Assessment of the use of RNA quality metrics for the screening of articular cartilage specimens from clinically normal dogs and dogs with osteoarthritis

RNA Extraction from Cartilage: Issues, Methods, Tips

The increase in degenerative diseases involving articular cartilage has pushed research to focus on their pathogenesis and treatment, exploiting increasingly complex techniques. Gene expression analyses from tissue are representative of the in vivo situation, but the protocols to be applied to obtain a reliable analysis are not completely cleared through customs. Thus, RNA extraction from fresh samples and specifically from musculoskeletal tissue such as cartilage is still a challenging issue. The aim of the review is to provide an overview of the techniques described in the literature for RNA extraction, highlighting limits and possibilities. The research retrieved 65 papers suitable for the purposes. The results highlighted the great difficulty in comparing the different studies, both for the sources of tissue used and for the techniques employed, as well as the details about protocols. Few papers compared different RNA extraction methods or homogenization techniques; the case study reported by authors about RNA extraction from sheep cartilage has not found an analog in the literature, confirming the existence of a relevant blank on studies about RNA extraction from cartilage tissue. However, the state of the art depicted can be used as a starting point to improve and expand studies on this topic.

Optimizations for identifying reference genes in bone and cartilage bioengineering

BACKGROUND

Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) remains one of the best-established techniques to assess gene expression patterns. However, appropriate reference gene(s) selection remains a critical and challenging subject in which inappropriate reference gene selction can distort results leading to false interpretations. To date, mixed opinions still exist in how to choose the most optimal reference gene sets in accodrance to the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guideline. Therefore, the purpose of this study was to investigate which schemes were the most feasible for the identification of reference genes in a bone and cartilage bioengineering experimental setting. In this study, rat bone mesenchymal stem cells (rBMSCs), skeletal muscle tissue and adipose tissue were utilized, undergoing either chondrogenic or osteogenic induction, to investigate the optimal reference gene set identification scheme that would subsequently ensure stable and accurate interpretation of gene expression in bone and cartilage bioengineering.

RESULTS

The stability and pairwise variance of eight candidate reference genes were analyzed using geNorm. The V_0.15- vs. V_min-based normalization scheme in rBMSCs had no significant effect on the eventual normalization of target genes. In terms of the muscle tissue, the results of the correlation of NF values between the V_0.15 and V_min schemes and the variance of target genes expression levels generated by these two schemes showed that different schemes do indeed have a significant effect on the eventual normalization of target genes. Three selection schemes were adopted in terms of the adipose tissue, including the three optimal reference genes (Opt₃), V_0.20 and V_min schemes, and the analysis of NF values with eventual normalization of target genes showed that the different selection schemes also have a significant effect on the eventual normalization of target genes.

CONCLUSIONS

Based on these results, the proposed cut-off value of Vn/n + 1 under 0.15, according to the geNorm algorithm, should be considered with caution. For cell only experiments, at least rBMSCs, a Vn/n + 1 under 0.15 is sufficient in RT-qPCR studies. However, when using certain tissue types such as skeletal muscle and adipose tissue the minimum Vn/n + 1 should be used instead as this provides a far superior mode of generating accurate gene expression results. We thus recommended that when the stability and variation of a candidate reference genes in a specific study is unclear the minimum Vn/n + 1 should always be used as this ensures the best and most accurate gene expression value is achieved during RT-qPCR assays.

RNA-seq in Skeletal Biology

PURPOSE OF REVIEW

The goal of this paper is to review state-of-the-art transcriptome profiling methods and their recent applications in the field of skeletal biology.

RECENT FINDINGS

Next-generation sequencing of mRNA (RNA-seq) methods have been established and routinely used in skeletal biology research. RNA-seq has led to the identification of novel genes and transcription factors involved in skeletal development and disease, through its application in small and large animal models, as well as human tissue and cells. With the availability of advanced techniques such as single-cell RNA-seq, novel cell types in skeletal tissues are being identified. As the sequencing technologies are rapidly evolving, the exciting discoveries supported by transcriptomics will continue to emerge and improve our understanding of the biology of the skeleton.

Optimised isolation method for RNA extraction suitable for RNA sequencing from feline teeth collected in a clinical setting and at post mortem

Advanced next generation sequencing approaches have started to reveal the cellular and molecular complexity of the microenvironment in many tissues. It is challenging to obtain high quality RNA from mineralised tissues. We developed an optimised method of RNA extraction from feline teeth collected in a clinical setting and at post mortem. Teeth were homogenised in phenol-guanidinium solution at near-freezing temperatures and followed by solid-phase nucleic acid extraction utilising a commercially available kit. This method produced good RNA yields and improved RNA quality based on RNA integrity numbers equivalent (RIN^e) from an average of 3.6 to 5.6. No correlation was found between RNA purity parameters measured by A_260:280 or A_230:260 ratios and degree of RNA degradation. This implies that RNA purity indicators cannot be reliably used as parameters of RNA integrity. Two reference genes (GAPDH, RPS19) showed significant changes in expression levels by qPCR at low and moderate RIN^e values, while RPL17 was stable at all RIN^e values tested. Furthermore, we investigated the effect of quantity and quality of RNA on the quality of the resultant RNA sequencing (RNA-Seq) data. Thirteen RNA-seq data showed similar duplication and mapping rates (94 to 95%) against the feline genome regardless of RIN^e values. However one low yield sample with a high RIN^e value showed a high duplication rate and it was an outlier on the RNA-seq multidimensional scaling plot. We conclude that the overall yield of RNA was more important than quality of RNA for RNA-seq quality control. These results will guide researchers who wish to perform RNA extractions from mineralised tissues, especially if collecting in a clinical setting with the recognised restraints that this imposes.

Differential inflammatory responses of bovine foot skin fibroblasts and keratinocytes to digital dermatitis treponemes

Bovine digital dermatitis (BDD) is a serious infectious inflammatory lameness causing pain and suffering to many cattle worldwide and which has severe economic implications. This study set out to investigate relationships between the treponemes considered causal of BDD and the local inflammatory response of the bovine host. Here we describe, for the first time, the isolation of bovine foot skin keratinocytes and fibroblasts as separate cell lineages. These cell lines were then exposed to treponeme whole-cell sonicates, and the gene expression of selected host inflammatory mediators investigated using quantitative reverse transcriptase PCR. Several genes, including those encoding RANTES/CCL5, MMP12, TNFα, TGFβ and TIMP3 were significantly upregulated in fibroblasts exposed to whole-cell sonicates derived from BDD treponeme phylotypes. For each of the above genes there were similar fibroblast expression increases for all three BDD treponeme phylotypes tested, suggesting common virulence mechanisms. With bovine foot skin keratinocytes, we were unable to detect expression of RANTES/CCL5 and after incubation with BDD treponeme constituents we were unable to observe any significant changes in expression of inflammatory mediators tested. These contrasting results suggest fibroblasts rather than keratinocytes may be an important shared target of pathogenesis for BDD treponemes.

Histological and molecular characterisation of feline humeral condylar osteoarthritis

Background

Osteoarthritis (OA) is a clinically important and common disease of older cats. The pathological changes and molecular mechanisms which underpin the disease have yet to be described. In this study we evaluated selected histological and transcriptomic measures in the articular cartilage and subchondral bone (SCB) of the humeral condyle of cats with or without OA.

Results

The histomorphometric changes in humeral condyle were concentrated in the medial aspect of the condyle. Cats with OA had a reduction in articular chondrocyte density, an increase in the histopathological score of the articular cartilage and a decrease in the SCB porosity of the medial part of the humeral condyle. An increase in LUM gene expression was observed in OA cartilage from the medial part of the humeral condyle.

Conclusions

Histopathological changes identified in OA of the feline humeral condyle appear to primarily affect the medial aspect of the joint. Histological changes suggest that SCB is involved in the OA process in cats. Differentiating which changes represent OA rather than the aging process, or the effects of obesity and or bodyweight requires further investigation.

Canine tissue-specific expression of multiple small leucine rich proteoglycans

Small leucine rich proteoglycans (SLRPs) are important constituents of extracellular matrix (ECM) and contribute to the production, organization and remodelling of collagen and elastin through complex biological systems. The relative expression and distribution of SLRPs in a variety of different mammalian tissues is poorly characterized. The aim of this study was to map the expression of seven SLRPs (biglycan, versican, prolargin, fibromodulin, osteoglycin, decorin and lumican) in seven tissues (bone, cartilage, cruciate ligament, skin, ventricular myocardium, mitral valve and cornea) in young adult dogs using a combination of quantitative real-time PCR, immunohistochemistry and protein immunoblotting. Clear and consistent patterns of SLRP expression and distribution were identified for the seven tissues examined, with the greatest SLRP expression in cartilage, skin, cornea and mitral valve, and the least expression in myocardium. In general, lumican and prolargin had the greatest expression across the seven tissues whilst osteoglycin was the least abundantly expressed SLRP. These data provide a SLRP profile for different canine tissues which can inform future studies of SLRP expression in development and disease.

Gene expression in canine atopic dermatitis and correlation with clinical severity scores

BACKGROUND

Canine atopic dermatitis (cAD) is a common condition in dogs that may be a naturally occurring model for human atopic dermatitis (hAD). Despite this, comparative research is limited, particularly into the genetic background of cAD.

OBJECTIVES

1. Measure candidate gene expression in cAD skin using quantitative real time PCR (qPCR). 2. Correlate gene expression to clinical cAD scores (Canine Atopic Dermatitis Extent and Severity Index[CADESI]-03 and intradermal allergen test [IDT]).

METHODS

mRNA was extracted from biopsies of non-lesional and lesional skin from atopic dogs, and healthy skin from non-atopic dogs. Gene expression was quantified using qPCR, and compared between non-lesional atopic, lesional atopic and healthy skin. Gene expression in atopic skin was correlated with clinical severity (CADESI-03) and the number of positive reactions on an IDT.

RESULTS

Of the 20 quantified genes, 11 demonstrated statistically significant altered mRNA expression between atopic and healthy skin; dipeptidyl-peptidase-4 (DPP4), phosphatidylinositol-3,4,5-trisphosphate-5-phosphatase-2 (INPPL1), serine protease inhibitor kazal type-5 (SPINK5), sphingosine-1-phosphate lyase-1 (SGPL1), peroxisome proliferator-activated receptor gamma (PPARgamma), S100 calcium-binding protein A8 (S100A8), Plakophilin-2 (PKP2), Periostin (POSTN), Cullin4A, TNF-alpha and metalloproteinase inhibitor-1 (TIMP-1). Three genes correlated with CADESI-03: serum amyloid A 1 (SAA-1), S100A8, and PKP2; and four with IDT results: mast cell protease I (CMA1), SAA-1, S100A8 and SPINK5.

CONCLUSION

Genes with altered expression included those relevant to skin barrier formation and immune function, suggesting both are relevant in the pathogenesis of AD. Many of these genes reflect the proposed pathogenesis in hAD, supporting the use of dogs as a model for hAD. Furthermore, these genes may be considered suitable targets for future genetic and protein function studies in human and canine AD.

Gene expression markers of tendon fibroblasts in normal and diseased tissue compared to monolayer and three dimensional culture systems

BACKGROUND

There is a paucity of data regarding molecular markers that identify the phenotype of the tendon cell. This study aims to quantify gene expression markers that distinguish between tendon fibroblasts and other mesenchymal cells which may be used to investigate tenogenesis.

METHODS

Expression levels for 12 genes representative of musculoskeletal tissues, including the proposed tendon progenitor marker scleraxis, relative to validated reference genes, were evaluated in matched samples of equine tendon (harvested from the superficial digital flexor tendon), cartilage and bone using quantitative PCR (qPCR). Expression levels of genes associated with tendon phenotype were then evaluated in healthy, including developmental, and diseased equine tendon tissue and in tendon fibroblasts maintained in both monolayer culture and in three dimensional (3D) collagen gels.

RESULTS

Significantly increased expression of scleraxis was found in tendon compared with bone (P = 0.002) but not compared to cartilage. High levels of COL1A2 and scleraxis and low levels of tenascin-C were found to be most representative of adult tensional tendon phenotype. While, relative expression of scleraxis in developing mid-gestational tendon or in acute or chronically diseased tendon did not differ significantly from normal adult tendon, tenascin-C message was significantly upregulated in acutely injured equine tendon (P = 0.001). Relative scleraxis gene expression levels in tendon cell monolayer and 3D cultures were significantly lower than in normal adult tendon (P = 0.002, P = 0.02 respectively).

CONCLUSION

The findings of this study indicate that high expression of both COL1A2 and scleraxis, and low expression of tenascin-C is representative of a tensional tendon phenotype. The in vitro culture methods used in these experiments however, may not recapitulate the phenotype of normal tensional tendon fibroblasts in tissues as evidenced by gene expression.

Gene expression profiling of normal and ruptured canine anterior cruciate ligaments

OBJECTIVE

To identify genes which may be involved in the development of anterior cruciate ligament (ACL) laxity and rupture in a naturally occurring canine osteoarthritis (OA) model.

DESIGN

Three groups of dog were studied: (1) dogs with ACL rupture; (2) dogs with intact ACLs from a breed predisposed to ACL rupture; (3) dogs with intact ACLs from a breed at very low risk of rupture. The transcriptomes of the ACLs from each group were compared using a whole genome microarray and quantitative reverse transcriptase polymerase chain reaction. Differential gene expression in ruptured canine ACLs was compared with that published in the literature for ruptured human ACLs.

RESULTS

No significant differences were identified between the gene expression profiles of normal ACLs of a breed predisposed to ACL rupture when compared to a breed relatively resistant to ACL rupture. A general pattern of increased protease and extracellular structural matrix gene expression was identified in the ruptured ACLs when compared to intact ACLs. The gene expression profiles of ruptured canine ACLs demonstrate similar patterns to those previously reported for ruptured human ACLs.

CONCLUSIONS

A transcriptomic basis to breed specific risk for the development of canine ACL rupture was not identified. Although changes in matrix associated gene expression in the ruptured ACL are similar between humans and dogs, the molecular events which may predispose to ACL laxity and rupture were not defined.

Cartilage gene expression correlates with radiographic severity of canine elbow osteoarthritis

The relationship between radiographic measures of severity of osteoarthritis (OA) and changes in gene expression in joints are not well characterised. In this study, the expression of 11 candidate genes was characterised by quantitative reverse transcriptase polymerase chain reaction in normal and OA cartilage and bone from the elbows of dogs with fragmented coronoid disease. The levels of expression of type I collagen alpha2 chain (COL1A2), type III collagen alpha1 chain (COL3A1), lumican (LUM), matrix metalloproteinase-2 (MMP2), -9 (MMP9) and -13 (MMP13) genes were increased and the expression of tissue inhibitor of metalloproteinase-2 (TIMP2) and cathepsin D (CTSD) genes were decreased in OA cartilage relative to normal cartilage. All differences correlated with radiographic measures of severity of OA. Levels of expression of COL1A2, MMP2, MMP9, MMP13 and TIMP1 were increased, whereas expression of TIMP2 was decreased in OA bone relative to normal bone. Cartilage gene expression may be correlated with the radiographic severity of OA.

Identification of new reference genes for the normalisation of canine osteoarthritic joint tissue transcripts from microarray data

BACKGROUND

Real-time reverse transcriptase quantitative polymerase chain reaction (real-time RT-qPCR) is the most accurate measure of gene expression in biological systems. The comparison of different samples requires the transformation of data through a process called normalisation. Reference or housekeeping genes are candidate genes which are selected on the basis of constitutive expression across samples, and allow the quantification of changes in gene expression. At present, no reference gene has been identified for any organism which is universally optimal for use across different tissue types or disease situations. We used microarray data to identify new reference genes generated from total RNA isolated from normal and osteoarthritic canine articular tissues (bone, ligament, cartilage, synovium and fat). RT-qPCR assays were designed and applied to each different articular tissue. Reference gene expression stability and ranking was compared using three different mathematical algorithms.

RESULTS

Twelve new potential reference genes were identified from microarray data. One gene (mitochondrial ribosomal protein S7 [MRPS7]) was stably expressed in all five of the articular tissues evaluated. One gene HIRA interacting protein 5 isoform 2 [HIRP5]) was stably expressed in four of the tissues evaluated. A commonly used reference gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was not stably expressed in any of the tissues evaluated. Most consistent agreement between rank ordering of reference genes was observed between Bestkeeper(c) and geNorm, although each method tended to agree on the identity of the most stably expressed genes and the least stably expressed genes for each tissue. New reference genes identified using microarray data normalised in a conventional manner were more stable than those identified by microarray data normalised by using a real-time RT-qPCR methodology.

CONCLUSION

Microarray data normalised by a conventional manner can be filtered using a simple stepwise procedure to identify new reference genes, some of which will demonstrate good measures of stability. Mitochondrial ribosomal protein S7 is a new reference gene worthy of investigation in other canine tissues and diseases. Different methods of reference gene stability assessment will generally agree on the most and least stably expressed genes, when co-regulation is not present.

Expression stability of commonly used reference genes in canine articular connective tissues

Background

The quantification of gene expression in tissue samples requires the use of reference genes to normalise transcript numbers between different samples. Reference gene stability may vary between different tissues, and between the same tissue in different disease states. We evaluated the stability of 9 reference genes commonly used in human gene expression studies. Real-time reverse transcription PCR and a mathematical algorithm were used to establish which reference genes were most stably expressed in normal and diseased canine articular tissues and two canine cell lines stimulated with lipolysaccaride (LPS).

Results

The optimal reference genes for comparing gene expression data between normal and diseased infrapatella fat pad were RPL13A and YWHAZ (M = 0.56). The ideal reference genes for comparing normal and osteoarthritic (OA) cartilage were RPL13A and SDHA (M = 0.57). The best reference genes for comparing normal and ruptured canine cranial cruciate ligament were B2M and TBP (M = 0.59). The best reference genes for normalising gene expression data from normal and LPS stimulated cell lines were SDHA and YWHAZ (K6) or SDHA and HMBS (DH82), which had expression stability (M) values of 0.05 (K6) and 0.07 (DH82) respectively. The number of reference genes required to reduce pairwise variation (V) to <0.20 was 4 for cell lines, 5 for cartilage, 7 for cranial cruciate ligament and 8 for fat tissue. Reference gene stability was not related to the level of gene expression.

Conclusion

The reference genes demonstrating the most stable expression within each different canine articular tissue were identified, but no single reference gene was identified as having stable expression in all different tissue types. This study underlines the necessity to select reference genes on the basis of tissue and disease specific expression profile evaluation and highlights the requirement for the identification of new reference genes with greater expression stability for use in canine articular tissue gene expression studies.

Expression profiling of select cytokines in canine osteoarthritis tissues

The objective of this study was to investigate the level of expression of five cytokines in four different articular tissues from the joints of dogs with and without osteoarthritis (OA). Articular tissues were harvested from the stifle (fat, cranial cruciate ligament, synovial membrane) or hip (articular cartilage) from eight dogs with OA secondary to cranial cruciate ligament disease (stifle) or hip dysplasia (hip), undergoing routine surgical treatment for the condition, and from five dogs euthanatized without orthopaedic disease. The mRNA transcript numbers for interleukin-1beta (IL-1beta), interleukin-6 (IL-6), interleukin-8 (IL-8), interleukin-10 (IL-10) and interleukin-17 (IL-17) were determined by quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR). Increased expression of IL-1beta, IL-6 and IL-10 in OA synovial membrane, increased expression of IL-1beta and IL-6 in ruptured (OA) ligament, and reduced expression of IL-8 in OA synovial membrane were identified. Cytokine expression was detected in multiple tissues within the articular joint, but differential expression in OA was detected primarily in the synovial membrane and cranial cruciate ligament.

Analysis of normal and osteoarthritic canine cartilage mRNA expression by quantitative polymerase chain reaction

The molecular basis to mammalian osteoarthritis (OA) is unknown. We hypothesised that the expression of selected proteases, matrix molecules, and collagens believed to have a role in the pathogenesis of OA would be changed in naturally occurring canine OA cartilage when compared to normal articular cartilage. Quantitative (real-time) reverse transcriptase-polymerase chain reaction assays were designed measuring the expression of selected matrix molecules (collagens and small leucine-rich proteoglycans), key mediators of the proteolytic degradation of articular cartilage (metalloproteinases, cathepsins), and their inhibitors (tissue inhibitors of matrix metalloproteinases). All data were normalised using a geometric mean of three housekeeping genes, and the results subjected to power calculations and corrections for multiple hypothesis testing. We detected increases in the expression of BGN, COL1A2, COL2A1, COL3A1, COL5A1, CSPG2, CTSB, CTSD, LUM, MMP13, TIMP1, and TNC in naturally occurring canine OA. The expression of TIMP2 and TIMP4 was significantly reduced in canine OA cartilage. The patterns of gene expression change observed in naturally occurring canine OA were similar to those reported in naturally occurring human OA and experimental canine OA. We conclude that the expression profiles of matrix-associated molecules in end-stage mammalian OA may be comparable but that the precise aetiologies of OA affecting specific joints in different species are presently unknown.