baylor College of Medicine, Houston, Texas
| | - Yiqun Zhang
- Division of Biostatistics, Dan L. Duncan Comprehensive Cancer Center Baylor College of Medicine, Houston, Texas
| | - Sooryanarayana Varambally
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Pathology, Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Chad J Creighton
- Division of Biostatistics, Dan L. Duncan Comprehensive Cancer Center Baylor College of Medicine, Houston, Texas.
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
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Yamamoto CM, Oakes ML, Murakami T, Muto MG, Berkowitz RS, Ng SW. Comparison of benign peritoneal fluid- and ovarian cancer ascites-derived extracellular vesicle RNA biomarkers. J Ovarian Res 2018; 11:20. [PMID: 29499737 PMCID: PMC5834862 DOI: 10.1186/s13048-018-0391-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Extracellular vesicles (EVs) are considered as a new class of resources for potential biomarkers. We analyzed expression of specific mRNA and miRNA in EVs derived from ovarian cancer ascites and the ideal controls, peritoneal fluids from benign patients for potential early detection and prognostic biomarkers. METHODS Fluids were collected from subjects with benign cysts or endometrioma (n = 10), or low/high grade serous ovarian carcinoma (n = 8). EV particles were captured using primarily ExoComplete filterplate or ultracentrifugation and analyzed by nanoparticle tracking analysis, ELISA, and scanning electron microscopy. EV RNAs extracted from two ascites and three peritoneal fluids were submitted for next-generation sequencing. The expression of 34 mRNA and 18 miRNAs in the EVs isolated from patient fluids and cell line media was determined using qPCR. RESULTS EVs isolated from patient samples had concentrations greater than 1010 EV particles/mL and 30% were EpCAM-positive based on ELISA. EV particle sizes averaged 113 ± 11.5 nm. The qPCR studies identified five mRNA (CA11, MEDAG, LAMA4, SPINT2, NANOG) and six miRNA (let-7b, miR23b, miR29a, miR30d, miR205, miR720) that were significantly differentially expressed between cancer ascites and peritoneal fluids. In addition, CA11 mRNA was decreased to 0.5-fold and SPINT2 and NANOG mRNA were significantly increased up to 100-fold in conditioned media of cancer cells compared to immortalized ovarian surface and fallopian tube epithelial cell lines, the hypothesized cells of origin for ovarian cancer development. CONCLUSIONS This study indicates that EV mRNA profiles can reflect the disease stage and may provide a potentially novel source for discovery of biomarkers in ovarian cancer.
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Affiliation(s)
- Cindy M. Yamamoto
- Hitachi Chemical Co. America, Ltd. R and D Center, 1003 Health Sciences Rd, Irvine, CA 92617 USA
| | - Melanie L. Oakes
- Hitachi Chemical Co. America, Ltd. R and D Center, 1003 Health Sciences Rd, Irvine, CA 92617 USA
| | - Taku Murakami
- Hitachi Chemical Co. America, Ltd. R and D Center, 1003 Health Sciences Rd, Irvine, CA 92617 USA
| | - Michael G. Muto
- Department of Obstetrics, Gynecology and Reproductive Biology, Gynecologic Oncology Division, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA
| | - Ross S. Berkowitz
- Department of Obstetrics, Gynecology and Reproductive Biology, Gynecologic Oncology Division, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA
| | - Shu-Wing Ng
- Department of Obstetrics, Gynecology and Reproductive Biology, Gynecologic Oncology Division, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA
- Department of Obstetrics and Gynecology, Tuft Medical Center, 800 Washington Street, Boston, MA 02111 USA
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36
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Circular RNAs and their associations with breast cancer subtypes. Oncotarget 2018; 7:80967-80979. [PMID: 27829232 PMCID: PMC5348369 DOI: 10.18632/oncotarget.13134] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 10/29/2016] [Indexed: 12/22/2022] Open
Abstract
Circular RNAs (circRNAs) are highly stable forms of non-coding RNAs with diverse biological functions. They are implicated in modulation of gene expression thus affecting various cellular and disease processes. Based on existing bioinformatics approaches, we developed a comprehensive workflow called Circ-Seq to identify and report expressed circRNAs. Circ-Seq also provides informative genomic annotation along circRNA fused junctions thus allowing prioritization of circRNA candidates. We applied Circ-Seq first to RNA-sequence data from breast cancer cell lines and validated one of the large circRNAs identified. Circ-Seq was then applied to a larger cohort of breast cancer samples (n = 885) provided by The Cancer Genome Atlas (TCGA), including tumors and normal-adjacent tissue samples. Notably, circRNA results reveal that normal-adjacent tissues in estrogen receptor positive (ER+) subtype have relatively higher numbers of circRNAs than tumor samples in TCGA. Similar phenomenon of high circRNA numbers were observed in normal breast-mammary tissues from the Genotype-Tissue Expression (GTEx) project. Finally, we observed that number of circRNAs in normal-adjacent samples of ER+ subtype is inversely correlated to the risk-of-relapse proliferation (ROR-P) score for proliferating genes, suggesting that circRNA frequency may be a marker for cell proliferation in breast cancer. The Circ-Seq workflow will function for both single and multi-threaded compute environments. We believe that Circ-Seq will be a valuable tool to identify circRNAs useful in the diagnosis and treatment of other cancers and complex diseases.
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37
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MiRNAs at the Crossroads between Innate Immunity and Cancer: Focus on Macrophages. Cells 2018; 7:cells7020012. [PMID: 29419779 PMCID: PMC5850100 DOI: 10.3390/cells7020012] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/01/2018] [Accepted: 02/06/2018] [Indexed: 12/12/2022] Open
Abstract
Innate immune cells form an integrative component of the tumor microenvironment (TME), which can control or prevent tumor initiation and progression, due to the simultaneous processing of both anti- and pro-growth signals. This decision-making process is a consequence of gene expression changes, which are in part dependent on post-transcriptional regulatory mechanisms. In this context, microRNAs have been shown to regulate both recruitment and activation of specific tumor-associated immune cells in the TME. This review aims to describe the most important microRNAs that target cancer-related innate immune pathways. The role of exosomal microRNAs in tumor progression and microRNA-based therapeutic strategies are also discussed.
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38
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miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer. Oncotarget 2017; 7:25930-48. [PMID: 27036018 PMCID: PMC5041955 DOI: 10.18632/oncotarget.8412] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 03/13/2016] [Indexed: 12/13/2022] Open
Abstract
Ovarian cancer presents as an aggressive, advanced stage cancer with widespread metastases that depend primarily on multicellular spheroids in the peritoneal fluid. To identify new druggable pathways related to metastatic progression and spheroid formation, we integrated microRNA and mRNA sequencing data from 293 tumors from The Cancer Genome Atlas (TCGA) ovarian cancer cohort. We identified miR-509-3p as a clinically significant microRNA that is more abundant in patients with favorable survival in both the TCGA cohort (P = 2.3E–3), and, by in situ hybridization (ISH), in an independent cohort of 157 tumors (P < 1.0E–3). We found that miR-509-3p attenuated migration and disrupted multi-cellular spheroids in HEYA8, OVCAR8, SKOV3, OVCAR3, OVCAR4 and OVCAR5 cell lines. Consistent with disrupted spheroid formation, in TCGA data miR-509-3p's most strongly anti-correlated predicted targets were enriched in components of the extracellular matrix (ECM). We validated the Hippo pathway effector YAP1 as a direct miR-509-3p target. We showed that siRNA to YAP1 replicated 90% of miR-509-3p-mediated migration attenuation in OVCAR8, which contained high levels of YAP1 protein, but not in the other cell lines, in which levels of this protein were moderate to low. Our data suggest that the miR-509-3p/YAP1 axis may be a new druggable target in cancers with high YAP1, and we propose that therapeutically targeting the miR-509-3p/YAP1/ECM axis may disrupt early steps in multi-cellular spheroid formation, and so inhibit metastasis in epithelial ovarian cancer and potentially in other cancers.
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39
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Comprehensive Analysis of Cancer-Proteogenome to Identify Biomarkers for the Early Diagnosis and Prognosis of Cancer. Proteomes 2017; 5:proteomes5040028. [PMID: 29068423 PMCID: PMC5748563 DOI: 10.3390/proteomes5040028] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 10/13/2017] [Accepted: 10/17/2017] [Indexed: 02/07/2023] Open
Abstract
During the past century, our understanding of cancer diagnosis and treatment has been based on a monogenic approach, and as a consequence our knowledge of the clinical genetic underpinnings of cancer is incomplete. Since the completion of the human genome in 2003, it has steered us into therapeutic target discovery, enabling us to mine the genome using cutting edge proteogenomics tools. A number of novel and promising cancer targets have emerged from the genome project for diagnostics, therapeutics, and prognostic markers, which are being used to monitor response to cancer treatment. The heterogeneous nature of cancer has hindered progress in understanding the underlying mechanisms that lead to abnormal cellular growth. Since, the start of The Cancer Genome Atlas (TCGA), and the International Genome consortium projects, there has been tremendous progress in genome sequencing and immense numbers of cancer genomes have been completed, and this approach has transformed our understanding of the diagnosis and treatment of different types of cancers. By employing Genomics and proteomics technologies, an immense amount of genomic data is being generated on clinical tumors, which has transformed the cancer landscape and has the potential to transform cancer diagnosis and prognosis. A complete molecular view of the cancer landscape is necessary for understanding the underlying mechanisms of cancer initiation to improve diagnosis and prognosis, which ultimately will lead to personalized treatment. Interestingly, cancer proteome analysis has also allowed us to identify biomarkers to monitor drug and radiation resistance in patients undergoing cancer treatment. Further, TCGA-funded studies have allowed for the genomic and transcriptomic characterization of targeted cancers, this analysis aiding the development of targeted therapies for highly lethal malignancy. High-throughput technologies, such as complete proteome, epigenome, protein-protein interaction, and pharmacogenomics data, are indispensable to glean into the cancer genome and proteome and these approaches have generated multidimensional universal studies of genes and proteins (OMICS) data which has the potential to facilitate precision medicine. However, due to slow progress in computational technologies, the translation of big omics data into their clinical aspects have been slow. In this review, attempts have been made to describe the role of high-throughput genomic and proteomic technologies in identifying a panel of biomarkers which could be used for the early diagnosis and prognosis of cancer.
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40
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Kuznetsov VA, Tang Z, Ivshina AV. Identification of common oncogenic and early developmental pathways in the ovarian carcinomas controlling by distinct prognostically significant microRNA subsets. BMC Genomics 2017; 18:692. [PMID: 28984201 PMCID: PMC5629558 DOI: 10.1186/s12864-017-4027-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background High-grade serous ovarian carcinoma (HG-SOC) is the dominant tumor histologic type in epithelial ovarian cancers, exhibiting highly aberrant microRNA expression profiles and diverse pathways that collectively determine the disease aggressiveness and clinical outcomes. However, the functional relationships between microRNAs, the common pathways controlled by the microRNAs and their prognostic and therapeutic significance remain poorly understood. Methods We investigated the gene expression patterns of microRNAs in the tumors of 582 HG-SOC patients to identify prognosis signatures and pathways controlled by tumor miRNAs. We developed a variable selection and prognostic method, which performs a robust selection of small-sized subsets of the predictive features (e.g., expressed microRNAs) that collectively serves as the biomarkers of cancer risk and progression stratification system, interconnecting these features with common cancer-related pathways. Results Across different cohorts, our meta-analysis revealed two robust and unbiased miRNA-based prognostic classifiers. Each classifier reproducibly discriminates HG-SOC patients into high-confidence low-, intermediate- or high-prognostic risk subgroups with essentially different 5-year overall survival rates of 51.6-85%, 20-38.1%, and 0-10%, respectively. Significant correlations of the risk subgroup’s stratification with chemotherapy treatment response were observed. We predicted specific target genes involved in nine cancer-related and two oocyte maturation pathways (neurotrophin and progesterone-mediated oocyte maturation), where each gene can be controlled by more than one miRNA species of the distinct miRNA HG-SOC prognostic classifiers. Conclusions We identified robust and reproducible miRNA-based prognostic subsets of the of HG-SOC classifiers. The miRNAs of these classifiers could control nine oncogenic and two developmental pathways, highlighting common underlying pathologic mechanisms and perspective targets for the further development of a personalized prognosis assay(s) and the development of miRNA-interconnected pathway-centric and multi-agent therapeutic intervention. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4027-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vladimir A Kuznetsov
- Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A-STAR, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore. .,School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore.
| | - Zhiqun Tang
- Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A-STAR, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Anna V Ivshina
- Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A-STAR, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
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Thomas SN, Chen L, Liu Y, Höti N, Zhang H. Targeted Proteomic Analyses of Histone H4 Acetylation Changes Associated with Homologous-Recombination-Deficient High-Grade Serous Ovarian Carcinomas. J Proteome Res 2017; 16:3704-3710. [PMID: 28866885 DOI: 10.1021/acs.jproteome.7b00405] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Approximately 20% of high-grade serous ovarian cancers are homologous-recombination (HR)-deficient due to genetic and epigenetic mutations of HR pathway genes including the tumor suppressor genes BRCA1 and 2. HR deficiency (HRD) compromises cells' ability to efficiently repair DNA damage, but it also increases sensitivity to chemotherapeutic treatment strategies; however, not all ovarian cancer patients with HRD tumors exhibit positive responses to chemotherapy. Our previous iTRAQ-based comprehensive proteomic characterization of high-grade serous ovarian carcinomas found that lower levels of histone H4 acetylation at Lys12 and Lys16 (H4-K12acK16ac) were associated with HRD tumors compared with non-HRD tumors. In the current study, we developed and validated an H4-K12acK16ac parallel-reaction-monitoring (PRM)-targeted mass-spectrometry-based assay to analyze acetylation changes of histone H4 and to determine the association of these changes with total H4, histone acetyltransferase, and histone deacetylase (HDAC) levels. Whereas the levels of H4 and histone acetyltransferases were stable irrespective of HRD status, the levels of histone H4 acetylation and one HDAC, HDAC6, were elevated in the HRD tumors. Relative H4 acetylation levels were also analyzed by an antibody-based approach in additional ovarian tumors. It is possible that specific H4 acetylation at Lys12 and Lys16 associated with HRD could inform chemotherapeutic treatment modalities to improve ovarian cancer patients' treatment response.
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Affiliation(s)
- Stefani N Thomas
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine , Baltimore, Maryland 21231, United States
| | - Lijun Chen
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine , Baltimore, Maryland 21231, United States
| | - Yang Liu
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine , Baltimore, Maryland 21231, United States
| | - Naseruddin Höti
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine , Baltimore, Maryland 21231, United States
| | - Hui Zhang
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine , Baltimore, Maryland 21231, United States
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Yu X, Zheng H, Chan MTV, Wu WKK. Modulation of chemoresponsiveness to platinum-based agents by microRNAs in cancer. Am J Cancer Res 2017; 7:1769-1778. [PMID: 28979802 PMCID: PMC5622214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 01/12/2016] [Indexed: 06/07/2023] Open
Abstract
Ovarian cancer accounts for the highest mortality among all gynecologic cancers. Cytoreductive surgery followed by chemotherapy with a platinum-based agent (cisplatin or carboplatin) plus paclitaxel is the first-line option for treatment of epithelial ovarian cancer. However, primary or acquired resistance to platinum-based agents is a major clinical challenge. MicroRNAs are a group of small non-coding RNAs that regulate gene expression post-transcriptionally and may function as oncogenes or tumor-suppressor genes through extensive crosstalk with intracellular signaling pathways. Importantly, their dysregulation has been implicated in ovarian tumorigenesis. Pertinent to chemotherapy, increasing evidence has revealed that miRNAs can be directly linked to chemosensitivity to platinum-based agents in ovarian cancer. In this review, we summarize current evidence concerning the role of miRNAs in prediction and modulation of cellular responses to cisplatin and carboplatin in ovarian cancer.
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Affiliation(s)
- Xin Yu
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, 100042, China
| | - Heyi Zheng
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, 100042, China
| | - Matthew TV Chan
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong KongHong Kong
| | - William KK Wu
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong KongHong Kong
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Wang X, Ivan M, Hawkins SM. The role of MicroRNA molecules and MicroRNA-regulating machinery in the pathogenesis and progression of epithelial ovarian cancer. Gynecol Oncol 2017; 147:481-487. [PMID: 28866430 DOI: 10.1016/j.ygyno.2017.08.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/03/2017] [Accepted: 08/26/2017] [Indexed: 12/20/2022]
Abstract
MicroRNA molecules are small, single-stranded RNA molecules that function to regulate networks of genes. They play important roles in normal female reproductive tract biology, as well as in the pathogenesis and progression of epithelial ovarian cancer. DROSHA, DICER, and Argonaute proteins are components of the microRNA-regulatory machinery and mediate microRNA production and function. This review discusses aberrant expression of microRNA molecules and microRNA-regulating machinery associated with clinical features of epithelial ovarian cancer. Understanding the regulation of microRNA molecule production and function may facilitate the development of novel diagnostic and therapeutic strategies to improve the prognosis of women with epithelial ovarian cancer. Additionally, understanding microRNA molecules and microRNA-regulatory machinery associations with clinical features may influence prevention and early detection efforts.
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Affiliation(s)
- Xiyin Wang
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Mircea Ivan
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Shannon M Hawkins
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, United States; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States.
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Wu F, Tao L, Gao S, Ren L, Wang Z, Wang S, Tian J, An L. miR-6539 is a novel mediator of somatic cell reprogramming that represses the translation of Dnmt3b. J Reprod Dev 2017; 63:415-423. [PMID: 28603220 PMCID: PMC5593093 DOI: 10.1262/jrd.2016-170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/12/2017] [Indexed: 12/14/2022] Open
Abstract
Global DNA hypomethylation has been shown to be involved in the pluripotency of induced pluripotent stem (iPS) cells. Relatedly, DNA methyltransferases (DNMTs) are believed to be a substantial barrier to genome-wide demethylation. There are two distinct stages of DNMT expression during iPS cell generation. In the earlier stage of reprogramming, the expression of DNMTs is repressed to overcome epigenetic barriers. During the late stage, the expression of DNMTs is upregulated to ensure iPS cells obtain the full pluripotency required for further development. This fact is strongly reminiscent of microRNAs (miRNAs), critical regulators of precise gene expression, may be central to coordinate the expression of DNMTs during reprogramming. Using a secondary inducible system, we found that miR-6539 had a unique expression dynamic during iPS cell generation that inversely correlated with DNMT3B protein levels. Enforced upregulation of miR-6539 during the early stage of reprogramming increased the efficiency of iPS cell generation, while enforced downregulation impaired efficiency. Further analysis showed that Dnmt3b mRNA is the likely target of miR-6539. Notably, miR-6539 repressed Dnmt3b translation via a target site located in the coding sequence. Our study has therefore identified miR-6539 as a novel mediator of somatic cell reprogramming and, to the best of our knowledge, is the first to demonstrate miRNA-mediated translation inhibition in somatic cell reprogramming via targeting the coding sequence. Our study contributes to understand the mechanisms that underlie the miRNA-mediated epigenetic remodeling that occurs during somatic cell reprogramming.
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Affiliation(s)
- Fujia Wu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China
| | - Li Tao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China
| | - Shuai Gao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China
| | - Likun Ren
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China
| | - Zhuqing Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China
| | - Shumin Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China
| | - Jianhui Tian
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China
| | - Lei An
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China
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45
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Li C, Duan P, Wang J, Lu X, Cheng J. miR-320 inhibited ovarian cancer oncogenicity via targeting TWIST1 expression. Am J Transl Res 2017; 9:3705-3713. [PMID: 28861161 PMCID: PMC5575184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 03/21/2017] [Indexed: 06/07/2023]
Abstract
Ovarian cancer is the most lethal gynecological cancer in most countries. Increasing studies have demonstrated that dysregulation of microRNAs (miRNAs) can contribute to cancer progression. In this study, we showed that miR-320 was underexpressed in ovarian cancer samples compared to their non-tumor tissues. The expression of Twist homolog 1 (TWIST1) in ovarian cancer tissues was upregulated compared with that in the non-tumorous tissues. We found that the expression of TWIST1 was inversely correlated with that of miR-320 in the ovarian cancer. Overexpression of miR-320 suppressed cell proliferation, cell cycle and invasion in ovarian cancer. We identified TWIST1 as a direct target gene of miR-320 in the ovarian cancer cell. Overexpression of TWIST1 promoted the ovarian cancer cell proliferation, cell cycle and invasion. Ectopic expression of TWIST1 restored the effects of miR-320 on cell proliferation, cell cycle and invasion. These findings revealed that miR-320 was a tumor suppressive gene that supressed cell prloferation, cycle and invasion through targeting TWIST1 in ovarian cancer.
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Affiliation(s)
- Chunyang Li
- Department of Biochemistry, School of Basic Sciences, Wenzhou Medical UniversityWenzhou 325000, Zhejiang, China
| | - Ping Duan
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical UniversityWenzhou 325027, Zhejiang, China
| | - Jianguang Wang
- Department of Biochemistry, School of Basic Sciences, Wenzhou Medical UniversityWenzhou 325000, Zhejiang, China
| | - Xiaosheng Lu
- Reproductive Health Center, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical UniversityWenzhou 325027, Zhejiang, China
| | - Jing Cheng
- Reproductive Health Center, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical UniversityWenzhou 325027, Zhejiang, China
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46
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Schliekelman MJ, Creighton CJ, Baird BN, Chen Y, Banerjee P, Bota-Rabassedas N, Ahn YH, Roybal JD, Chen F, Zhang Y, Mishra DK, Kim MP, Liu X, Mino B, Villalobos P, Rodriguez-Canales J, Behrens C, Wistuba II, Hanash SM, Kurie JM. Thy-1 + Cancer-associated Fibroblasts Adversely Impact Lung Cancer Prognosis. Sci Rep 2017; 7:6478. [PMID: 28744021 PMCID: PMC5527099 DOI: 10.1038/s41598-017-06922-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 06/22/2017] [Indexed: 12/11/2022] Open
Abstract
Cancer-associated fibroblasts (CAFs) regulate diverse intratumoral biological programs and can promote or inhibit tumorigenesis, but those CAF populations that negatively impact the clinical outcome of lung cancer patients have not been fully elucidated. Because Thy-1 (CD90) marks CAFs that promote tumor cell invasion in a murine model of KrasG12D-driven lung adenocarcinoma (KrasLA1), here we postulated that human lung adenocarcinomas containing Thy-1+ CAFs have a worse prognosis. We first examined the location of Thy-1+ CAFs within human lung adenocarcinomas. Cells that co-express Thy-1 and α-smooth muscle actin (αSMA), a CAF marker, were located on the tumor periphery surrounding collectively invading tumor cells and in perivascular regions. To interrogate a human lung cancer database for the presence of Thy-1+ CAFs, we isolated Thy-1+ CAFs and normal lung fibroblasts (LFs) from the lungs of KrasLA1 mice and wild-type littermates, respectively, and performed global proteomic analysis on the murine CAFs and LFs, which identified 425 proteins that were differentially expressed. Used as a probe to identify Thy-1+ CAF-enriched tumors in a compendium of 1,586 lung adenocarcinomas, the presence of the 425-gene signature predicted a significantly shorter survival. Thus, Thy-1 marks a CAF population that adversely impacts clinical outcome in human lung cancer.
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Affiliation(s)
- Mark J Schliekelman
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Chad J Creighton
- Department of Medicine and Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America.,Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Brandi N Baird
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Yulong Chen
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Priyam Banerjee
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Neus Bota-Rabassedas
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Young-Ho Ahn
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America.,Department of Molecular Medicine and Tissue Injury Defense Research Center, Ewha Womans University School of Medicine, Seoul, Korea
| | - Jonathon D Roybal
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Fengju Chen
- Department of Medicine and Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Yiqun Zhang
- Department of Medicine and Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Dhruva K Mishra
- Department of Surgery, Houston Methodist Research Institute, Houston, Texas, United States of America
| | - Min P Kim
- Department of Surgery, Houston Methodist Research Institute, Houston, Texas, United States of America
| | - Xin Liu
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Barbara Mino
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Pamela Villalobos
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jaime Rodriguez-Canales
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Carmen Behrens
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Samir M Hanash
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.,Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jonathan M Kurie
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America.
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Abstract
Cellular heterogeneity is a common feature in breast cancer, yet an understanding of the coexistence and regulation of various tumor cell subpopulations remains a significant challenge in cancer biology. In the current study, we approached tumor cell heterogeneity from the perspective of Wnt pathway biology to address how different modes of Wnt signaling shape the behaviors of diverse cell populations within a heterogeneous tumor landscape. Using a syngeneic TP53-null mouse model of breast cancer, we identified distinctions in the topology of canonical Wnt β-catenin-dependent signaling activity and non-canonical β-catenin-independent Ror2-mediated Wnt signaling across subtypes and within tumor cell subpopulations in vivo. We further discovered an antagonistic role for Ror2 in regulating canonical Wnt/β-catenin activity in vivo, where lentiviral shRNA depletion of Ror2 expression augmented canonical Wnt/β-catenin signaling activity across multiple basal-like models. Depletion of Ror2 expression yielded distinct phenotypic outcomes and divergent alterations in gene expression programs among different tumors, despite all sharing basal-like features. Notably, we uncovered cell state plasticity and adhesion dynamics regulated by Ror2, which influenced Ras Homology Family Member A (RhoA) and Rho-Associated Coiled-Coil Kinase 1 (ROCK1) activity downstream of Dishevelled-2 (Dvl2). Collectively, these studies illustrate the integration and collaboration of Wnt pathways in basal-like breast cancer, where Ror2 provides a spatiotemporal function to regulate the balance of Wnt signaling and cellular heterogeneity during tumor progression.
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48
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Gov E, Kori M, Arga KY. RNA-based ovarian cancer research from 'a gene to systems biomedicine' perspective. Syst Biol Reprod Med 2017; 63:219-238. [PMID: 28574782 DOI: 10.1080/19396368.2017.1330368] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ovarian cancer remains the leading cause of death from a gynecologic malignancy, and treatment of this disease is harder than any other type of female reproductive cancer. Improvements in the diagnosis and development of novel and effective treatment strategies for complex pathophysiologies, such as ovarian cancer, require a better understanding of disease emergence and mechanisms of progression through systems medicine approaches. RNA-level analyses generate new information that can help in understanding the mechanisms behind disease pathogenesis, to identify new biomarkers and therapeutic targets and in new drug discovery. Whole RNA sequencing and coding and non-coding RNA expression array datasets have shed light on the mechanisms underlying disease progression and have identified mRNAs, miRNAs, and lncRNAs involved in ovarian cancer progression. In addition, the results from these analyses indicate that various signalling pathways and biological processes are associated with ovarian cancer. Here, we present a comprehensive literature review on RNA-based ovarian cancer research and highlight the benefits of integrative approaches within the systems biomedicine concept for future ovarian cancer research. We invite the ovarian cancer and systems biomedicine research fields to join forces to achieve the interdisciplinary caliber and rigor required to find real-life solutions to common, devastating, and complex diseases such as ovarian cancer. ABBREVIATIONS CAF: cancer-associated fibroblasts; COG: Cluster of Orthologous Groups; DEA: disease enrichment analysis; EOC: epithelial ovarian carcinoma; ESCC: oesophageal squamous cell carcinoma; GSI: gamma secretase inhibitor; GO: Gene Ontology; GSEA: gene set enrichment analyzes; HAS: Hungarian Academy of Sciences; lncRNAs: long non-coding RNAs; MAPK/ERK: mitogen-activated protein kinase/extracellular signal-regulated kinases; NGS: next-generation sequencing; ncRNAs: non-coding RNAs; OvC: ovarian cancer; PI3K/Akt/mTOR: phosphatidylinositol-3-kinase/protein kinase B/mammalian target of rapamycin; RT-PCR: real-time polymerase chain reaction; SNP: single nucleotide polymorphism; TF: transcription factor; TGF-β: transforming growth factor-β.
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Affiliation(s)
- Esra Gov
- a Department of Bioengineering , Marmara University , Istanbul , Turkey.,b Department of Bioengineering , Adana Science and Technology University , Adana , Turkey
| | - Medi Kori
- a Department of Bioengineering , Marmara University , Istanbul , Turkey
| | - Kazim Yalcin Arga
- a Department of Bioengineering , Marmara University , Istanbul , Turkey
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Gibbons DL, Creighton CJ. Pan-cancer survey of epithelial-mesenchymal transition markers across the Cancer Genome Atlas. Dev Dyn 2017; 247:555-564. [PMID: 28073171 DOI: 10.1002/dvdy.24485] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/14/2016] [Accepted: 12/28/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND While epithelial-mesenchymal transition (EMT) can be readily induced experimentally in cancer cells, the EMT process as manifested in human tumors needs to be better understood. Pan-cancer genomic datasets from The Cancer Genome Atlas (TCGA), representing over 10,000 patients and 32 distinct cancer types, provide a rich resource for examining correlative patterns involving EMT mediators in the setting of human cancers. RESULTS Here, we surveyed a 16-gene signature of canonical EMT markers in TCGA pan-cancer cohort. The histology or cell-of-origin of a tumor sample may align more with mesenchymal or epithelial phenotype, and noncancer as well as cancer cells can contribute to the overall molecular patterns observed within a tumor sample; correlation models involving EMT markers can factor in both of the above variables. EMT-associated genes appear coordinately expressed across all cancers and within each cancer type surveyed. Gene signatures of immune cells correlate highly with EMT marker expression in tumors. In pan-cancer analysis, several EMT-related genes can be significantly associated with worse patient outcome. CONCLUSIONS Gene correlates of EMT phenotype in human tumors could include novel mediators of EMT that might be confirmed experimentally, by which TCGA datasets may serve as a platform for discovery in ongoing studies. Developmental Dynamics 247:555-564, 2018. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, Texas.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Medicine, Baylor College of Medicine, Houston, Texas
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50
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Prahm KP, Høgdall C, Karlsen MA, Christensen IJ, Novotny GW, Knudsen S, Hansen A, Jensen PB, Jensen T, Mirza MR, Ekmann-Gade AW, Nedergaard L, Høgdall E. Clinical validation of chemotherapy predictors developed on global microRNA expression in the NCI60 cell line panel tested in ovarian cancer. PLoS One 2017; 12:e0174300. [PMID: 28334047 PMCID: PMC5363866 DOI: 10.1371/journal.pone.0174300] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/07/2017] [Indexed: 01/31/2023] Open
Abstract
OBJECTIVE Ovarian cancer is the leading cause of death among gynecologic malignancies. This is partly due to a non-durable response to chemotherapy. Prediction of resistance to chemotherapy could be a key role in more personalized treatment. In the current study we aimed to examine if microRNA based predictors could predict resistance to chemotherapy in ovarian cancer, and to investigate if the predictors could be prognostic factors for progression free and overall survival. METHODS Predictors of chemotherapy-resistance were developed based on correlation between miRNA expression and differences in measured growth inhibition in a variety of human cancer cell lines in the presence of Carboplatin, Paclitaxel and Docetaxel. These predictors were then, retrospectively, blindly validated in a cohort of 170 epithelial ovarian cancer patients treated with Carboplatin and Paclitaxel or Docetaxel as first line treatment. RESULTS In a multivariate cox proportional analysis the predictors of chemotherapy-resistance were not able to predict time to progression after end of chemotherapy (hazard ratio: 0.64, 95% CI: 0.36-1.12, P = 0.117). However, in a multivariate logistic analysis, where time to progression was considered as either more or less than 6 months, the predictors match clinical observed chemotherapy-resistance (odds ratio: 0.19, 95% CI: 0.05-0.73, P = 0.015). Neither univariate nor multivariate, time-dependent, cox analysis for progression free survival (PFS) or overall survival (OS) in all 170 patients showed to match predicted resistance to chemotherapy (PFS: hazard ratio: 0.69, 95% CI: 0.40-1.19, P = 0.183, OS: hazard ratio: 0.76, 95% CI: 0.42-1.40, P = 0.386). CONCLUSION In the current study, microRNA based predictors of chemotherapy-resistance did not demonstrate any convincing correlation to clinical observed chemotherapy-resistance, progression free survival, or overall survival, in patients with epithelial ovarian cancer. However the predictors did reflect relapse more or less than 6 months.
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Affiliation(s)
- Kira Philipsen Prahm
- Department of Pathology, Molecular unit, Danish CancerBiobank, Herlev University Hospital, Herlev, Denmark
- Department of Gynecology, The Juliane Marie Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Claus Høgdall
- Department of Gynecology, The Juliane Marie Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mona Aarenstrup Karlsen
- Department of Pathology, Molecular unit, Danish CancerBiobank, Herlev University Hospital, Herlev, Denmark
- Department of Gynecology, The Juliane Marie Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ib Jarle Christensen
- Department of Pathology, Molecular unit, Danish CancerBiobank, Herlev University Hospital, Herlev, Denmark
| | - Guy Wayne Novotny
- Department of Pathology, Molecular unit, Danish CancerBiobank, Herlev University Hospital, Herlev, Denmark
| | | | | | | | | | - Mansoor Raza Mirza
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne Weng Ekmann-Gade
- Department of Gynecology, The Juliane Marie Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lotte Nedergaard
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Estrid Høgdall
- Department of Pathology, Molecular unit, Danish CancerBiobank, Herlev University Hospital, Herlev, Denmark
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