COL3A1, COL6A3, and SERPINH1 Are Related to Glucocorticoid-Induced Osteoporosis Occurrence According to Integrated Bioinformatics Analysis

Li, Liuxun; Yang, Meiling; Jin, Anmin

doi:10.12659/msm.925474

Cited by 5 publications

(8 citation statements)

References 55 publications

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“…A detailed list of hub genes and top edges for breast cancer data analysis is provided in Section C of the Supplementary Material. From our analyses, multiple collagen genes are detected as hub genes in tumor clusters such as COL6A2, COL3A1 which control the tumor migration involving metastasis (Li et al, 2020). Transcription factors, signaling pathways, and receptors related to cancer can all be modulated by collagen biosynthesis (Xu et al, 2019).…”

Section: Breast Cancer Datamentioning

confidence: 95%

SpaceX: gene co-expression network estimation for spatial transcriptomics

2022

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Motivation The analysis of spatially-resolved transcriptome enables the understanding of the spatial interactions between the cellular environment and transcriptional regulation. In particular, the characterization of the gene-gene co-expression at distinct spatial locations or cell types in the tissue enables delineation of spatial co-regulatory patterns as opposed to standard differential single gene analyses. To enhance the ability and potential of spatial transcriptomics technologies to drive biological discovery, we develop a statistical framework to detect gene co-expression patterns in a spatially structured tissue consisting of different clusters in the form of cell classes or tissue domains. Results We develop SpaceX (spatially dependent gene co-expression network), a Bayesian methodology to identify both shared and cluster-specific co-expression network across genes. SpaceX uses an over-dispersed spatial Poisson model coupled with a high-dimensional factor model which is based on a dimension reduction technique for computational efficiency. We show via simulations, accuracy gains in co-expression network estimation and structure by accounting for (increasing) spatial correlation and appropriate noise distributions. In-depth analysis of two spatial transcriptomics datasets in mouse hypothalamus and human breast cancer using SpaceX, detected multiple hub genes which are related to cognitive abilities for the hypothalamus data and multiple cancer genes (e.g. collagen family) from the tumor region for the breast cancer data. Availability and implementation The SpaceX R-package is available at github.com/bayesrx/SpaceX. Supplementary information Supplementary data are available at bookdown.org/satwik91/SpaceX_supplementary/.

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Section: Breast Cancer Datamentioning

confidence: 95%

SpaceX: gene co-expression network estimation for spatial transcriptomics

2022

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“…It is estimated that osteoporosis affects 200 million people worldwide [ 2 ]. Osteoporosis is a common disorder in women after menopause, and it may also develop in men or in people with hormonal disorders or conditions that require chronic glucocorticoid medications [ 3 ]. Age-related osteoporosis occurs in both women and man, with bone loss beginning from the age of 40 years and continuing for the remainder of adult life [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

Association of Hydrogen Sulfide with Femoral Bone Mineral Density in Osteoporosis Patients: A Preliminary Study

Hao

Gao

et al. 2021

Med Sci Monit

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Background Accumulated evidence has suggested that hydrogen sulfide (H 2 S) has a role in bone formation and bone tissue regeneration. However, it is unknown whether the H 2 S content is associated with bone mineral density (BMD) in patients with osteopenia/osteoporosis. Material/Methods In the present study, we aimed to explore the changes of serum H 2 S in osteopenia and osteoporosis patients. We analyzed femur expression of cystathionine β synthase (CBS), cystathionine γ lyase (CSE), and 3-mercaptopyruvate sulfurtransferase (3-MST), which are key enzymes for generating H 2 S. Results Sixteen (16%) patients had osteopenia, 9 (9%) had osteoporosis, and 75 (75%) had normal BMD. In comparison with patients with normal BMD (controls), the serum levels of H 2 S were unexpectedly increased in patients with osteopenia and osteoporosis. This increase was much higher in patients with osteoporosis than in those with osteopenia. Serum H 2 S levels were negatively correlated with femoral BMD, but not lumbar BMD. Interestingly, the expression of CBS and CSE were downregulated in femur tissues in patients with osteoporosis, whereas the expression of 3-MST remained unchanged. Serum phosphorus levels, alkaline phosphatase, hemoglobin, and triglycerides were found to be closely associated with CBS and CSE scores in femur tissues. Conclusions Serum H 2 S levels and femur CBS and CSE expression may be involved in osteoporosis pathogenesis.

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“…Between ETB and poly, COL3A1, HAPLN1, and SFRP4 are differentially expressed within single cells from each subtype. Mutations in the COL3A1 gene have been linked to arthritis and bone disorders [ 30 ]. HAPLN1 has been linked to RA [ 31 ].…”

Section: Discussionmentioning

confidence: 99%

Single-cell analysis reveals heterogeneity of juvenile idiopathic arthritis fibroblast-like synoviocytes with implications for disease subtype

2022

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Background Fibroblast-like synoviocytes (FLS) play a crucial role in JIA pathogenesis; however, the mechanisms by which they contribute to disease progression are not well described. Previous studies demonstrated that rheumatoid arthritis FLS are heterogeneous, and subpopulations with transformed, aggressive phenotypes cause invasive and destructive disease activity. We employ single-cell RNA-sequencing (scRNA-seq) to investigate JIA FLS heterogeneity and gene expression that distinguishes JIA subtypes. Methods JIA FLS cell lines from three persistent oligoarticular, three pre-extension oligoarticular, and three polyarticular subtypes were cultured. scRNA-seq was performed by Genewiz according to 10 × Genomics Chromium protocols. SeuratR package was used for QC, analysis, and exploration of data. Results FLS are heterogeneous and have characteristics of fibroblasts, chondrocytes, and smooth muscle cells. The chondrocyte-like subpopulation is the predominant cell type and percentages of this subpopulation increase with disease severity. Despite overlapping subpopulations, the chondrocyte-like cells have unique genetic fingerprints that distinguish between JIA subtypes. LRRC15, GREM1, and GREM2 are overexpressed in chondrocyte-like cells from persistent oligoarticular JIA FLS compared to pre-extension oligoarticular JIA FLS. S100A4, TIMP3, and NBL1 are overexpressed in pre-extension oligoarticular JIA FLS compared to polyarticular JIA FLS. CRLF1, MFAP5, and TNXB are overexpressed in persistent oligoarticular JIA FLS compared to polyarticular JIA FLS. Conclusions We found biologically relevant differences in gene expression between JIA subtypes that support a critical role for FLS in pathogenesis. We also demonstrate that gene expression within the chondrocyte-like subpopulation can be used to distinguish between these subtypes.

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COL3A1, COL6A3, and SERPINH1 Are Related to Glucocorticoid-Induced Osteoporosis Occurrence According to Integrated Bioinformatics Analysis

Cited by 5 publications

References 55 publications

SpaceX: gene co-expression network estimation for spatial transcriptomics

SpaceX: gene co-expression network estimation for spatial transcriptomics

Association of Hydrogen Sulfide with Femoral Bone Mineral Density in Osteoporosis Patients: A Preliminary Study

Single-cell analysis reveals heterogeneity of juvenile idiopathic arthritis fibroblast-like synoviocytes with implications for disease subtype

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