1
|
Mitchell MI, Ben‐Dov IZ, Ye K, Liu C, Shi M, Sadoughi A, Shah C, Siddiqui T, Okorozo A, Gutierrez M, Unawane R, Biamonte L, Parikh K, Spivack S, Loudig O. Exhaled breath condensate contains extracellular vesicles (EVs) that carry miRNA cargos of lung tissue origin that can be selectively purified and analyzed. J Extracell Vesicles 2024; 13:e12440. [PMID: 38659349 PMCID: PMC11043690 DOI: 10.1002/jev2.12440] [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: 09/27/2023] [Accepted: 03/24/2024] [Indexed: 04/26/2024] Open
Abstract
Lung diseases, including lung cancer, are rising causes of global mortality. Despite novel imaging technologies and the development of biomarker assays, the detection of lung cancer remains a significant challenge. However, the lung communicates directly with the external environment and releases aerosolized droplets during normal tidal respiration, which can be collected, stored and analzsed as exhaled breath condensate (EBC). A few studies have suggested that EBC contains extracellular vesicles (EVs) whose microRNA (miRNA) cargos may be useful for evaluating different lung conditions, but the cellular origin of these EVs remains unknown. In this study, we used nanoparticle tracking, transmission electron microscopy, Western blot analyses and super resolution nanoimaging (ONi) to detect and validate the identity of exhaled EVs (exh-EVs). Using our customizable antibody-purification assay, EV-CATCHER, we initially determined that exh-EVs can be selectively enriched from EBC using antibodies against three tetraspanins (CD9, CD63 and CD81). Using ONi we also revealed that some exh-EVs harbour lung-specific proteins expressed in bronchiolar Clara cells (Clara Cell Secretory Protein [CCSP]) and Alveolar Type II cells (Surfactant protein C [SFTPC]). When conducting miRNA next generation sequencing (NGS) of airway samples collected at five different anatomic levels (i.e., mouth rinse, mouth wash, bronchial brush, bronchoalveolar lavage [BAL] and EBC) from 18 subjects, we determined that miRNA profiles of exh-EVs clustered closely to those of BAL EVs but not to those of other airway samples. When comparing the miRNA profiles of EVs purified from matched BAL and EBC samples with our three tetraspanins EV-CATCHER assay, we captured significant miRNA expression differences associated with smoking, asthma and lung tumor status of our subjects, which were also reproducibly detected in EVs selectively purified with our anti-CCSP/SFTPC EV-CATCHER assay from the same samples, but that confirmed their lung tissue origin. Our findings underscore that enriching exh-EV subpopulations from EBC allows non-invasive sampling of EVs produced by lung tissues.
Collapse
Affiliation(s)
- Megan I. Mitchell
- Center for Discovery and InnovationHackensack Meridian HealthNutleyNew JerseyUSA
| | - Iddo Z. Ben‐Dov
- Laboratory of Medical Transcriptomics, Internal Medicine BHadassah‐Hebrew University Medical CenterJerusalemIsrael
| | - Kenny Ye
- The Albert Einstein College of MedicineMontefiore Medical CenterBronxNew JerseyUSA
| | - Christina Liu
- Center for Discovery and InnovationHackensack Meridian HealthNutleyNew JerseyUSA
| | - Miao Shi
- The Albert Einstein College of MedicineMontefiore Medical CenterBronxNew JerseyUSA
| | - Ali Sadoughi
- The Albert Einstein College of MedicineMontefiore Medical CenterBronxNew JerseyUSA
| | - Chirag Shah
- The Albert Einstein College of MedicineMontefiore Medical CenterBronxNew JerseyUSA
| | - Taha Siddiqui
- The Albert Einstein College of MedicineMontefiore Medical CenterBronxNew JerseyUSA
| | - Aham Okorozo
- The Albert Einstein College of MedicineMontefiore Medical CenterBronxNew JerseyUSA
| | - Martin Gutierrez
- Department of Thoracic OncologyHackensack University Medical Center, Hackensack Meridian HealthHackensackNew JerseyUSA
| | - Rashmi Unawane
- Department of Thoracic OncologyHackensack University Medical Center, Hackensack Meridian HealthHackensackNew JerseyUSA
| | - Lisa Biamonte
- Department of Thoracic OncologyHackensack University Medical Center, Hackensack Meridian HealthHackensackNew JerseyUSA
| | - Kaushal Parikh
- Department of Thoracic OncologyThe Mayo ClinicRochesterMinnesotaUSA
| | - Simon Spivack
- The Albert Einstein College of MedicineMontefiore Medical CenterBronxNew JerseyUSA
| | - Olivier Loudig
- Center for Discovery and InnovationHackensack Meridian HealthNutleyNew JerseyUSA
| |
Collapse
|
2
|
Wickramage I, VanWye J, Max K, Lockhart JH, Hortu I, Mong EF, Canfield J, Lamabadu Warnakulasuriya Patabendige HM, Guzeloglu-Kayisli O, Inoue K, Ogura A, Lockwood CJ, Akat KM, Tuschl T, Kayisli UA, Totary-Jain H. SINE RNA of the imprinted miRNA clusters mediates constitutive type III interferon expression and antiviral protection in hemochorial placentas. Cell Host Microbe 2023; 31:1185-1199.e10. [PMID: 37315561 PMCID: PMC10524649 DOI: 10.1016/j.chom.2023.05.018] [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: 09/28/2022] [Revised: 03/23/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023]
Abstract
Hemochorial placentas have evolved defense mechanisms to prevent the vertical transmission of viruses to the immunologically underdeveloped fetus. Unlike somatic cells that require pathogen-associated molecular patterns to stimulate interferon production, placental trophoblasts constitutively produce type III interferons (IFNL) through an unknown mechanism. We demonstrate that transcripts of short interspersed nuclear elements (SINEs) embedded in miRNA clusters within the placenta trigger a viral mimicry response that induces IFNL and confers antiviral protection. Alu SINEs within primate-specific chromosome 19 (C19MC) and B1 SINEs within rodent-specific microRNA cluster on chromosome 2 (C2MC) produce dsRNAs that activate RIG-I-like receptors (RLRs) and downstream IFNL production. Homozygous C2MC knockout mouse trophoblast stem (mTS) cells and placentas lose intrinsic IFN expression and antiviral protection, whereas B1 RNA overexpression restores C2MCΔ/Δ mTS cell viral resistance. Our results uncover a convergently evolved mechanism whereby SINE RNAs drive antiviral resistance in hemochorial placentas, placing SINEs as integral players in innate immunity.
Collapse
Affiliation(s)
- Ishani Wickramage
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Jeffrey VanWye
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Klaas Max
- Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - John H Lockhart
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Ismet Hortu
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Ezinne F Mong
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - John Canfield
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | | | - Ozlem Guzeloglu-Kayisli
- Department of Obstetrics and Gynecology, Morsani College of Medicine, University of South Florida, Tampa, FL 33602, USA
| | - Kimiko Inoue
- Bioresource Engineering Division, BioResource Research Center, RIKEN, Tsukuba 305-0074, Ibaraki, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Ibaraki, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, BioResource Research Center, RIKEN, Tsukuba 305-0074, Ibaraki, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Ibaraki, Japan
| | - Charles J Lockwood
- Department of Obstetrics and Gynecology, Morsani College of Medicine, University of South Florida, Tampa, FL 33602, USA
| | - Kemal M Akat
- Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA; Division of Cardiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Thomas Tuschl
- Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Umit A Kayisli
- Department of Obstetrics and Gynecology, Morsani College of Medicine, University of South Florida, Tampa, FL 33602, USA
| | - Hana Totary-Jain
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; USF Heart Institute, University of South Florida, Tampa, FL 33602, USA.
| |
Collapse
|
3
|
Nøst TH, Skogholt AH, Urbarova I, Mjelle R, Paulsen E, Dønnem T, Andersen S, Markaki M, Røe OD, Johansson M, Johansson M, Grønberg BH, Sandanger TM, Sætrom P. Increased levels of microRNA-320 in blood serum and plasma is associated with imminent and advanced lung cancer. Mol Oncol 2023; 17:312-327. [PMID: 36337027 PMCID: PMC9892825 DOI: 10.1002/1878-0261.13336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/04/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Lung cancer (LC) incidence is increasing globally and altered levels of microRNAs (miRNAs) in blood may contribute to identification of individuals with LC. We identified miRNAs differentially expressed in peripheral blood at LC diagnosis and evaluated, in pre-diagnostic blood specimens, how long before diagnosis expression changes in such candidate miRNAs could be detected. We identified upregulated candidate miRNAs in plasma specimens from a hospital-based study sample of 128 patients with confirmed LC and 62 individuals with suspected but confirmed negative LC (FalsePos). We then evaluated the expression of candidate miRNAs in pre-diagnostic plasma or serum specimens of 360 future LC cases and 375 matched controls. There were 1663 miRNAs detected in diagnostic specimens, nine of which met our criteria for candidate miRNAs. Higher expression of three candidates, miR-320b, 320c, and 320d, was associated with poor survival, independent of LC stage and subtype. Moreover, miR-320c and miR-320d expression was higher in pre-diagnostic specimens collected within 2 years of LC diagnosis. Our results indicated that elevated levels of miR-320c and miR-320d may be early indications of imminent and advanced LC.
Collapse
Affiliation(s)
- Therese Haugdahl Nøst
- Department of Community Medicine, Faculty of Health SciencesUiT The Arctic University of NorwayTromsøNorway
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic EpidemiologyNTNU – Norwegian University of Science and TechnologyTrondheimNorway
| | - Anne Heidi Skogholt
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic EpidemiologyNTNU – Norwegian University of Science and TechnologyTrondheimNorway
| | - Ilona Urbarova
- Department of Community Medicine, Faculty of Health SciencesUiT The Arctic University of NorwayTromsøNorway
| | - Robin Mjelle
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic EpidemiologyNTNU – Norwegian University of Science and TechnologyTrondheimNorway
- Department of Clinical and Molecular MedicineNTNU – Norwegian University of Science and TechnologyTrondheimNorway
- Bioinformatics Core FacilityNTNU – Norwegian University of Science and TechnologyTrondheimNorway
| | - Erna‐Elise Paulsen
- Department of Clinical Medicine, Faculty of Health SciencesUiT The Arctic University of NorwayTromsøNorway
- Department of PulmonologyUniversity Hospital of North NorwayTromsøNorway
| | - Tom Dønnem
- Department of Clinical Medicine, Faculty of Health SciencesUiT The Arctic University of NorwayTromsøNorway
- Department of OncologyUniversity Hospital of North NorwayTromsøNorway
| | - Sigve Andersen
- Department of Clinical Medicine, Faculty of Health SciencesUiT The Arctic University of NorwayTromsøNorway
- Department of OncologyUniversity Hospital of North NorwayTromsøNorway
| | | | - Oluf Dimitri Røe
- Department of Clinical and Molecular MedicineNTNU – Norwegian University of Science and TechnologyTrondheimNorway
- Cancer Clinic, Levanger HospitalNord‐Trøndelag Health TrustLevangerNorway
| | | | | | - Bjørn Henning Grønberg
- Department of Clinical and Molecular MedicineNTNU – Norwegian University of Science and TechnologyTrondheimNorway
- Department of Oncology, St. Olavs HospitalTrondheim University HospitalNorway
| | - Torkjel Manning Sandanger
- Department of Community Medicine, Faculty of Health SciencesUiT The Arctic University of NorwayTromsøNorway
| | - Pål Sætrom
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic EpidemiologyNTNU – Norwegian University of Science and TechnologyTrondheimNorway
- Department of Clinical and Molecular MedicineNTNU – Norwegian University of Science and TechnologyTrondheimNorway
- Bioinformatics Core FacilityNTNU – Norwegian University of Science and TechnologyTrondheimNorway
- Department of Computer ScienceNorwegian University of Science and TechnologyTrondheimNorway
| |
Collapse
|
4
|
Blanco LP, Wang X, Carlucci PM, Torres-Ruiz JJ, Romo-Tena J, Sun HW, Hafner M, Kaplan MJ. RNA Externalized by Neutrophil Extracellular Traps Promotes Inflammatory Pathways in Endothelial Cells. Arthritis Rheumatol 2021; 73:2282-2292. [PMID: 33983685 PMCID: PMC8589882 DOI: 10.1002/art.41796] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 04/29/2021] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Neutrophil extracellular traps (NETs) are extracellular lattices composed of nucleic material bound to neutrophil granule proteins. NETs may play pathogenic roles in the development and severity of autoimmune diseases such as systemic lupus erythematosus (SLE), at least in part, through induction of type I interferon (IFN) responses via externalization of oxidized immunostimulatory DNA. A distinct subset of SLE proinflammatory neutrophils (low-density granulocytes [LDGs]) displays enhanced ability to form proinflammatory NETs that damage the vasculature. We undertook this study to assess whether NET-bound RNA can contribute to inflammatory responses in endothelial cells (ECs) and the pathways that mediate this effect. METHODS Expression of newly synthesized and total RNA was quantified in NETs from healthy controls and lupus patients. The ability of ECs to take up NET-bound RNA and downstream induction of type I IFN responses were quantified. RNAs present in NETs were sequenced and specific small RNAs were tested for induction of endothelial type I IFN pathways. RESULTS NETs extruded RNA that was internalized by ECs, and this was enhanced when NET-bound nucleic acids were oxidized, particularly in lupus LDG-derived NETs. Internalization of NET-bound RNA by ECs was dependent on endosomal Toll-like receptors (TLRs) and the actin cytoskeleton and induced type I IFN-stimulated genes (ISGs). This ISG induction was dependent on NET-associated microRNA let-7b, a small RNA expressed at higher levels in LDG-derived NETs, which acted as a TLR-7 agonist. CONCLUSION These findings highlight underappreciated roles for small RNAs externalized in NETs in the induction of proinflammatory responses in vascular cells, with implications for lupus vasculopathy.
Collapse
Affiliation(s)
- Luz P. Blanco
- Systemic Autoimmunity Branch, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Xinghao Wang
- Systemic Autoimmunity Branch, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Philip M. Carlucci
- Systemic Autoimmunity Branch, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Jose Jiram Torres-Ruiz
- Systemic Autoimmunity Branch, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Jorge Romo-Tena
- Systemic Autoimmunity Branch, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, Maryland, USA
- Medical Science PhD Program, School of Medicine, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Markus Hafner
- RNA Molecular Biology Group, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Mariana J. Kaplan
- Systemic Autoimmunity Branch, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, Maryland, USA
| |
Collapse
|
5
|
Max KEA, Wang VR, Chang MS, Liau J, Weiss ZR, Morgan S, Li J, Bogardus KA, Morozov P, Suryawanshi H, Akat KM, Ben-Dov IZ, Hurley AM, Dowd K, Williams Z, Tuschl T. Plasma microRNA Interindividual Variability in Healthy Individuals, Pregnant Women, and an Individual with a Stably Altered Neuroendocrine Phenotype. Clin Chem 2021; 67:1676-1688. [PMID: 34850840 DOI: 10.1093/clinchem/hvab193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/01/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Extracellular RNAs (exRNAs) in biofluids are amenable to quantitative analysis and proposed as noninvasive biomarkers for monitoring organ function. Cell-lineage-specific microRNAs (miRNAs) are present in plasma as soluble ribonucleoproteins or enclosed in exRNA carriers and transported through the vasculature. However, more extensive studies of healthy individuals are needed to gain insights into the variability of plasma miRNA abundance and composition. METHODS The exRNA composition of platelet-depleted plasma collected twice from 236 healthy individuals was characterized by small RNA sequencing. Plasma of pregnant women featuring dramatically increased placental miRNAs and samples from subject P12 with noticeably increased epithelial- and neuroendocrine-origin miRNAs were included for comparison. The miRNA content of 10 000g and 100 000g pellet fractions of plasma generated by ultracentrifugation was also determined. Data analysis methods included Pearson correlation, differential gene expression, and unsupervised clustering. RESULTS The abundance changes for more variable miRNAs in plasma of normal individuals correlated between coexpressed cell-lineage-specific miRNAs of the liver, neuroendocrine organs, epithelial cells, and muscle. ExRNA of pellet fractions contained <2% of total plasma miRNA with modest enrichment of lineage-specific and variable miRNAs compared to supernatant. The abundance fold changes of miRNAs observed in pregnancy and P12 compared to normal exceeded interquartile variability of healthy individuals. The neuroendocrine miRNA signature of P12 persisted for more than 4 years and was absent in other individuals. CONCLUSIONS This study defines the framework and effect size for screening of extensive plasma collections for miRNA phenotypes and biomarker discovery.
Collapse
Affiliation(s)
- Klaas E A Max
- Rockefeller University, Laboratory for RNA Molecular Biology, New York, NY
| | - Victoria R Wang
- Rockefeller University, Laboratory for RNA Molecular Biology, New York, NY
| | - Michael S Chang
- Rockefeller University, Laboratory for RNA Molecular Biology, New York, NY
| | - Jonathan Liau
- Rockefeller University, Laboratory for RNA Molecular Biology, New York, NY
| | - Zachary R Weiss
- Department of Obstetrics and Gynecology, Columbia University Medical Center, Columbia University Irving Medical Center, New York, NY
| | - Stephanie Morgan
- Department of Obstetrics and Gynecology, Columbia University Medical Center, Columbia University Irving Medical Center, New York, NY
| | - Jenny Li
- Rockefeller University, Laboratory for RNA Molecular Biology, New York, NY
| | | | - Pavel Morozov
- Rockefeller University, Laboratory for RNA Molecular Biology, New York, NY
| | - Hemant Suryawanshi
- Rockefeller University, Laboratory for RNA Molecular Biology, New York, NY.,Department of Obstetrics and Gynecology, Columbia University Medical Center, Columbia University Irving Medical Center, New York, NY
| | - Kemal M Akat
- Rockefeller University, Laboratory for RNA Molecular Biology, New York, NY.,Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Iddo Z Ben-Dov
- Department of Nephrology, Hadassah-Hebrew University Medical Center, Jerusalem, IL
| | - Arlene M Hurley
- Clinical Research Facilitation Office, Rockefeller University, New York, NY
| | - Kathleen Dowd
- Clinical Research Facilitation Office, Rockefeller University, New York, NY
| | - Zev Williams
- Department of Obstetrics and Gynecology, Columbia University Medical Center, Columbia University Irving Medical Center, New York, NY
| | - Thomas Tuschl
- Rockefeller University, Laboratory for RNA Molecular Biology, New York, NY
| |
Collapse
|
6
|
Qin LX, Zou J, Shi J, Lee A, Mihailovic A, Farazi TA, Tuschl T, Singer S. Statistical Assessment of Depth Normalization for Small RNA Sequencing. JCO Clin Cancer Inform 2021; 4:567-582. [PMID: 32598180 PMCID: PMC7330947 DOI: 10.1200/cci.19.00118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
PURPOSE Methods for depth normalization have been assessed primarily with simulated data or cell-line–mixture data. There is a pressing need for benchmark data enabling a more realistic and objective assessment, especially in the context of small RNA sequencing. METHODS We collected a unique pair of microRNA sequencing data sets for the same set of tumor samples; one data set was collected with and the other without uniform handling and balanced design. The former provided a benchmark for evaluating evidence of differential expression and the latter served as a test bed for normalization. Next, we developed a data perturbation algorithm to simulate additional data set pairs. Last, we assembled a set of computational tools to visualize and quantify the assessment. RESULTS We validated the quality of the benchmark data and showed the need for normalization of the test data. For illustration, we applied the data and tools to assess the performance of 9 existing normalization methods. Among them, trimmed mean of M-values was a better scaling method, whereas the median and the upper quartiles were consistently the worst performers; one variation of remove unwanted variation had the best chance of capturing true positives but at the cost of increased false positives. In general, these methods were, at best, moderately helpful when the level of differential expression was extensive and asymmetric. CONCLUSION Our study (1) provides the much-needed benchmark data and computational tools for assessing depth normalization, (2) shows the dependence of normalization performance on the underlying pattern of differential expression, and (3) calls for continued research efforts to develop more effective normalization methods.
Collapse
Affiliation(s)
- Li-Xuan Qin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jian Zou
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jiejun Shi
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ann Lee
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Thalia A Farazi
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
7
|
Sauer M, Was N, Ziegenhals T, Wang X, Hafner M, Becker M, Fischer U. The miR-26 family regulates neural differentiation-associated microRNAs and mRNAs by directly targeting REST. J Cell Sci 2021; 134:jcs257535. [PMID: 34151974 PMCID: PMC11443607 DOI: 10.1242/jcs.257535] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/11/2021] [Indexed: 01/13/2023] Open
Abstract
Repressor element 1-silencing transcription factor (REST) plays a crucial role in the differentiation of neural progenitor cells (NPCs). C-terminal domain small phosphatases (CTDSPs) are REST effector proteins that reduce RNA polymerase II activity on genes required for neurogenesis. miR-26b regulates neurogenesis in zebrafish by targeting ctdsp2 mRNA, but the molecular events triggered by this microRNA (miR) remain unknown. Here, we show in a murine embryonic stem cell differentiation paradigm that inactivation of miR-26 family members disrupts the formation of neurons and astroglia and arrests neurogenesis at the neural progenitor level. Furthermore, we show that miR-26 directly targets Rest, thereby inducing the expression of a large set of REST complex-repressed neuronal genes, including miRs required for induction of the neuronal gene expression program. Our data identify the miR-26 family as the trigger of a self-amplifying system required for neural differentiation that acts upstream of REST-controlled miRs.
Collapse
Affiliation(s)
- Mark Sauer
- Institute for Medical Radiology and Cell Research (MSZ) in the Center for Experimental Molecular Medicine (ZEMM), University of Würzburg, D-97078 Würzburg, Germany
| | - Nina Was
- Institute for Medical Radiology and Cell Research (MSZ) in the Center for Experimental Molecular Medicine (ZEMM), University of Würzburg, D-97078 Würzburg, Germany
| | - Thomas Ziegenhals
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, D-97074 Würzburg, Germany
| | - Xiantao Wang
- RNA Molecular Biology Group, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Markus Hafner
- RNA Molecular Biology Group, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Matthias Becker
- Institute for Medical Radiology and Cell Research (MSZ) in the Center for Experimental Molecular Medicine (ZEMM), University of Würzburg, D-97078 Würzburg, Germany
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, D-97074 Würzburg, Germany
| |
Collapse
|
8
|
Kennel PJ, Yahi A, Naka Y, Mancini DM, Marboe CC, Max K, Akat K, Tuschl T, Vasilescu EM, Zorn E, Tatonetti NP, Schulze PC. Longitudinal profiling of circulating miRNA during cardiac allograft rejection: a proof-of-concept study. ESC Heart Fail 2021; 8:1840-1849. [PMID: 33713567 PMCID: PMC8120386 DOI: 10.1002/ehf2.13238] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/09/2021] [Accepted: 01/19/2021] [Indexed: 12/30/2022] Open
Abstract
AIMS Allograft rejection following heart transplantation (HTx) is a serious complication even in the era of modern immunosuppressive regimens and causes up to a third of early deaths after HTx. Allograft rejection is mediated by a cascade of immune mechanisms leading to acute cellular rejection (ACR) and/or antibody-mediated rejection (AMR). The gold standard for monitoring allograft rejection is invasive endomyocardial biopsy that exposes patients to complications. Little is known about the potential of circulating miRNAs as biomarkers to detect cardiac allograft rejection. We here present a systematic analysis of circulating miRNAs as biomarkers and predictors for allograft rejection after HTx using next-generation small RNA sequencing. METHODS AND RESULTS We used next-generation small RNA sequencing to investigate circulating miRNAs among HTx recipients (10 healthy controls, 10 heart failure patients, 13 ACR, and 10 AMR). MiRNA profiling was performed at different time points before, during, and after resolution of the rejection episode. We found three miRNAs with significantly increased serum levels in patients with biopsy-proven cardiac rejection when compared with patients without rejection: hsa-miR-139-5p, hsa-miR-151a-5p, and hsa-miR-186-5p. We identified miRNAs that may serve as potential predictors for the subsequent development of ACR: hsa-miR-29c-3p (ACR) and hsa-miR-486-5p (AMR). Overall, hsa-miR-486-5p was most strongly associated with acute rejection episodes. CONCLUSIONS Monitoring cardiac allograft rejection using circulating miRNAs might represent an alternative strategy to invasive endomyocardial biopsy.
Collapse
Affiliation(s)
- Peter J. Kennel
- Division of Cardiology, Department of MedicineColumbia UniversityNew YorkNYUSA
- Department of Medicine I, Division of CardiologyUniversity Hospital of Friedrich Schiller University JenaAm Klinikum 1Jena07747Germany
| | - Alexandre Yahi
- Department of Biomedical InformaticsColumbia UniversityNew YorkNYUSA
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Department of MedicineColumbia UniversityNew YorkNYUSA
| | | | | | - Charles C. Marboe
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNYUSA
| | - Klaas Max
- Laboratory of RNA Molecular BiologyRockefeller UniversityNew YorkNYUSA
| | - Kemal Akat
- Laboratory of RNA Molecular BiologyRockefeller UniversityNew YorkNYUSA
| | - Thomas Tuschl
- Laboratory of RNA Molecular BiologyRockefeller UniversityNew YorkNYUSA
| | | | - Emmanuel Zorn
- Columbia Center for Translational ImmunologyColumbia UniversityNew YorkNYUSA
| | - Nicholas P. Tatonetti
- Department of Biomedical InformaticsColumbia UniversityNew YorkNYUSA
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Department of MedicineColumbia UniversityNew YorkNYUSA
| | - Paul Christian Schulze
- Department of Medicine I, Division of CardiologyUniversity Hospital of Friedrich Schiller University JenaAm Klinikum 1Jena07747Germany
| |
Collapse
|
9
|
Yang X, Nanayakkara J, Claypool D, Saghafinia S, Wong JJM, Xu M, Wang X, Nicol CJB, Michael IP, Hafner M, Yang X, Renwick N. A miR-375/YAP axis regulates neuroendocrine differentiation and tumorigenesis in lung carcinoid cells. Sci Rep 2021; 11:10455. [PMID: 34001972 PMCID: PMC8129150 DOI: 10.1038/s41598-021-89855-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 04/30/2021] [Indexed: 02/03/2023] Open
Abstract
Lung carcinoids are variably aggressive and mechanistically understudied neuroendocrine neoplasms (NENs). Here, we identified and elucidated the function of a miR-375/yes-associated protein (YAP) axis in lung carcinoid (H727) cells. miR-375 and YAP are respectively high and low expressed in wild-type H727 cells. Following lentiviral CRISPR/Cas9-mediated miR-375 depletion, we identified distinct transcriptomic changes including dramatic YAP upregulation. We also observed a significant decrease in neuroendocrine differentiation and substantial reductions in cell proliferation, transformation, and tumor growth in cell culture and xenograft mouse disease models. Similarly, YAP overexpression resulted in distinct and partially overlapping transcriptomic changes, phenocopying the effects of miR-375 depletion in the same models as above. Transient YAP knockdown in miR-375-depleted cells reversed the effects of miR-375 on neuroendocrine differentiation and cell proliferation. Pathways analysis and confirmatory real-time PCR studies of shared dysregulated target genes indicate that this axis controls neuroendocrine related functions such as neural differentiation, exocytosis, and secretion. Taken together, we provide compelling evidence that a miR-375/YAP axis is a critical mediator of neuroendocrine differentiation and tumorigenesis in lung carcinoid cells.
Collapse
Affiliation(s)
- Xiaojing Yang
- grid.410356.50000 0004 1936 8331Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, 88 Stuart St, Kingston, ON K7L 3N6 Canada
| | - Jina Nanayakkara
- grid.410356.50000 0004 1936 8331Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, 88 Stuart St, Kingston, ON K7L 3N6 Canada
| | - Duncan Claypool
- grid.420086.80000 0001 2237 2479Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, 50 South Drive, Bethesda, MD 20892 USA
| | - Sadegh Saghafinia
- grid.5333.60000000121839049Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Justin J. M. Wong
- grid.410356.50000 0004 1936 8331Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, 88 Stuart St, Kingston, ON K7L 3N6 Canada
| | - Minqi Xu
- grid.410356.50000 0004 1936 8331Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, 88 Stuart St, Kingston, ON K7L 3N6 Canada
| | - Xiantao Wang
- grid.420086.80000 0001 2237 2479Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, 50 South Drive, Bethesda, MD 20892 USA
| | - Christopher J. B. Nicol
- grid.410356.50000 0004 1936 8331Department of Pathology and Molecular Medicine, Queen’s University, 88 Stuart St, Kingston, ON K7L 3N6 Canada ,Division of Cancer Biology and Genetics, Queen’s Cancer Research Institute, 10 Stuart St, Kingston, ON K7L 3N6 Canada
| | - Iacovos P. Michael
- grid.5333.60000000121839049Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Markus Hafner
- grid.420086.80000 0001 2237 2479Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, 50 South Drive, Bethesda, MD 20892 USA
| | - Xiaolong Yang
- grid.410356.50000 0004 1936 8331Cancer Research Laboratory, Department of Pathology and Molecular Medicine, Queen’s University, 88 Stuart St, Kingston, ON K7L 3N6 Canada
| | - Neil Renwick
- grid.410356.50000 0004 1936 8331Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, 88 Stuart St, Kingston, ON K7L 3N6 Canada
| |
Collapse
|
10
|
Wang L, Guan X, Hu Q, Wu Z, Chen W, Song L, Wang K, Tian K, Cao C, Zhang D, Ma J, Tong X, Zhang B, Zhang J, Zeng C. TGFB3 downregulation causing chordomagenesis and its tumor suppression role maintained by Smad7. Carcinogenesis 2021; 42:913-923. [PMID: 34057989 DOI: 10.1093/carcin/bgab022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 02/02/2021] [Accepted: 04/06/2021] [Indexed: 12/19/2022] Open
Abstract
Chordoma is a rare bone tumor arising from notochordal remnants, but the underlying mechanism remains elusive. By integrated mRNA and microRNA analyses, we found significant downregulation of TGFB3 along with upregulation of its inhibitor, miR-29 family in chordoma comparing with notochord. Somatic copy number gains of miR-29 loci in chordoma highlighted a mechanism of inactivation of TGFB3 signaling in tumor formation. In zebrafish, knockout and knockdown homologous tgfb3 resulted in a chordoma-like neoplasm. On the other hand, Smad7 negative feedback regulation of transforming growth factor-β (TGF-β) signaling is retentive in chordoma cell UM-Chor1 despite its disruption in most cancer cells (e.g. A549). Therefore, contrary to other cancers, exogenous TGF-β activated Smad7 by downregulating miR-182 and inhibited cell migration and invasion in UM-Chor1. Meanwhile, TGF-β decreased chordoma characteristic protein Brachyury. Altogether, downregulation of TGFB3 causes chordomagenesis, showing a feasible target for therapies. The retention of Smad7 negative regulation may maintain the suppressor role of TGF-β in chordoma.
Collapse
Affiliation(s)
- Liang Wang
- Neurosurgery Department, Beijing Tiantan Hospital, Capital Medical University, Tiantan Xili, Dongcheng District, Beijing, China.,China National Clinical Research Center for Neurological Diseases, NCRC-ND, Tiantan Xili, Dongcheng District, Beijing, China
| | - Xiaonan Guan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qingtao Hu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhen Wu
- Neurosurgery Department, Beijing Tiantan Hospital, Capital Medical University, Tiantan Xili, Dongcheng District, Beijing, China.,China National Clinical Research Center for Neurological Diseases, NCRC-ND, Tiantan Xili, Dongcheng District, Beijing, China
| | - Wei Chen
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Lairong Song
- Neurosurgery Department, Beijing Tiantan Hospital, Capital Medical University, Tiantan Xili, Dongcheng District, Beijing, China.,China National Clinical Research Center for Neurological Diseases, NCRC-ND, Tiantan Xili, Dongcheng District, Beijing, China
| | - Ke Wang
- Neurosurgery Department, Beijing Tiantan Hospital, Capital Medical University, Tiantan Xili, Dongcheng District, Beijing, China.,China National Clinical Research Center for Neurological Diseases, NCRC-ND, Tiantan Xili, Dongcheng District, Beijing, China
| | - Kaibing Tian
- Neurosurgery Department, Beijing Tiantan Hospital, Capital Medical University, Tiantan Xili, Dongcheng District, Beijing, China.,China National Clinical Research Center for Neurological Diseases, NCRC-ND, Tiantan Xili, Dongcheng District, Beijing, China
| | - Chunwei Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Dake Zhang
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Junpeng Ma
- Neurosurgery Department, Beijing Tiantan Hospital, Capital Medical University, Tiantan Xili, Dongcheng District, Beijing, China.,China National Clinical Research Center for Neurological Diseases, NCRC-ND, Tiantan Xili, Dongcheng District, Beijing, China
| | - Xiangjun Tong
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Bo Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Junting Zhang
- Neurosurgery Department, Beijing Tiantan Hospital, Capital Medical University, Tiantan Xili, Dongcheng District, Beijing, China.,China National Clinical Research Center for Neurological Diseases, NCRC-ND, Tiantan Xili, Dongcheng District, Beijing, China
| | - Changqing Zeng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
11
|
Azar S, Udi S, Drori A, Hadar R, Nemirovski A, Vemuri KV, Miller M, Sherill-Rofe D, Arad Y, Gur-Wahnon D, Li X, Makriyannis A, Ben-Zvi D, Tabach Y, Ben-Dov IZ, Tam J. Reversal of diet-induced hepatic steatosis by peripheral CB1 receptor blockade in mice is p53/miRNA-22/SIRT1/PPARα dependent. Mol Metab 2020; 42:101087. [PMID: 32987186 PMCID: PMC7563015 DOI: 10.1016/j.molmet.2020.101087] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/03/2020] [Accepted: 09/17/2020] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE The endocannabinoid (eCB) system is increasingly recognized as being crucially important in obesity-related hepatic steatosis. By activating the hepatic cannabinoid-1 receptor (CB1R), eCBs modulate lipogenesis and fatty acid oxidation. However, the underlying molecular mechanisms are largely unknown. METHODS We combined unbiased bioinformatics techniques, mouse genetic manipulations, multiple pharmacological, molecular, and cellular biology approaches, and genomic sequencing to systematically decipher the role of the hepatic CB1R in modulating fat utilization in the liver and explored the downstream molecular mechanisms. RESULTS Using an unbiased normalized phylogenetic profiling analysis, we found that the CB1R evolutionarily coevolves with peroxisome proliferator-activated receptor-alpha (PPARα), a key regulator of hepatic lipid metabolism. In diet-induced obese (DIO) mice, peripheral CB1R blockade (using AM6545) induced the reversal of hepatic steatosis and improved liver injury in WT, but not in PPARα-/- mice. The antisteatotic effect mediated by AM6545 in WT DIO mice was accompanied by increased hepatic expression and activity of PPARα as well as elevated hepatic levels of the PPARα-activating eCB-like molecules oleoylethanolamide and palmitoylethanolamide. Moreover, AM6545 was unable to rescue hepatic steatosis in DIO mice lacking liver sirtuin 1 (SIRT1), an upstream regulator of PPARα. Both of these signaling molecules were modulated by the CB1R as measured in hepatocytes exposed to lipotoxic conditions or treated with CB1R agonists in the absence/presence of AM6545. Furthermore, using microRNA transcriptomic profiling, we found that the CB1R regulated the hepatic expression, acetylation, and transcriptional activity of p53, resulting in the enhanced expression of miR-22, which was found to specifically target SIRT1 and PPARα. CONCLUSIONS We provide strong evidence for a functional role of the p53/miR-22/SIRT1/PPARα signaling pathway in potentially mediating the antisteatotic effect of peripherally restricted CB1R blockade.
Collapse
Affiliation(s)
- Shahar Azar
- Obesity and Metabolism Laboratory, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shiran Udi
- Obesity and Metabolism Laboratory, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adi Drori
- Obesity and Metabolism Laboratory, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rivka Hadar
- Obesity and Metabolism Laboratory, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alina Nemirovski
- Obesity and Metabolism Laboratory, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Kiran V Vemuri
- Center for Drug Discovery, Northeastern University, Boston, MA, USA
| | - Maya Miller
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical School, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dana Sherill-Rofe
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical School, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yhara Arad
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical School, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Devorah Gur-Wahnon
- Laboratory of Medical Transcriptomics, Department of Nephrology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Xiaoling Li
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | | | - Danny Ben-Zvi
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical School, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical School, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Iddo Z Ben-Dov
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Joseph Tam
- Obesity and Metabolism Laboratory, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| |
Collapse
|
12
|
Wong JJM, Ginter PS, Tyryshkin K, Yang X, Nanayakkara J, Zhou Z, Tuschl T, Chen YT, Renwick N. Classifying Lung Neuroendocrine Neoplasms through MicroRNA Sequence Data Mining. Cancers (Basel) 2020; 12:E2653. [PMID: 32957587 PMCID: PMC7564332 DOI: 10.3390/cancers12092653] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022] Open
Abstract
Lung neuroendocrine neoplasms (NENs) can be challenging to classify due to subtle histologic differences between pathological types. MicroRNAs (miRNAs) are small RNA molecules that are valuable markers in many neoplastic diseases. To evaluate miRNAs as classificatory markers for lung NENs, we generated comprehensive miRNA expression profiles from 14 typical carcinoid (TC), 15 atypical carcinoid (AC), 11 small cell lung carcinoma (SCLC), and 15 large cell neuroendocrine carcinoma (LCNEC) samples, through barcoded small RNA sequencing. Following sequence annotation and data preprocessing, we randomly assigned these profiles to discovery and validation sets. Through high expression analyses, we found that miR-21 and -375 are abundant in all lung NENs, and that miR-21/miR-375 expression ratios are significantly lower in carcinoids (TC and AC) than in neuroendocrine carcinomas (NECs; SCLC and LCNEC). Subsequently, we ranked and selected miRNAs for use in miRNA-based classification, to discriminate carcinoids from NECs. Using miR-18a and -155 expression, our classifier discriminated these groups in discovery and validation sets, with 93% and 100% accuracy. We also identified miR-17, -103, and -127, and miR-301a, -106b, and -25, as candidate markers for discriminating TC from AC, and SCLC from LCNEC, respectively. However, these promising findings require external validation due to sample size.
Collapse
Affiliation(s)
- Justin J. M. Wong
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (J.J.M.W.); (K.T.); (X.Y.); (J.N.); (Z.Z.)
| | - Paula S. Ginter
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; (P.S.G.); (Y.-T.C.)
| | - Kathrin Tyryshkin
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (J.J.M.W.); (K.T.); (X.Y.); (J.N.); (Z.Z.)
| | - Xiaojing Yang
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (J.J.M.W.); (K.T.); (X.Y.); (J.N.); (Z.Z.)
| | - Jina Nanayakkara
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (J.J.M.W.); (K.T.); (X.Y.); (J.N.); (Z.Z.)
| | - Zier Zhou
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (J.J.M.W.); (K.T.); (X.Y.); (J.N.); (Z.Z.)
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA;
| | - Yao-Tseng Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; (P.S.G.); (Y.-T.C.)
| | - Neil Renwick
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (J.J.M.W.); (K.T.); (X.Y.); (J.N.); (Z.Z.)
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA;
| |
Collapse
|
13
|
Nanayakkara J, Tyryshkin K, Yang X, Wong JJM, Vanderbeck K, Ginter PS, Scognamiglio T, Chen YT, Panarelli N, Cheung NK, Dijk F, Ben-Dov IZ, Kim MK, Singh S, Morozov P, Max KEA, Tuschl T, Renwick N. Characterizing and classifying neuroendocrine neoplasms through microRNA sequencing and data mining. NAR Cancer 2020; 2:zcaa009. [PMID: 32743554 PMCID: PMC7380486 DOI: 10.1093/narcan/zcaa009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/22/2020] [Accepted: 06/06/2020] [Indexed: 12/13/2022] Open
Abstract
Neuroendocrine neoplasms (NENs) are clinically diverse and incompletely characterized cancers that are challenging to classify. MicroRNAs (miRNAs) are small regulatory RNAs that can be used to classify cancers. Recently, a morphology-based classification framework for evaluating NENs from different anatomical sites was proposed by experts, with the requirement of improved molecular data integration. Here, we compiled 378 miRNA expression profiles to examine NEN classification through comprehensive miRNA profiling and data mining. Following data preprocessing, our final study cohort included 221 NEN and 114 non-NEN samples, representing 15 NEN pathological types and 5 site-matched non-NEN control groups. Unsupervised hierarchical clustering of miRNA expression profiles clearly separated NENs from non-NENs. Comparative analyses showed that miR-375 and miR-7 expression is substantially higher in NEN cases than non-NEN controls. Correlation analyses showed that NENs from diverse anatomical sites have convergent miRNA expression programs, likely reflecting morphological and functional similarities. Using machine learning approaches, we identified 17 miRNAs to discriminate 15 NEN pathological types and subsequently constructed a multilayer classifier, correctly identifying 217 (98%) of 221 samples and overturning one histological diagnosis. Through our research, we have identified common and type-specific miRNA tissue markers and constructed an accurate miRNA-based classifier, advancing our understanding of NEN diversity.
Collapse
Affiliation(s)
- Jina Nanayakkara
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen's University, 88 Stuart Street, Kingston, ON K7L 3N6, Canada
| | - Kathrin Tyryshkin
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen's University, 88 Stuart Street, Kingston, ON K7L 3N6, Canada
| | - Xiaojing Yang
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen's University, 88 Stuart Street, Kingston, ON K7L 3N6, Canada
| | - Justin J M Wong
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen's University, 88 Stuart Street, Kingston, ON K7L 3N6, Canada
| | - Kaitlin Vanderbeck
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen's University, 88 Stuart Street, Kingston, ON K7L 3N6, Canada
| | - Paula S Ginter
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Theresa Scognamiglio
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Yao-Tseng Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Nicole Panarelli
- Department of Pathology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Nai-Kong Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Frederike Dijk
- Department of Pathology, Amsterdam University Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Iddo Z Ben-Dov
- Department of Nephrology and Hypertension, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Michelle Kang Kim
- Center for Carcinoid and Neuroendocrine Tumors of Mount Sinai, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Simron Singh
- Odette Cancer Center, Sunnybrook Health Sciences Center, Toronto, ON M4N 3M5, Canada
| | - Pavel Morozov
- Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Klaas E A Max
- Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Neil Renwick
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen's University, 88 Stuart Street, Kingston, ON K7L 3N6, Canada
| |
Collapse
|
14
|
Chakraborty N, Gautam A, Holmes-Hampton GP, Kumar VP, Biswas S, Kumar R, Hamad D, Dimitrov G, Olabisi AO, Hammamieh R, Ghosh SP. microRNA and Metabolite Signatures Linked to Early Consequences of Lethal Radiation. Sci Rep 2020; 10:5424. [PMID: 32214144 PMCID: PMC7096415 DOI: 10.1038/s41598-020-62255-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/11/2020] [Indexed: 12/12/2022] Open
Abstract
Lethal total body irradiation (TBI) triggers multifactorial health issues in a potentially short time frame. Hence, early signatures of TBI would be of great clinical value. Our study aimed to interrogate microRNA (miRNA) and metabolites, two biomolecules available in blood serum, in order to comprehend the immediate impacts of TBI. Mice were exposed to a lethal dose (9.75 Gy) of Cobalt-60 gamma radiation and euthanized at four time points, namely, days 1, 3, 7 and 9 post-TBI. Serum miRNA libraries were sequenced using the Illumina small RNA sequencing protocol, and metabolites were screened using a mass spectrometer. The degree of early impacts of irradiation was underscored by the large number of miRNAs and metabolites that became significantly expressed during the Early phase (day 0 and 1 post-TBI). Radiation-induced inflammatory markers for bone marrow aplasia and pro-sepsis markers showed early elevation with longitudinal increment. Functional analysis integrating miRNA-protein-metabolites revealed inflammation as the overarching host response to lethal TBI. Early activation of the network linked to the synthesis of reactive oxygen species was associated with the escalated regulation of the fatty acid metabolism network. In conclusion, we assembled a list of time-informed critical markers and mechanisms of significant translational potential in the context of a radiation exposure event.
Collapse
Affiliation(s)
- Nabarun Chakraborty
- The Geneva Foundation, Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Fort Detrick, MD, 21702-5010, USA
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Fort Detrick, MD, 21702-5010, USA
| | - Aarti Gautam
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Fort Detrick, MD, 21702-5010, USA
| | - Gregory P Holmes-Hampton
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD, 20889, USA
| | - Vidya P Kumar
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD, 20889, USA
| | - Shukla Biswas
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD, 20889, USA
| | - Raina Kumar
- The Geneva Foundation, Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Fort Detrick, MD, 21702-5010, USA
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Fort Detrick, MD, 21702-5010, USA
| | - Dana Hamad
- ORISE, Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Fort Detrick, MD, 21702-5010, USA
| | - George Dimitrov
- The Geneva Foundation, Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Fort Detrick, MD, 21702-5010, USA
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Fort Detrick, MD, 21702-5010, USA
| | - Ayodele O Olabisi
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD, 20889, USA
| | - Rasha Hammamieh
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Fort Detrick, MD, 21702-5010, USA
| | - Sanchita P Ghosh
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD, 20889, USA.
| |
Collapse
|
15
|
Mong EF, Yang Y, Akat KM, Canfield J, VanWye J, Lockhart J, Tsibris JCM, Schatz F, Lockwood CJ, Tuschl T, Kayisli UA, Totary-Jain H. Chromosome 19 microRNA cluster enhances cell reprogramming by inhibiting epithelial-to-mesenchymal transition. Sci Rep 2020; 10:3029. [PMID: 32080251 PMCID: PMC7033247 DOI: 10.1038/s41598-020-59812-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 02/04/2020] [Indexed: 02/08/2023] Open
Abstract
During implantation, cytotrophoblasts undergo epithelial-to-mesenchymal transition (EMT) as they differentiate into invasive extravillous trophoblasts (EVTs). The primate-specific microRNA cluster on chromosome 19 (C19MC) is exclusively expressed in the placenta, embryonic stem cells and certain cancers however, its role in EMT gene regulation is unknown. In situ hybridization for miR-517a/c, a C19MC cistron microRNA, in first trimester human placentas displayed strong expression in villous trophoblasts and a gradual decrease from proximal to distal cell columns as cytotrophoblasts differentiate into invasive EVTs. To investigate the role of C19MC in the regulation of EMT genes, we employed the CRISPR/dCas9 Synergistic Activation Mediator (SAM) system, which induced robust transcriptional activation of the entire C19MC cistron and resulted in suppression of EMT associated genes. Exposure of human iPSCs to hypoxia or differentiation of iPSCs into either cytotrophoblast-stem-like cells or EVT-like cells under hypoxia reduced C19MC expression and increased EMT genes. Furthermore, transcriptional activation of the C19MC cistron induced the expression of OCT4 and FGF4 and accelerated cellular reprogramming. This study establishes the CRISPR/dCas9 SAM as a powerful tool that enables activation of the entire C19MC cistron and uncovers its novel role in suppressing EMT genes critical for maintaining the epithelial cytotrophoblasts stem cell phenotype.
Collapse
Affiliation(s)
- Ezinne F Mong
- Department of Molecular Pharmacology and Physiology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Ying Yang
- Department of Molecular Pharmacology and Physiology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Kemal M Akat
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York, USA
| | - John Canfield
- Department of Molecular Pharmacology and Physiology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Jeffrey VanWye
- Department of Molecular Pharmacology and Physiology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - John Lockhart
- Department of Molecular Pharmacology and Physiology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - John C M Tsibris
- Department of Obstetrics and Gynecology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Frederick Schatz
- Department of Obstetrics and Gynecology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Charles J Lockwood
- Department of Obstetrics and Gynecology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Thomas Tuschl
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York, USA
| | - Umit A Kayisli
- Department of Obstetrics and Gynecology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Hana Totary-Jain
- Department of Molecular Pharmacology and Physiology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA.
| |
Collapse
|
16
|
Liu S, Guo X, Zhong W, Weng R, Liu J, Gu X, Zhong Z. Circulating MicroRNA Expression Profiles in Patients with Stable and Unstable Angina. Clinics (Sao Paulo) 2020; 75:e1546. [PMID: 32667489 PMCID: PMC7337223 DOI: 10.6061/clinics/2020/e1546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 04/07/2020] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVES High incidence and case fatality of unstable angina (UA) is, to a large extent, a consequence of the lack of highly sensitive and specific non-invasive markers. Circulating microRNAs (miRNAs) have been widely recommended as potential biomarkers for numerous diseases. In the present study, we characterized distinctive miRNA expression profiles in patients with stable angina (SA), UA, and normal coronary arteries (NCA), and identified promising candidates for UA diagnosis. METHODS Serum was collected from patients with SA, UA, and NCA who visited the Department of Cardiovascular Diseases of the Meizhou People's Hospital. Small RNA sequencing was carried out on an Illumina HiSeq 2500 platform. miRNA expression in different groups of patients was profiled and then confirmed based on that in an independent set of patients. Functions of differentially expressed miRNAs were predicted using gene ontology classification and Kyoto Encyclopedia of Genes and Genomes pathway analysis. RESULTS Our results indicated that circulating miRNA expression profiles differed between SA, UA, and NCA patients. A total of 36 and 161 miRNAs were dysregulated in SA and UA patients, respectively. miRNA expression was validated by reverse transcription quantitative polymerase chain reaction. CONCLUSION The results suggest that circulating miRNAs are potential biomarkers of UA.
Collapse
Affiliation(s)
- Sudong Liu
- Research Experimental Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou 514031, P. R. China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou 514031, P. R. China
| | - Xuemin Guo
- Research Experimental Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou 514031, P. R. China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou 514031, P. R. China
| | - Wei Zhong
- Center for Cardiovascular Diseases, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou 514031, P. R. China
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou 514031, P. R. China
| | - Ruiqiang Weng
- Research Experimental Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou 514031, P. R. China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou 514031, P. R. China
| | - Jing Liu
- Research Experimental Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou 514031, P. R. China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou 514031, P. R. China
| | - Xiaodong Gu
- Research Experimental Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou 514031, P. R. China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou 514031, P. R. China
| | - Zhixiong Zhong
- Center for Cardiovascular Diseases, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou 514031, P. R. China
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou 514031, P. R. China
- *Corresponding author. E-mail:
| |
Collapse
|
17
|
Chiou NT, Kageyama R, Ansel KM. Selective Export into Extracellular Vesicles and Function of tRNA Fragments during T Cell Activation. Cell Rep 2019; 25:3356-3370.e4. [PMID: 30566862 PMCID: PMC6392044 DOI: 10.1016/j.celrep.2018.11.073] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 10/29/2018] [Accepted: 11/15/2018] [Indexed: 12/12/2022] Open
Abstract
The discovery of microRNA (miRNA) sorting into extracellular vesicles (EVs) revealed a novel mode of intercellular communication and uncovered a link between cellular endomembrane compartments and small RNAs in EV-secreting cells. Using a two-step ultracentrifugation procedure to isolate EVs released by T cells, we found that 45% of tRNA fragments (tRFs), but fewer than 1% of miRNAs, were significantly enriched in EVs compared with the corresponding cellular RNA. T cell activation induced the EV-mediated release of a specific set of tRFs derived from the 5' end and 3'-internal region of tRNAs without variable loops. Inhibition of EV biogenesis pathways specifically led to the accumulation of these activation-induced EV-enriched tRFs within multivesicular bodies (MVBs). Introducing antisense oligonucleotides to inhibit these tRFs enhanced T cell activation. Taken together, these results demonstrate that T cells selectively release tRFs into EVs via MVBs and suggest that this process may remove tRFs that repress immune activation.
Collapse
Affiliation(s)
- Ni-Ting Chiou
- Sandler Asthma Basic Research Center and Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Robin Kageyama
- Sandler Asthma Basic Research Center and Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - K Mark Ansel
- Sandler Asthma Basic Research Center and Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
18
|
Computational Workflow for Small RNA Profiling in Virus-Infected Plants. Methods Mol Biol 2019; 2028:185-214. [PMID: 31228116 DOI: 10.1007/978-1-4939-9635-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
In this chapter we describe a series of computational pipelines for the in silico analysis of small RNAs (sRNA) produced in response to viral infections in plants. Our workflow is primarily focused on the analysis of sRNA populations derived from known or previously undescribed viruses infecting host plants. Furthermore, we provide an additional pipeline to examine host-specific endogenous sRNAs activated or specifically expressed during viral infections in plants. We present some key points for a successful and cost-efficient processing of next generation sequencing sRNA libraries, from purification of high quality RNA to guidance for library preparation and sequencing strategies. We report a series of free available tools and programs as well as in-house Perl scripts to perform customized sRNA-seq data mining. Previous bioinformatic background is not required, but experience with basic Unix commands is desirable.
Collapse
|
19
|
Meningher T, Boleslavsky D, Barshack I, Tabibian-Keissar H, Kohen R, Gur-Wahnon D, Ben-Dov IZ, Sidi Y, Avni D, Schwartz E. Giardia lamblia miRNAs as a new diagnostic tool for human giardiasis. PLoS Negl Trop Dis 2019; 13:e0007398. [PMID: 31206518 PMCID: PMC6597124 DOI: 10.1371/journal.pntd.0007398] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 06/27/2019] [Accepted: 04/16/2019] [Indexed: 01/15/2023] Open
Abstract
Background Giardia lamblia is a very common cause of gastrointestinal symptoms worldwide. There are several methods for the diagnosis of Giardia infection, however none are ideal. We aim to find a new, microRNA-based method that will improve the currently available diagnostic methods for giardiasis. Methods Deep-sequence profiling of Giardia small-RNA revealed that miR5 and miR6 are highly expressed in Giardia. These miRNAs were tested by qRT-PCR in duodenal biopsies of patients with giardiasis who were positive by microscopic pathological evaluation. The gastric biopsies of the same patients served as negative control tissues. Additionally, these miRNAs were evaluated in stool samples of patients with proven giardiasis. Results All histologically proven duodenal biopsies of patients with Giardia infection were positive for Giardia miR5, with a mean threshold cycle (Ct) of 23.7, as well as for Giardia DNA qPCR (16S-like gene, mean Ct 26.3). Gastric biopsies which were tested as a control all were negative. Stool evaluation of miR6 in patients with giardiasis showed 90% specificity but only 66% sensitivity, and a lower accuracy rate was obtained with miR5. Conclusion Giardia miR5 testing in duodenal biopsies may be a new method for the diagnosis of giardiasis. It seems to be more sensitive when compared with testing for Giardia DNA by qPCR in duodenal biopsies. It will be important to investigate the contribution of routine Giardia miRNA testing in duodenal biopsies from patients with persistent abdominal symptoms Giardiasis is a major cause of diarrheal disease throughout the world. It is more common in areas with poor sanitation such as in many low-income countries, but it occurs in high-income countries as well. It is the most commonly identified intestinal parasite in the United States and it is endemic in other industrialized countries. The causative agent is the flagellate protozoan Giardia lamblia, and transmission is mainly by the fecal-oral route. The basic method of diagnosis is stool examination. It is usually found through stool microscopy examination which should be performed on fresh stool and repeated in 3 days. Despite some newer diagnostic methods, Giardia is still difficult to detect, often leading to misdiagnoses. In this study we show that using Giardia microRNA (miR5) as a marker for Giardia infection in duodenal biopsies may be a new method for diagnosis of giardiasis. It appears to be more sensitive than histological diagnosis and also more sensitive than Giardia DNA testing in duodenal biopsies. Interestingly, in our patients, duodenal biopsies were done for persistent abdominal symptoms and the finding of Giardia in their biopsy was unexpected. Thus, testing duodenal biopsies for Giardia miRNA in patients with persistent abdominal symptoms might contribute to diagnosis and prompt treatment for those with giardiasis.
Collapse
Affiliation(s)
- Tal Meningher
- Laboratory of Molecular Cell Biology, Sheba Medical Center, Ramat Gan, Israel
- Department of Medicine C, Sheba Medical Center, Ramat Gan, Israel
- Molecular Laboratory for the Study of Tropical Diseases, Sheba Medical Center, Ramat Gan, Israel
| | | | - Iris Barshack
- Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hila Tabibian-Keissar
- Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Refael Kohen
- Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Devorah Gur-Wahnon
- Laboratory of Medical Transcriptomics, Nephrology and Hypertension Services, Hadassah—Hebrew University Medical Center, Jerusalem, Israel
| | - Iddo Z. Ben-Dov
- Laboratory of Medical Transcriptomics, Nephrology and Hypertension Services, Hadassah—Hebrew University Medical Center, Jerusalem, Israel
| | - Yechezkel Sidi
- Laboratory of Molecular Cell Biology, Sheba Medical Center, Ramat Gan, Israel
- Department of Medicine C, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dror Avni
- Laboratory of Molecular Cell Biology, Sheba Medical Center, Ramat Gan, Israel
- Department of Medicine C, Sheba Medical Center, Ramat Gan, Israel
- Molecular Laboratory for the Study of Tropical Diseases, Sheba Medical Center, Ramat Gan, Israel
- * E-mail: , (DA); (ES)
| | - Eli Schwartz
- Molecular Laboratory for the Study of Tropical Diseases, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Center for Geographic Medicine, Sheba Medical Center, Ramat Gan, Israel
- * E-mail: , (DA); (ES)
| |
Collapse
|
20
|
Muys BR, Sousa JF, Plaça JR, de Araújo LF, Sarshad AA, Anastasakis DG, Wang X, Li XL, de Molfetta GA, Ramão A, Lal A, Vidal DO, Hafner M, Silva WA. miR-450a Acts as a Tumor Suppressor in Ovarian Cancer by Regulating Energy Metabolism. Cancer Res 2019; 79:3294-3305. [PMID: 31101765 DOI: 10.1158/0008-5472.can-19-0490] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/12/2019] [Accepted: 05/13/2019] [Indexed: 01/17/2023]
Abstract
Dysregulation of miRNA expression is associated with multiple diseases, including cancers, in which small RNAs can have either oncogenic or tumor suppressive functions. Here we investigated the potential tumor suppressive function of miR-450a, one of the most significantly downregulated miRNAs in ovarian cancer. RNA-seq analysis of the ovarian cancer cell line A2780 revealed that overexpression of miR-450a suppressed multiple genes involved in the epithelial-to-mesenchymal transition (EMT). Overexpression of miR-450a reduced tumor migration and invasion and increased anoikis in A2780 and SKOV-3 cell lines and reduced tumor growth in an ovarian tumor xenographic model. Combined AGO-PAR-CLIP and RNA-seq analysis identified a panel of potential miR-450a targets, of which many, including TIMMDC1, MT-ND2, ACO2, and ATP5B, regulate energetic metabolism. Following glutamine withdrawal, miR-450a overexpression decreased mitochondrial membrane potential but increased glucose uptake and viability, characteristics of less invasive ovarian cancer cell lines. In summary, we propose that miR-450a acts as a tumor suppressor in ovarian cancer cells by modulating targets associated with glutaminolysis, which leads to decreased production of lipids, amino acids, and nucleic acids, as well as inhibition of signaling pathways associated with EMT. SIGNIFICANCE: miR-450a limits the metastatic potential of ovarian cancer cells by targeting a set of mitochondrial mRNAs to reduce glycolysis and glutaminolysis.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/13/3294/F1.large.jpg.
Collapse
Affiliation(s)
- Bruna Rodrigues Muys
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil.,Center for Medical Genomics (HCFMRP/USP), Center for Integrative Systems Biology (CISBi-NAP/USP), Ribeirão Preto, Brazil.,Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, Maryland.,Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Josane F Sousa
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil.,Center for Medical Genomics (HCFMRP/USP), Center for Integrative Systems Biology (CISBi-NAP/USP), Ribeirão Preto, Brazil.,Genetics and Molecular Biology Program, Institute of Biological Sciences, Federal University of Para-UFPA, Belem, Brazil
| | - Jessica Rodrigues Plaça
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil.,Center for Medical Genomics (HCFMRP/USP), Center for Integrative Systems Biology (CISBi-NAP/USP), Ribeirão Preto, Brazil
| | - Luíza Ferreira de Araújo
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil.,Center for Medical Genomics (HCFMRP/USP), Center for Integrative Systems Biology (CISBi-NAP/USP), Ribeirão Preto, Brazil.,Medical Genomics Laboratory, AC Camargo Cancer Center, São Paulo, Brazil
| | - Aishe A Sarshad
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, Maryland
| | - Dimitrios G Anastasakis
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, Maryland
| | - Xiantao Wang
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, Maryland
| | - Xiao Ling Li
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Greice Andreotti de Molfetta
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil.,Center for Medical Genomics (HCFMRP/USP), Center for Integrative Systems Biology (CISBi-NAP/USP), Ribeirão Preto, Brazil
| | - Anelisa Ramão
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Daniel Onofre Vidal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, Maryland.
| | - Wilson A Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil. .,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil.,Center for Medical Genomics (HCFMRP/USP), Center for Integrative Systems Biology (CISBi-NAP/USP), Ribeirão Preto, Brazil
| |
Collapse
|
21
|
Akat KM, Lee YA, Hurley A, Morozov P, Max KE, Brown M, Bogardus K, Sopeyin A, Hildner K, Diacovo TG, Neurath MF, Borggrefe M, Tuschl T. Detection of circulating extracellular mRNAs by modified small-RNA-sequencing analysis. JCI Insight 2019; 5:127317. [PMID: 30973829 DOI: 10.1172/jci.insight.127317] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Extracellular mRNAs (ex-mRNAs) potentially supersede extracellular miRNAs (ex-miRNAs) and other RNA classes as biomarkers. We performed conventional small-RNA-sequencing (sRNA-seq) and sRNA-seq with T4 polynucleotide kinase (PNK) end-treatment of total exRNA isolated from serum and platelet-poor EDTA, ACD, and heparin plasma to study the effect on ex-mRNA capture. Compared to conventional sRNA-seq PNK-treatment increased the detection of informative ex-mRNAs reads up to 50-fold. The exRNA pool was dominated by hematopoietic cells and platelets, with additional contribution from the liver. About 60% of the 15- to 42-nt reads originated from the coding sequences, in a pattern reminiscent of ribosome-profiling. Blood sample type had a considerable influence on the exRNA profile. On average approximately 350 to 1,100 distinct ex-mRNA transcripts were detected depending on plasma type. In serum, additional transcripts from neutrophils and hematopoietic cells increased this number to near 2,300. EDTA and ACD plasma showed a destabilizing effect on ex mRNA and non-coding RNA ribonucleoprotein complexes compared to other plasma types. In a proof-of-concept study, we investigated differences between the exRNA profiles of patients with acute coronary syndrome (ACS) and healthy controls. The improved tissue resolution of ex mRNAs after PNK-treatment enabled us to detect a neutrophil-signature in ACS that escaped detection by ex miRNA analysis.
Collapse
Affiliation(s)
| | | | - Arlene Hurley
- Center for Translational Science, The Rockefeller University, New York, New York, USA
| | | | | | | | | | | | - Kai Hildner
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Kussmaul Campus for Medical Research, Erlangen, Bavaria, Germany
| | - Thomas G Diacovo
- Departments of Pediatrics and Cell Biology and Pathology, Columbia University Medical Center, New York, New York, USA
| | - Markus F Neurath
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Kussmaul Campus for Medical Research, Erlangen, Bavaria, Germany
| | - Martin Borggrefe
- First Department of Medicine, University Medical Center Mannheim, Faculty of Medicine Mannheim, University of Heidelberg, European Center for AngioScience, and DZHK (German Center for Cardiovascular Research), partner site Heidelberg/Mannheim, Mannheim, Baden-Wuerttemberg, Germany
| | | |
Collapse
|
22
|
Rohan TE, Wang T, Weinmann S, Wang Y, Lin J, Ginsberg M, Loudig O. A miRNA Expression Signature in Breast Tumor Tissue Is Associated with Risk of Distant Metastasis. Cancer Res 2019; 79:1705-1713. [PMID: 30760517 DOI: 10.1158/0008-5472.can-18-2779] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/17/2018] [Accepted: 02/06/2019] [Indexed: 11/16/2022]
Abstract
Dysregulation of miRNA expression may influence breast cancer progression, and experimental evidence suggests that miRNA silencing might suppress breast cancer metastasis. However, the relationship between miRNA and metastasis must be confirmed before this approach can be applied in the clinic. To this end, we conducted a two-stage study in a cohort of 3,760 patients with breast cancer to first identify and then validate the association between miRNA expression and risk of distant metastasis. The first stage (discovery) entailed miRNA sequencing of 126 case-control pairs; qPCR was used to validate the findings in a separate set of 80 case-control pairs. The 13 miRNAs most differentially expressed between cases and controls were combined into an miRNA score that was significantly associated with risk of distant metastasis in a logistic regression model that also included clinical variables (tumor size and number of positive lymph nodes) (ORper unit increase in score = 1.30; 95% confidence interval, 1.03-1.66). The results of this study suggest that in women with invasive breast cancer, a miRNA score that incorporates both clinical variables and miRNA expression levels in breast tumor tissue is moderately predictive of risk of subsequent distant metastasis. SIGNIFICANCE: A novel predictive scoring system for patients with breast cancer includes clinical variables and the expression levels of 13 miRNAs and may help to identify those at increased risk of distant metastasis.
Collapse
Affiliation(s)
- Thomas E Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York.
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Sheila Weinmann
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon
| | - Yihong Wang
- Department of Pathology and Laboratory of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Juan Lin
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Mindy Ginsberg
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Olivier Loudig
- Hackensack University Medical Center, Hackensack, New Jersey
| |
Collapse
|
23
|
Panarelli N, Tyryshkin K, Wong JJM, Majewski A, Yang X, Scognamiglio T, Kim MK, Bogardus K, Tuschl T, Chen YT, Renwick N. Evaluating gastroenteropancreatic neuroendocrine tumors through microRNA sequencing. Endocr Relat Cancer 2019; 26:47-57. [PMID: 30021866 DOI: 10.1530/erc-18-0244] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 12/27/2022]
Abstract
Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) can be challenging to evaluate histologically. MicroRNAs (miRNAs) are small RNA molecules that often are excellent biomarkers due to their abundance, cell-type and disease stage specificity and stability. To evaluate miRNAs as adjunct tissue markers for classifying and grading well-differentiated GEP-NETs, we generated and compared miRNA expression profiles from four pathological types of GEP-NETs. Using quantitative barcoded small RNA sequencing and state-of-the-art sequence annotation, we generated comprehensive miRNA expression profiles from archived pancreatic, ileal, appendiceal and rectal NETs. Following data preprocessing, we randomly assigned sample profiles to discovery (80%) and validation (20%) sets prior to data mining using machine-learning techniques. High expression analyses indicated that miR-375 was the most abundant individual miRNA and miRNA cistron in all samples. Leveraging prior knowledge that GEP-NET behavior is influenced by embryonic derivation, we developed a dual-layer hierarchical classifier for differentiating GEP-NET types. In the first layer, our classifier discriminated midgut (ileum, appendix) from non-midgut (rectum, pancreas) NETs based on miR-615 and -92b expression. In the second layer, our classifier discriminated ileal from appendiceal NETs based on miR-125b, -192 and -149 expression, and rectal from pancreatic NETs based on miR-429 and -487b expression. Our classifier achieved overall accuracies of 98.5% and 94.4% in discovery and validation sets, respectively. We also found provisional evidence that low- and intermediate-grade pancreatic NETs can be discriminated based on miR-328 expression. GEP-NETs can be reliably classified and potentially graded using a limited panel of miRNA markers, complementing morphological and immunohistochemistry-based approaches to histologic evaluation.
Collapse
Affiliation(s)
- Nicole Panarelli
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Kathrin Tyryshkin
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Justin Jong Mun Wong
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Adrianna Majewski
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Xiaojing Yang
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Theresa Scognamiglio
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Michelle Kang Kim
- Center for Carcinoid and Neuroendocrine Tumors of Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kimberly Bogardus
- HHMI, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York, USA
| | - Thomas Tuschl
- HHMI, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York, USA
| | - Yao-Tseng Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Neil Renwick
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- HHMI, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York, USA
| |
Collapse
|
24
|
Mazeh H, Deutch T, Karas A, Bogardus KA, Mizrahi I, Gur-Wahnon D, Ben-Dov IZ. Next-Generation Sequencing Identifies a Highly Accurate miRNA Panel That Distinguishes Well-Differentiated Thyroid Cancer from Benign Thyroid Nodules. Cancer Epidemiol Biomarkers Prev 2018; 27:858-863. [PMID: 30049841 DOI: 10.1158/1055-9965.epi-18-0055] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/19/2018] [Accepted: 05/09/2018] [Indexed: 01/04/2023] Open
Abstract
Background: Fine needle aspiration biopsy (FNAB) is the gold-standard procedure for diagnosing malignant thyroid nodules. Indeterminate cytology is identified in 10% to 40% of cases, and molecular testing may guide management in this setting. Current commercial options are expensive, and are either sensitive or specific. The aim of this study was to utilize next-generation sequencing (NGS) technology to identify informative diversities in the miRNA expression profile of benign versus malignant thyroid nodules.Methods:Ex vivo FNAB samples were obtained from thyroid specimens of patients who underwent thyroidectomy at a referral center. miRNA levels were determined using NGS and multiplexing technologies. Statistical analyses identified differences between normal and malignant samples and miRNA expression profiles that associate with malignancy were established. The accuracy of the miRNA signature in predicting histologic malignancy was validated using a group of patient specimens with indeterminate cytology results.Results: A total of 274 samples were obtained from 102 patients undergoing thyroidectomy. Of these samples, 71% were benign and 29% were malignant. Nineteen miRNAs were identified as statistically different between benign and malignant samples and were used to classify 35 additional nodules with indeterminate cytology (validation). The miRNA panel's sensitivity, specificity, negative and positive predictive values, and overall accuracy were 91%, 100%, 87%, 100%, and 94%, respectively.Conclusions: Using NGS technology, we identified a panel of 19 miRNAs that may be utilized to distinguish benign from malignant thyroid nodules with indeterminate cytology.Impact: Our panel may classify indeterminate thyroid nodules at higher accuracy than commercially available molecular tests. Cancer Epidemiol Biomarkers Prev; 27(8); 858-63. ©2018 AACR.
Collapse
Affiliation(s)
- Haggi Mazeh
- Department of Surgery, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Tova Deutch
- Laboratory of Medical Transcriptomics, Department of Nephrology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Adi Karas
- Department of Surgery, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Kimberly A Bogardus
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York
| | - Ido Mizrahi
- Department of Surgery, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Devorah Gur-Wahnon
- Laboratory of Medical Transcriptomics, Department of Nephrology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Iddo Z Ben-Dov
- Laboratory of Medical Transcriptomics, Department of Nephrology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.
| |
Collapse
|
25
|
Human plasma and serum extracellular small RNA reference profiles and their clinical utility. Proc Natl Acad Sci U S A 2018; 115:E5334-E5343. [PMID: 29777089 PMCID: PMC6003356 DOI: 10.1073/pnas.1714397115] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nucleic acids mediate storage and expression of genetic information. Extracellular DNA (exDNA) and exRNA are traces of nucleic acids released from cells into the extracellular environment. Their use as disease biomarkers has been limited by technical challenges in their isolation caused by abundant RNA- and DNA-degrading enzymes in biofluids. Using isolation protocols developed especially for biofluids, we generated plasma and serum exRNA reference profiles from 13 healthy volunteers over time and determined the effect of critical clinical parameters such as gender and fasting. Surprisingly, we encountered one participant with dramatically increased endocrine-origin exRNA contributions stable over 1 year and detectable in all of his samples, thereby demonstrating the robustness of this approach and the clinical potential of circulating RNAs as biomarkers. Circulating extracellular RNAs (exRNAs) have the potential to serve as biomarkers for a wide range of medical conditions. However, limitations in existing exRNA isolation methods and a lack of knowledge on parameters affecting exRNA variability in human samples may hinder their successful discovery and clinical implementation. Using combinations of denaturants, reducing agents, proteolysis, and revised organic extraction, we developed an automated, high-throughput approach for recovery of exRNAs and exDNA from the same biofluid sample. We applied this method to characterize exRNAs from 312 plasma and serum samples collected from 13 healthy volunteers at 12 time points over a 2-month period. Small RNA cDNA library sequencing identified nearly twofold increased epithelial-, muscle-, and neuroendocrine-cell–specific miRNAs in females, while fasting and hormonal cycle showed little effect. External standardization helped to detect quantitative differences in erythrocyte and platelet-specific miRNA contributions and in miRNA concentrations between biofluids. It also helped to identify a study participant with a unique exRNA phenotype featuring a miRNA signature of up to 20-fold elevated endocrine-cell–specific miRNAs and twofold elevated total miRNA concentrations stable for over 1 year. Collectively, these results demonstrate an efficient and quantitative method to discern exRNA phenotypes and suggest that plasma and serum RNA profiles are stable over months and can be routinely monitored in long-term clinical studies.
Collapse
|
26
|
Mong EF, Akat KM, Canfield J, Lockhart J, VanWye J, Matar A, Tsibris JCM, Wu JK, Tuschl T, Totary-Jain H. Modulation of LIN28B/Let-7 Signaling by Propranolol Contributes to Infantile Hemangioma Involution. Arterioscler Thromb Vasc Biol 2018; 38:1321-1332. [PMID: 29724816 DOI: 10.1161/atvbaha.118.310908] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/18/2018] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Infantile hemangiomas (IHs) are the most common benign vascular neoplasms of infancy, characterized by a rapid growth phase followed by a spontaneous involution, or triggered by propranolol treatment by poorly understood mechanisms. LIN28/let-7 axis plays a central role in the regulation of stem cell self-renewal and tumorigenesis. However, the role of LIN28B/let-7 signaling in IH pathogenesis has not yet been elucidated. APPROACH AND RESULTS LIN28B is highly expressed in proliferative IH and is less expressed in involuted and in propranolol-treated IH samples as measured by immunofluorescence staining and quantitative RT-PCR. Small RNA sequencing analysis of IH samples revealed a decrease in microRNAs that target LIN28B, including let-7, and an increase in microRNAs in the mir-498(46) cistron. Overexpression of LIN28B in HEK293 cells induced the expression of miR-516b in the mir-498(46) cistron. Propranolol treatment of induced pluripotent stem cells, which express mir-498(46) endogenously, reduced the expression of both LIN28B and mir-498(46) and increased the expression of let-7. Furthermore, propranolol treatment reduced the proliferation of induced pluripotent stem cells and induced epithelial-mesenchymal transition. CONCLUSIONS This work uncovers the role of the LIN28B/let-7 switch in IH pathogenesis and provides a novel mechanism by which propranolol induces IH involution. Furthermore, it provides therapeutic implications for cancers in which the LIN28/let-7 pathway is imbalanced.
Collapse
Affiliation(s)
- Ezinne Francess Mong
- From the Department of Molecular Pharmacology and Physiology (E.F.M., J.C., J.L., J.V., A.M., H.T.-J.)
| | - Kemal Marc Akat
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, New York (K.M.A., T.T.)
| | - John Canfield
- From the Department of Molecular Pharmacology and Physiology (E.F.M., J.C., J.L., J.V., A.M., H.T.-J.)
| | - John Lockhart
- From the Department of Molecular Pharmacology and Physiology (E.F.M., J.C., J.L., J.V., A.M., H.T.-J.)
| | - Jeffrey VanWye
- From the Department of Molecular Pharmacology and Physiology (E.F.M., J.C., J.L., J.V., A.M., H.T.-J.)
| | - Andrew Matar
- From the Department of Molecular Pharmacology and Physiology (E.F.M., J.C., J.L., J.V., A.M., H.T.-J.)
| | - John C M Tsibris
- Department of Obstetrics and Gynecology (J.C.M.T.), Morsani College of Medicine, University of South Florida, Tampa
| | - June K Wu
- Department of Surgery, Columbia University College of Physicians and Surgeons, New York (J.K.W.)
| | - Thomas Tuschl
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, New York (K.M.A., T.T.)
| | - Hana Totary-Jain
- From the Department of Molecular Pharmacology and Physiology (E.F.M., J.C., J.L., J.V., A.M., H.T.-J.)
| |
Collapse
|
27
|
Abstract
MicroRNAs are a class of small noncoding RNAs that function as regulators involving in many biological processes. The evaluation of miRNAs and their targets has been aided by miRNA expression profiling studies including multiplex PCR, microarrays, and recent next-generation sequencing tools. Next-generation sequencing has enabled us to profile thousands of genes in a single experiment and overcome the background signal and cross-hybridization issues of microarrays. Next-generation sequencing also allows for the simultaneous confirmation of known miRNAs and discovery of new miRNAs, and significantly reduces costs while providing billions of nucleotide information within a single experiment. Here we describe a detailed procedure of generation of miRNA library for next-generation sequencing to increase the efficiency of adapter ligation and finally construct a more specific cDNA library for sequencing and analyses for miRNA expression profiling.
Collapse
Affiliation(s)
- Poching Liu
- DNA Sequencing and Genomics Core-NHLBI, National Institute of Health, Bethesda, MD, USA.
| |
Collapse
|
28
|
Geva GA, Gielchinsky I, Aviv N, Max KEA, Gofrit ON, Gur-Wahnon D, Ben-Dov IZ. Urine cell-free microRNA as biomarkers for transitional cell carcinoma. BMC Res Notes 2017; 10:641. [PMID: 29187235 PMCID: PMC5708087 DOI: 10.1186/s13104-017-2950-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/21/2017] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE MicroRNA (miRNA) are short nucleotide strands with a regulatory function in the cell. Several miRNAs have been shown to be useful as biomarkers for different neoplasms. The aim of this project was to assess whether levels of miRNA in cell free urine could be used as a biomarker in transitional cell carcinoma (TCC). RESULTS cDNA libraries were produced based on small RNAs in urine samples of fourteen TCC patients and twenty healthy volunteers. Resulting reads were deep sequenced on Illumina HiSeq sequencer with the intent of characterizing cell free urine miRNA profiles. A statistically significant difference was found for a single miRNA; miR-210 was > sixfold higher in the TCC group compared to the control group. Furthermore, we were able to produce a diagnostic score by summing of standardized levels of overexpressed miRNA. This score was considerably higher in TCC patients with a sensitivity of 0.93, specificity of 0.76 and negative predictive value > 0.97.
Collapse
Affiliation(s)
- Gil A. Geva
- Nephrology and Hypertension, Hadassah-Hebrew University Medical Center, POB 12000, 91120 Jerusalem, Israel
| | - Ilan Gielchinsky
- Department of Urology, Hadassah-Hebrew University Medical Center, POB 12000, 91120 Jerusalem, Israel
| | - Nina Aviv
- Nephrology and Hypertension, Hadassah-Hebrew University Medical Center, POB 12000, 91120 Jerusalem, Israel
| | - Klaas E. A. Max
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065 USA
| | - Ofer N. Gofrit
- Department of Urology, Hadassah-Hebrew University Medical Center, POB 12000, 91120 Jerusalem, Israel
| | - Devorah Gur-Wahnon
- Nephrology and Hypertension, Hadassah-Hebrew University Medical Center, POB 12000, 91120 Jerusalem, Israel
| | - Iddo Z. Ben-Dov
- Nephrology and Hypertension, Hadassah-Hebrew University Medical Center, POB 12000, 91120 Jerusalem, Israel
| |
Collapse
|
29
|
Plasma microRNA profiling: Exploring better biomarkers for lymphoma surveillance. PLoS One 2017; 12:e0187722. [PMID: 29131834 PMCID: PMC5683633 DOI: 10.1371/journal.pone.0187722] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 10/24/2017] [Indexed: 12/14/2022] Open
Abstract
Early detection of relapsed lymphoma improves response and survival. Current tools lack power for detection of early relapse, while being cumbersome and expensive. We searched for sensitive biomarkers that precede clinical relapse, and serve for further studies on therapy response and relapse. We recruited 20 healthy adults, 14 diffuse large B-cell lymphoma (DLBCL) patients and 11 Hodgkin lymphoma (HL) patients at diagnosis. Using small-RNA sequencing we identified in DLBCL patients increased plasma levels of miR-124 and miR-532-5p, and decreased levels of miR-425, miR-141, miR-145, miR-197, miR-345, miR-424, miR-128 and miR-122. In the HL group, we identified miR-25, miR-30a/d, miR-26b, miR-182, miR-186, miR-140* and miR-125a to be up-regulated, while miR-23a, miR-122, miR-93 and miR-144 were down-regulated. Pathway analysis of potential mRNAs targets of these miRNA revealed in the DLBCL group potential up-regulation of STAT3, IL8, p13k/AKT and TGF-B signaling, and potential down-regulation of the PTEN and p53 pathways; while in the HL group we have found the cAMP-mediated pathway and p53 pathway to be potentially down-regulated. Survival analyses revealed that plasma levels of miR-20a/b, miR-93 and miR-106a/b were associated with higher mortality. In conclusion, we identified sets of dysregulated circulating miRNA that might serve as reliable biomarkers for relapsed lymphoma.
Collapse
|
30
|
Mizrahi A, Barzilai A, Gur-Wahnon D, Ben-Dov IZ, Glassberg S, Meningher T, Elharar E, Masalha M, Jacob-Hirsch J, Tabibian-Keissar H, Barshack I, Roszik J, Leibowitz-Amit R, Sidi Y, Avni D. Alterations of microRNAs throughout the malignant evolution of cutaneous squamous cell carcinoma: the role of miR-497 in epithelial to mesenchymal transition of keratinocytes. Oncogene 2017; 37:218-230. [PMID: 28925390 DOI: 10.1038/onc.2017.315] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 07/05/2017] [Accepted: 07/31/2017] [Indexed: 12/18/2022]
Abstract
Skin carcinogenesis is known to be a multi-step process with several stages along its malignant evolution. We hypothesized that transformation of normal epidermis to cutaneous squamous cell carcinoma (cSCC) is causally linked to alterations in microRNAs (miRNA) expression. For this end we decided to evaluate their alterations in the pathologic states ending in cSCC. Total RNA was extracted from formalin fixed paraffin embedded biopsies of five stages along the malignant evolution of keratinocytes towards cSCC: Normal epidermis, solar elastosis, actinic keratosis KIN1-2, advanced actinic keratosis KIN3 and well-differentiated cSCC. Next-generation small RNA sequencing was performed. We found that 18 miRNAs are overexpressed and 28 miRNAs are underexpressed in cSCC compared to normal epidermis. miR-424, miR-320, miR-222 and miR-15a showed the highest fold change among the overexpressed miRNAs. And miR-100, miR-101 and miR-497 showed the highest fold change among the underexpressed miRNAs. Heat map of hierarchical clustering analysis of significantly changed miRNAs and principle component analysis disclosed that the most prominent change in miRNAs expression occurred in the switch from 'early' stages; normal epidermis, solar elastosis and early actinic keratosis to the 'late' stages of epidermal carcinogenesis; late actinic keratosis and cSCC. We found several miRNAs with 'stage specific' alterations while others display a clear 'gradual', either progressive increase or decrease in expression along the malignant evolution of keratinocytes. The observed alterations focused in miRNAs involved in the regulation of AKT/mTOR or in those involved in epithelial to mesenchymal transition. We chose to concentrate on the evaluation of the molecular role of miR-497. We found that it induces reversion of epithelial to mesenchymal transition. We proved that SERPINE-1 is its biochemical target. The present study allows us to further study the pathways that are regulated by miRNAs along the malignant evolution of keratinocytes towards cSCC.
Collapse
Affiliation(s)
- A Mizrahi
- Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashomer, Israel
| | - A Barzilai
- Department of Dermatology and Institute of Pathology, Sheba Medical Center, Tel Hashomer, Israel
| | - D Gur-Wahnon
- Laboratory of Medical Transcriptomics, Nephrology and Hypertension Services, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - I Z Ben-Dov
- Laboratory of Medical Transcriptomics, Nephrology and Hypertension Services, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - S Glassberg
- Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashomer, Israel
| | - T Meningher
- Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashomer, Israel
| | - E Elharar
- Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashomer, Israel
| | - M Masalha
- Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashomer, Israel.,Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - J Jacob-Hirsch
- Center for Cancer Research, Sheba Medical Center, Tel Hashomer, Israel
| | - H Tabibian-Keissar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.,Department of Pathology, Sheba Medical Center, Tel Hashomer, Israel
| | - I Barshack
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Pathology, Sheba Medical Center, Tel Hashomer, Israel
| | - J Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - R Leibowitz-Amit
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Institute of Oncology, Sheba Medical Center, Tel Hashomer, Israel
| | - Y Sidi
- Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashomer, Israel.,Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - D Avni
- Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashomer, Israel
| |
Collapse
|
31
|
Manasa VG, Kannan S. Impact of microRNA dynamics on cancer hallmarks: An oral cancer scenario. Tumour Biol 2017; 39:1010428317695920. [PMID: 28347239 DOI: 10.1177/1010428317695920] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
MicroRNAs are endogenous small noncoding RNAs that negatively regulate gene expression at posttranscriptional level. The discovery of microRNAs has identified a new layer of gene regulation mechanisms, which play a pivotal role in development as well as in various cellular processes, such as proliferation, differentiation, cell growth, and cell death. Deregulated microRNA expression favors acquisition of cancer hallmark traits as well as transforms the tumor microenvironment, leading to tumor development and progression. Many recent studies have revealed altered expression of microRNAs in oral carcinoma with several microRNAs shown to have key biological role in tumorigenesis functioning either as tumor suppressors or as tumor promoters. MicroRNA expression levels correlate with clinicopathological variables and have a diagnostic and prognostic value in oral carcinoma. For these reasons, microRNA has been a hot topic in oral cancer research for the last few years. In this review, we attempt to summarize the present understanding of microRNA deregulation in oral carcinoma, their role in acquiring cancer hallmarks, and their potential diagnostic and prognostic value for oral cancer management.
Collapse
Affiliation(s)
- V G Manasa
- Laboratory of Cell Cycle Regulation and Molecular Oncology, Division of Cancer Research, Regional Cancer Centre, Thiruvananthapuram, India
| | - S Kannan
- Laboratory of Cell Cycle Regulation and Molecular Oncology, Division of Cancer Research, Regional Cancer Centre, Thiruvananthapuram, India
| |
Collapse
|
32
|
Rotem N, Magen I, Ionescu A, Gershoni-Emek N, Altman T, Costa CJ, Gradus T, Pasmanik-Chor M, Willis DE, Ben-Dov IZ, Hornstein E, Perlson E. ALS Along the Axons - Expression of Coding and Noncoding RNA Differs in Axons of ALS models. Sci Rep 2017; 7:44500. [PMID: 28300211 PMCID: PMC5353576 DOI: 10.1038/srep44500] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/08/2017] [Indexed: 12/18/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a multifactorial lethal motor neuron disease with no known treatment. Although the basic mechanism of its degenerative pathogenesis remains poorly understood, a subcellular spatial alteration in RNA metabolism is thought to play a key role. The nature of these RNAs remains elusive, and a comprehensive characterization of the axonal RNAs involved in maintaining neuronal health has yet to be described. Here, using cultured spinal cord (SC) neurons grown using a compartmented platform followed by next-generation sequencing (NGS) technology, we find that RNA expression differs between the somatic and axonal compartments of the neuron, for both mRNA and microRNA (miRNA). Further, the introduction of SOD1G93A and TDP43A315T, established ALS-related mutations, changed the subcellular expression and localization of RNAs within the neurons, showing a spatial specificity to either the soma or the axon. Altogether, we provide here the first combined inclusive profile of mRNA and miRNA expression in two ALS models at the subcellular level. These data provide an important resource for studies on the roles of local protein synthesis and axon degeneration in ALS and can serve as a possible target pool for ALS treatment.
Collapse
Affiliation(s)
- Nimrod Rotem
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and the Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Iddo Magen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ariel Ionescu
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and the Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noga Gershoni-Emek
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and the Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Topaz Altman
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and the Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Christopher J Costa
- Brain and Mind Research Institute, Weill Cornell Medicine, Burke Medical Research Institute, White Plains, NY, USA
| | - Tal Gradus
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and the Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | | | - Dianna E Willis
- Brain and Mind Research Institute, Weill Cornell Medicine, Burke Medical Research Institute, White Plains, NY, USA
| | - Iddo Z Ben-Dov
- Department of Nephrology and Hypertension, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Perlson
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and the Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
33
|
Loudig O, Wang T, Ye K, Lin J, Wang Y, Ramnauth A, Liu C, Stark A, Chitale D, Greenlee R, Multerer D, Honda S, Daida Y, Spencer Feigelson H, Glass A, Couch FJ, Rohan T, Ben-Dov IZ. Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens. Int J Mol Sci 2017; 18:ijms18030627. [PMID: 28335433 PMCID: PMC5372640 DOI: 10.3390/ijms18030627] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/02/2017] [Accepted: 03/08/2017] [Indexed: 01/30/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years. We then evaluated this cDNA library preparation protocol by performing a miRNA expression analysis of archived breast ductal carcinoma in situ (DCIS) specimens, selected for their relation to the risk of subsequent breast cancer development and obtained from six different institutions. Our analyses identified six miRNAs (miR-29a, miR-221, miR-375, miR-184, miR-363, miR-455-5p) differentially expressed between DCIS lesions from women who subsequently developed an invasive breast cancer (cases) and women who did not develop invasive breast cancer within the same time interval (control). Our thorough evaluation and application of this laboratory-based miRNA sequencing analysis indicates that the preparation of small RNA cDNA libraries can reliably be performed on older, archived, clinically-classified specimens.
Collapse
Affiliation(s)
- Olivier Loudig
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Kenny Ye
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Juan Lin
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Yihong Wang
- Department of Pathology, Rhode Island Hospital, Providence, RI 02903, USA.
| | - Andrew Ramnauth
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Christina Liu
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Azadeh Stark
- Department of Pathology and Breast Oncology Program, Henry Ford Health System, Detroit, MI 48202, USA.
| | - Dhananjay Chitale
- Department of Pathology and Breast Oncology Program, Henry Ford Health System, Detroit, MI 48202, USA.
| | - Robert Greenlee
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA.
| | - Deborah Multerer
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA.
| | - Stacey Honda
- Department of Pathology, Center for Health Research, Kaiser Permanente, 3288 Moanalua Road, Honolulu, HI 96819, USA.
| | - Yihe Daida
- Department of Pathology, Center for Health Research, Kaiser Permanente, 3288 Moanalua Road, Honolulu, HI 96819, USA.
| | | | - Andrew Glass
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR 97227, USA.
| | - Fergus J Couch
- Health Sciences Research, Mayo Clinic, Rochester, NY 55902, USA.
| | - Thomas Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
- Montefiore Medical Center, Bronx, NY 10467, USA.
| | - Iddo Z Ben-Dov
- Laboratory of Medical Transcriptomics, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel.
| |
Collapse
|
34
|
Lee HW, Khan SQ, Khaliqdina S, Altintas MM, Grahammer F, Zhao JL, Koh KH, Tardi NJ, Faridi MH, Geraghty T, Cimbaluk DJ, Susztak K, Moita LF, Baltimore D, Tharaux PL, Huber TB, Kretzler M, Bitzer M, Reiser J, Gupta V. Absence of miR-146a in Podocytes Increases Risk of Diabetic Glomerulopathy via Up-regulation of ErbB4 and Notch-1. J Biol Chem 2016; 292:732-747. [PMID: 27913625 DOI: 10.1074/jbc.m116.753822] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/01/2016] [Indexed: 12/31/2022] Open
Abstract
Podocyte injury is an early event in diabetic kidney disease and is a hallmark of glomerulopathy. MicroRNA-146a (miR-146a) is highly expressed in many cell types under homeostatic conditions, and plays an important anti-inflammatory role in myeloid cells. However, its role in podocytes is unclear. Here, we show that miR-146a expression levels decrease in the glomeruli of patients with type 2 diabetes (T2D), which correlates with increased albuminuria and glomerular damage. miR-146a levels are also significantly reduced in the glomeruli of albuminuric BTBR ob/ob mice, indicating its significant role in maintaining podocyte health. miR-146a-deficient mice (miR-146a-/-) showed accelerated development of glomerulopathy and albuminuria upon streptozotocin (STZ)-induced hyperglycemia. The miR-146a targets, Notch-1 and ErbB4, were also significantly up-regulated in the glomeruli of diabetic patients and mice, suggesting induction of the downstream TGFβ signaling. Treatment with a pan-ErbB kinase inhibitor erlotinib with nanomolar activity against ErbB4 significantly suppressed diabetic glomerular injury and albuminuria in both WT and miR-146a-/- animals. Treatment of podocytes in vitro with TGF-β1 resulted in increased expression of Notch-1, ErbB4, pErbB4, and pEGFR, the heterodimerization partner of ErbB4, suggesting increased ErbB4/EGFR signaling. TGF-β1 also increased levels of inflammatory cytokine monocyte chemoattractant protein-1 (MCP-1) and MCP-1 induced protein-1 (MCPIP1), a suppressor of miR-146a, suggesting an autocrine loop. Inhibition of ErbB4/EGFR with erlotinib co-treatment of podocytes suppressed this signaling. Our findings suggest a novel role for miR-146a in protecting against diabetic glomerulopathy and podocyte injury. They also point to ErbB4/EGFR as a novel, druggable target for therapeutic intervention, especially because several pan-ErbB inhibitors are clinically available.
Collapse
Affiliation(s)
- Ha Won Lee
- From the Departments of Internal Medicine and
| | | | | | | | - Florian Grahammer
- the Department of Medicine IV, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Jimmy L Zhao
- the Department of Medicine, New York Presbyterian/Weill Cornell Medical Center, New York, New York 10065.,the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Kwi Hye Koh
- From the Departments of Internal Medicine and
| | | | | | | | - David J Cimbaluk
- Pathology, Rush University Medical Center, Chicago, Illinois 60612
| | - Katalin Susztak
- the Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Luis F Moita
- the Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - David Baltimore
- the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Pierre-Louis Tharaux
- the Paris Cardiovascular Centre (PARCC), Institut National de la Santé et de la Recherche Médicale (INSERM), 75015 Paris, France and the Université Paris Descartes, Sorbonne Paris Cité, 75270 Paris, France
| | - Tobias B Huber
- the Department of Medicine IV, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany.,the BIOSS Center for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,the FRIAS, Freiburg Institute for Advanced Studies and ZBSA-Center for Systems Biology, Albert-Ludwigs-University, 79104 Freiburg, Germany, and
| | - Matthias Kretzler
- the Division of Nephrology, University of Michigan, Ann Arbor, Michigan 48109
| | - Markus Bitzer
- the Division of Nephrology, University of Michigan, Ann Arbor, Michigan 48109
| | | | | |
Collapse
|
35
|
Basika T, Macchiaroli N, Cucher M, Espínola S, Kamenetzky L, Zaha A, Rosenzvit M, Ferreira HB. Identification and profiling of microRNAs in two developmental stages of the model cestode parasite Mesocestoides corti. Mol Biochem Parasitol 2016; 210:37-49. [DOI: 10.1016/j.molbiopara.2016.08.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 12/21/2022]
|
36
|
Abstract
miRNA-guided diagnostics is a powerful molecular approach for evaluating clinical samples through miRNA detection and/or visualization. To date, this approach has been successfully used to diagnose, manage, and/or monitor a wide range of neoplastic and non-neoplastic diseases. Despite the promise of miRNA-guided diagnostics, particularly in the field of minimally invasive biomarkers, several knowledge and practical issues confound or hinder translation into routine clinical practice including: miRNA sequence database errors, suboptimal RNA extraction methods, detection assay variability, a vast array of online resources for bioinformatic analyses, and non-standardized statistical analyses for miRNA clinical testing. In this review, we raise awareness of these issues and recommend research directions to help specialists in endocrinology and metabolism integrate miRNA testing into clinical decision-making.
Collapse
Affiliation(s)
- Dakota Gustafson
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Kathrin Tyryshkin
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Neil Renwick
- Laboratory of Translational RNA Biology, Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON K7L 3N6, Canada.
| |
Collapse
|
37
|
Ziemann M, Kaspi A, El-Osta A. Evaluation of microRNA alignment techniques. RNA (NEW YORK, N.Y.) 2016; 22:1120-38. [PMID: 27284164 PMCID: PMC4931105 DOI: 10.1261/rna.055509.115] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 05/04/2016] [Indexed: 05/26/2023]
Abstract
Genomic alignment of small RNA (smRNA) sequences such as microRNAs poses considerable challenges due to their short length (∼21 nucleotides [nt]) as well as the large size and complexity of plant and animal genomes. While several tools have been developed for high-throughput mapping of longer mRNA-seq reads (>30 nt), there are few that are specifically designed for mapping of smRNA reads including microRNAs. The accuracy of these mappers has not been systematically determined in the case of smRNA-seq. In addition, it is unknown whether these aligners accurately map smRNA reads containing sequence errors and polymorphisms. By using simulated read sets, we determine the alignment sensitivity and accuracy of 16 short-read mappers and quantify their robustness to mismatches, indels, and nontemplated nucleotide additions. These were explored in the context of a plant genome (Oryza sativa, ∼500 Mbp) and a mammalian genome (Homo sapiens, ∼3.1 Gbp). Analysis of simulated and real smRNA-seq data demonstrates that mapper selection impacts differential expression results and interpretation. These results will inform on best practice for smRNA mapping and enable more accurate smRNA detection and quantification of expression and RNA editing.
Collapse
Affiliation(s)
- Mark Ziemann
- Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, AustraliaEpigenomics Profiling Facility, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia
| | - Antony Kaspi
- Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, AustraliaEpigenomics Profiling Facility, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, AustraliaEpigenomics Profiling Facility, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia
| |
Collapse
|
38
|
Vaknin-Dembinsky A, Charbit H, Brill L, Abramsky O, Gur-Wahnon D, Ben-Dov IZ, Lavon I. Circulating microRNAs as biomarkers for rituximab therapy, in neuromyelitis optica (NMO). J Neuroinflammation 2016; 13:179. [PMID: 27393339 PMCID: PMC4939003 DOI: 10.1186/s12974-016-0648-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/29/2016] [Indexed: 12/23/2022] Open
Abstract
Background Neuromyelitis optica (NMO) is a chronic autoimmune disease of the central nervous system (CNS). The main immunological feature of the disease is the presence of autoantibodies to Aquaporin 4 (AQP4+), identified in about 82 % of cases. Currently, there are no reliable biomarkers for monitoring treatment response in patients with NMO. In an effort to identify biomarkers, we analyzed microRNAs (miRNAs) in the blood of rituximab-treated NMO patients before and after therapy. Methods Total RNA extracted from whole blood of nine rituximab-responsive NMO patients before and 6 months following treatment was subjected to small RNAseq analysis. The study included an additional group of seven untreated AQP4+ seropositive NMO patients and 15 healthy controls (HCs). Results Fourteen miRNAs were up regulated and 32 were downregulated significantly in the blood of NMO patients following effective therapy with rituximab (all p < 0.05). Furthermore, we show that expression of 17 miRNAs was significantly higher and of 25 miRNAs was significantly lower in untreated NMO patients compared with HCs (all p < 0.05). Following rituximab treatment, the expression levels of 10 of the 17 miRNAs that show increased expression in NMO reverted to the levels seen in HCs. Six of these “normalized” miRNAs are known as brain-specific/enriched miRNAs. Conclusions Specific miRNA signatures in whole blood of patients with NMO might serve as biomarkers for therapy response. Furthermore, monitoring the levels of brain-specific/enriched miRNAs in the blood might reflect the degree of disease activity in the CNS of inflammatory demyelinating disorders. Electronic supplementary material The online version of this article (doi:10.1186/s12974-016-0648-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Adi Vaknin-Dembinsky
- Department of Neurology, Multiple Sclerosis Center and Laboratory of Neuroimmunology, and the Agnes-Ginges Center for Neurogenetics, Hadassah Hebrew University Medical Center, Ein-Karem, Jerusalem, 91120, Israel.
| | - Hanna Charbit
- Department of Neurology, Multiple Sclerosis Center and Laboratory of Neuroimmunology, and the Agnes-Ginges Center for Neurogenetics, Hadassah Hebrew University Medical Center, Ein-Karem, Jerusalem, 91120, Israel
| | - Livnat Brill
- Department of Neurology, Multiple Sclerosis Center and Laboratory of Neuroimmunology, and the Agnes-Ginges Center for Neurogenetics, Hadassah Hebrew University Medical Center, Ein-Karem, Jerusalem, 91120, Israel
| | - Oded Abramsky
- Department of Neurology, Multiple Sclerosis Center and Laboratory of Neuroimmunology, and the Agnes-Ginges Center for Neurogenetics, Hadassah Hebrew University Medical Center, Ein-Karem, Jerusalem, 91120, Israel
| | - Devorah Gur-Wahnon
- Nephrology and Hypertension Services, Internal Medicine Wing, Hadassah Hebrew University Medical Center, Ein-Karem, Jerusalem, 91120, Israel
| | - Iddo Z Ben-Dov
- Nephrology and Hypertension Services, Internal Medicine Wing, Hadassah Hebrew University Medical Center, Ein-Karem, Jerusalem, 91120, Israel
| | - Iris Lavon
- Department of Neurology, Multiple Sclerosis Center and Laboratory of Neuroimmunology, and the Agnes-Ginges Center for Neurogenetics, Hadassah Hebrew University Medical Center, Ein-Karem, Jerusalem, 91120, Israel.,Department of Neurology, the Agnes-Ginges Center for Neurogenetics and Leslie and Michel Gaffin Center for Neuro-Oncology, Hadassah Hebrew University Medical Center, Ein-Karem, Jerusalem, 91120, Israel
| |
Collapse
|
39
|
Empirical insights into the stochasticity of small RNA sequencing. Sci Rep 2016; 6:24061. [PMID: 27052356 PMCID: PMC4823707 DOI: 10.1038/srep24061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/21/2016] [Indexed: 11/08/2022] Open
Abstract
The choice of stochasticity distribution for modeling the noise distribution is a fundamental assumption for the analysis of sequencing data and consequently is critical for the accurate assessment of biological heterogeneity and differential expression. The stochasticity of RNA sequencing has been assumed to follow Poisson distributions. We collected microRNA sequencing data and observed that its stochasticity is better approximated by gamma distributions, likely because of the stochastic nature of exponential PCR amplification. We validated our findings with two independent datasets, one for microRNA sequencing and another for RNA sequencing. Motivated by the gamma distributed stochasticity, we provided a simple method for the analysis of RNA sequencing data and showed its superiority to three existing methods for differential expression analysis using three data examples of technical replicate data and biological replicate data.
Collapse
|
40
|
Gulati N, Løvendorf MB, Zibert JR, Akat KM, Renwick N, Tuschl T, Krueger JG. Unique microRNAs appear at different times during the course of a delayed-type hypersensitivity reaction in human skin. Exp Dermatol 2015. [PMID: 26205579 DOI: 10.1111/exd.12813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Diphencyprone (DPCP) is a hapten that induces delayed-type hypersensitivity (DTH) reactions. MicroRNAs (miRNAs) are short non-coding RNAs that negatively regulate gene expression and have been implicated in various inflammatory skin diseases, but their role in DTH reactions is not well understood. We generated global miRNA expression profiles (using next-generation sequencing) of DPCP reactions in skin of seven healthy volunteers at 3, 14 and 120 days after challenge. Compared to placebo-treated sites, DPCP-challenged skin at 3 days (peak inflammation) had 127 miRNAs significantly deregulated. At 14 days (during resolution of inflammation), 43 miRNAs were deregulated and, at 120 days (when inflammation had completely resolved), six miRNAs were upregulated. While some miRNAs have been observed in psoriasis or atopic dermatitis, most of the deregulated miRNAs have not yet been studied in the context of skin biology or immunology. Across the three time points studied, many but not all miRNAs were uniquely expressed. As various miRNAs may influence T cell activation, this may indicate that the miRNAs exclusively expressed at different time points function to promote or resolve skin inflammation, and therefore, may inform on the paradoxical ability of DPCP to treat both autoimmune conditions (alopecia areata) and conditions of ineffective immunity (melanoma).
Collapse
Affiliation(s)
- Nicholas Gulati
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY, USA
| | - Marianne B Løvendorf
- LEO Pharma A/S, Ballerup, Denmark.,Department of Dermato-Allergology, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | | | - Kemal M Akat
- HHMI Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Neil Renwick
- HHMI Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Thomas Tuschl
- HHMI Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - James G Krueger
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY, USA
| |
Collapse
|
41
|
Shilo V, Ben-Dov IZ, Nechama M, Silver J, Naveh-Many T. Parathyroid-specific deletion of dicer-dependent microRNAs abrogates the response of the parathyroid to acute and chronic hypocalcemia and uremia. FASEB J 2015; 29:3964-76. [PMID: 26054367 DOI: 10.1096/fj.15-274191] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/26/2015] [Indexed: 11/11/2022]
Abstract
MicroRNAs (miRNAs) down-regulate gene expression and have vital roles in biology but their functions in the parathyroid are unexplored. To study this, we generated parathyroid-specific Dicer1 knockout (PT-Dicer(-/-) ) mice where parathyroid miRNA maturation is blocked. Remarkably, the PT-Dicer(-/-) mice did not increase serum parathyroid hormone (PTH) in response to acute hypocalcemia compared with the >5-fold increase in controls. PT-Dicer(-/-) glands cultured in low-calcium medium secreted 5-fold less PTH at 1.5 h than controls. Chronic hypocalcemia increased serum PTH >4-fold less in PT-Dicer(-/-) mice compared with control mice with no increase in PTH mRNA levels and parathyroid cell proliferation compared with the 2- to 3-fold increase in hypocalcemic controls. Moreover, uremic PT-Dicer(-/-) mice increased serum PTH and FGF23 significantly less than uremic controls. Therefore, stimulation of the parathyroid by both hypocalcemia and uremia is dependent upon intact dicer function and miRNAs. In contrast, the PT-Dicer(-/-) mice responded normally to activation of the parathyroid calcium-sensing receptor (Casr) by both hypercalcemia and a calcimimetic that decreases PTH secretion, demonstrating that they are dicer-independent. Therefore, miRNAs are essential for the response of the parathyroid to both acute and chronic hypocalcemia and uremia, the major stimuli for PTH secretion.
Collapse
Affiliation(s)
- Vitali Shilo
- *Minerva Center for Calcium and Bone Metabolism, Nephrology Services, Hadassah Hebrew University Medical Center, Jerusalem, Israel; and Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Iddo Z Ben-Dov
- *Minerva Center for Calcium and Bone Metabolism, Nephrology Services, Hadassah Hebrew University Medical Center, Jerusalem, Israel; and Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Morris Nechama
- *Minerva Center for Calcium and Bone Metabolism, Nephrology Services, Hadassah Hebrew University Medical Center, Jerusalem, Israel; and Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Justin Silver
- *Minerva Center for Calcium and Bone Metabolism, Nephrology Services, Hadassah Hebrew University Medical Center, Jerusalem, Israel; and Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Tally Naveh-Many
- *Minerva Center for Calcium and Bone Metabolism, Nephrology Services, Hadassah Hebrew University Medical Center, Jerusalem, Israel; and Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| |
Collapse
|
42
|
Tam S, Tsao MS, McPherson JD. Optimization of miRNA-seq data preprocessing. Brief Bioinform 2015; 16:950-63. [PMID: 25888698 PMCID: PMC4652620 DOI: 10.1093/bib/bbv019] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Indexed: 12/05/2022] Open
Abstract
The past two decades of microRNA (miRNA) research has solidified the role of these small non-coding RNAs as key regulators of many biological processes and promising biomarkers for disease. The concurrent development in high-throughput profiling technology has further advanced our understanding of the impact of their dysregulation on a global scale. Currently, next-generation sequencing is the platform of choice for the discovery and quantification of miRNAs. Despite this, there is no clear consensus on how the data should be preprocessed before conducting downstream analyses. Often overlooked, data preprocessing is an essential step in data analysis: the presence of unreliable features and noise can affect the conclusions drawn from downstream analyses. Using a spike-in dilution study, we evaluated the effects of several general-purpose aligners (BWA, Bowtie, Bowtie 2 and Novoalign), and normalization methods (counts-per-million, total count scaling, upper quartile scaling, Trimmed Mean of M, DESeq, linear regression, cyclic loess and quantile) with respect to the final miRNA count data distribution, variance, bias and accuracy of differential expression analysis. We make practical recommendations on the optimal preprocessing methods for the extraction and interpretation of miRNA count data from small RNA-sequencing experiments.
Collapse
|
43
|
Abstract
In recent years, there has been a tremendous and growing interest among researchers to investigate the role of mircoRNA (miRNA) in normal cellular as well as in disease processes. miRNAs are a family of small non-coding RNAs which were reported to regulate the expression of various oncogenes or tumor suppressor genes. The expression profiling of miRNAs has already entered into cancer clinics as diagnostic and prognostic biomarkers to assess tumor initiation, progression and response to treatment in cancer patients. This review summarizes: (i) the current understanding of interactions between miRNAs and their target genes, (ii) recent advances in the regulatory mechanisms that control the expression of genes related to carcinogenesis, and (iii) the role of miRNAs in cancer diagnosis and therapy.
Collapse
Affiliation(s)
- Kaladhar B Reddy
- Department of Pathology, Wayne State University School of Medicine, 540 E. Canfield Anvenue, Detroit, MI 48201 USA ; Karmanos Cancer Institute, Wayne State University, Detroit, MI USA
| |
Collapse
|
44
|
Løvendorf MB, Mitsui H, Zibert JR, Røpke MA, Hafner M, Dyring-Andersen B, Bonefeld CM, Krueger JG, Skov L. Laser capture microdissection followed by next-generation sequencing identifies disease-related microRNAs in psoriatic skin that reflect systemic microRNA changes in psoriasis. Exp Dermatol 2015; 24:187-93. [PMID: 25431026 PMCID: PMC11214776 DOI: 10.1111/exd.12604] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2014] [Indexed: 12/16/2022]
Abstract
Psoriasis is a systemic disease with cutaneous manifestations. MicroRNAs (miRNAs) are small non-coding RNA molecules that are differentially expressed in psoriatic skin; however, only few cell- and region-specific miRNAs have been identified in psoriatic lesions. We used laser capture microdissection (LCM) and next-generation sequencing (NGS) to study the specific miRNA expression profiles in the epidermis (Epi) and dermal inflammatory infiltrates (RD) of psoriatic skin (N = 6). We identified 24 deregulated miRNAs in the Epi and 37 deregulated miRNAs in the RD of psoriatic plaque compared with normal psoriatic skin (FCH > 2, FDR < 0.05). Interestingly, 9 of the 37 miRNAs in RD, including miR-193b and miR-223, were recently described as deregulated in circulating peripheral blood mononuclear cells (PBMCs) from patients with psoriasis. Using flow cytometry and qRT-PCR, we found that miR-193b and miR-223 were expressed in Th17 cells. In conclusion, we demonstrate that LCM combined with NGS provides a robust approach to explore the global miRNA expression in the epidermal and dermal compartments of psoriatic skin. Furthermore, our results indicate that the altered local miRNA changes seen in the RD are reflected in the circulating immune cells, suggesting that miRNAs may contribute to the pathogenesis of psoriasis.
Collapse
Affiliation(s)
- Marianne B. Løvendorf
- Department of Dermato-Allergology, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- LEO Pharma A/S, Ballerup, Denmark
| | - Hiroshi Mitsui
- The Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY, USA
| | | | | | - Markus Hafner
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Beatrice Dyring-Andersen
- Department of Dermato-Allergology, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- Department of International Health, Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte M. Bonefeld
- Department of International Health, Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - James G. Krueger
- The Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY, USA
| | - Lone Skov
- Department of Dermato-Allergology, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| |
Collapse
|
45
|
Cucher M, Macchiaroli N, Kamenetzky L, Maldonado L, Brehm K, Rosenzvit MC. High-throughput characterization of Echinococcus spp. metacestode miRNomes. Int J Parasitol 2015; 45:253-67. [PMID: 25659494 DOI: 10.1016/j.ijpara.2014.12.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 12/04/2014] [Accepted: 12/08/2014] [Indexed: 01/06/2023]
Abstract
Echinococcosis is a worldwide zoonosis of great public health concern, considered a neglected disease by the World Health Organisation. The cestode parasites Echinococcus granulosus sensu lato (s. l.) and Echinococcus multilocularis are the main aetiological agents. In the intermediate host, these parasites display particular developmental traits that lead to different patterns of disease progression. In an attempt to understand the causes of these differences, we focused on the analysis of microRNAs (miRNAs), small non-coding regulatory RNAs with major roles in development of animals and plants. In this work, we analysed the small RNA expression pattern of the metacestode, the stage of sanitary relevance, and provide a detailed description of Echinococcus miRNAs. Using high-throughput small RNA sequencing, we believe that we have carried out the first experimental identification of miRNAs in E. multilocularis and have expanded the Echinococcus miRNA catalogue to 38 miRNA genes, including one miRNA only present in E. granulosus s. l. Our findings show that although both species share the top five highest expressed miRNAs, 13 are differentially expressed, which could be related to developmental differences. We also provide evidence that uridylation is the main miRNA processing mechanism in Echinococcus spp. These results provide detailed information on Echinococcus miRNAs, which is the first step in understanding their role in parasite biology and disease establishment and/or progression, and their future potential use as drug or diagnostic targets.
Collapse
Affiliation(s)
- Marcela Cucher
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina.
| | - Natalia Macchiaroli
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Laura Kamenetzky
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Lucas Maldonado
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Klaus Brehm
- Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Mara Cecilia Rosenzvit
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina.
| |
Collapse
|
46
|
Hayes J, Peruzzi PP, Lawler S. MicroRNAs in cancer: biomarkers, functions and therapy. Trends Mol Med 2014; 20:460-9. [PMID: 25027972 DOI: 10.1016/j.molmed.2014.06.005] [Citation(s) in RCA: 1503] [Impact Index Per Article: 150.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/18/2014] [Accepted: 06/18/2014] [Indexed: 12/12/2022]
Abstract
The emergence of microRNAs has been one of the defining developments in cancer biology over the past decade, and the explosion of knowledge in this area has brought forward new diagnostic and therapeutic opportunities. The importance of microRNAs in cancer has been underlined by the identification of alterations in microRNA target binding sites and the microRNA processing machinery in tumor cells. Clinical trials utilizing microRNA profiling for patient prognosis and clinical response are now underway, and the first microRNA mimic entered the clinic for cancer therapy in 2013. In this article we review the potential applications of microRNAs for the clinical assessment of patient outcome in cancer, as well as in cancer monitoring and therapy.
Collapse
Affiliation(s)
- Josie Hayes
- Leeds Institute of Cancer and Pathology and Yorkshire Regional Cytogenetics Unit, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Pier Paolo Peruzzi
- Department of Neurosurgery, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Sean Lawler
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
47
|
Comparative RNA-sequencing analysis of myocardial and circulating small RNAs in human heart failure and their utility as biomarkers. Proc Natl Acad Sci U S A 2014; 111:11151-6. [PMID: 25012294 DOI: 10.1073/pnas.1401724111] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heart failure (HF) is associated with high morbidity and mortality and its incidence is increasing worldwide. MicroRNAs (miRNAs) are potential markers and targets for diagnostic and therapeutic applications, respectively. We determined myocardial and circulating miRNA abundance and its changes in patients with stable and end-stage HF before and at different time points after mechanical unloading by a left ventricular assist device (LVAD) by small RNA sequencing. miRNA changes in failing heart tissues partially resembled that of fetal myocardium. Consistent with prototypical miRNA-target-mRNA interactions, target mRNA levels were negatively correlated with changes in abundance for highly expressed miRNAs in HF and fetal hearts. The circulating small RNA profile was dominated by miRNAs, and fragments of tRNAs and small cytoplasmic RNAs. Heart- and muscle-specific circulating miRNAs (myomirs) increased up to 140-fold in advanced HF, which coincided with a similar increase in cardiac troponin I (cTnI) protein, the established marker for heart injury. These extracellular changes nearly completely reversed 3 mo following initiation of LVAD support. In stable HF, circulating miRNAs showed less than fivefold differences compared with normal, and myomir and cTnI levels were only captured near the detection limit. These findings provide the underpinning for miRNA-based therapies and emphasize the usefulness of circulating miRNAs as biomarkers for heart injury performing similar to established diagnostic protein biomarkers.
Collapse
|
48
|
Stokowy T, Eszlinger M, Świerniak M, Fujarewicz K, Jarząb B, Paschke R, Krohn K. Analysis options for high-throughput sequencing in miRNA expression profiling. BMC Res Notes 2014; 7:144. [PMID: 24625073 PMCID: PMC4007773 DOI: 10.1186/1756-0500-7-144] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 02/28/2014] [Indexed: 12/11/2022] Open
Abstract
Background Recently high-throughput sequencing (HTS) using next generation sequencing techniques became useful in digital gene expression profiling. Our study introduces analysis options for HTS data based on mapping to miRBase or counting and grouping of identical sequence reads. Those approaches allow a hypothesis free detection of miRNA differential expression. Methods We compare our results to microarray and qPCR data from one set of RNA samples. We use Illumina platforms for microarray analysis and miRNA sequencing of 20 samples from benign follicular thyroid adenoma and malignant follicular thyroid carcinoma. Furthermore, we use three strategies for HTS data analysis to evaluate miRNA biomarkers for malignant versus benign follicular thyroid tumors. Results High correlation of qPCR and HTS data was observed for the proposed analysis methods. However, qPCR is limited in the differential detection of miRNA isoforms. Moreover, we illustrate a much broader dynamic range of HTS compared to microarrays for small RNA studies. Finally, our data confirm hsa-miR-197-3p, hsa-miR-221-3p, hsa-miR-222-3p and both hsa-miR-144-3p and hsa-miR-144-5p as potential follicular thyroid cancer biomarkers. Conclusions Compared to microarrays HTS provides a global profile of miRNA expression with higher specificity and in more detail. Summarizing of HTS reads as isoform groups (analysis pipeline B) or according to functional criteria (seed analysis pipeline C), which better correlates to results of qPCR are promising new options for HTS analysis. Finally, data opens future miRNA research perspectives for HTS and indicates that qPCR might be limited in validating HTS data in detail.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Knut Krohn
- Interdisciplinary Center for Clinical Research (IZKF), University of Leipzig, Liebigstr, 21, 04103 Leipzig, Germany.
| |
Collapse
|
49
|
Brown M, Suryawanshi H, Hafner M, Farazi TA, Tuschl T. Mammalian miRNA curation through next-generation sequencing. Front Genet 2013; 4:145. [PMID: 23935604 PMCID: PMC3731538 DOI: 10.3389/fgene.2013.00145] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 07/18/2013] [Indexed: 01/24/2023] Open
Abstract
Characteristic small RNA biogenesis processing patterns are used for the discovery of novel microRNAs (miRNAs) from next-generation sequencing data. Here, we highlight and discuss key criteria for mammalian – specifically human – miRNA database curation based on small RNA sequencing data. Sequence reads obtained from small RNA cDNA libraries are aligned to reference genomic regions, and miRNA genes are revealed by their distinct read length and bimodal read frequency distribution, the predicted secondary structure of the deduced miRNA stem-loop precursor molecule, and, to a lesser degree, based on evolutionary conservation of small RNAs from other vertebrates. Properly curated miRNA databases are an important resource for investigators interested in miRNA biology, diagnostics, and therapeutics.
Collapse
Affiliation(s)
- Miguel Brown
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University New York, NY, USA
| | | | | | | | | |
Collapse
|
50
|
Qin LX, Tuschl T, Singer S. An Empirical Evaluation of Normalization Methods for MicroRNA Arrays in a Liposarcoma Study. Cancer Inform 2013; 12:83-101. [PMID: 23589668 PMCID: PMC3615992 DOI: 10.4137/cin.s11384] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Methods for array normalization, such as median and quantile normalization, were developed for mRNA expression arrays. These methods assume few or symmetric differential expression of genes on the array. However, these assumptions are not necessarily appropriate for microRNA expression arrays because they consist of only a few hundred genes and a reasonable fraction of them are anticipated to have disease relevance. METHODS We collected microRNA expression profiles for human tissue samples from a liposarcoma study using the Agilent microRNA arrays. For a subset of the samples, we also profiled their microRNA expression using deep sequencing. We empirically evaluated methods for normalization of microRNA arrays using deep sequencing data derived from the same tissue samples as the benchmark. RESULTS In this study, we demonstrated array effects in microRNA arrays using data from a liposarcoma study. We found moderately high correlation between Agilent data and sequence data on the same tumors, with the Pearson correlation coefficients ranging from 0.6 to 0.9. Array normalization resulted in some improvement in the accuracy of the differential expression analysis. However, even with normalization, there is still a significant number of false positive and false negative microRNAs, many of which are expressed at moderate to high levels. CONCLUSIONS Our study demonstrated the need to develop more efficient normalization methods for microRNA arrays to further improve the detection of genes with disease relevance. Until better methods are developed, an existing normalization method such as quantile normalization should be applied when analyzing microRNA array data.
Collapse
Affiliation(s)
- Li-Xuan Qin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | |
Collapse
|