The analysis of microRNA expression in tears of Kazakh patients with climatic droplet keratopathy in Xinjiang, China
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ABSTRACT:
PROVIDER: PRJNA859767 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20281222.fastq.gz | Fastqsanger.gz | |||
| SRR20281223.fastq.gz | Fastqsanger.gz | |||
| SRR20281224.fastq.gz | Fastqsanger.gz | |||
| SRR20281225.fastq.gz | Fastqsanger.gz | |||
| SRR20281226.fastq.gz | Fastqsanger.gz |
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Project description:Climatic droplet keratopathy (CDK) is characterized by increased oil-like deposits on the anterior elastic lamina and anterior stromal layer. The pathogenic mechanisms of CDK are poorly understood. Sampling corneal tissue from CDK patients is challenging. Therefore, in this study, we analyzed the microRNA (miRNA) expression profile in tear samples of CDK patients and their putative roles in CDK pathogenesis to identify possible biomarkers.
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Project description:Investigate long non-coding RNA (lncRNA) expression characteristics in the peripheral blood lymphocytes of Xinjiang Kazakh people with essential hypertension.
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Project description:Climatic droplet keratopathy (CDK) is a corneal diseases, which is characterized by increased oil-like deposits on the anterior elastic lamina and anterior stromal layer. Severe CDK can even cause blindness, with no specific available treatment. Besides. CDK is poorly understood in terms of its pathogenic mechanisms. Thus, to determine potential biomarkers for CDK, we analyzed the microRNA expression profile in tear samples from CDK patients and investigated their putative roles in the pathogenesis of CDK. Herein, miRNA sequencing and following bioinformatics analysis was performed to explore the roles of their target genes in CDK. A total of 67 differentially expressed miRNAs were identified, of which 25 were upregulated and 42 were downregulated. qPCR verification showed that among the up- and down-regulated miRNAs, expression of five and six, respectively, was most significantly different.The target genes of the differentially expressed miRNAs are involved in the FoxO signaling pathway, tumor necrosis factor (TNF) signaling pathway, and steroid hormone biosynthesis. Protein-protein interaction network analyses identified 20 hub genes, including PTEN, GSK3B, and SMAD3. In conclusion, the panel of differentially expressed miRNAs identified may have potential utility as early diagnostic biomarkers for CDK. Moreover, the TNF signaling pathway is a new potential target in CDK for the development of treatments.
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Project description:Esophageal squamous cell carcinoma (ESCC) is characterized as a metabolic disorder characterized by lipid metabolic reprogramming. To investigate the regional characteristics of ESCC patients in Xinjiang Province, China, and lipid metabolism, in this study, we described the characteristics of the serum lipid composition in Kazakh ESCC patients by performing an integrated analysis of the transcriptome and lipidomic data. Serum samples from 30 Kazakh ESCC patients and 30 healthy individuals were subjected to targeted lipid metabolomics analysis via UPLC‒MS/MS, while 3 tumor samples and matched adjacent normal tissues from 30 ESCC patients were subjected to transcriptome analysis. Compared with those in the healthy group, we observed obvious changes in the serum lipid subclass content, chain length and unsaturation in the ESCC patients. Integrated lipidomic and transcriptomic analyses revealed that unsaturated fatty acid biosynthesis, fatty acid metabolism, lipid degradation, cholesterol metabolism and the AMPK signaling pathway were enriched in tumor tissues. In addition, RT–qPCR results demonstrated that genes closely related to these pathways were differentially expressed between the ESCC group and the healthy control group. Considering the key role of AMPK in lipid metabolism, we conducted a targeted lipid metabolomics analysis on AMPK-knockdown esophageal cancer cells by UPLC‒MS/MS. These findings suggested that AMPK might be correlated with lipid metabolism in Kazakh ESCC patients, identifying potential therapeutic targets of AMPK and other lipid metabolism-related markers against the progression of ESCC.
2024-01-17 | GSE253171 | GEO
Project description:Differential expression of lncRNA in peripheral blood lymphocytes of Xinjiang Kazakh patients with essential hypertension
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Project description:Genotyping of hundreds of healthy individuals with Kazakh ethnicity as a reference cohort for further genetic investigations
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Project description:The anterior cruciate ligament (ACL) is an essential stabilizer of the tibiofemoral articulation. ACL tears often lead to functional instability and are associated with an increased risk for osteoarthritis. The healing potential of the injured ACL is poorly understood and is considered to be limited. Transcriptome-wide expression profiles of 24 human ACL remnants recovered at the time of surgical reconstruction were analyzed utilizing the Agilent human 8x60K microarray platform. Gene ontology was performed on differentially expressed transcripts based on time-from-injury (acute, <3 months; intermediate, 3-12 months; chronic, >12 months). A subset of transcripts was validated via microfluidic digital polymerase-chain-reaction. Expression of periostin, a highly differentially expressed transcript, was tested by immunohistochemistry. Numerous transcripts covering important functional classifications were differentially expressed by time-from-injury. In acute tears, processes representing angiogenesis were repressed while those representing stem-cell differentiation were elevated. In intermediate tears, processes representing stem-cell proliferation concomitant with cellular component organization/cellular localization were elevated. In chronic tears, processes denoting myosin filament organization were elevated while those representing cellular component organization/cell localization and extracellular matrix organization were repressed. Expression levels of periostin were down-regulated in chronic tears compared to acute (42-fold) and intermediate (29-fold) tears. Immunohistochemistry confirmed a decline in periostin expression in tissues from chronic tears. These findings suggest an initial attempt of the injured ACL to repair, which declines with time-from-injury. These findings have implications for efforts to repair the ACL and may be relevant for reconstruction of the ACL. The functional role of periostin in ACL injuries, and the potential implication for surgical treatment, warrants further investigation. Total RNA obtained frominjured anterior cruciate ligament (ACL) tissues from pateints undergoing ACL surgery.
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Project description:Objective To identify transcript level differences between traumatic and degenerative tears of tendon tissues in shoulder joint using RNA-seq. Methods Tendon tissues were isolated from female and male patients with traumatic or degenerative tears during arthroscopic surgery (N = 31). Differentially expressed transcript were identified and biological processes enriched in traumatic and degenerative tears were probed computationally. Expression pattern of selected transcripts was validated by real-time qPCR. Results We identified 339 and 336 transcripts differentially expressed between traumatic and degenerative tears in females and males respectively at a fold-change greater than |2| and a p-value 0.05. In females, GSTM1, MT1G, S1008A, ACSM3, DSC, FAM110C and VNN2 were the most prominent transcripts elevated in traumatic tears and CHAD, CLEC3A, IBSP, TNMD, APLNR, and CPA3 were most highly repressed in traumatic tears. Transcripts elevated in traumatic tears represented catabolic processes, immune response, and metabolic processes while those repressed in traumatic tears represented tissue morphogenesis and developmental processes, angiogenesis, and extracellular matrix organization. In males, ELOA3B, CXCL8, ADM, TNS4 and SPOCK1 were the most prominent transcripts elevated in traumatic tears and MYL2, TNNC1, MB, CPA3, APLNR, and CA3 were most highly repressed in traumatic tears. Transcripts elevated in traumatic tears represented localization of endoplasmic reticulum, chromosome organization, leukocyte/neutrophil degranulation, and protein transport whereas those repressed in traumatic tears represented muscle development, blood circulation (angiogenesis), and muscle cell differentiation. Numerous novel lncRNAs were also identified to be differentially expressed between traumatic and degenerative tears in both sexes. Conclusions and Clinical Relevance This study improves our molecular understanding of tendon tissues in patients with rotator cuff tendinopathy based on underlying etiology (trauma and degeneration). It also provides new insights into sex-based transcript differences that may help drive clinical decision making in female and male patients with traumatic and degenerative shoulder injuries.
2022-03-15 | GSE180836 | GEO
Project description:Objective: To identify transcript level differences between traumatic and degenerative tears of subacromial bursal tissues in shoulder joint using RNA-seq. Methods: Bursal tissues were collected from female and male patients with traumatic or degenerative tears during arthroscopic surgery (N=32). Differentially expressed transcript between traumatic and degenerative tears were detected by RNA-seq and biological processes were identified computationally. RNA-seq results were selectively validated by real-time qPCR. Results: We identified 334 protein-coding transcripts differentially expressed between traumatic and degenerative tears in females and 167 in males at a fold-change greater than |2| and a P < 0.05. In females, XIRP2, MYL1, MYBPC1, TNNT1, and LMOD2, were the highly expressed in traumatic tears and TPSD1, CDSN, RCVRN, LTBP4, and PTGS1 were prominently repressed in traumatic tears. Transcripts elevated in traumatic tears represented muscle cell differentiation and development, and muscle contraction whereas those elevated in degenerative tears represented cell activation, neutrophil granulation, immune response, and protein transport. In males, AZGP1, CNTFR, COL9A1, ZNF98 and EREG were highly elevated in traumatic tears whereas MYL2, HOXD11, SLC6A7, CADM1, and MMP17 were most highly repressed in traumatic tears. Transcripts elevated in traumatic tears represented metabolic processes, catabolic processes, and transmembrane protein transport while processes related to cell cycle were mainly repressed in traumatic tears. We also identified a number of novel lncRNAs differentially expressed between traumatic and degenerative tears in both females and males. Conclusions: This study increases our molecular understanding of bursal tissues in patients with rotator cuff tendinopathy based on the nature of disease that is trauma or degeneration. These finding also provide new insights into sex-based transcript differences that could inform clinical decision making in treating patients with traumatic and degenerative shoulder injuries.
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