Normalization strategies for mRNA expression data in cartilage research

OBJECTIVE: Normalization of mRNA data, i.e., the calculation of mRNA expression values comparable in between different experiments, is a major issue in biomedical and orthopaedic/rheumatology research, both for single-gene technologies [Northern blotting, conventional and quantitative polymerase chain reaction (qPCR)] and large-scale gene expression experiments. In this study, we tested several established normalization methods for their effects on gene expression measurements. METHOD: Five standard normalization strategies were applied on a previously published data set comparing peripheral and central late stage osteoarthritic cartilage samples. RESULTS: The different normalization procedures had profound effects on the distribution as well as the significance values of the gene expression levels. All applied normalization procedures, except the median absolute deviation scaling, showed a bias towards up- or down-regulation of genes as visualized in volcano plots. Of interest, the P-values were much more depending on the normalization procedure than the fold changes. Ten commonly used housekeeping genes showed a significant variability in between the different specimens investigated. The gene expression analysis by cDNA arrays was confirmed for these genes by qPCR. CONCLUSION: This study documents how much normalization strategies influence the outcome of gene expression profiling analysis (i.e., the detection of regulated genes). Different normalization approaches can significantly change the P-values and fold changes of a large number of genes. Thus, it is of vital importance to check every individual step of gene expression data analysis for its appropriateness. The use of global robustness and quality measures for analyzing individual outcomes can help in estimating the reliability of final microarray study results.     

微小RNAs在骨与软骨组织中的调节作用

目的对微小RNAs(microRNAs,miRNAs)在骨与软骨组织中的调控作用和作用机制作一综述。方法广泛查阅近年来有关miRNAs在骨与软骨组织的调控作用及作用机制的文献,进行总结与分析。结果 miRNAs是近年来骨关节疾病研究的热点,越来越多研究显示其在骨与软骨组织形成和代谢过程中,对于细胞分化、细胞基质分泌等方面发挥重要的调控作用,但确切机制尚不清楚。结论 通过对miRNAs在骨与软骨组织中的调控作用及作用机制的研究,可能为了解退行性骨关节疾病开辟新的领域。     

Developmental expression of creatine kinase isoenzymes in chicken growth cartilage.

We have shown previously that creatine kinase (CK) activity is required for normal development and mineralization of chicken growth cartilage and that expression of the cytosolic isoforms of CK is related to the biosynthetic and energy status of the chondrocyte. In this study, we have characterized changes in isoenzyme activity and mRNA levels of CK (muscle-specific CK, M-CK; brain-type CK, B-CK; and mitochondrial CK subunits, MiaCK and MibCK) in the growth plate in situ and in chondrocyte culture systems that model the development/maturation program of the cartilage. The in vitro culture systems analyzed were as follows: tibial chondrocytes, which undergo hypertrophy; embryonic cephalic and caudal sternal chondrocytes, which differ from each other in their mineralization response to retinoic acid; and long-term micromass cultures of embryonic limb mesenchymal cells, which recapitulate the chondrocyte differentiation program. In all systems analyzed, B-CK was found to be the predominant isoform. In the growth plate, B-CK expression was highest in the most calcified regions, and M-CK was less abundant than B-CK in all regions of the growth plate. In tibial chondrocytes, an increase in B-CK expression was seen when the cells became hypertrophic. Expression of B-CK increased slightly over 15 days in mineralizing, retinoic acid-treated cephalic chondrocytes, but it decreased in nonmineralizing caudal chondrocytes, while there was little expression of M-CK. Interestingly, in limb mesenchyme cultures, significant M-CK expression was detected during chondrogenesis (days 2-7), whereas hypertrophic cells expressed only B-CK. Finally, expression of MiaCK and MibCK was low both in situ and in vitro. These observations suggest that the CK genes are differentially regulated during cartilage development and maturation and that an increase in CK expression is important in initiating chondrocyte maturation.     

骨形态发生蛋白-2对椎间盘细胞软骨特异性基因 mRNA的调节作用

目的探讨骨形态发生蛋白(BMP)-2对椎间盘细胞软骨特异性基因Sox9、Ⅱ型胶原和蛋白聚糖基因的调控作用.方法应用逆转录-聚合酶链反应(RT-PCR)技术检测BMP-2对培养的人椎间盘细胞中Sox9、Ⅱ型胶原和蛋白聚糖基因 mRNA表达的调控作用.结果在BMP-2浓度为100 μg/L(0.149±0.006,P<0.05)和1 000 μg/L(0.163±0.006,P<0.01)时,其对椎间盘细胞中Sox9基因 mRNA可起到显著的正向调控作用;在此浓度下,它也可以对Ⅱ型胶原和蛋白聚糖基因mRNA起到正向调控作用.结论 BMP-2可以按照剂量依赖方式正向调控椎间盘细胞中Sox9、Ⅱ型胶原和蛋白聚糖基因的表达.     

Developmental changes in cyclooxygenase mRNA expression in the kidney of rats

Prostaglandins, synthesized by cyclooxygenase (COX), regulate renal hemodynamics and also epithelial water and solute transport. To determine whether COX mRNA expression changes with age, we studied expression in renal medulla and in cortex in developing rats at various ages. We also examined age-related changes in COX mRNA expression induced by lipopolysaccharide (LPS). COX mRNA was quantitatively analyzed in a real-time polymerase chain reaction (PCR) with dual-labeled fluorogenic probes. COX-1 mRNA expression did not change with age in cortex or medulla. COX-2 mRNA expression was highest in 1-week-old rats and lowest in 4- and 8-week-old rats. Lipopolysaccharide treatment did not alter COX-1 mRNA expression in infantile or adult rats. In adults, LPS at 1, 5, and 10 mg/kg induced COX-2 mRNA expression in renal medulla; the higher doses, 5 and 10 mg/kg, induced COX-2 expression in cortex. In infantile rats, COX-2 mRNA, already high in the unmanipulated state, was further increased by only 1 mg/kg LPS in both renal cortex and medulla. Age-related changes in the expression of COX-2 mRNA might be responsible for changing physiologic characteristics of renal function during postnatal development in rats, and may be important in renal cortical development.     

Developmental regulation of creatine kinase activity in cells of the epiphyseal growth cartilage.

During the process of endochondral bone formation, the maturing chondrocyte exhibits profound changes in energy metabolism. To explore the mechanism of energy conservation in cartilage we examined the expression of creatine kinase, an enzyme that catalyzes the formation of ATP in tissues under oxygen stress. Measurement of creatine kinase activity and cytochemical assessment of enzyme distribution clearly showed that the level of enzyme activity was related to chondrocyte maturation. Thus, as the cells hypertrophied, there was a progressive increase in creatine kinase activity. Similarly, an elevation in creatine kinase activity was noted in chondrocyte cultures as the cells assumed an hypertrophic state. When cartilage calcification was disturbed by rickets, there was a decrease in enzyme activity in the hypertrophic region. Studies were performed to examine the creatine kinase isozyme profile of cells of the epiphysis. In resting and proliferating cartilage, the isoform was MM. In hypertrophic cartilage, the predominant isoforms were MB and BB. In terms of the creatine phosphate content, the highest values were seen in the proliferative region; lower amounts were present in hypertrophic and resting cartilage; and no creatine phosphate was detected in calcified cartilage. These data suggest that turnover of creatine phosphate is greatest in the mineralized region of the epiphysis. The results of these investigations point to creatine kinase as being under developmental control. The activity of the enzyme in cartilage cells should serve as a marker of developmental events associated with chondrocyte proliferation, hypertrophy, and mineralization.     

白细胞介素1对椎间盘细胞软骨特异性基因Sox9 mRNA的调节作用

目的探讨白细胞介素1（interleukin-1,IL-1）对人椎间盘细胞软骨特异性基因Sox9和Ⅱ型胶原基因表达的调节作用。方法应用RT—PCR技术检测IL-1对培养的椎间盘细胞中软骨特异性基因so西和Ⅱ型胶原基因mRNA表达的调节作用。结果在IL-1浓度为0．1ng／ml、1ng／ml和10ng／ml培养24h时,其对椎间盘细胞Sox9和Ⅱ型胶原基因mRNA可起到显著的负向调控作用;10ng／ml的IL-1随着培养时间的延长对椎间盘细胞中Sox9和Ⅱ型胶原基因mRNA出现显著的负向调控作用。结论IL-1可以按照剂量及时间依赖方式负向调节椎间盘细胞Sox9和Ⅱ型胶原基因的表达。     

Wnt-mediated reciprocal regulation between cartilage and bone development during endochondral ossification

The role of Wnt signaling is extensively studied in skeletal development and postnatal bone remodeling, mostly based on the genetic approaches of β-catenin manipulation. However, given their independent function, a requirement for β-catenin is not the same as that for Wnt. Here, we investigated the effect of Wnt proteins in both tissues through generating cartilage- or bone-specific Wls null mice, respectively. Depletion of Wls by Col2-Cre, which would block Wnt secretion in the chondrocytes and perichondrium, delayed chondrocyte hypertrophy in the growth plate and impaired perichondrial osteogenesis. Loss of Wls in chondrocytes also disturbed the proliferating chondrocyte morphology and division orientation, which was similar to the defect observed in Wnt5a null mice. On the other hand, inactivation of Wls in osteoblasts by Col1-Cre resulted in a shorter hypertrophic zone and an increase of TRAP positive cell number in the chondro-osseous junction of growth plate, coupled with a decrease in bone mass. Taken together, our studies reveal that Wnt proteins not only modulate differentiation and cellular communication within populations of chondrocytes, but also mediate the cross regulation between the chondrocytes and osteoblasts in growth plate.     

Genetic and nongenetic regulation of CAPN10 mRNA expression in skeletal muscle

The gene encoding calpain-10 (CAPN10) has been identified as a candidate gene for type 2 diabetes. Our aim was to study the impact of genetic (heritability and polymorphisms) and nongenetic (insulin, free fatty acids, and age) factors on CAPN10 mRNA expression in skeletal muscle using two different study designs. Muscle biopsies were obtained before and after hyperinsulinemic-euglycemic clamps from 166 young and elderly monozygotic and dizygotic twins as well as from 15 subjects with normal (NGT) or impaired glucose tolerance (IGT) exposed to an Intralipid infusion. We found hereditary effects on both basal and insulin-exposed CAPN10 mRNA expression. Carriers of the type 2 diabetes-associated single nucleotide polymorphism (SNP)-43 G/G genotype had reduced CAPN10 mRNA levels compared with subjects carrying the SNP-43 A-allele. Age had no significant influence on CAPN10 mRNA levels. Insulin had no significant effect on CAPN10 mRNA levels, neither in the twins nor in the basal state of the Intralipid study. However, after a 24-h infusion of Intralipid, we noted a significant increase in CAPN10 mRNA in response to insulin in subjects with NGT but not in subjects with IGT. In conclusion, we provide evidence that mRNA expression of CAPN10 in skeletal muscle is under genetic control. Glucose-tolerant but not glucose-intolerant individuals upregulate their CAPN10 mRNA levels in response to prolonged exposure to fat.     

趋化素样因子超家族在小鼠睾丸中的基因发育表达调控和蛋白表达定位

目的研究CKLFSF2小鼠同源序列cklfsf26基因在睾丸组织发育中的表达和定位,为其功能研究做出提示。方法利用RT-PCR方法检测cklfsf26基因在不同周龄小鼠睾丸组织中的表达情况；制备cklfsf2b多克隆抗体,利用免疫组织化学方法,检测cklfsf2b蛋白在小鼠睾丸组织中的表达定位。结果cklfsf2bmRNA在出生后第2周内出现,表达量逐渐增加,在成年前即达高峰并持续表达。cklfsf2b蛋白特异性的表达于睾丸Leydig细胞和Sertoli细胞,阳性信号均位于胞质内。结论cklfsf2b基因存在发育的表达调控,随着睾丸发育的日趋成熟,表达量逐渐增加：在Leydig细胞和Sertoli细胞的特异性表达表明其在睾酮合成和精子发生中均可能发挥作用,但其具体功能还需深入研究。     

Gene and protein expression of brain-derived neurotrophic factor and TrkB in bone and cartilage

Gene and protein expressions of brain-derived neurotrophic factor (BDNF) and TrkB, the high-affinity receptor of BDNF, were investigated in the femur and mandibular condyle of rats by in situ hybridization and immunohistochemistry. BDNF and TrkB mRNA showed overlapped expression in chondrocytes in proliferating and mature zones of the epiphyseal growth plate cartilage and mandibular condylar cartilage, and in cuboidal-shaped active osteoblasts at the site of endochondral and intramembranous ossification and in trabecular bone. Expression of BDNF protein also showed a similar localization. The present study suggests that BDNF may participate in regulating the development and remodeling of bony tissue in the developing rat.     

骨调素在骨骼代谢中的表达与调控

本文对骨调素（OPN）的分子结构及其基因表达与调控和在骨骼重建过程中的作用进行了详细的综述。