Comprehensive selection of reference genes for expression studies in meniscus injury using quantitative real-time PCR

Identification of optimal reference genes in golden Syrian hamster with ethanol- and palmitoleic acid-induced acute pancreatitis using quantitative real-time polymerase chain reaction

BACKGROUND

Acute pancreatitis (AP) is a severe disorder that leads to high morbidity and mortality. Appropriate reference genes are important for gene analysis in AP. This study sought to study the expression stability of several reference genes in the golden Syrian hamster, a model of AP.

METHODS

AP was induced in golden Syrian hamster by intraperitoneal injection of ethanol (1.35 g/kg) and palmitoleic acid (2 mg/kg). The expression of candidate genes, including Actb, Gapdh, Eef2, Ywhaz, Rps18, Hprt1, Tubb, Rpl13a, Nono, and B2m, in hamster pancreas at different time points (1, 3, 6, 9, and 24 h) posttreatment was analyzed using quantitative polymerase chain reaction. The expression stability of these genes was calculated using BestKeeper, Comprehensive Delta CT, NormFinder, and geNorm algorithms and RefFinder software.

RESULTS

Our results show that the expression of these reference genes fluctuated during AP, of which Ywhaz and Gapdh were the most stable genes, whereas Tubb, Eef2, and Actb were the least stable genes. Furthermore, these genes were used to normalize the expression of TNF-α messenger ribonucleic acid in inflamed pancreas.

CONCLUSIONS

In conclusion, Ywhaz and Gapdh were suitable reference genes for gene expression analysis in AP induced in Syrian hamster.

A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets

In the next-generation sequencing era, RT-qPCR is still widely employed to quantify levels of nucleic acids of interest due to its popularity, versatility, and limited costs. The measurement of transcriptional levels through RT-qPCR critically depends on reference genes used for normalization. Here, we devised a strategy to select appropriate reference genes for a specific clinical/experimental setting based on publicly available transcriptomic datasets and a pipeline for RT-qPCR assay design and validation. As a proof-of-principle, we applied this strategy to identify and validate reference genes for transcriptional studies of bone-marrow plasma cells from patients with AL amyloidosis. We performed a systematic review of published literature to compile a list of 163 candidate reference genes for RT-qPCR experiments employing human samples. Next, we interrogated the Gene Expression Omnibus to assess expression levels of these genes in published transcriptomic studies on bone-marrow plasma cells from patients with different plasma cell dyscrasias and identified the most stably expressed genes as candidate normalizing genes. Experimental validation on bone-marrow plasma cells showed the superiority of candidate reference genes identified through this strategy over commonly employed "housekeeping" genes. The strategy presented here may apply to other clinical and experimental settings for which publicly available transcriptomic datasets are available.

Ppia is the most stable housekeeping gene for qRT-PCR normalization in kidneys of three Pkd1-deficient mouse models

Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most common inherited renal disorder, characterized by renal cyst development leading to end-stage renal disease. Although the appropriate choice of suitable reference is critical for quantitative RNA analysis, no comparison of frequently used “housekeeping” genes is available. Here, we determined the validity of 7 candidate housekeeping genes (Actb, Actg1, B2m, Gapdh, Hprt, Pgam1 and Ppia) in kidney tissues from mouse models orthologous to ADPKD, including a cystic mice (CY) 10–12 weeks old (Pkd1^flox/flox:Nestin^cre/Pkd1^flox/−:Nestin^cre, n = 10) and non-cystic (NC) controls (Pkd1^flox/^flox/Pkd1^flox/^-, n = 10), Pkd1-haploinsufficient (HT) mice (Pkd1^+/−, n = 6) and wild-type (WT) controls (Pkd1^+/+, n = 6) and a severely cystic (SC) mice 15 days old (Pkd1^V/V, n = 7) and their controls (CO, n = 5). Gene expression data were analyzed using six distinct statistical softwares. The estimation of the ideal number of genes suggested the use of Ppia alone as sufficient, although not ideal, to analyze groups altogether. Actb, Hprt and Ppia expression profiles were correlated in all samples. Ppia was identified as the most stable housekeeping gene, while Gapdh was the least stable for all kidney samples. Stat3 expression level was consistent with upregulation in SC compared to CO when normalized by Ppia expression. In conclusion, present findings identified Ppia as the best housekeeping gene for CY + NC and SC + CO groups, while Hprt was the best for the HT + WT group.

Stability of housekeeping genes in inflamed joints of spontaneous and collagen-induced arthritis in DBA/1 mice

BACKGROUND

DBA/1 mice arthritis models have contributed to our understanding of human rheumatoid arthritis (RA) and spondyloarthritis (SpA) pathogenesis, as well as the exploration of therapeutic targets for treatment. Quantitative polymerase chain reaction (qPCR) is an indispensable tool in molecular research, which requires reference gene validation to obtain consistent and reliable results.

OBJECTIVE

To determine the stability of candidate reference genes for qPCR in the joint of collagen-induced arthritis (CIA) and spontaneous arthritis (SpAD) DBA/1 mice.

METHODS

The expression of eleven commonly used reference genes (ACTB, B2M, EF1a, GAPDH, HMBS, HPRT, PPIB, RPL13A, SDHA, TBP, and YWHAZ) was assessed by qPCR and the data were compared using delta-Ct methods and the geNorm, NormFinder, and RefFinder software packages. Genes identified as stable in each model were used for the quantification of inflammatory cytokines RESULTS: The gene stabilities differed between the two arthritis models in the DBA/1 mice. EF1a and RPL13A were the best reference genes for SpAD, while RPL13A and TBP were the best for the CIA. These genes allowed the data normalization for the quantification of the inflammatory cytokines in both models; these results showed an increase in the expression of IL-1B, IL-12B, IL-17A, and IL-6 in the inflamed joints. The use of different primer sequences for the same reference gene resulted in different relative quantification values.

CONCLUSION

This study demonstrates that commonly used reference genes may not be suitable for arthritic tissues from DBA/1 mice, and strengthening the principle that meticulous validation of reference genes is essential before each experiment to obtain valid and reproducible qPCR data for analysis or interpretation.

Core-Shell Nanofibrous Scaffolds for Repair of Meniscus Tears

Electrospinning is an attractive method of fabricating nanofibers that replicate the ultrastructure of the human meniscus. However, it is challenging to approximate the mechanical properties of meniscal tissue while maintaining the biocompatibility of collagen fibers. Our objective was to determine if functionalizing polylactic acid (PLA) nanofibers with collagen would enhance their biocompatibility. We therefore used coaxial electrospinning to generate core-shell nanofibers with a core of PLA for mechanical strength and a shell of collagen to enhance cell attachment and matrix synthesis. We characterized the nanostructure of the engineered scaffolds and measured the hydrophilic and mechanical properties. We assessed the performance of human meniscal cells seeded on coaxial electrospun scaffolds to produce meniscal tissue by gene expression and histology. Finally, we investigated whether these cell-seeded scaffolds could repair surgical tears created ex vivo in avascular meniscal explants. Histology, immunohistochemistry, and mechanical testing of ex vivo repair provided evidence of neotissue that was significantly better integrated with the native tissue than with the acellular coaxial electrospun scaffolds. Human meniscal cell-seeded coaxial electrospun scaffolds may have potential in enhancing repair of avascular meniscus tears. Impact Statement The success of any tissue-engineered meniscus graft relies on its ability to mimic native three-dimensional microstructure, support cell growth, produce tissue-specific matrix, and enhance graft integration into the repair site. Polylactic acid scaffolds possess the desired mechanical properties, whereas collagen scaffolds induce better cell attachment and enhanced tissue regeneration. We therefore fabricated nanofibrous scaffolds that combined the properties of two biomaterials. These novel coaxial scaffolds more closely emulated the structure, mechanical properties, and biochemical composition of native meniscal tissue. Our findings of meniscogenic tissue generation and integration in meniscus defects have the potential to be translated to clinical use.

Changes in the expression of matrix extracellular genes and TGFB family members in rotator cuff tears

Lack of synthesis of extracellular matrix compounds may contribute to degeneration of the tendons. Thus, we aimed to evaluate the expression of extracellular matrix and TGFB family members in ruptured and non-ruptured tendons of the rotator cuff, as well as the effect of clinical factors on gene expression in tendon samples, and the relationship between histological findings and altered gene expression. Injured and non-injured supraspinatus tendon samples and subscapular non-injured tendon samples were collected from 38 patients with rotator cuff tears. Non-injured supraspinatus tendons were obtained from eight controls. Specimens were used for histological evaluation, quantification of collagen fibers, and mRNA and protein expression analyses. Increased COL1A1, COL1A2, COL3A1, COL5A1, FN1, TNC, and TGFBR1 mRNA expression was observed in the tear samples (p < 0.05). Duration of symptoms was correlated with the levels of collagen type I/III fibers (p = 0.032; ρ = 0.0447) and FN1 immunostaining (p = 0.031; ρ = 0.417). Smoking was associated with increased frequency of microcysts, myxoid degeneration, and COL5A1, FN1, TNC, and TGFB1 mRNA expression (p < 0.05). FN1 immunostaining was correlated with the number of years of smoking (p = 0.048; ρ = 0.384). Lower levels of collagen type I/III fibers were detected in samples with fissures (0 = 0.046). High frequency of microcysts was associated with increased COL5A1, FN1, and TNC expression (p < 0.05, for all comparisons). Neovascularization was associated with reduced FN1 (p = 0.035) and TGFBR1 expression (p = 0.034). Our findings show differential expression of matrix extracellular genes and TGFB family members in the degeneration process involved in rotator cuff tears. These molecular alterations are influenced by clinical factors. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:2542-2553, 2018.

Selection and validation of suitable reference genes for qRT-PCR analysis in pear leaf tissues under distinct training systems

Training systems generally alter tree architecture, which modulates light microclimate within the canopy, for the purpose of improving photosynthetic efficiency and fruit quality. Gene expression quantification is one of the most important methods for exploring the molecular mechanisms underlying the influence of training systems on pear photosynthesis, and suitable reference genes for gene expression normalization are a prerequisite for this method. In this study, the expression stability of nine common and four novel candidate genes were evaluated in 14 different pear leaf samples in two training systems, including those at four developmental stages (training_period) and from different parts of the trees (training_space), using two distinct algorithms, geNorm and NormFinder. Our results revealed that SKD1 (Suppressor of K⁺Transport Growth Defect1)/ YLS8 (Yellow Leaf Specific 8) and ARM (Armadillo) were the most stable single reference genes for the ‘training_period’ and ‘training_space’ subsets, respectively, although these single genes were not as stable as the optimal pairs of reference genes, SKD1+YLS8 and ARM+YLS8, respectively. Furthermore, the expression levels of the PpsAPX (Ascorbate peroxidase) gene showed that the arbitrary use of reference genes without previous testing could lead to misinterpretation of data. This work constitutes the first systematic analysis regarding the selection of superior reference genes in training system studies, facilitating the elucidation of gene function in pear and providing valuable information for similar studies in other higher plants.

Suitable reference gene selection for gene expression studies in knee osteoarthritis synovium using quantitative PCR analysis

Osteoarthritis (OA) is the leading cause of musculoskeletal disability in the elderly. Insights into the biological features of OA are obtained by characterization of the molecular features by gene expression profiling using reverse transcription-quantitative PCR (RT-qPCR). However, it has recently become evident that the use of suitable reference genes is required for appropriate normalization of this technique. Here total RNA was isolated from the synovium of 18 men and 20 women who underwent total knee arthroplasty for knee OA (KOA). We validated the expression stability of 7 candidate housekeeping genes (ACTB, B2M, GAPDH, HPRT1, RPL13A, SDHA, and YWHAZ) in the synovium of KOA with 3 commonly used algorithms (geNorm, NormFinder, and BestKeeper). Additionally, we evaluated expression profiles of the steroid hormone receptor (AR, ESR1, ESR2, GR, MR, and PR) and proinflammatory cytokines (IL1B and IL6) genes in the synovium and their correlations with the risk factors of KOA, using the most and least stable housekeeping genes for comparison. Results showed that HPRT1 was the most stable gene, whereas B2M was the least stable. RT-qPCR analysis revealed sexually dimorphic expression of AR, IL1B, and IL6; intercorrelations between steroid hormone receptor expression levels and female-specific correlations of IL1B expression with ESR1 and PR expression, IL6 expression with ESR1 and GR expression, and body mass index with AR and PR expression; and the choice of the least stable reference gene altered several correlations and statistical significances. In conclusion, HPRT1 was identified as the suitable reference gene for normalization in the OA synovium.

Identifying optimal reference genes for the normalization of microRNA expression in cucumber under viral stress

Cucumber green mottle mosaic virus (CGMMV) is an economically important pathogen and causes significant reduction of both yield and quality of cucumber (Cucumis sativus). Currently, there were no satisfied strategies for controlling the disease. A better understanding of microRNA (miRNA) expression related to the regulation of plant-virus interactions and virus resistance would be of great assistance when developing control strategies for CGMMV. However, accurate expression analysis is highly dependent on robust and reliable reference gene used as an internal control for normalization of miRNA expression. Most commonly used reference genes involved in CGMMV-infected cucumber are not universally expressed depending on tissue types and stages of plant development. It is therefore crucial to identify suitable reference genes in investigating the role of miRNA expression. In this study, seven reference genes, including Actin, Tubulin, EF-1α, 18S rRNA, Ubiquitin, GAPDH and Cyclophilin, were evaluated for the most accurate results in analyses using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Gene expression was assayed on cucumber leaves, stems and roots that were collected at different days post inoculation with CGMMV. The expression data were analyzed using algorithms including delta-Ct, geNorm, NormFinder, and BestKeeper as well as the comparative tool RefFinder. The reference genes were subsequently validated using miR159. The results showed that EF-1α and GAPDH were the most reliable reference genes for normalizing miRNA expression in leaf, root and stem samples, while Ubiquitin and EF-1α were the most suitable combination overall.

Meniscal Tissue Engineering Using Aligned Collagen Fibrous Scaffolds: Comparison of Different Human Cell Sources

Hydrogel and electrospun scaffold materials support cell attachment and neotissue development and can be tuned to structurally and mechanically resemble native extracellular matrix by altering either electrospun fiber or hydrogel properties. In this study, we examined meniscus tissue generation from different human cell sources including meniscus cells derived from vascular and avascular regions, human bone marrow-derived mesenchymal stem cells, synovial cells, and cells from the infrapatellar fat pad (IPFP). All cells were seeded onto aligned electrospun collagen type I scaffolds and were optionally encapsulated in a tricomponent hydrogel. Single or multilayered constructs were generated and cultivated in defined medium with selected growth factors for 2 weeks. Cell viability, cell morphology, and gene-expression profiles were monitored using confocal microscopy, scanning electron microscopy, and quantitative polymerase chain reaction (qPCR), respectively. Multilayered constructs were examined with histology, immunohistochemistry, qPCR, and for tensile mechanical properties. For all cell types, TGFβ1 and TGFβ3 treatment increased COL1A1, COMP, Tenascin C (TNC), and Scleraxis (SCX) gene expression and deposition of collagen type I protein. IPFP cells generated meniscus-like tissues with higher meniscogenic gene expression, mechanical properties, and better cell distribution compared to other cell types studied. We show proof of concept that electrospun collagen scaffolds support neotissue formation and IPFP cells have potential for use in cell-based meniscus regeneration strategies.

Evaluation of candidate reference genes for RT-qPCR studies in three metabolism related tissues of mice after caloric restriction

Reverse transcription quantitative-polymerase chain reaction (RT-qPCR) is a routine method for gene expression analysis, and reliable results depend on proper normalization by stable reference genes. Caloric restriction (CR) is a robust lifestyle intervention to slow aging and delay onset of age-associated diseases via inducing global changes in gene expression. Reliable normalization of RT-qPCR data becomes crucial in CR studies. In this study, the expression stability of 12 candidate reference genes were evaluated in inguinal white adipose tissue (iWAT), skeletal muscle (Sk.M) and liver of CR mice by using three algorithms, geNorm, NormFinder, and Bestkeeper. Our results showed β2m, Ppia and Hmbs as the most stable genes in iWAT, Sk.M and liver, respectively. Moreover, two reference genes were sufficient to normalize RT-qPCR data in each tissue and the suitable pair of reference genes was β2m-Hprt in iWAT, Ppia-Gusb in Sk.M and Hmbs-β2m in liver. By contrast, the least stable gene in iWAT or Sk.M was Gapdh, and in liver was Pgk1. Furthermore, the expression of Leptin and Ppar-γ were profiled in these tissues to validate the selected reference genes. Our data provided a basis for gene expression analysis in future CR studies.

Differential expression of extracellular matrix genes in glenohumeral capsule of shoulder instability patients

Anterior shoulder instability is a common orthopedic problem. After a traumatic shoulder dislocation, patients present a plastic deformation of the capsule. The shoulder instability biology remains poorly understood. We evaluated the expression of genes that encode the cartilage oligomeric matrix protein (COMP), fibronectin 1 (FN1), tenascin C (TNC) and tenascin XB (TNXB) in the glenohumeral capsule of anterior shoulder instability patients and controls. Moreover, we investigated the associations between gene expression and clinical parameters. The gene expression was evaluated by quantitative reverse transcription-polymerase chain reaction in the antero-inferior (macroscopically injured region), antero-superior and posterior regions of the capsule of 29 patients with shoulder instability and 8 controls. COMP expression was reduced and FN1 and TNC expression was increased in the antero-inferior capsule region of cases compared to controls (p < 0.05). TNC expression was increased in the posterior capsule portion of shoulder instability patients (p = 0.022). COMP expression was reduced in the antero-inferior region compared to the posterior region of shoulder instability patients (p = 0.007). In the antero-inferior region, FN1 expression was increased in the capsule of patients with more than one year of symptoms (p = 0.003) and with recurrent dislocations (p = 0.004) compared with controls. FN1 and TNXB expression was correlated with the duration of symptoms in the posterior region (p < 0.05). Thus, COMP, FN1, TNC and TNXB expression was altered across the capsule of shoulder instability patients. Dislocation episodes modify FN1, TNC and TNXB expression in the injured tissue. COMP altered expression may be associated with capsule integrity after shoulder dislocation, particularly in the macroscopically injured portion.