title: Single Nucleotide Variants of Candidate Genes in Aggrecan Metabolic Pathway Are Associated with Lumbar Disc Degeneration and Modic Changes.
abstract: BACKGROUND
  Lumbar disc degeneration (LDD) is genetically determined and severity of LDD is associated with Modic changes. Aggrecan is a major proteoglycan in the intervertebral disc and end plate. Progressive reduction of aggrecan is a main feature of LDD and Modic changes.
  
  
  OBJECTIVE
  The study investigated the associations of single nucleotide variants (SNVs) of candidate genes in the aggrecan metabolic pathway with the severity of LDD and Modic changes. In-silico functional analysis of significant SNVs was also assessed.
  
  
  METHODS
  A descriptive cross sectional study was carried out on 106 patients with chronic mechanical low back pain. T1, T2 sagittal lumbar MRI scans were used to assess the severity of LDD and Modic changes. 62 SNVs in ten candidate genes (ACAN, IL1A, IL1B, IL6, MMP3, ADAMTS4, ADAMTS5, TIMP1, TIMP2 and TIMP3) were genotyped on Sequenom MassARRAY iPLEX platform. Multiple linear regression analysis was carried out using PLINK 1.9 in accordance with additive genetic model. In-silico functional analysis was carried out using Provean, SIFT, PolyPhen and Mutation Taster.
  
  
  RESULTS
  Mean age was 52.42±9.42 years. 74 (69.8%) were females. The rs2856836, rs1304037, rs17561 and rs1800587 variants of the IL1A gene were associated with the severity of LDD and Modic changes. The rs41270041 variant of the ADAMTS4 gene and the rs226794 variant of the ADAMTS5 gene were associated with severity of LDD while the rs34884997 variant of the ADAMTS4 gene, the rs55933916 variant of the ADAMTS5 gene and the rs9862 variant of the TIMP3 gene were associated with severity of Modic changes. The rs17561 variant of the IL1A gene was predicted as pathogenic by the PolyPhen prediction tool.
  
  
  CONCLUSIONS
  SNVs of candidate genes in ACAN metabolic pathway are associated with severity of LDD and Modic changes in patients with chronic mechanical low back pain. Predictions of in-silico functional analysis of significant SNVs are inconsistent.
authors.affiliation: Department of Allied Health Sciences, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.
authors.forename: Romain Shanil
authors.identifier: http://orcid.org/0000-0002-9682-5642
authors.initials: RS
authors.lastname: Perera
authors.affiliation: Department of Anatomy, Faculty of Medical Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda, Sri Lanka.
authors.forename: Poruwalage Harsha
authors.initials: PH
authors.lastname: Dissanayake
authors.affiliation: Department of Community Medicine, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.
authors.forename: Upul
authors.initials: U
authors.lastname: Senarath
authors.affiliation: National Hospital of Sri Lanka, Colombo, Sri Lanka.
authors.forename: Lalith Sirimevan
authors.initials: LS
authors.lastname: Wijayaratne
authors.affiliation: Department of Anatomy, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka.
authors.forename: Aranjan Lional
authors.initials: AL
authors.lastname: Karunanayake
authors.affiliation: Human Genetics Unit, Department of Anatomy, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.
authors.forename: Vajira Harshadeva Weerabaddana
authors.initials: VH
authors.lastname: Dissanayake
mesh_terms: D000071121:ADAMTS4 Protein / Q000235:genetics*; D000071116:ADAMTS5 Protein / Q000235:genetics*; D000328:Adult; D053674:Aggrecans / Q000235:genetics*; D059350:Chronic Pain / Q000000981:diagnostic imaging / Q000235:genetics*; D005260:Female; D006801:Humans; D053582:Interleukin-1alpha / Q000235:genetics*; D055959:Intervertebral Disc Degeneration / Q000000981:diagnostic imaging / Q000235:genetics*; D007405:Intervertebral Disc Displacement / Q000000981:diagnostic imaging / Q000235:genetics*; D017116:Low Back Pain / Q000000981:diagnostic imaging / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide; D019717:Tissue Inhibitor of Metalloproteinase-3 / Q000235:genetics*
chemical_list: C508319:ACAN protein, human; D053674:Aggrecans; C508584:IL1A protein, human; D053582:Interleukin-1alpha; C088390:TIMP3 protein, human; D019717:Tissue Inhibitor of Metalloproteinase-3; D000071116:ADAMTS5 Protein; C121532:ADAMTS5 protein, human; D000071121:ADAMTS4 Protein; C000603918:ADAMTS4 protein, human