Wuhong Tan

Detection of serum proteomic changes and discovery of serum biomarkers for Kashin-Beck disease using surface-enhanced laser desorption ionization mass spectrometry (SELDI-TOF MS)

The purpose of the current study was to investigate the changes of serum proteome and discover potential biomarkers for Kashin-Beck disease (KBD) using surface-enhanced laser desorption ionization mass spectrometry (SELDI-TOF MS). The serum protein profiles from 102 cases (36 KBD patients, 16 controls in KBD areas, 33 controls in non-KBD areas, and 17 osteoarthritis controls) were detected by SELDI-TOF MS and weak cation-exchange protein chip. Differently expressed peaks in KBD were identified by comparing the data among the four groups using the nonparametric Mann-Whitney test with Bonferroni correction at a significance level of 0.05. Then, those 102 cases were used to generate a classification tree as the training set, and an additional 34 cases were collected as the test set. A classification tree was generated by Biomarker Patterns Software (Ciphergen). Multiple protein changes were detected in the KBD group, including three potential biomarkers (15 886, 5336, 6113 m/z). A classification tree with three distinct proteins was generated. The classification tree was able to distinguish the KBD patients from the controls with 88.89% specificity and 86.36% sensitivity. The study demonstrates that marked serum proteomic changes exist in KBD. The proteins represented by the differently expressed peaks are candidate biomarkers for KBD.

Association of TNF-α and Fas gene promoter polymorphism with the risk of Kashin–Beck disease in Northwest Chinese population

The objective of this study is to investigate the relationship between single-nucleotide polymorphisms (SNPs) of the tumor necrosis factor-α (TNF-α) and Fas genes and Kashin–Beck disease (KBD) in Shaanxi province, Northwest in China. Blood samples of 388 residents were collected from 14 KBD villages in Linyou and Yongshou counties, Shaanxi, Northern of China. One hundred eighty-six cases with KBD and 202 cases of health in KBD areas were diagnosed by “Diagnosis Criterion of Kashin–Beck disease in China (WS/T207- 2010)”. The TNF-α −308G/A, TNF-α −238G/A, and Fas −670A/G SNPs were determined by polymerase chain reaction-restriction fragment length polymorphism in combination with sequence analysis in KBD and healthy control groups. The genotypes and allele frequencies distribution of these SNPs were then analyzed. TNF-α −308A allele frequency in KBD patients were significantly higher than that in healthy controls. Although TNF-α −238 genotypes and allele frequencies were not significantly different between KBD patients and the healthy controls, GA genotype and A allele frequency in KBD patients were higher than those in healthy controls. The TNF-α −308G/A SNPs were associated with the susceptibility of KBD.

Comparing gene expression profiles of Kashin-Beck and Keshan diseases occurring within the same endemic areas of China

In this study, differentially expressed genes in peripheral blood from patients with Kashin-Beck disease and Keshan disease were compared to further investigate the etiology and pathogenesis of both diseases, which occur in a common endemic area of China. Twenty Kashin-Beck disease patients and 12 healthy controls, and 16 Keshan disease patients and 16 healthy controls, were grouped into four pairs. Patients and controls were selected from common endemic areas for the two diseases. Total RNA was isolated from peripheral blood mononuclear cells from all patients and controls, and gene expression profiles analyzed by oligonucleotide microarrays. Sixteen genes differentially expressed in both Kashin-Beck disease and Keshan disease (versus controls) were identified, and comprised nine genes showing synchronous and seven asynchronous expression. The Comparative Toxicogenomics Database shows that expression and biological function of these genes can be affected by multiple environmental factors, including mycotoxin and selenium content, potential environmental risk factors for the two diseases. Thus, these shared differentially expressed genes may contribute to the distinct organ lesions, caused by common environmental risk factors of Kashin-Beck disease and Keshan disease.

Mitochondrial-related gene expression profiles suggest an important role of PGC-1alpha in the compensatory mechanism of endemic dilated cardiomyopathy.

Keshan disease (KD) is an endemic dilated cardiomyopathy with unclear etiology. In this study, we compared mitochondrial-related gene expression profiles of peripheral blood mononuclear cells (PBMCs) derived from 16 KD patients and 16 normal controls in KD areas. Total RNA was isolated, amplified, labeled and hybridized to Agilent human 4 × 44k whole genome microarrays. Mitochondrial-related genes were screened out by the Third-Generation Human Mitochondria-Focused cDNA Microarray (hMitChip3). Quantitative real-time PCR, immunohistochemical and biochemical parameters related mitochondrial metabolism were conducted to validate our microarray results. In KD samples, 34 up-regulated genes (ratios ≥ 2.0) were detected by significance analysis of microarrays and ingenuity systems pathway analysis (IPA). The highest ranked molecular and cellular functions of the differentially regulated genes were closely related to amino acid metabolism, free radical scavenging, carbohydrate metabolism, and energy production. Using IPA, 40 significant pathways and four significant networks, involved mainly in apoptosis, mitochondrion dysfunction, and nuclear receptor signaling were identified. Based on our results, we suggest that PGC-1alpha regulated energy metabolism and anti-apoptosis might play an important role in the compensatory mechanism of KD. Our results may lead to the identification of potential diagnostic biomarkers for KD in PBMCs, and may help to understand the pathogenesis of KD.

Selenium deficiency induced damages and altered expressions of metalloproteinases and their inhibitors (MMP1/3, TIMP1/3) in the kidneys of growing rats

Selenium is an essential trace element for the maintenance of structures and functions of kidney. To evaluate the effects of low selenium on the kidneys of growing rats, newborn rats were fed with selenium deficient and normal diets respectively for 109 days. As a result, rats fed with low selenium diets resulted in a decline in the body weight and the concentration of selenium in the kidney, especially the male rats from the low selenium groups. Moreover, the ultrastructure of glomerulus and tubules were damaged in low selenium group: the glomeruli were observed with hyperplasia of mesangial cells, fusion of podocyte foot processes and thickening of basement membrane; and the tubules were observed with vacuolar degenerated epithelial cells, increased edema fluid or protein solution between cells, microvilli edema, increased cell gaps and decreased cell links. Furthermore, the pathological changes in selenium deficient group included the increase of fibers around renal hilum aorta and in the renal collecting duct, and shed of cells in the proximal convoluted tubules. In addition, up-regulated expressions of matrix metalloproteinases (MMP1/3) and down-regulated expressions of their inhibitors (TIMP1/3) at the mRNA and protein levels were also appeared to be relevant to low selenium. The results suggested that low selenium in diet may cause low selenium concentration in the kidney of growing rat and lead to damages of the ultrastructure and extracellular matrix (ECM) of kidney.

Population-based comparative analysis of differentially expressed genes between Kashin–Beck disease grades I and II

Objectives: To identify the differences and similarities of differentially expressed genes in peripheral blood mononuclear cells (PBMCs) between Kashin–Beck disease (KBD) grades I and II. Method: In total, 100 patients with KBD and 100 healthy controls were selected from a KBD endemic area and divided into 100 pairs of KBD vs. controls (50 pairs of patients with KBD grade I and healthy controls, 50 pairs of patients with KBD grade II and healthy controls). RNA was isolated from KBD PBMCs and healthy control PBMCs. Microarray analysis was conducted to identify differentially expressed genes in the different stages of KBD. The microarray data obtained were further confirmed using quantitative real-time polymerase chain reaction (qRT-PCR). Results: In total, eight differentially expressed genes in KBD grade I and 69 differentially expressed genes in KBD grade II were identified. Among these genes, six common genes were differentially expressed in both stages of the disease. The expression ratios of four common genes differed significantly between KBD grades I and II. Based on the expression ratios of the four genes, linear discriminant analysis (LDA) correctly classified the KBD grade (I or II) with 81% accuracy. Conclusions: The similarities and differences of differentially expressed genes in PBMCs of patients with different stages of KBD may play an important role in the pathogenesis of the early phase of KBD. Additionally, six common genes may be considered blood-based genetic biomarkers for the detection and treatment of KBD.

Gene Expression Analysis Suggests Bone Development-Related Genes GDF5 and DIO2 Are Involved in the Development of Kashin-Beck Disease in Children Rather than Adults

Objective To investigate the differences in gene expression between children and adults with Kashin-Beck disease (KBD). Methods 12 children with KBD and 12 healthy children were selected and divided into 4 KBD vs. control pairs matched according to age and gender, with each pair having 3 KBD children and 3 healthy children. Additionally, 15 adults with KBD and 15 healthy adults were selected and divided into 5 KBD vs. control pairs matched according to age and gender, with each pair having 3 KBD adults and 3 healthy adults. Total RNA was isolated from peripheral blood mononuclear cells (PBMCs) respectively. A total of 367 target genes were selected based on previous genome-wide gene expression profile analysis. Expression levels of the 367 genes were evaluated by customized oligonucleotide microarray and the differentially expressed genes were identified. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) was conducted to validate the microarray data. Results A total of 95 (25.9%) genes in KBD children and 158 (43.1%) genes in KBD adults were found to exhibit more than two-fold change in gene expression level relative to healthy controls. By comparing differentially expressed genes identified in KBD children to those of KBD adults, 42 genes were found to be differentially expressed only in KBD children. And 105 genes were found to be differentially expressed only in KBD adults. Further, 16 differentially expressed genes common to both KBD children and adults were found to be asynchronously expressed in KBD children compared to KBD adults. Conclusion Significant differences in gene expression pattern were identified between KBD children and KBD adults, indicating different molecular mechanisms underlying cartilage lesions of KBD children and KBD adults. In addition, bone development-related genes GDF5 (expression ratio = 2.14±0.02) and DIO2 (expression ratio = 0.11±0.05) may contribute to the development of KBD in children rather than in adults.

Mass spectrometry-based proteomic analysis of Kashin-Beck disease

Kashin-Beck disease (KBD) is a degenerative osteoarticular disease of unknown etiology. The management of KBD would benefit from the identification of the biomarkers related to this disease. In this study, mass spectrometry (MS)-based proteomic profiling was used to identify potential biomarkers of the disease. One hundred and sixteen serum samples of KBD cases and healthy controls were collected and analyzed. A framework for data analysis was implemented, which included normalization, denoising using undecimated discrete wavelet transforms, baseline subtraction, peak detection and alignment, non-parametric testing and classification by support vector machine. The method identified correlative mass points and obtained a discriminative pattern with 90.91% sensitivity and 82.61% specificity. The results of this study, although preliminary, suggest that further proteomics study may be useful with a larger number of appropriate specimens, careful experiment manipulation and improved MS techniques.

Serum Biomarkers of Keshan Disease Assessed Using a Protein Profiling Approach Based on ClinProt Technique

The etiology of Keshan disease (KD), an endemic myocardiopathy in regions of China, is largely unknown. To show the protein changes in serum from KD patients versus controls and idiopathic dilated cardiomyopathy (IDCM) and to search specific biological markers for differential diagnosis for KD. Serum of 65 patients with KD was compared with 29 patients with IDCM, 62 controls from KD areas and 28 controls from non-KD areas by ClinProt/MALDI-ToF technique. The genetic algorithm, quick classifier algorithm and supervised neural network algorithm methods were used to screen marker proteins and establish diagnostic model. Thirty-four differential peaks were identified in KD patients compared with the healthy controls from non-KD areas. Thirty-eight differentially peaks were identified in KD patients and controls from KD areas; and sixty-seven differentially peaks were identified in patients with KD and patients with IDCM. We believe that marker protein peaks screened in KD patients, healthy controls and IDCM patients may provide clues for the differential diagnosis and treatment of KD.

Prediction of co-expression genes and integrative analysis of gene microarray and proteomics profile of Keshan disease

Keshan disease (KD) is a kind of endemic cardiomyopathy which has a high mortality. However, molecular mechanism in the pathogenesis of KD remains poorly understood. Serum samples were collected from 112 KD patients and 112 normal controls. Gene microarray was used to screen differently expressed genes. Genevestigator was applied to forecast co-expression genes of significant gene. iTRAQ proteomics analysis was used to verify significant genes and their co-expression genes. GO, COG, IPA and STRING were applied to undertake function categorization, pathway and network analysis separately. We identified 32 differentially expressed genes; IDH2, FEM1A, SSPB1 and their respective 30 co-expression genes; 68 differential proteins in KD. Significant proteins were categorized into 23 biological processes, 16 molecular functions, 16 cellular components, 15 function classes, 13 KD pathways and 1 network. IDH2, FEM1A, SSBP1, CALR, NDUFS2, IDH3A, GAPDH, TCA Cycle II (Eukaryotic) pathway and NADP repair pathway may play important roles in the pathogenesis of KD.