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Cocostîrc V, Paștiu AI, Pusta DL. An Overview of Canine Inherited Neurological Disorders with Known Causal Variants. Animals (Basel) 2023; 13:3568. [PMID: 38003185 PMCID: PMC10668755 DOI: 10.3390/ani13223568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Hereditary neurological conditions documented in dogs encompass congenital, neonatal, and late-onset disorders, along with both progressive and non-progressive forms. In order to identify the causal variant of a disease, the main two approaches are genome-wide investigations and candidate gene investigation. Online Mendelian Inheritance in Animals currently lists 418 Mendelian disorders specific to dogs, of which 355 have their likely causal genetic variant identified. This review aims to summarize the current knowledge on the canine nervous system phenes and their genetic causal variant. It has been noted that the majority of these diseases have an autosomal recessive pattern of inheritance. Additionally, the dog breeds that are more prone to develop such diseases are the Golden Retriever, in which six inherited neurological disorders with a known causal variant have been documented, and the Belgian Shepherd, in which five such disorders have been documented. DNA tests can play a vital role in effectively managing and ultimately eradicating inherited diseases.
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Affiliation(s)
- Vlad Cocostîrc
- Department of Genetics and Hereditary Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (A.I.P.); (D.L.P.)
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2
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Bionda A, Cortellari M, Liotta L, Crepaldi P. The Shepherd and the Hunter: A Genomic Comparison of Italian Dog Breeds. Animals (Basel) 2023; 13:2438. [PMID: 37570247 PMCID: PMC10417656 DOI: 10.3390/ani13152438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Shepherd and hunting dogs have undergone divergent selection for specific tasks, resulting in distinct phenotypic and behavioural differences. Italy is home to numerous recognized and unrecognized breeds of both types, providing an opportunity to compare them genomically. In this study, we analysed SNP data obtained from the CanineHD BeadChip, encompassing 116 hunting dogs (representing 6 breeds) and 158 shepherd dogs (representing 9 breeds). We explored the population structure, genomic background, and phylogenetic relationships among the breeds. To compare the two groups, we employed three complementary methods for selection signature detection: FST, XP-EHH, and ROH. Our results reveal a clear differentiation between shepherd and hunting dogs as well as between gun dogs vs. hounds and guardian vs. herding shepherd dogs. The genomic regions distinguishing these groups harbour several genes associated with domestication and behavioural traits, including gregariousness (WBSRC17) and aggressiveness (CDH12 and HTT). Additionally, genes related to morphology, such as size and coat colour (ASIP and TYRP1) and texture (RSPO2), were identified. This comparative genomic analysis sheds light on the genetic underpinnings of the phenotypic and behavioural variations observed in Italian hunting and shepherd dogs.
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Affiliation(s)
- Arianna Bionda
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milano, Via Celoria 2, 20133 Milano, Italy; (A.B.); (P.C.)
| | - Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milano, Via Celoria 2, 20133 Milano, Italy; (A.B.); (P.C.)
| | - Luigi Liotta
- Dipartimento di Scienze Veterinarie, University of Messina, Viale Palatucci 13, 98168 Messina, Italy;
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milano, Via Celoria 2, 20133 Milano, Italy; (A.B.); (P.C.)
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3
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Gutierrez‐Quintana R, Christen M, Faller KME, Guevar J, Jagannathan V, Leeb T. SCN9A variant in a family of mixed breed dogs with congenital insensitivity to pain. J Vet Intern Med 2023; 37:230-235. [PMID: 36630088 PMCID: PMC9889608 DOI: 10.1111/jvim.16610] [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: 09/26/2022] [Accepted: 12/08/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Congenital insensitivity to pain (CIP) and hereditary sensory and autonomic neuropathies (HSANs) are a rare group of genetic disorders causing inability to feel pain. Three different associated variants have been identified in dogs: 1 in Border Collies, 1 in mixed breed dogs, and 1 in Spaniels and Pointers. OBJECTIVES To clinically and genetically characterize CIP in a family of mixed breed dogs. ANIMALS Two mixed breed dogs from the same litter were independently presented: 1 for evaluation of painless fractures, and the other for chronic thermal skin injuries. METHODS Physical, neurological, and histopathological evaluations were performed. Whole genome sequencing of 1 affected dog was used to identify homozygous protein-changing variants that were not present in 926 control genomes from diverse dog breeds. RESULTS Physical and neurological examinations showed the absence of superficial and deep pain perception in the entire body. Histopathological evaluations of the brain, spinal cord and sensory ganglia were normal. Whole genome sequencing identified a homozygous missense variant in SCN9A, XM_038584713.1:c.2761C>T or XP_038440641.1:(p.Arg921Cys). Both affected dogs were homozygous for the mutant allele, which was not detected in 926 dogs of different breeds. CONCLUSIONS AND CLINICAL IMPORTANCE We confirmed the diagnosis of CIP in a family of mixed breed dogs and identified a likely pathogenic variant in the SCN9A gene. The clinical signs observed in these dogs mimic those reported in humans with pathogenic SCN9A variants causing CIP. This report is the first of a spontaneous pathogenic SCN9A variant in domestic animals.
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Affiliation(s)
- Rodrigo Gutierrez‐Quintana
- Small Animal Hospital, School of Biodiversity, One Health and Veterinary MedicineUniversity of GlasgowGlasgowUK
| | - Matthias Christen
- Institute of Genetics, Vetsuisse FacultyUniversity of BernBernSwitzerland
| | - Kiterie M. E. Faller
- Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
| | - Julien Guevar
- Department of Clinical Veterinary Sciences, Vetsuisse FacultyUniversity of BernBernSwitzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse FacultyUniversity of BernBernSwitzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse FacultyUniversity of BernBernSwitzerland
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4
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Inheritance of Monogenic Hereditary Skin Disease and Related Canine Breeds. Vet Sci 2022; 9:vetsci9080433. [PMID: 36006348 PMCID: PMC9412528 DOI: 10.3390/vetsci9080433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/20/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
The plasticity of the genome is an evolutionary factor in all animal species, including canines, but it can also be the origin of diseases caused by hereditary genetic mutation. Genetic changes, or mutations, that give rise to a pathology in most cases result from recessive alleles that are normally found with minority allelic frequency. The use of genetic improvement increases the consanguinity within canine breeds and, on many occasions, also increases the frequency of these recessive alleles, increasing the prevalence of these pathologies. This prevalence has been known for a long time, but mutations differ according to the canine breed. These genetic diseases, including skin diseases, or genodermatosis, which is narrowly defined as monogenic hereditary dermatosis. In this review, we focus on genodermatosis sensu estricto, i.e., monogenic, and hereditary dermatosis, in addition to the clinical features, diagnosis, pathogeny, and treatment. Specifically, this review analyzes epidermolytic and non-epidermolytic ichthyosis, junctional epidermolysis bullosa, nasal parakeratosis, mucinosis, dermoid sinus, among others, in canine breeds, such as Golden Retriever, German Pointer, Australian Shepherd, American Bulldog, Great Dane, Jack Russell Terrier, Labrador Retriever, Shar-Pei, and Rhodesian Ridgeback.
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5
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Leonard C, Van Soens I, Fontaine J. Inherited Sensory and Autonomic Neuropathy in a Border Collie, Interest of Oclacitinib for the Control of Self-Mutilation. Vet Sci 2022; 9:vetsci9030127. [PMID: 35324855 PMCID: PMC8955948 DOI: 10.3390/vetsci9030127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 02/05/2023] Open
Abstract
Sensory and autonomic neuropathy was diagnosed in a five-month-old Border Collie puppy, who presented with progressive self-mutilation, proprioceptive ataxia and urinary incontinence. In the Border Collie, sensory neuropathy is different from what is observed in acral mutilation syndrome, as the genetic mutation is linked to an inversion disrupting the FAM134B gene. Diagnosis was based on history, clinical signs and genetic testing. The prognosis of sensory neuropathies is poor and no curative treatment is available. In the present case, oclacitinib was started for symptomatic treatment of the self-mutilation. A good control of the self-mutilation was quickly observed with an improvement in quality of life for five months. Unfortunately, progression of neurological signs with severe proprioceptive deficits, ataxia, muscular atrophy and urinary/fecal incontinence was observed. Five months after diagnosis, the owner elected for euthanasia.
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6
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Hu C, He M, Xu Q, Tian W. Advances With Non-coding RNAs in Neuropathic Pain. Front Neurosci 2022; 15:760936. [PMID: 35002601 PMCID: PMC8733285 DOI: 10.3389/fnins.2021.760936] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/29/2021] [Indexed: 12/22/2022] Open
Abstract
Neuropathic pain (NP) is one of the most common types of clinical pain. The common causes of this syndrome include injury to the central or peripheral nervous systems and pathological changes. NP is characterized by spontaneous pain, hyperalgesia, abnormal pain, and paresthesia. Because of its diverse etiology, the pathogenesis of NP has not been fully elucidated and has become one of the most challenging problems in clinical medicine. This kind of pain is extremely resistant to conventional treatment and is accompanied by serious complications. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), contribute to diverse biological processes by regulating the expression of various mRNAs involved in pain-related pathways, at the posttranscriptional level. Abnormal regulation of ncRNAs is closely related to the occurrence and development of NP. In this review, we summarize the current state of understanding of the roles of different ncRNAs in the development of NP. Understanding these mechanisms can help develop novel therapeutic strategies to prevent or treat chronic pain.
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Affiliation(s)
- Cheng Hu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Menglin He
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Qian Xu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Weiqian Tian
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
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7
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Genes of Congenital Dermatologic Disorders in Dogs—A Review. FOLIA VETERINARIA 2021. [DOI: 10.2478/fv-2021-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
This article presents an overview of up-to-date identified genes responsible for congenital canine skin diseases of dogs and the characteristics of these diseases. Congenital skin diseases constitute a specific group of dermatologic disorders that plays an important role in breeding of purebred dogs. They include primary seborrhoea, ichthyosis, hereditary nasal parakeratosis, dermatomyositis, colour dilution alopecia, skin mucinosis, dermoid sinus, lethal acrodermatitis, acral mutilation syndrome, keratoconjunctivitis sicca, ichthyosiform dermatosis, bullous epidermolysis, exfoliative dermal lupus erythematosus, congenital footpad hyperkeratosis and sebaceous adenitis. In the majority of cases, their occurrence is linked to particular breeds. In more than half of these diseases a specific defective gene variant responsible for the disease has been identified. Genetic tests for identification of the relevant defective genes serve as an important tool in the diagnostics of diseases in veterinary practice and in breeding of purebred dogs.
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8
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Leeb T, Roosje P, Welle M. Genetics of inherited skin disorders in dogs. Vet J 2021; 279:105782. [PMID: 34861369 DOI: 10.1016/j.tvjl.2021.105782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/16/2021] [Accepted: 11/29/2021] [Indexed: 01/22/2023]
Abstract
Canine genodermatoses represent a broad spectrum of diseases with diverse phenotypes. Modern genetic technology including whole genome sequencing has expedited the identification of novel genes and greatly simplified the establishment of genetic diagnoses in such heterogeneous disorders. The precise genetic diagnosis of a heritable skin disorder is essential for the appropriate counselling of owners regarding the course of the disease, prognosis and implications for breeding. Understanding the underlying pathophysiology is a prerequisite to developing specific, targeted or individualized therapeutic approaches. This review aims to create a comprehensive overview of canine genodermatoses and their respective genetic aetiology known to date. Raising awareness of genodermatoses in dogs is important and this review may help clinicians to apply modern genetics in daily clinical practice, so that a precise diagnoses can be established in suspected genodermatoses.
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Affiliation(s)
- Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; Dermfocus, University of Bern, 3001 Bern, Switzerland.
| | - Petra Roosje
- Dermfocus, University of Bern, 3001 Bern, Switzerland; Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Monika Welle
- Dermfocus, University of Bern, 3001 Bern, Switzerland; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
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9
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Gutierrez-Quintana R, Mellersh C, Wessmann A, Ortega M, Penderis J, Sharpe S, Freeman E, Stevenson L, Burmeister L. Hereditary sensory and autonomic neuropathy in a family of mixed breed dogs associated with a novel RETREG1 variant. J Vet Intern Med 2021; 35:2306-2314. [PMID: 34387380 PMCID: PMC8478055 DOI: 10.1111/jvim.16242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/19/2022] Open
Abstract
Background Hereditary sensory and autonomic neuropathies (HSANs) are a group of genetic disorders affecting the peripheral nervous system. Two different associated variants have been identified in dogs: 1 in Border Collies and 1 in Spaniels and Pointers. Objectives Clinically and genetically characterize HSAN in a family of mixed breed dogs. Animals Five 7‐month‐old mixed breed dogs from 2 related litters were presented for evaluation of a 2‐month history of acral mutilation and progressive pelvic limb gait abnormalities. Methods Complete physical, neurological, electrodiagnostic, and histopathological evaluations were performed. Whole genome sequencing of 2 affected dogs (1 from each litter) was used to identify variants that were homozygous or heterozygous in both cases, but wild type in 217 control genomes of 100 breeds. Immunohistochemistry was used to assess protein expression. Results Complete physical, neurological, electrodiagnostic, and histopathological evaluations confirmed a disorder affecting sensory and autonomic nerves. Whole genome sequencing identified a missense variant in the RETREG1 (reticulophagy regulator 1) gene (c.656C > T, p.P219L). All affected dogs were homozygous for the variant, which was not detected in 1193 dogs from different breeds. Immunohistochemistry showed no expression of RETREG1 in the cerebellum of affected dogs. One of the affected dogs lived for 5 years and showed gradual progression of the clinical signs. Conclusions and Clinical Importance We confirmed the diagnosis of HSAN in a family of mixed breed dogs and identified a novel and possibly pathogenic RETREG1 variant. Affected dogs experienced gradual deterioration over several years.
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Affiliation(s)
| | | | | | | | | | - Samuel Sharpe
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Lynn Stevenson
- Pathology Department, School of Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
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10
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An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues. Sci Rep 2020; 10:20457. [PMID: 33235280 PMCID: PMC7686352 DOI: 10.1038/s41598-020-77586-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (LNC) regulate numerous biological processes. In contrast to human, the identification of LNC in farm species, like chicken, is still lacunar. We propose a catalogue of 52,075 chicken genes enriched in LNC (http://www.fragencode.org/), built from the Ensembl reference extended using novel LNC modelled here from 364 RNA-seq and LNC from four public databases. The Ensembl reference grew from 4,643 to 30,084 LNC, of which 59% and 41% with expression ≥ 0.5 and ≥ 1 TPM respectively. Characterization of these LNC relatively to the closest protein coding genes (PCG) revealed that 79% of LNC are in intergenic regions, as in other species. Expression analysis across 25 tissues revealed an enrichment of co-expressed LNC:PCG pairs, suggesting co-regulation and/or co-function. As expected LNC were more tissue-specific than PCG (25% vs. 10%). Similarly to human, 16% of chicken LNC hosted one or more miRNA. We highlighted a new chicken LNC, hosting miR155, conserved in human, highly expressed in immune tissues like miR155, and correlated with immunity-related PCG in both species. Among LNC:PCG pairs tissue-specific in the same tissue, we revealed an enrichment of divergent pairs with the PCG coding transcription factors, as for example LHX5, HXD3 and TBX4, in both human and chicken.
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11
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Xavier PLP, Müller S, Fukumasu H. Epigenetic Mechanisms in Canine Cancer. Front Oncol 2020; 10:591843. [PMID: 33194754 PMCID: PMC7646326 DOI: 10.3389/fonc.2020.591843] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/05/2020] [Indexed: 01/18/2023] Open
Abstract
A plethora of data has highlighted the role of epigenetics in the development of cancer. Initiation and progression of different cancer types are associated with a variety of changes of epigenetic mechanisms, including aberrant DNA methylation, histone modifications, and miRNA expression. At the same time, advances in the available epigenetic tools allow to investigate and reverse these epigenetic changes and form the basis for the development of anticancer drugs in human oncology. Although human and canine cancer shares several common features, only recently that studies emerged investigating the epigenetic landscape in canine cancer and applying epigenetic modulators to canine cancer. This review focuses on the existing studies involving epigenetic changes in different types of canine cancer and the use of small-molecule inhibitors in canine cancer cells.
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Affiliation(s)
- Pedro Luiz Porfirio Xavier
- Laboratory of Comparative and Translational Oncology (LOCT), Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Brazil
| | - Susanne Müller
- Structural Genomics Consortium and Institute of Pharmaceutical Chemistry, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Heidge Fukumasu
- Laboratory of Comparative and Translational Oncology (LOCT), Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Brazil
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12
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Feng T, Feng N, Zhu T, Li Q, Zhang Q, Wang Y, Gao M, Zhou B, Yu H, Zheng M, Qian B. A SNP-mediated lncRNA (LOC146880) and microRNA (miR-539-5p) interaction and its potential impact on the NSCLC risk. J Exp Clin Cancer Res 2020; 39:157. [PMID: 32795333 PMCID: PMC7427888 DOI: 10.1186/s13046-020-01652-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Many cancer-associated single nucleotide polymorphisms (SNPs) are located in the genomic regions of long non-coding RNAs (lncRNAs). Mechanisms of these SNPs in connection to cancer risk are not fully understood. METHODS Association of SNP (rs140618127) in lncRNA LOC146880 with non-small cell lung cancer (NSCLC) was evaluated in a case-control study of 2707 individuals. The mechanism of the SNP's biologic influence was explored with in vitro and in vivo experiments, including plasmid transfection, siRNA knockdown, flow cytometry assessment, and assays of cell proliferation, migration, invasion, and colony formation. RESULTS Association analysis showed that A allele of SNP rs140618127 was associated with low risk of NSCLC in the Chinese population. Lab experiments indicated that SNP rs140618127 contained a binding site for miR-539-5p and the binding between miR-539-5p and LOC146880 resulted in declined phosphorylation of an oncogene, ENO1. The reduced phosphorylation of ENO1 led to decreased phosphorylation of PI3K and Akt, which is further linked to the decline in cell proliferation and tumor progression. CONCLUSION The study demonstrates that SNP rs140618127 in lncRNA loc146880 provides an alternate binding site for microRNA miR-539-5p which affects the phosphorylation of ENO1 and activation of the PI3K and Akt pathway.
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MESH Headings
- Animals
- Apoptosis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/pathology
- Case-Control Studies
- Cell Movement
- Cell Proliferation
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- MicroRNAs/genetics
- Middle Aged
- Phosphopyruvate Hydratase/genetics
- Phosphopyruvate Hydratase/metabolism
- Polymorphism, Single Nucleotide
- Prognosis
- RNA, Long Noncoding/genetics
- Tumor Cells, Cultured
- Tumor Suppressor Proteins/genetics
- Tumor Suppressor Proteins/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Tienan Feng
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Clinical Research Promotion and Development Center, Shanghai Shenkang Hospital Development Center, Shanghai, 200041, China
| | - Nannan Feng
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Tengteng Zhu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qiang Li
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qi Zhang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yu Wang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ming Gao
- Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Baosen Zhou
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110013, China
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA
| | - Min Zheng
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Biyun Qian
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Second Affiliated hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, 610051, Sichuan, China.
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13
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Baker L, Muir P, Sample SJ. Genome-wide association studies and genetic testing: understanding the science, success, and future of a rapidly developing field. J Am Vet Med Assoc 2020; 255:1126-1136. [PMID: 31687891 DOI: 10.2460/javma.255.10.1126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Dog owners are increasingly interested in using commercially available testing panels to learn about the genetics of their pets, both to identify breed ancestry and to screen for specific genetic diseases. Helping owners interpret and understand results from genetic screening panels is becoming an important issue facing veterinarians. The objective of this review article is to introduce basic concepts behind genetic studies and current genetic screening tests while highlighting their value in veterinary medicine. The potential uses and limitations of commercially available genetic testing panels as screening tests are discussed, including appropriate cautions regarding the interpretation of results. Future directions, particularly with regard to the study of common complex genetic diseases, are also described.
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14
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Du X, Liu L, Li Q, Zhang L, Pan Z, Li Q. NORFA, long intergenic noncoding RNA, maintains sow fertility by inhibiting granulosa cell death. Commun Biol 2020; 3:131. [PMID: 32188888 PMCID: PMC7080823 DOI: 10.1038/s42003-020-0864-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/27/2020] [Indexed: 02/07/2023] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) have been proved to be involved in regulating female reproduction. However, to what extent lincRNAs are involved in ovarian functions and fertility is incompletely understood. Here we show that a lincRNA, NORFA is involved in granulosa cell apoptosis, follicular atresia and sow fertility. We found that NORFA was down-regulated during follicular atresia, and inhibited granulosa cell apoptosis. NORFA directly interacted with miR-126 and thereby preventing it from binding to TGFBR2 3'-UTR. miR-126 enhanced granulosa cell apoptosis by attenuating NORFA-induced TGF-β signaling pathway. Importantly, a breed-specific 19-bp duplication was detected in NORFA promoter, which proved association with sow fertility through enhancing transcription activity of NORFA by recruiting transcription factor NFIX. In summary, our findings identified a candidate lincRNA for sow prolificacy, and provided insights into the mechanism of follicular atresia and female fertility.
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Affiliation(s)
- Xing Du
- College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Lu Liu
- College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Qiqi Li
- College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Lifan Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zengxiang Pan
- College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Qifa Li
- College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China.
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15
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Minnema L, Wheeler J, Enomoto M, Pitake S, Mishra SK, Lascelles BDX. Correlation of Artemin and GFRα3 With Osteoarthritis Pain: Early Evidence From Naturally Occurring Osteoarthritis-Associated Chronic Pain in Dogs. Front Neurosci 2020; 14:77. [PMID: 32116521 PMCID: PMC7031206 DOI: 10.3389/fnins.2020.00077] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 01/20/2020] [Indexed: 12/11/2022] Open
Abstract
Arthritis, including osteoarthritis (OA) and other musculoskeletal-associated pain, is a worldwide problem, however, effective drug options are limited. Several receptors, neurotransmitters, and endogenous mediators have been identified in rodent models, but the relevance of these molecules in disease-associated pain is not always clear. Artemin, a neurotrophic factor, and its receptor, glial-derived neurotrophic factor (GDNF) family receptor alpha-3 (GFRα3), have been identified as involved in pain in rodents. Their role in OA-associated pain is unknown. To explore a possible association, we analyzed tissue from naturally occurring OA in dogs to characterize the correlation with chronic pain. We used behavioral assessment, objective measures of limb use, and molecular tools to identify whether artemin and GFRα3 might be associated with OA pain. Our results using banked tissue from well-phenotyped dogs indicates that artemin/GFRα3 may play an important, and hitherto unrecognized, role in chronic OA-associated pain. Elevated serum levels of artemin from osteoarthritic humans compared to healthy individuals suggest translational relevance. Our data provide compelling evidence that the artemin/GFRα3 signaling pathway may be important in OA pain in both non-humans and humans and may ultimately lead to novel therapeutics.
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Affiliation(s)
- Laura Minnema
- Translational Research in Pain Program, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States.,Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Joshua Wheeler
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States.,Comparative Pain Research and Education Center, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Masataka Enomoto
- Translational Research in Pain Program, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States.,Comparative Pain Research and Education Center, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Saumitra Pitake
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Santosh K Mishra
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States.,Comparative Pain Research and Education Center, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - B Duncan X Lascelles
- Translational Research in Pain Program, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States.,Comparative Pain Research and Education Center, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States.,Thurston Arthritis Research Center, UNC School of Medicine, Chapel Hill, NC, United States.,Center for Translational Pain Research, Department of Anesthesiology, Duke University, Durham, NC, United States
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16
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Granger N, Luján Feliu-Pascual A, Spicer C, Ricketts S, Hitti R, Forman O, Hersheson J, Houlden H. Charcot-Marie-Tooth type 4B2 demyelinating neuropathy in miniature Schnauzer dogs caused by a novel splicing SBF2 (MTMR13) genetic variant: a new spontaneous clinical model. PeerJ 2019; 7:e7983. [PMID: 31772832 PMCID: PMC6875392 DOI: 10.7717/peerj.7983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/02/2019] [Indexed: 01/23/2023] Open
Abstract
Background Charcot-Marie-Tooth (CMT) disease is the most common neuromuscular disorder in humans affecting 40 out of 100,000 individuals. In 2008, we described the clinical, electrophysiological and pathological findings of a demyelinating motor and sensory neuropathy in Miniature Schnauzer dogs, with a suspected autosomal recessive mode of inheritance based on pedigree analysis. The discovery of additional cases has followed this work and led to a genome-wide association mapping approach to search for the underlying genetic cause of the disease. Methods For genome wide association screening, genomic DNA samples from affected and unaffected dogs were genotyped using the Illumina CanineHD SNP genotyping array. SBF2 and its variant were sequenced using primers and PCRs. RNA was extracted from muscle of an unaffected and an affected dog and RT-PCR performed. Immunohistochemistry for myelin basic protein was performed on peripheral nerve section specimens. Results The genome-wide association study gave an indicative signal on canine chromosome 21. Although the signal was not of genome-wide significance due to the small number of cases, the SBF2 (also known as MTMR13) gene within the region of shared case homozygosity was a strong positional candidate, as 22 genetic variants in the gene have been associated with demyelinating forms of Charcot-Marie-Tooth disease in humans. Sequencing of SBF2 in cases revealed a splice donor site genetic variant, resulting in cryptic splicing and predicted early termination of the protein based on RNA sequencing results. Conclusions This study reports the first genetic variant in Miniature Schnauzer dogs responsible for the occurrence of a demyelinating peripheral neuropathy with abnormally folded myelin. This discovery establishes a genotype/phenotype correlation in affected Miniature Schnauzers that can be used for the diagnosis of these dogs. It further supports the dog as a natural model of a human disease; in this instance, Charcot-Marie-Tooth disease. It opens avenues to search the biological mechanisms responsible for the disease and to test new therapies in a non-rodent large animal model. In particular, recent gene editing methods that led to the restoration of dystrophin expression in a canine model of muscular dystrophy could be applied to other canine models such as this before translation to humans.
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Affiliation(s)
- Nicolas Granger
- Royal Veterinary College, University of London, Hatfield, United Kingdom.,Bristol Veterinary Specialists, CVS Referrals, Bristol, United Kingdom
| | | | - Charlotte Spicer
- Department of Molecular Neuroscience, UCL Institute of Neurology & National Hospital for Neurology and Neurosurgery & London, London, United Kingdom
| | - Sally Ricketts
- Kennel Club Genetics Centre, Animal Health Trust, Newmarket, United Kingdom
| | - Rebekkah Hitti
- Kennel Club Genetics Centre, Animal Health Trust, Newmarket, United Kingdom
| | - Oliver Forman
- Kennel Club Genetics Centre, Animal Health Trust, Newmarket, United Kingdom
| | - Joshua Hersheson
- Department of Molecular Neuroscience, UCL Institute of Neurology & National Hospital for Neurology and Neurosurgery & London, London, United Kingdom
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology & National Hospital for Neurology and Neurosurgery & London, London, United Kingdom
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17
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Song S, Tian D, Li C, Tang B, Dong L, Xiao J, Bao Y, Zhao W, He H, Zhang Z. Genome Variation Map: a data repository of genome variations in BIG Data Center. Nucleic Acids Res 2019; 46:D944-D949. [PMID: 29069473 PMCID: PMC5753358 DOI: 10.1093/nar/gkx986] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 10/11/2017] [Indexed: 11/16/2022] Open
Abstract
The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes.
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Affiliation(s)
- Shuhui Song
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dongmei Tian
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Cuiping Li
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bixia Tang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lili Dong
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingfa Xiao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China
| | - Yiming Bao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenming Zhao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hang He
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhang Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China
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18
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Canine neuropathies: powerful spontaneous models for human hereditary sensory neuropathies. Hum Genet 2019; 138:455-466. [PMID: 30955094 DOI: 10.1007/s00439-019-02003-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 03/18/2019] [Indexed: 12/16/2022]
Abstract
In humans, hereditary sensory neuropathies (HSN), also known as hereditary sensory and autonomic neuropathies (HSAN), constitute a clinically and genetically heterogeneous group of disorders characterized by progressive sensory loss, often accompanied by chronic skin ulcerations and nail dystrophic changes. To date, although around 20 genes have already been discovered, they do not explain the genetic causes of all patients. In dogs, similar neuropathies are also diagnosed, several breeds being predisposed to specific forms of the disease. Indeed, the breed specificity of most canine genetic diseases is due to the small numbers of founders and high levels of inbreeding. Recent knowledge and tools developed to study the canine genome efficiently allows deciphering the genetic bases of such diseases. To date, a dozen breeds are recognized to develop specific HSN. For the Border collie and hunting dog breeds, the genes involved have recently been discovered. Other affected breeds thus constitute potential genetic models, with new genes to be found in dogs that can be considered as candidate genes for human HSAN/HSN. Here, we review the different forms of human and canine HSAN/HSN and we present a novel form in Fox terrier cases, highlighting the advantages of the dog model for such rare human diseases.
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19
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Natural models for retinitis pigmentosa: progressive retinal atrophy in dog breeds. Hum Genet 2019; 138:441-453. [PMID: 30904946 DOI: 10.1007/s00439-019-01999-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/14/2019] [Indexed: 01/24/2023]
Abstract
Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal disorders eventually leading to blindness with different ages of onset, progression and severity. Human RP, first characterized by the progressive degeneration of rod photoreceptor cells, shows high genetic heterogeneity with more than 90 genes identified. However, about one-third of patients have no known genetic causes. Interestingly, dogs are also severely affected by similar diseases, called progressive retinal atrophy (PRA). Indeed, RP and PRA have comparable clinical signs, physiopathology and outcomes, similar diagnosis methods and most often, orthologous genes are involved. The many different dog PRAs often segregate in specific breeds. Indeed, undesired alleles have been selected and amplified through drastic selection and excessive use of inbreeding. Out of the 400 breeds, nearly 100 have an inherited form of PRA, which are natural animal models that can be used to investigate the genetics, disease progression and therapies in dogs for the benefit of both dogs and humans. Recent knowledge on the canine genome and access to new genotyping and sequencing technologies now efficiently allows the identification of mutations involved in canine genetic diseases. To date, PRA genes identified in dog breeds correspond to the same genes in humans and represent relevant RP models, and new genes found in dogs represent good candidate for still unknown human RP. We present here a review of the main advantages of the dog models for human RP with the genes already identified and an X-linked PRA in the Border collie as a model for orphan X-linked RPs in human.
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20
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Hu JZ, Rong ZJ, Li M, Li P, Jiang LY, Luo ZX, Duan CY, Cao Y, Lu HB. Silencing of lncRNA PKIA-AS1 Attenuates Spinal Nerve Ligation-Induced Neuropathic Pain Through Epigenetic Downregulation of CDK6 Expression. Front Cell Neurosci 2019; 13:50. [PMID: 30873006 PMCID: PMC6401634 DOI: 10.3389/fncel.2019.00050] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/01/2019] [Indexed: 01/07/2023] Open
Abstract
Neuropathic pain (NP) is among the most intractable comorbidities of spinal cord injury. Dysregulation of non-coding RNAs has also been implicated in the development of neuropathic pain. Here, we identified a novel lncRNA, PKIA-AS1, by using lncRNA array analysis in spinal cord tissue of spinal nerve ligation (SNL) model rats, and investigated the role of PKIA-AS1 in SNL-mediated neuropathic pain. We observed that PKIA-AS1 was significantly upregulated in SNL model rats and that PKIA-AS1 knockdown attenuated neuropathic pain progression. Alternatively, overexpression of PKIA-AS1 was sufficient to induce neuropathic pain-like symptoms in uninjured rats. We also found that PKIA-AS1 mediated SNL-induced neuropathic pain by directly regulating the expression and function of CDK6, which is essential for the initiation and maintenance of neuroinflammation and neuropathic pain. Therefore, our study identifies PKIA-AS1 as a novel therapeutic target for neuroinflammation related neuropathic pain.
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Affiliation(s)
- Jian-Zhong Hu
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Zi-Jie Rong
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Miao Li
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Ping Li
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China.,Department of Obstetrics, Xiangya Hospital, Central South University, Changsha, China
| | - Li-Yuan Jiang
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Zi-Xiang Luo
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Chun-Yue Duan
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Yong Cao
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Hong-Bin Lu
- Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China.,Department of Sports Medicine, Xiangya Hospital, Central South University, Changsha, China
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21
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Zucchelli S, Fedele S, Vatta P, Calligaris R, Heutink P, Rizzu P, Itoh M, Persichetti F, Santoro C, Kawaji H, Lassmann T, Hayashizaki Y, Carninci P, Forrest ARR, Gustincich S. Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases. Mol Neurobiol 2019; 56:5392-5415. [PMID: 30610612 PMCID: PMC6614138 DOI: 10.1007/s12035-018-1465-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022]
Abstract
Natural antisense transcripts are common features of mammalian genes providing additional regulatory layers of gene expression. A comprehensive description of antisense transcription in loci associated to familial neurodegenerative diseases may identify key players in gene regulation and provide tools for manipulating gene expression. We take advantage of the FANTOM5 sequencing datasets that represent the largest collection to date of genome-wide promoter usage in almost 2000 human samples. Transcription start sites (TSSs) are mapped at high resolution by the use of a modified protocol of cap analysis of gene expression (CAGE) for high-throughput single molecule next-generation sequencing with Helicos (hCAGE). Here we present the analysis of antisense transcription at 17 loci associated to hereditary Alzheimer’s disease, Frontotemporal Dementia, Parkinson’s disease, Amyotrophic Lateral Sclerosis, and Huntington’s disease. We focused our analysis on libraries derived from brain tissues and primary cells. We also screened libraries from total blood and blood cell populations in the quest for peripheral biomarkers of neurodegenerative diseases. We identified 63 robust promoters in antisense orientation to genes associated to familial neurodegeneration. When applying a less stringent cutoff, this number increases to over 400. A subset of these promoters represents alternative TSSs for 24 FANTOM5 annotated long noncoding RNA (lncRNA) genes, in antisense orientation to 13 of the loci analyzed here, while the remaining contribute to the expression of additional transcript variants. Intersection with GWAS studies, sample ontology, and dynamic expression reveals association to specific genetic traits as well as cell and tissue types, not limited to neurodegenerative diseases. Antisense transcription was validated for a subset of genes, including those encoding for Microtubule-Associated Protein Tau, α-synuclein, Parkinsonism-associated deglycase DJ-1, and Leucin-Rich Repeat Kinase 2. This work provides evidence for the existence of additional regulatory mechanisms of the expression of neurodegenerative disease-causing genes by previously not-annotated and/or not-validated antisense long noncoding RNAs.
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Affiliation(s)
- Silvia Zucchelli
- Area of Neuroscience, SISSA, Trieste, Italy
- Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), Novara, Italy
| | | | - Paolo Vatta
- Area of Neuroscience, SISSA, Trieste, Italy
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Raffaella Calligaris
- Area of Neuroscience, SISSA, Trieste, Italy
- Department of Medical, Surgical and Health Sciences, Clinical Neurology Unit, Cattinara University Hospital, Trieste, Italy
| | - Peter Heutink
- Section Medical Genomics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
- Genome Biology of Neurodegenerative Diseases, Deutsches Zentrum fur Neurodegenerative Erkrankungen (DZNE), Standort, Tübingen, Germany
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
| | - Patrizia Rizzu
- Section Medical Genomics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
- Applied Genomics for Neurodegenerative Diseases, Deutsches Zentrum fur Neurodegenerative Erkrankungen (DZNE), Standort, Tübingen, Germany
| | - Masayoshi Itoh
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wakō, Japan
| | - Francesca Persichetti
- Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Claudio Santoro
- Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Hideya Kawaji
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wakō, Japan
- Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Timo Lassmann
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
- Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, WA 6008 Australia
- Laboratory for Applied Computational Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wakō, Japan
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Alistair R. R. Forrest
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
- Laboratory for Genome Information Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Stefano Gustincich
- Area of Neuroscience, SISSA, Trieste, Italy
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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22
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Wang GD, Shao XJ, Bai B, Wang J, Wang X, Cao X, Liu YH, Wang X, Yin TT, Zhang SJ, Lu Y, Wang Z, Wang L, Zhao W, Zhang B, Ruan J, Zhang YP. Structural variation during dog domestication: insights from gray wolf and dhole genomes. Natl Sci Rev 2019; 6:110-122. [PMID: 34694297 PMCID: PMC8291444 DOI: 10.1093/nsr/nwy076] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/27/2018] [Accepted: 07/17/2018] [Indexed: 12/11/2022] Open
Abstract
Several processes like phenotypic evolution, disease susceptibility and environmental adaptations, which fashion the domestication of animals, are largely attributable to structural variations (SVs) in the genome. Here, we present high-quality draft genomes of the gray wolf (Canis lupus) and dhole (Cuon alpinus) with scaffold N50 of 6.04 Mb and 3.96 Mb, respectively. Sequence alignment comprising genomes of three canid species reveals SVs specific to the dog, particularly 16 315 insertions, 2565 deletions, 443 repeats, 16 inversions and 15 translocations. Functional annotation of the dog SVs associated with genes indicates their enrichments in energy metabolisms, neurological processes and immune systems. Interestingly, we identify and verify at population level an insertion fully covering a copy of the AKR1B1 (Aldo-Keto Reductase Family 1 Member B) transcript. Transcriptome analysis reveals a high level of expression of the new AKR1B1 copy in the small intestine and liver, implying an increase in de novo fatty acid synthesis and antioxidant ability in dog compared to gray wolf, likely in response to dietary shifts during the agricultural revolution. For the first time, we report a comprehensive analysis of the evolutionary dynamics of SVs during the domestication step of dogs. Our findings demonstrate that retroposition can birth new genes to facilitate domestication, and affirm the importance of large-scale genomic variants in domestication studies.
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Affiliation(s)
- Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, 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
| | - Xiu-Juan Shao
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Bing Bai
- Medical Faculty, Kunming University of Science and Technology, Kunming 650504, China
- Department of Pediatrics, the First People's Hospital of Yunnan Province, Kunming 650032, China
| | - Junlong Wang
- College of Pharmacology, Soochow University, Suzhou 215123, China
- 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
| | - Xiaobo Wang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xue Cao
- Department of Laboratory Animal Science, Kunming Medical University, Kunming 650500, China
| | - Yan-Hu Liu
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Xuan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Shao-Jie Zhang
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Yan Lu
- Beijing Zoo, Beijing 100044, China
| | | | - Lu Wang
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Wenming Zhao
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhang
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jue Ruan
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, 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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23
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Amengual-Batle P, Rusbridge C, José-López R, Golini L, Shelton GD, Mellersh CS, Gutierrez-Quintana R. Two mixed breed dogs with sensory neuropathy are homozygous for an inversion disrupting FAM134B previously identified in Border Collies. J Vet Intern Med 2018; 32:2082-2087. [PMID: 30307654 PMCID: PMC6272042 DOI: 10.1111/jvim.15312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 05/19/2018] [Accepted: 07/31/2018] [Indexed: 01/21/2023] Open
Abstract
Two unrelated 8‐month‐old male mixed breed dogs were presented for evaluation of progressive ataxia, knuckling, and lack of pain perception in the distal limbs. Because of the similarity in age of onset, progression, and clinical findings with previously described sensory neuropathy in Border Collies, the affected dogs were screened for an FAM134B mutation and were determined to be homozygous for the mutation. Despite few phenotypic similarities with other breeds, genetic testing for specific diseases should be considered in mixed breed dogs with compatible clinical signs, especially if ancestry is unknown.
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Affiliation(s)
- Pablo Amengual-Batle
- Small Animal Hospital, School of Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Clare Rusbridge
- Fitzpatrick Referrals, Eashing, Surrey, United Kingdom.,Faculty of Health & Medical Sciences, University of Surrey, School of Veterinary Medicine, Vet School Main Building, Daphne Jackson Road, Guildford, GU2 7AL, United Kingdom
| | - Roberto José-López
- Small Animal Hospital, School of Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Lorenzo Golini
- Northwest Veterinary Specialists, Cheshire, United Kingdom
| | - G Diane Shelton
- Department of Pathology, School of Medicine, University of California, San Diego, San Diego, California
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Le Béguec C, Wucher V, Lagoutte L, Cadieu E, Botherel N, Hédan B, De Brito C, Guillory AS, André C, Derrien T, Hitte C. Characterisation and functional predictions of canine long non-coding RNAs. Sci Rep 2018; 8:13444. [PMID: 30194329 PMCID: PMC6128939 DOI: 10.1038/s41598-018-31770-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/24/2018] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are a family of heterogeneous RNAs that play major roles in multiple biological processes. We recently identified an extended repertoire of more than 10,000 lncRNAs of the domestic dog however, predicting their biological functionality remains challenging. In this study, we have characterised the expression profiles of 10,444 canine lncRNAs in 26 distinct tissue types, representing various anatomical systems. We showed that lncRNA expressions are mainly clustered by tissue type and we highlighted that 44% of canine lncRNAs are expressed in a tissue-specific manner. We further demonstrated that tissue-specificity correlates with specific families of canine transposable elements. In addition, we identified more than 900 conserved dog-human lncRNAs for which we show their overall reproducible expression patterns between dog and human through comparative transcriptomics. Finally, co-expression analyses of lncRNA and neighbouring protein-coding genes identified more than 3,400 canine lncRNAs, suggesting that functional roles of these lncRNAs act as regulatory elements. Altogether, this genomic and transcriptomic integrative study of lncRNAs constitutes a major resource to investigate genotype to phenotype relationships and biomedical research in the dog species.
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Affiliation(s)
- Céline Le Béguec
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Valentin Wucher
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Lætitia Lagoutte
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France.,UMR PEGASE, Agrocampus Ouest, INRA, 35042, Rennes, France
| | - Edouard Cadieu
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Nadine Botherel
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Benoît Hédan
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Clotilde De Brito
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Anne-Sophie Guillory
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Catherine André
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France.
| | - Christophe Hitte
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France.
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25
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Ostrander EA, Wayne RK, Freedman AH, Davis BW. Demographic history, selection and functional diversity of the canine genome. Nat Rev Genet 2017; 18:705-720. [DOI: 10.1038/nrg.2017.67] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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