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Home / Equine Research Bank / Int J Mol Sci / Small Non-Coding RNAome of Ageing Chondrocytes.
International journal of molecular sciences2020; 21(16); 5675; doi: 10.3390/ijms21165675

Small Non-Coding RNAome of Ageing Chondrocytes.

Abstract: Ageing is a leading risk factor predisposing cartilage to osteoarthritis. However, little research has been conducted on the effect of ageing on the expression of small non-coding RNAs (sncRNAs). RNA from young and old chondrocytes from macroscopically normal equine metacarpophalangeal joints was extracted and subjected to small RNA sequencing (RNA-seq). Differential expression analysis was performed in R using package DESeq2. For transfer RNA (tRNA) fragment analysis, tRNA reads were aligned to horse tRNA sequences using Bowtie2 version 2.2.5. Selected microRNA (miRNAs or miRs) and small nucleolar RNA (snoRNA) findings were validated using real-time quantitative Polymerase Chain Reaction (qRT-PCR) in an extended cohort of equine chondrocytes. tRNA fragments were further investigated in low- and high-grade OA human cartilage tissue. In total, 83 sncRNAs were differentially expressed between young and old equine chondrocytes, including miRNAs, snoRNAs, small nuclear RNAs (snRNAs), and tRNAs. qRT-PCR analysis confirmed findings. tRNA fragment analysis revealed that tRNA halves (tiRNAs), tiRNA-5035-GluCTC and tiRNA-5031-GluCTC-1 were reduced in both high grade OA human cartilage and old equine chondrocytes. For the first time, we have measured the effect of ageing on the expression of sncRNAs in equine chondrocytes. Changes were detected in a number of different sncRNA species. This study supports a role for sncRNAs in ageing cartilage and their potential involvement in age-related cartilage diseases.
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Publication Date: 2020-08-07 PubMed ID: 32784773PubMed Central: PMC7461137DOI: 10.3390/ijms21165675Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research investigates how aging impacts the expression of small non-coding RNAs (sncRNAs) in the cartilage cells of horses, contributing to understanding of age-related cartilage diseases, such as osteoarthritis.

Methodology

  • The researchers extracted RNA from young and old chondrocytes (cartilage cells) from equine metacarpophalangeal joints that were macroscopically normal – i.e., appearing normal under visible inspection.
  • They performed small RNA sequencing (RNA-seq), a technique that allows for the capturing, sequencing, and analysis of the small RNAs in the samples.
  • Differential expression analysis was done using the DESeq2 package in R software. This allowed the researchers to compare the difference in expression of sncRNAs between young and old chondrocytes.
  • For transfer RNA (tRNA) fragment analysis, they aligned tRNA reads to horse tRNA sequences using software called Bowtie2 version 2.2.5. This allowed the researchers to see if the sequences from their samples matched known horse tRNA sequences.
  • Selected findings relating to microRNA (miRNAs or miRs) and small nucleolar RNA (snoRNA) were validated using real-time quantitative Polymerase Chain Reaction (qRT-PCR) in a larger cohort of equine chondrocytes. qRT-PCR is a method used to measure the quantity of specific RNAs in a sample.
  • tRNA fragments were further investigated in human cartilage tissue with low and high grade osteoarthritis (OA).

Findings

  • In total, 83 sncRNAs had different expression levels between young and old equine chondrocytes. These encompassed miRNAs, snoRNAs, small nuclear RNAs (snRNAs), and tRNAs.
  • The qRT-PCR analysis confirmed these findings.
  • The tRNA fragment analysis revealed that specific tRNA halves (tiRNAs), namely tiRNA-5035-GluCTC and tiRNA-5031-GluCTC-1, were reduced in both high grade OA human cartilage as well as old equine chondrocytes.

Implications

  • This is the first study to measure the effect of ageing on the expression of sncRNAs in equine chondrocytes.
  • The changes detected support the idea that sncRNAs have a role in ageing cartilage, and might be involved in age-related cartilage diseases, such as osteoarthritis.

Cite This Article

APA
Balaskas P, Green JA, Haqqi TM, Dyer P, Kharaz YA, Fang Y, Liu X, Welting TJM, Peffers MJ. (2020). Small Non-Coding RNAome of Ageing Chondrocytes. Int J Mol Sci, 21(16), 5675. https://doi.org/10.3390/ijms21165675

Publication

International journal of molecular sciences
ISSN: 1422-0067
NlmUniqueID: 101092791
Country: Switzerland
Language: English
Volume: 21
Issue: 16
PII: 5675

Researcher Affiliations

Balaskas, Panagiotis
  • Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK.
Green, Jonathan A
  • Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272, USA.
Haqqi, Tariq M
  • Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272, USA.
Dyer, Philip
  • Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK.
Kharaz, Yalda A
  • Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK.
Fang, Yongxiang
  • Centre for Genomic Research, Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, UK.
Liu, Xuan
  • Centre for Genomic Research, Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, UK.
Welting, Tim J M
  • Department of Orthopaedic Surgery, Maastricht University Medical Centre, 6202 AZ Maastricht, The Netherlands.
Peffers, Mandy J
  • Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK.

MeSH Terms

  • Aging / genetics
  • Animals
  • Cartilage, Articular / pathology
  • Cellular Senescence / genetics
  • Chondrocytes / metabolism
  • Chondrocytes / pathology
  • Gene Expression Profiling
  • Gene Expression Regulation
  • Horses / genetics
  • Humans
  • MicroRNAs / genetics
  • MicroRNAs / metabolism
  • Osteoarthritis / genetics
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA, Small Untranslated / metabolism
  • RNA, Transfer / genetics
  • RNA, Transfer / metabolism
  • Real-Time Polymerase Chain Reaction
  • Reproducibility of Results
  • Sequence Analysis, RNA

Grant Funding

  • MR/K006312/1 / MRC-DTP studentship supported by the Medical Research Council (MRC) and Versus Arthritis as part of the MRC Versus Arthritis Centre for Integrated research into Musculoskeletal Ageing (CIMA)
  • MR/P020941/1 / Medical Research Council
  • R01-AT007373 / National Centre for Complementary and Integrative Health (NCCIH) of the National Institutes of Health (NIH)
  • R01-AR067056 / National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
  • 107471/Z/15/Z / Wellcome Trust

Conflict of Interest Statement

T.J.M Welting is listed as inventors on patents WO2017178251 and WO2017178253. T.J.M Welting has shares in Chondropeptix. The remaining authors declare that they have no competing interests.

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