Osteogenesis-Related Long Noncoding RNA GAS5 as a Novel Biomarker for Osteonecrosis of Femoral Head
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ABSTRACT:
PROVIDER: PRJEB51292 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR8982050_1.fastq.gz | Fastqsanger.gz | |||
| ERR8982050_2.fastq.gz | Fastqsanger.gz | |||
| ERR8982051_1.fastq.gz | Fastqsanger.gz | |||
| ERR8982051_2.fastq.gz | Fastqsanger.gz | |||
| ERR8982052_1.fastq.gz | Fastqsanger.gz |
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Project description:Subchondral bone samples from six patients who underwent primary total hip arthroplasty (three ONFH patients and three patients in control group with femoral neck fracture) were obtained.
2022-03-12 | E-MTAB-11493 | biostudies-arrayexpress
Project description:We recently showed that microRNA different profile from Trauma-induced osteonecrosis of the femoral head (TIONFH) and healing patients.
2017-09-14 | GSE89587 | GEO
Project description:Background: The lack of effective biomarkers makes it difficult to achieve early diagnosis and intervention for osteonecrosis of the femoral head (ONFH). Hence, we aimed to identify novel long noncoding RNA (lncRNA) biomarkers for ONFH. Methods: High-throughput RNA sequencing was performed to detect lncRNA and mRNA expression levels in subchondral bone samples from three patients with ONFH and three patients with femoral neck fractures. Integrated bioinformatics analyses were conducted to identify lncRNAs associated with ONFH development and their potential functions and signaling pathways. A co-expression network was constructed based on the gene time-series expression data in GSE113253. After selecting lncRNA GAS5 as a novel biomarker for ONFH, bone marrow mesenchymal stem cell (BMSC) osteogenic differentiation assays were performed to verify the association between lncRNA GAS5 and osteogenic differentiation. Alkaline phosphatase (ALP) staining and quantitative reverse transcription polymerase chain reaction (RT-qPCR) were used to measure the osteogenic phenotype and lncRNA GAS5 expression. Finally, for further validation, ONFH rat models were established, and lncRNA GAS5 expression in subchondral bone was detected by RT-qPCR. Results: We identified 126 and 959 differentially expressed lncRNAs and genes, respectively. lncRNA GAS5 expression level was significantly downregulated in patients with ONFH compared to the control group patients. The BMSC osteogenic differentiation assays showed that ALP activity increased gradually from days 3 to 7, while the lncRNA GAS5 expression level was significantly upregulated in the osteogenic differentiation induction groups. Furthermore, in vivo experiments suggested that the bone volume/tissue volume value and trabecular thickness significantly decreased in the ONFH rat model group compared to the control group, whereas the trabecular space significantly increased in the ONFH group compared to the control group. In addition, the lncRNA GAS5 expression level significantly decreased in the ONFH rat model group. Conclusion: The lncRNA GAS5 expression level was highly associated with BMSC osteogenic differentiation and was significantly downregulated in both the subchondral trabecular bone tissue of ONFH patients and ONFH rat models. Therefore, lncRNA GAS5 can serve as an ONFH osteogenic biomarker to provide an effective target for early diagnosis and molecular therapy of ONFH.
| S-EPMC8980611 | biostudies-literature
Project description:Early diagnosis is crucial to increase the chances of conservation treatment for patients with steroid-induced osteonecrosis of the femoral head (SIONFH). This study aimed to identify serum peptides as potential biomarkers to diagnose SIONFH.
2020-06-16 | PXD019805 |
Project description:data-independent Acquisition (DIA) proteomics technology was utilized to identify differentially expressed proteins within bone tissue in Osteonecrosis of the femoral head
2024-01-19 | PXD048708 |
Project description:Early diagnosis and prompt treatment are the key to prevent collapse and delay Steroid-induced Osteonecrosis of the Femoral Head(SONFH) progression.The aim of this study was to identify potential biomarkers for the diagnosis of SONFH, so to improve the efficiency of early diagnosis. Microarray analysis based on the 30 SONFH patients and 10 non-SONFH patients(following steroid administration) was performed to screen SONFH-related genes.
2019-12-31 | GSE123568 | GEO
Project description:Single nucleotide polymorphisms (SNPs) of factor V Leiden have been associated with osteonecrosis of the femoral head (ONFH) in Caucasians but remains controversial in Asians. We used an SNP microarray to screen 55 loci of factor V gene in patients with ONFH of Chinese. Significantly different candidate SNPs at 14 loci were analyzed in 146 patients and 116 healthy controls using MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry and gene sequencing. The factor V Leiden (rs6025) was not found in all participants. Six SNP loci (rs9332595, rs6020, rs9332647, rs3766110, rs10919186, and rs12040141) were confirmed with significant differences in patients but not in controls. The rs6020 G-to-A polymorphism was found in 88.9% of the patients. In addition, a high percentage (84.7%) of the patients had an abnormal coagulation profile that included hyperfibrinogen, elevated fibrinogen degradation products, elevated D-dimer, abnormal protein S, abnormal protein C, or a decrease in anti-thrombin III. Patients with the rs6020 G-to-A polymorphism (mutation) had a higher risk (odds ratio: 4.33; 95% confidence interval: 1.36-13.76) of having coagulation abnormalities than did those without the mutation (wild-type) (p = 0.008). Our findings suggested that the rs6020 polymorphism might be the genetic trait that accounts for the higher prevalence of ONFH in the Chinese population than in Westerners. Exposure to risk factors such as alcohol and steroids in patients with the rs6020 polymorphism causes coagulation abnormalities and, subsequently, thromboembolisms in the femoral head. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples. SNP genotype analysis of Affymetrix 6.0 Chip. SNP arrays was performed for 22 Chinese patients with Osteonecrosis of the Femoral Head.
2014-07-28 | E-GEOD-58951 | biostudies-arrayexpress
Project description:Aims: Steroid-induced osteonecrosis of the femoral head (SIONFH) is a debilitating condition often accompanied by cystic change in the affected bone. Previous studies and our clinical observation have suggested the potential for tissue repair within the cystic change, but the underlying cellular mechanisms remain unclear. This study aims to investigate the heterogeneity of cells in the cystic change region, focusing on chondrocytes and endothelial cells, using single-cell RNA sequencing (scRNA-seq) and subsequent histological validation. Method: Cystic change tissues were obtained from patients undergoing total hip arthroplasty. Single-cell RNA sequencing was performed to identify distinct cell populations, particularly chondrocytes and endothelial cells. Alcian blue staining was employed to detect chondrocytes, while immunohistochemistry (IHC) was used to verify the presence of repair-associated chondrocytes. Additionally, HE staining was performed to further analyze tissue architecture like blood vessels. Results: ScRNA-seq analysis identified two major cell types in the cystic change region: endothelial cells involved in angiogenesis and chondrocytes, which included subpopulations associated with cartilage repair. Alcian blue staining showed strong cartilage matrix staining within the cystic change. Immunohistochemistry further validated the expression of repair-associated markers in the chondrocyte population, suggesting active cartilage repair. Cellular communication analysis revealed intercellular interactions between reparative chondrocyte via matrix proteins (FN1, COL1A1) and integrin receptors on angiogenic endothelial cell, suggesting their potential collaboration in the repair process. Conclusion: This study highlights the positive effects of cystic change region of SIONFH in the process of repair based on clinical observations and single-cell RNA sequencing technology. The presence of functionally distinct cell populations, including angiogenic endothelial cells and repair-associated chondrocytes, within cystic change region of SIONFH. The findings suggest a biological basis for repair in the cystic change tissue, providing insights that may inform future therapeutic strategies targeting bone and cartilage regeneration in osteonecrosis.
2025-09-24 | GSE290411 | GEO
Project description:Single nucleotide polymorphisms (SNPs) of factor V Leiden have been associated with osteonecrosis of the femoral head (ONFH) in Caucasians but remains controversial in Asians. We used an SNP microarray to screen 55 loci of factor V gene in patients with ONFH of Chinese. Significantly different candidate SNPs at 14 loci were analyzed in 146 patients and 116 healthy controls using MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry and gene sequencing. The factor V Leiden (rs6025) was not found in all participants. Six SNP loci (rs9332595, rs6020, rs9332647, rs3766110, rs10919186, and rs12040141) were confirmed with significant differences in patients but not in controls. The rs6020 G-to-A polymorphism was found in 88.9% of the patients. In addition, a high percentage (84.7%) of the patients had an abnormal coagulation profile that included hyperfibrinogen, elevated fibrinogen degradation products, elevated D-dimer, abnormal protein S, abnormal protein C, or a decrease in anti-thrombin III. Patients with the rs6020 G-to-A polymorphism (mutation) had a higher risk (odds ratio: 4.33; 95% confidence interval: 1.36-13.76) of having coagulation abnormalities than did those without the mutation (wild-type) (p = 0.008). Our findings suggested that the rs6020 polymorphism might be the genetic trait that accounts for the higher prevalence of ONFH in the Chinese population than in Westerners. Exposure to risk factors such as alcohol and steroids in patients with the rs6020 polymorphism causes coagulation abnormalities and, subsequently, thromboembolisms in the femoral head.
2014-07-28 | GSE58951 | GEO
Project description:Jianpi Huogu Formula (JPF) has achieved good curative effects in nontraumatic osteonecrosis of the femoral head (NONFH) in clinical practice. However, its underlying pharmacological mechanisms remain unclear. Herein, chemical constituents of JPF were systematically identified by UPLC-Q-TOF-MS, and the putative targets were predicted using TCMIP v2.0 platform. Then, the transcriptomic profiling based on clinical cohorts were carried out to identify the early NONFH-related genes and JPF effective targets. Following network-based calculation and functional enrichment analysis, JPF candidate targets against early NONFH were screened and further validated by a series of in vivo experiments. As a result, a total of 299 chemical constituents in JPF were identified under positive and negative ion mode of mass spectrometry. Pharmacologically, JPF was demonstrated to effectively reduce the content of blood lipids and the number of adipocytes in bone marrow, decrease the serum levels of various inflammatory factors, relieve the joint pain, maintain the normal morphology of bone trabeculae and reduce bone loss of early NONFH rats. Mechanically, JPF markedly suppressed the activities of NAMPT, NMNAT1 and NMNAT3 in the affected femoral head tissues, leading to the reduce of NAD+ synthesis and its mediated ATP synthesis, subsequently promoted the combination of STK11 with energy receptor AMPK, which further reduced the accumulation of cholesterol esters in the liver and the amount of cholesterol esters transported to the blood. In conclusion, JPF may promote the repair of early NONFH with reducing lipid production, improving blood hypercoagulable state and restoring normal bone metabolism by regulating NAMPT/STK11/HMGCR/ACAT1 signal axis.
2025-08-20 | GSE254972 | GEO