1
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Varvil MS, dos Santos AP. A review on microRNA detection and expression studies in dogs. Front Vet Sci 2023; 10:1261085. [PMID: 37869503 PMCID: PMC10585042 DOI: 10.3389/fvets.2023.1261085] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/12/2023] [Indexed: 10/24/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that function by post-transcriptional regulation of gene expression. Their stability and abundance in tissue and body fluids makes them promising potential tools for both the diagnosis and prognosis of diseases and attractive therapeutic targets in humans and dogs. Studies of miRNA expression in normal and disease processes in dogs are scarce compared to studies published on miRNA expression in human disease. In this literature review, we identified 461 peer-reviewed papers from database searches using the terms "canine," "dog," "miRNA," and "microRNA"; we screened 244 for inclusion criteria and then included a total of 148 original research peer-reviewed publications relating to specific miRNA expression in canine samples. We found an overlap of miRNA expression changes between the four groups evaluated (normal processes, non-infectious and non-inflammatory conditions, infectious and/or inflammatory conditions, and neoplasia) in 39 miRNAs, 83 miRNAs in three of the four groups, 110 miRNAs in two of the three groups, where 158 miRNAs have only been reported in one of the groups. Additionally, the mechanism of action of these overlapping miRNAs varies depending on the disease process, elucidating a need for characterization of the mechanism of action of each miRNA in each disease process being evaluated. Herein we also draw attention to the lack of standardization of miRNA evaluation, consistency within a single evaluation method, and the need for standardized methods for a direct comparison.
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Affiliation(s)
- Mara S. Varvil
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, WA, United States
| | - Andrea Pires dos Santos
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
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2
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Mármol-Sánchez E, Fromm B, Oskolkov N, Pochon Z, Kalogeropoulos P, Eriksson E, Biryukova I, Sekar V, Ersmark E, Andersson B, Dalén L, Friedländer MR. Historical RNA expression profiles from the extinct Tasmanian tiger. Genome Res 2023; 33:1299-1316. [PMID: 37463752 PMCID: PMC10552650 DOI: 10.1101/gr.277663.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023]
Abstract
Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a ∼130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden;
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
| | - Bastian Fromm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, 9006 Tromsø, Norway
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 223 62 Lund, Sweden
| | - Zoé Pochon
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden
| | - Panagiotis Kalogeropoulos
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Eli Eriksson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Inna Biryukova
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Vaishnovi Sekar
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Erik Ersmark
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden
| | - Björn Andersson
- Department of Cell and Molecular Biology (CMB), Karolinska Institute, 171 77 Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden;
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Marc R Friedländer
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden;
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3
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Mármol-Sánchez E, Heidemann PL, Gredal H, Cirera S. MicroRNA profiling of cerebrospinal fluid from dogs with steroid responsive meningitis-arteritis and meningoencephalitis of unknown origin. Front Vet Sci 2023; 10:1144084. [PMID: 37215481 PMCID: PMC10196361 DOI: 10.3389/fvets.2023.1144084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/28/2023] [Indexed: 05/24/2023] Open
Abstract
Introduction Non-infectious inflammatory diseases of the central nervous system in dogs, such as steroid responsive meningitis-arteritis (SRMA) and meningoencephalitis of unknown origin (MUO), represent a common clinical challenge that needs extensive and multimodal work-up to reach a presumptive diagnosis. Both diseases are presumably caused by dysregulations of the immune system, but further research is needed in order to understand the molecular mechanisms behind each disease and to optimize treatment. Methods By next-generation sequencing and subsequent quantitative real-time PCR (qPCR) verification, we designed a prospective case-control pilot study to analyze the small RNA profiles of cerebrospinal fluid from dogs suffering from MUO (N = 5), dogs suffering from SRMA (N = 8), and healthy dogs (N = 5) presented for elective euthanasia used as the Control group. Results Our results showed an overall enrichment in Y-RNA fragments across all samples, followed by microRNAs (miRNAs) and ribosomal RNAs as the major findings. Additional traces of short RNA reads mapped to long non-coding RNAs and protein-coding genes were also found. From the detected canine miRNAs, miR-21, miR-486, miR-148a, miR-99a, miR-191 and miR-92a were among the most abundant. Dogs with SRMA showed higher differences in miRNA abundance than dogs with MUO when compared to healthy dogs, and miR-142-3p was consistently detected as differentially upregulated in both diseases, although at a low concentration. Moreover, miR-405-5p and miR-503-5p showed different profiles between SRMA and MUO dogs. Subsequent qPCR analyses confirmed miR-142-5p, miR-191-5p and miR-92a-3p as significantly upregulated miRNAs in dogs with SRMA and/or MUO. Discussion Cerebrospinal fluid is a challenging biological material to use for profiling miRNAs due to the low content of circulating RNAs. Despite this, we could confirm several miRNAs being differentially abundant when comparing healthy dogs and dogs with MUO and SRMA, respectively. The results of this study indicate a potential role of miRNAs in the underlying molecular mechanisms of these diseases and establish the basis for further studies.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Centre for Paleogenetics, Stockholm University, Stockholm, Sweden
| | - Pernille Lindholm Heidemann
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hanne Gredal
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Susanna Cirera
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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4
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Gòdia M, Brogaard L, Mármol-Sánchez E, Langhorn R, Nordang Kieler I, Jan Reezigt B, Nikolic Nielsen L, Rem Jessen L, Cirera S. Urinary microRNAome in healthy cats and cats with pyelonephritis or other urological conditions. PLoS One 2022; 17:e0270067. [PMID: 35857780 PMCID: PMC9299306 DOI: 10.1371/journal.pone.0270067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/03/2022] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression at the post-transcriptional level. miRNAs have been found in urine and have shown diagnostic potential in human nephropathies. Here, we aimed to characterize, for the first time, the feline urinary miRNAome and explore the use of urinary miRNA profiles as non-invasive biomarkers for feline pyelonephritis (PN). Thirty-eight cats were included in a prospective case-control study and classified in five groups: healthy Control cats (n = 11), cats with PN (n = 10), cats with subclinical bacteriuria or cystitis (SB/C, n = 5), cats with ureteral obstruction (n = 7) and cats with chronic kidney disease (n = 5). By small RNA sequencing we identified 212 miRNAs in cat urine, including annotated (n = 137) and putative novel (n = 75) miRNAs. The 15 most highly abundant urinary miRNAs accounted for nearly 71% of all detected miRNAs, most of which were previously identified in feline kidney. Ninety-nine differentially abundant (DA) miRNAs were identified when comparing Control cats to cats with urological conditions and 102 DA miRNAs when comparing PN to other urological conditions. Tissue clustering analysis revealed that the majority of urine samples clustered close to kidney, which confirm the likely cellular origin of the secreted urinary miRNAs. Relevant DA miRNAs were verified by quantitative real-time PCR (qPCR). Eighteen miRNAs discriminated Control cats from cats with a urological condition. Of those, seven miRNAs were DA by both RNAseq and qPCR methods between Control and PN cats (miR-125b-5p, miR-27a-3p, miR-21-5p, miR-27b-3p, miR-125a-5p, miR-17-5p and miR-23a-3p) or DA between Control and SB/C cats (miR-125b-5p). Six additional miRNAs (miR-30b-5p, miR-30c, miR-30e-5p, miR-27a-3p, miR-27b-39 and miR-222) relevant for discriminating PN from other urological conditions were identified by qPCR alone (n = 4) or by both methods (n = 2) (P<0.05). This panel of 13 miRNAs has potential as non-invasive urinary biomarkers for diagnostic of PN and other urological conditions in cats.
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Affiliation(s)
- Marta Gòdia
- Department of Animal Medicine and Surgery, School of Veterinary Sciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès, Catalonia, Spain
| | - Louise Brogaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Emilio Mármol-Sánchez
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Centre for Paleogenetics, Stockholm University, Stockholm, Sweden
| | - Rebecca Langhorn
- Faculty of Health and Medical Sciences, Department of Veterinary Clinical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Ida Nordang Kieler
- Faculty of Health and Medical Sciences, Department of Veterinary Clinical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Lise Nikolic Nielsen
- Faculty of Health and Medical Sciences, Department of Veterinary Clinical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Lisbeth Rem Jessen
- Faculty of Health and Medical Sciences, Department of Veterinary Clinical Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail: (LRJ); (SC)
| | - Susanna Cirera
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail: (LRJ); (SC)
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5
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Corbee RJ, Penning LC. COMMD1 Exemplifies the Power of Inbred Dogs to Dissect Genetic Causes of Rare Copper-Related Disorders. Animals (Basel) 2021; 11:ani11030601. [PMID: 33668783 PMCID: PMC7996361 DOI: 10.3390/ani11030601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
Wilson's Disease is a rare autosomal recessive disorder in humans, often presenting with hepatic copper overload. Finding the genetic cause of a rare disease, especially if it is related to food constituents like the trace element copper, is a Herculean task. This review describes examples of how the unique population structure of in-bred dog strains led to the discovery of a novel gene and two modifier genes involved in inherited copper toxicosis. COMMD1, after the discovery in 2002, was shown to be a highly promiscuous protein involved in copper transport, protein trafficking/degradation, regulation of virus replication, and inflammation. Mutations in the ATP7A and ATP7B proteins in Labrador retrievers and Dobermann dogs resulted in a wide variation in hepatic copper levels in these breeds. To our knowledge, numerous dog breeds with inherited copper toxicosis of unknown genetic origin exist. Therefore, the possibility that men's best friend will provide new leads in rare copper storage diseases seems realistic.
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Wang C, Wallerman O, Arendt ML, Sundström E, Karlsson Å, Nordin J, Mäkeläinen S, Pielberg GR, Hanson J, Ohlsson Å, Saellström S, Rönnberg H, Ljungvall I, Häggström J, Bergström TF, Hedhammar Å, Meadows JRS, Lindblad-Toh K. A novel canine reference genome resolves genomic architecture and uncovers transcript complexity. Commun Biol 2021; 4:185. [PMID: 33568770 PMCID: PMC7875987 DOI: 10.1038/s42003-021-01698-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
We present GSD_1.0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3.1. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of lifted over CanFam3.1 gaps harboured previously hidden functional elements, including promoters, genes and miRNAs in GSD_1.0. A catalogue of canine "dark" regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leucocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. 10x linked-read sequencing of 27 dogs (19 breeds) uncovered 22.1 million SNPs, indels and larger structural variants. Subsequent intersection with protein coding genes showed that 1.4% of these could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.
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Affiliation(s)
- Chao Wang
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Ola Wallerman
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Maja-Louise Arendt
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Clinical Sciences, University of Copenhagen, Frederiksberg D, Denmark
| | - Elisabeth Sundström
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Åsa Karlsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jessika Nordin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Suvi Mäkeläinen
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gerli Rosengren Pielberg
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jeanette Hanson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Åsa Ohlsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Saellström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Henrik Rönnberg
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ingrid Ljungvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jens Häggström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tomas F Bergström
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Åke Hedhammar
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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7
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Cao X, Liu WP, Cheng LG, Li HJ, Wu H, Liu YH, Chen C, Xiao X, Li M, Wang GD, Zhang YP. Whole genome analyses reveal significant convergence in obsessive-compulsive disorder between humans and dogs. Sci Bull (Beijing) 2021; 66:187-196. [PMID: 36654227 DOI: 10.1016/j.scib.2020.09.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 08/20/2020] [Accepted: 08/31/2020] [Indexed: 01/20/2023]
Abstract
Obsessive-compulsive disorder (OCD) represents a heterogeneous collection of diseases with diverse levels of phenotypic, genetic, and etiologic variability, making it difficult to identify the underlying genetic and biological mechanisms in humans. Domestic dogs exhibit several OCD-like behaviors. Using continuous circling as a representative phenotype for OCD, we screened two independent dog breeds, the Belgian Malinois and Kunming Dog and subsequently sequenced ten circling dogs and ten unaffected dogs for each breed. Using population differentiation analyses, we identified 11 candidate genes in the extreme tail of the differentiated regions between cases and controls. These genes overlap significantly with genes identified in a genome wide association study (GWAS) of human OCD, indicating strong convergence between humans and dogs. Through gene expressional analysis and functional exploration, we found that two candidate OCD risk genes, PPP2R2B and ADAMTSL3, affected the density and morphology of dendritic spines. Therefore, changes in dendritic spine may underlie some common biological and physiological pathways shared between humans and dogs. Our study revealed an unprecedented level of convergence in OCD shared between humans and dogs, and highlighted the importance of using domestic dogs as a model species for many human diseases including OCD.
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Affiliation(s)
- Xue Cao
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Department of Laboratory Animal Science, Kunming Medical University, Kunming 650500, China
| | - Wei-Peng Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Lu-Guang Cheng
- Kunming Police Dog Base, Ministry of Public Security, Kunming 650204, China
| | - Hui-Juan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Hong Wu
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Chao Chen
- Kunming Police Dog Base, Ministry of Public Security, Kunming 650204, China
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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8
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Fromm B, Tarbier M, Smith O, Marmol-Sanchez E, Dalen L, Gilbert TP, Friedlander MR. Ancient microRNA profiles of a 14,300-year-old canid samples confirm taxonomic origin and give glimpses into tissue-specific gene regulation from the Pleistocene. RNA (NEW YORK, N.Y.) 2020; 27:rna.078410.120. [PMID: 33323528 PMCID: PMC7901840 DOI: 10.1261/rna.078410.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/09/2020] [Indexed: 05/04/2023]
Abstract
DNA sequencing is the current key technology for historic or ancient biological samples and has led to many exciting discoveries in the field of paleogenomics. However, functional insights into tissue identity, cellular composition or gene regulation cannot be gained from DNA. Recent analyses have shown that, under favorable conditions, RNA can also be sequenced from ancient samples, enabling studies at the transcriptomic and regulatory level. Analyzing ancient RNA data from a Pleistocene canid, we find hundreds of intact microRNAs that are taxonomically informative, show tissue-specificity and have functionally predictive characteristics. With an extraordinary age of 14,300 years, these microRNA sequences are by far the oldest ever reported. The authenticity of the sequences is further supported by a) the presence of canid / Caniformia-specific sequences that never evolved outside of this clade, b) tissue-specific expression patterns (cartilage, liver and muscle) that resemble those of modern dogs and c) RNA damage patterns that are clearly distinct from those of fresh samples. By performing computational microRNA-target enrichment analyses on the ancient sequences, we predict microRNA functions consistent with their tissue pattern of expression. For instance, we find a liver-specific microRNA that regulates carbohydrate metabolism and starvation responses in canids. In summary, we show that straightforward paleotranscriptomic microRNA analyses can give functional glimpses into tissue identity, cellular composition and gene regulatory activity of ancient samples and biological processes that took place in the Pleistocene, thus holding great promise for deeper insights into gene regulation in extinct animals based on ancient RNA sequencing. .
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Affiliation(s)
- Bastian Fromm
- Stockholm University, The Wenner-Gren Institute, Department of Molecular Biosciences, SciLifelab;
| | - Marcel Tarbier
- Stockholm University, The Wenner-Gren Institute, Department of Molecular Biosciences, SciLifelab
| | - Oliver Smith
- University of Copenhagen, Section for Evolutionary Genomics, The Globe Institute, Faculty of Health and Medical Sciences
| | - Emilio Marmol-Sanchez
- Stockholm University, The Wenner-Gren Institute, Department of Molecular Biosciences, SciLifelab
| | - Love Dalen
- Stockholm University, Centre for Palaeogenetics
| | - Tom P Gilbert
- University of Copenhagen, Section for Evolutionary Genomics, The Globe Institute, Faculty of Health and Medical Sciences
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9
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Koller D, Kubinyi E, Elek Z, Nemeth H, Miklosi A, Sasvari-Szekely M, Ronai Z. The molecular effect of a polymorphic microRNA binding site of Wolfram syndrome 1 gene in dogs. BMC Genet 2020; 21:82. [PMID: 32723293 PMCID: PMC7390163 DOI: 10.1186/s12863-020-00879-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/29/2020] [Indexed: 11/10/2022] Open
Abstract
Background Although the molecular function of wolframin remains unclear, the lack of this protein is known to cause stress in the endoplasmic reticulum. Some variants in the Wolfram Syndrome 1 gene (WFS1) were associated with various neuropsychiatric disorders in humans, such as aggressiveness, impulsivity and anxiety. Results Here we present an in silico study predicting a single nucleotide polymorphism (rs852850348) in the canine WFS1 gene which was verified by direct sequencing and was genotyped by a PCR-based technique. We found that the rs852850348 polymorphism is located in a putative microRNA (cfa-miR-8834a and cfa-miR-1838) binding site. Therefore, the molecular effect of allelic variants was studied in a luciferase reporter system that allowed assessing gene expression. We demonstrated that the variant reduced the activity of the reporter protein expression in an allele-specific manner. Additionally, we performed a behavioral experiment and investigated the association with this locus to different performance in this test. Association was found between food possessivity and the studied WFS1 gene polymorphism in the Border collie breed. Conclusions Based on our findings, the rs852850348 locus might contribute to the genetic risk of possessivity behavior of dogs in at least one breed and might influence the regulation of wolframin expression.
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Affiliation(s)
- Dora Koller
- Comparative Ethology Research Group, MTA-ELTE, Budapest, Hungary. .,Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary. .,Department of Ethology, ELTE Eötvös Loránd University, Budapest, Hungary.
| | - Eniko Kubinyi
- Comparative Ethology Research Group, MTA-ELTE, Budapest, Hungary.,Department of Ethology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Zsuzsanna Elek
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Helga Nemeth
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Adam Miklosi
- Comparative Ethology Research Group, MTA-ELTE, Budapest, Hungary.,Department of Ethology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Maria Sasvari-Szekely
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Zsolt Ronai
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
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10
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Sándor S, Kubinyi E. Genetic Pathways of Aging and Their Relevance in the Dog as a Natural Model of Human Aging. Front Genet 2019; 10:948. [PMID: 31681409 PMCID: PMC6813227 DOI: 10.3389/fgene.2019.00948] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022] Open
Abstract
Aging research has experienced a burst of scientific efforts in the last decades as the growing ratio of elderly people has begun to pose an increased burden on the healthcare and pension systems of developed countries. Although many breakthroughs have been reported in understanding the cellular mechanisms of aging, the intrinsic and extrinsic factors that contribute to senescence on higher biological levels are still barely understood. The dog, Canis familiaris, has already served as a valuable model of human physiology and disease. The possible role the dog could play in aging research is still an open question, although utilization of dogs may hold great promises as they naturally develop age-related cognitive decline, with behavioral and histological characteristics very similar to those of humans. In this regard, family dogs may possess unmatched potentials as models for investigations on the complex interactions between environmental, behavioral, and genetic factors that determine the course of aging. In this review, we summarize the known genetic pathways in aging and their relevance in dogs, putting emphasis on the yet barely described nature of certain aging pathways in canines. Reasons for highlighting the dog as a future aging and gerontology model are also discussed, ranging from its unique evolutionary path shared with humans, its social skills, and the fact that family dogs live together with their owners, and are being exposed to the same environmental effects.
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Affiliation(s)
- Sára Sándor
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
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Brain-enriched microRNAs circulating in plasma as novel biomarkers for Rett syndrome. PLoS One 2019; 14:e0218623. [PMID: 31291284 PMCID: PMC6619658 DOI: 10.1371/journal.pone.0218623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 06/05/2019] [Indexed: 12/13/2022] Open
Abstract
Rett syndrome (RTT) is a severe neurodevelopmental disorder caused by mutations in the X-linked gene MECP2 (methyl-CpG-binding protein 2). Minimally invasive and accurate biomarkers of disease progression and treatment response could facilitate screening of therapeutic compounds in animal models, enrollment of better-defined participants into clinical trials, and treatment monitoring. In this study, we used a targeted approach based on analysis of brain-enriched microRNAs (miRNAs) circulating in plasma to identify miRNA biomarkers of RTT using Mecp2-mutant mice as a model system and human plasma samples. An “miRNA pair” approach, i.e. the ratio between two miRNAs, was used for data normalization. Specific miRNA pairs and their combinations (classifiers) analyzed in plasma differentiated wild-type from Mecp2 male and female mice with >90% accuracy. Individual miRNA pairs were more effective in distinguishing male (homozygous) animals than female (heterozygous) animals, suggesting that disease severity correlated with the levels of the miRNA biomarkers. In the human study, 30 RTT patients were compared with age-matched controls. The results of this study showed that miRNA classifiers were able to differentiate RTT patients from controls with 85–100% sensitivity. In addition, a comparison of various age groups demonstrated that the dynamics in levels of miRNAs appear to be associated with disease development (involvement of liver, muscle and lipid metabolism in the pathology). Importantly, certain miRNA biomarker pairs were common to both the animal models and human subjects, indicating the similarity between the underlying pathological processes. The data generated in this feasibility study suggest that circulating miRNAs have the potential to be developed as markers of RTT progression and treatment response. Larger clinical studies are needed to further evaluate the findings presented here.
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Pinhal D, Bovolenta LA, Moxon S, Oliveira AC, Nachtigall PG, Acencio ML, Patton JG, Hilsdorf AWS, Lemke N, Martins C. Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs' transcription, sex-biased arm switching and increasing complexity of expression throughout development. Sci Rep 2018; 8:8248. [PMID: 29844338 PMCID: PMC5974277 DOI: 10.1038/s41598-018-26607-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 05/15/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression in multicellular organisms. The elucidation of miRNA function and evolution depends on the identification and characterization of miRNA repertoire of strategic organisms, as the fast-evolving cichlid fishes. Using RNA-seq and comparative genomics we carried out an in-depth report of miRNAs in Nile tilapia (Oreochromis niloticus), an emergent model organism to investigate evo-devo mechanisms. Five hundred known miRNAs and almost one hundred putative novel vertebrate miRNAs have been identified, many of which seem to be teleost-specific, cichlid-specific or tilapia-specific. Abundant miRNA isoforms (isomiRs) were identified with modifications in both 5p and 3p miRNA transcripts. Changes in arm usage (arm switching) of nine miRNAs were detected in early development, adult stage and even between male and female samples. We found an increasing complexity of miRNA expression during ontogenetic development, revealing a remarkable synchronism between the rate of new miRNAs recruitment and morphological changes. Overall, our results enlarge vertebrate miRNA collection and reveal a notable differential ratio of miRNA arms and isoforms influenced by sex and developmental life stage, providing a better picture of the evolutionary and spatiotemporal dynamics of miRNAs.
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Affiliation(s)
- Danillo Pinhal
- Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil.
| | - Luiz A Bovolenta
- Department of Physics and Biophysics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia (UEA), Norwich Research Park, Norwich, United Kingdom
| | - Arthur C Oliveira
- Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Pedro G Nachtigall
- Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Marcio L Acencio
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - James G Patton
- Stevenson Center, Vanderbilt University, Nashville, TN, USA
| | | | - Ney Lemke
- Department of Physics and Biophysics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Cesar Martins
- Department of Morphology, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
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Ye X, Wei W, Zhang Z, He C, Yang R, Zhang J, Wu Z, Huang Q, Jiang Q. Identification of microRNAs associated with glioma diagnosis and prognosis. Oncotarget 2018; 8:26394-26403. [PMID: 28060761 PMCID: PMC5432266 DOI: 10.18632/oncotarget.14445] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/15/2016] [Indexed: 12/21/2022] Open
Abstract
The sensitivity and specificity of microRNAs (miRNAs) for diagnosing glioma are controversial. We therefore performed a meta-analysis to systematically identify glioma-associated miRNAs. We initially screened five miRNA microarray datasets to evaluate the differential expression of miRNAs between glioma and normal tissues. We next compared the expression of the miRNAs in different organs and tissues to assess the sensitivity and specificity of the differentially expressed miRNAs in the diagnosis of glioma. Finally, pathway analysis was performed using GeneGO. We identified 27 candidate miRNAs associated with glioma initiation, progression, and patient prognosis. Sensitivity and specificity analysis indicated miR-15a, miR-16, miR-21, miR-23a, and miR-9 were up-regulated, while miR-124 was down-regulated in glioma. Ten signaling pathways showed the strongest association with glioma development and progression: the p53 pathway feedback loops 2, Interleukin signaling pathway, Toll receptor signaling pathway, Parkinson's disease, Notch signaling pathway, Cadherin signaling pathway, Apoptosis signaling pathway, VEGF signaling pathway, Alzheimer disease-amyloid secretase pathway, and the FGF signaling pathway. Our results indicate that the integration of miRNA, gene, and protein expression data can yield valuable biomarkers for glioma diagnosis and treatment. Indeed, six of the miRNAs identified in this study may be useful diagnostic and prognostic biomarkers in glioma.
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Affiliation(s)
- Xinyun Ye
- Department of Neurosurgery, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi 341000, China
| | - Wenjin Wei
- Department of Neurosurgery, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi 341000, China
| | - Zhengyu Zhang
- Department of Neurosurgery, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi 341000, China
| | - Chunming He
- Department of Neurosurgery, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi 341000, China
| | - Ruijin Yang
- Department of Neurosurgery, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi 341000, China
| | - Jinshi Zhang
- Department of Neurosurgery, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi 341000, China
| | - Zhiwu Wu
- Department of Neurosurgery, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi 341000, China
| | - Qianliang Huang
- Department of Neurosurgery, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi 341000, China
| | - Qiuhua Jiang
- Department of Neurosurgery, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi 341000, China
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Sheinerman KS, Toledo JB, Tsivinsky VG, Irwin D, Grossman M, Weintraub D, Hurtig HI, Chen-Plotkin A, Wolk DA, McCluskey LF, Elman LB, Trojanowski JQ, Umansky SR. Circulating brain-enriched microRNAs as novel biomarkers for detection and differentiation of neurodegenerative diseases. ALZHEIMERS RESEARCH & THERAPY 2017; 9:89. [PMID: 29121998 PMCID: PMC5679501 DOI: 10.1186/s13195-017-0316-0] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/19/2017] [Indexed: 12/11/2022]
Abstract
Background Minimally invasive specific biomarkers of neurodegenerative diseases (NDs) would facilitate patient selection and disease progression monitoring. We describe the assessment of circulating brain-enriched microRNAs as potential biomarkers for Alzheimer’s disease (AD), frontotemporal dementia (FTD), Parkinson’s disease (PD), and amyotrophic lateral sclerosis (ALS). Methods In this case-control study, the plasma samples were collected from 250 research participants with a clinical diagnosis of AD, FTD, PD, and ALS, as well as from age- and sex-matched control subjects (n = 50 for each group), recruited from 2003 to 2015 at the University of Pennsylvania Health System, including the Alzheimer’s Disease Center, the Parkinson’s Disease and Movement Disorders Center, the Frontotemporal Degeneration Center, and the Amyotrophic Lateral Sclerosis Clinic. Each group was randomly divided into training and confirmation sets of equal size. To evaluate the potential of circulating microRNAs enriched in specific brain regions affected by NDs and present in synapses as biomarkers of NDs, the levels of 37 brain-enriched and inflammation-associated microRNAs in the plasma of all participants were measured using individual qRT-PCR. A “microRNA pair” approach was used for data normalization. Results MicroRNA pairs and their combinations (classifiers) capable of differentiating NDs from control and from each other were defined using independently and jointly analyzed training and confirmation datasets. AD, PD, FTD, and ALS are differentiated from control with accuracy of 0.89, 0.90, 0.88, and 0.83 (AUCs, 0.96, 0.96, 0.94, and 0.93), respectively; NDs are differentiated from each other with accuracy ranging from 0.77 (AUC, 0.87) for AD vs. FTD to 0.93 (AUC, 0.98) for AD vs. ALS. The data further indicate sex dependence of some microRNA markers. The average increase in accuracy in distinguishing ND from control for all and male/female groups is 0.06; the largest increase is for ALS, from 0.83 for all participants to 0.92/0.98 for male/female participants. Conclusions The work presented here suggests the possibility of developing microRNA-based diagnostics for detection and differentiation of NDs. Larger multicenter clinical studies are needed to further evaluate circulating brain-enriched microRNAs as biomarkers for NDs and to investigate their association with other ND biomarkers in clinical trial settings. Electronic supplementary material The online version of this article (doi:10.1186/s13195-017-0316-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Jon B Toledo
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Present address: Department of Neurology, Houston Methodist Hospital, Houston, TX, 77030, USA
| | | | - David Irwin
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Murray Grossman
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Daniel Weintraub
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Howard I Hurtig
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alice Chen-Plotkin
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - David A Wolk
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Leo F McCluskey
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lauren B Elman
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - John Q Trojanowski
- Institute on Aging, Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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Bortolomeazzi M, Gaffo E, Bortoluzzi S. A survey of software tools for microRNA discovery and characterization using RNA-seq. Brief Bioinform 2017; 20:918-930. [DOI: 10.1093/bib/bbx148] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/12/2017] [Indexed: 01/08/2023] Open
Affiliation(s)
| | - Enrico Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
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Craft S, Ekena J, Mayer B, Thamm DH, Saba C, Chun R, Trepanier LA. Characterization of a low expression haplotype in canine glutathione S-transferase (GSTT1) and its prevalence in golden retrievers. Vet Comp Oncol 2017; 16:E61-E67. [PMID: 28840668 DOI: 10.1111/vco.12333] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 06/05/2017] [Accepted: 06/11/2017] [Indexed: 12/12/2022]
Abstract
Glutathione S-transferase-theta (GSTT1) is a carcinogen detoxification enzyme, and low activity variants are associated with lymphoma in humans. We recently found a variant in the 3' untranslated region (UTR) of canine GSTT1, *101_102insT, which was predicted to change miRNA binding and was found in 5 of 17 golden retriever (GR) dogs with lymphoma but none of 14 healthy GRs. The aim of this study was to determine whether this variant led to decreased GSTT1 expression and was a discernible risk factor for lymphoma within the GR breed. On resequencing, *101_102insT appeared to be in complete linkage disequilibrium with 3 additional 3'UTR variants, leading to the inferred haplotype *3T>C; *101_102insT; *190C>A; *203T>C. In canine livers that were heterozygous for this variant haplotype, GSTT1 protein expression was significantly lower compared to the reference haplotype (densitometry .40 vs .64, P = .022), and GSTT1 transcript levels by qPCR were also significantly lower (fold difference .52, P = .012), without evidence of substantial allelic expression imbalance. The variant haplotype led to >50% decrease in expression in vitro (.31 ± .07 vs .64 ± .19; P = .019). We found no significant difference in minor allele frequencies between 71 GR dogs with lymphoma (MAF .162) and 33 healthy age-matched controls (MAF .136, P = .69). Our results indicate that the variant GSTT1 3'UTR haplotype containing *101_102insT reduces gene expression, which could lead to impaired carcinogen detoxification, but was not a detectable risk factor for lymphoma in GR dogs.
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Affiliation(s)
- S Craft
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin
| | - J Ekena
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin
| | - B Mayer
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin
| | - D H Thamm
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado
| | - C Saba
- Department of Small Animal Medicine and Surgery, University of Georgia, Athens, Georgia
| | - R Chun
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin
| | - L A Trepanier
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin
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Restriction of Aerobic Metabolism by Acquired or Innate Arylsulfatase B Deficiency: A New Approach to the Warburg Effect. Sci Rep 2016; 6:32885. [PMID: 27605497 PMCID: PMC5015117 DOI: 10.1038/srep32885] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/16/2016] [Indexed: 11/09/2022] Open
Abstract
Aerobic respiration is required for optimal efficiency of metabolism in mammalian cells. Under circumstances when oxygen utilization is impaired, cells survive by anerobic metabolism. The malignant cell has cultivated the use of anerobic metabolism in an aerobic environment, the Warburg effect, but the explanation for this preference is not clear. This paper presents evidence that deficiency of the enzyme arylsulfatase B (ARSB; N-acetylgalactosamine 4-sulfatase), either innate or acquired, helps to explain the Warburg phenomenon. ARSB is the enzyme that removes 4-sulfate groups from the non-reducing end of chondroitin 4-sulfate and dermatan sulfate. Previous reports indicated reduced ARSB activity in malignancy and replication of the effects of hypoxia by decline in ARSB. Hypoxia reduced ARSB activity, since molecular oxygen is needed for post-translational modification of ARSB. In this report, studies were performed in human HepG2 cells and in hepatocytes from ARSB-deficient and normal C57BL/6J control mice. Decline of ARSB, in the presence of oxygen, profoundly reduced the oxygen consumption rate and increased the extracellular acidification rate, indicating preference for aerobic glycolysis. Specific study findings indicate that decline in ARSB activity enhanced aerobic glycolysis and impaired normal redox processes, consistent with a critical role of ARSB and sulfate reduction in mammalian metabolism.
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