Aqueous extract of Rehmanniae Radix Praeparata improves bone health in ovariectomized rats by modulating the miR-29a-3p/NFIA/Wnt signaling pathway axis

ETHNOPHARMACOLOGICAL RELEVANCE

Rehmanniae Radix Praeparata (RRP), a widely used traditional Chinese medicine and a processed form of Rehmannia glutinosa, is primarily utilized to supplement kidney function and promote bone health. Clinical evidence suggests that RRP exhibits significant efficacy in the treatment of osteoporosis (OP). However, the precise mechanisms underlying its therapeutic effects remain incompletely understood.

AIM OF THE STUDY

OP is a systemic skeletal disorder characterized by reduced bone density and quality, leading to an increased risk of fractures. The aim of this study is to evaluate the effectiveness and underlying mechanisms of RRP in treating OP.

MATERIALS AND METHODS

Ovariectomized (OVX) rats were administered RRP aqueous extract via gavage for three months. After the treatment period, femoral microstructure and osteogenic protein levels were assessed to evaluate the efficacy of RRP. Serum exosomes (Exos) derived from different groups of rats were isolated and characterized. The levels of miR-29a-3p in serum-derived Exos and femoral tissue were quantified. Subsequently, Exos were co-cultured with rat bone marrow mesenchymal stem cells (rBMSCs) to investigate their role in promoting osteogenic differentiation and explore the molecular mechanisms underlying this process, particularly through the miR-29a-3p/NFIA/Wnt signaling pathway axis.

RESULTS

OVX rats exhibited significant bone microdamage. In contrast, the RRP-treated OVX rats showed marked improvements in femoral bone microstructure and increased osteogenic protein expression. MiR-29a-3p levels were elevated in serum-derived Exos from the RRP-treated rats. Furthermore, rBMSCs treated with these Exos displayed an increase in miR-29a-3p expression. Further investigations revealed that miR-29a-3p promoted osteogenesis by inhibiting NFIA expression in both bone tissue and rBMSCs. Overexpression of NFIA reversed the osteogenic effects of miR-29a-3p, confirming NFIA as its direct target and suggesting that miR-29a-3p enhances osteogenesis by inhibiting NFIA. Additionally, NFIA was found to promote the transcription of SFRP1, an inhibitor of the Wnt signaling pathway. Our findings suggest that the RRP aqueous extract increases miR-29a-3p levels in serum Exos, which in turn inhibits NFIA and activates the Wnt signaling pathway, thereby promoting osteogenesis.

CONCLUSION

These findings suggest that the RRP aqueous extract improves bone health and mitigates bone microstructural damage caused by OP through the regulation of the miR-29a-3p/NFIA/Wnt signaling pathway axis.

Single-cell transcriptomic analysis of chondrocytes in cartilage and pathogenesis of osteoarthritis

Chondrocyte is considered the only cell type in cartilage. However, the cell heterogeneity of chondrocytes in human articular cartilage is still not well defined, which hinders our understanding of the pathogenesis of osteoarthritis (OA). Here, we constructed a single-cell transcriptomic atlas of chondrocytes in healthy cartilage and identified nine chondrocyte subsets including homeostatic chondrocytes, proliferate fibrochondrocytes, and hypertrophic chondrocytes (HTC). Interestingly, we identified two distinct HTC subpopulations, among which HTC-1 specifically expressed genes associated with apoptosis and programmed cell death. We identified two main trajectories of chondrocytes, one of which differentiates into fibrochondrocytes, while the other terminates in apoptosis. Comparison of chondrocyte subsets between healthy and OA cartilage showed that proliferate fibrochondrocytes and HTC-1 expanded in OA patients, whereas homeostatic chondrocytes decreased. Interestingly, we discovered an OA-specific proliferate fibrochondrocyte subset that may contribute to the development of OA via inflammation. In summary, this study significantly enhanced our understanding of cell heterogeneity of chondrocytes in articular cartilage and provides insight into the pathogenesis of OA.

Investigating Angiogenesis-Related Biomarkers in Osteoarthritis Patients Through Transcriptomic Profiling

BACKGROUND

Osteoarthritis (OA) is a common age-related joint disease characterized by joint destruction and impaired quality of life. Angiogenesis plays a vital role in OA progression. This study aimed to identify key angiogenesis-related genes (ARGs) in OA using transcriptomic and machine learning methods.

METHODS

The GSE55235 dataset (10 OA and 10 healthy synovial tissue samples) was analyzed for differentially expressed genes (DEGs), integrated with weighted gene co-expression network analysis (WGCNA), and ARGs to identify differentially expressed ARGs (DE-ARGs). Candidate genes were identified through three machine learning algorithms and evaluated using ROC curve analysis. Gene set enrichment analysis (GSEA), immune cell infiltration analysis, and therapeutic agent prediction were performed. Synovial samples from 5 OA patients and 5 matched controls were collected for RT-qPCR validation of biomarkers.

RESULTS

From 1552 DEGs, 11 DE-ARGs were identified, and six candidate genes were selected using machine learning. Four genes-COL3A1, OLR1, STC1, and KCNJ8-showed AUC >0.8 in both GSE55235 and GSE1919, indicating strong diagnostic value. GSEA linked biomarkers to the "lysosome" pathway, and eosinophils and Th2 cells were significantly associated with biomarkers. Potential therapeutic agents included bisphenol A, tetrachlorodibenzo-p-dioxin, and valproic acid. Clinical validation confirmed that COL3A1, OLR1, and STC1 expression levels were consistent with database findings.

CONCLUSION

The study identified COL3A1, OLR1, STC1, and KCNJ8 as key angiogenesis-related biomarkers in osteoarthritis, which could serve as potential diagnostic tools and therapeutic targets. The research underscores the importance of angiogenesis in osteoarthritis progression and suggests that targeting angiogenesis-related pathways may offer new treatment strategies.

Genomic analysis of Nigerian indigenous chickens reveals their genetic diversity and adaptation to heat-stress

Indigenous poultry breeds from Africa can survive in harsh tropical environments (such as long arid seasons, excessive rain and humidity, and extreme heat) and are resilient to disease challenges, but they are not productive compared to their commercial counterparts. Their adaptive characteristics are in response to natural selection or to artificial selection for production traits that have left selection signatures in the genome. Identifying these signatures of positive selection can provide insight into the genetic bases of tropical adaptations observed in indigenous poultry and thereby help to develop robust and high-performing breeds for extreme tropical climates. Here, we present the first large-scale whole-genome sequencing analysis of Nigerian indigenous chickens from different agro-climatic conditions, investigating their genetic diversity and adaptation to tropical hot climates (extreme arid and extreme humid conditions). The study shows a large extant genetic diversity but low level of population differentiation. Using different selection signature analyses, several candidate genes for adaptation were detected, especially in relation to thermotolerance and immune response (e.g., cytochrome P450 2B4-like, TSHR, HSF1, CDC37, SFTPB, HIF3A, SLC44A2, and ILF3 genes). These results have important implications for conserving valuable genetic resources and breeding improvement of chickens for thermotolerance.

NFIA haploinsufficiency: case series and literature review

Background

NFIA-related disorder (OMIM #613735) is an autosomal dominant neurodevelopmental disorder characterized by a variable degree of cognitive impairment and non-specific dysmorphic features. To date, fewer than thirty patients affected by this disorder have been described.

Methods

Our study included three children with NFIA haploinsufficiency recruited from three medical genetics centers. Clinical presentations were recorded on a standardized case report form.

Results

All patients presented a variable degree of intellectual disability. None of the individuals in our cohort had urinary tract malformations. Three novel mutations, c.344G>A, c.261T>G, and c.887_888del are reported here.

Conclusion

NFIA haploinsufficiency can be suspected through careful observation of specific dysmorphisms, including macrocephaly and craniofacial abnormalities. Instrumental tests such as MRI and renal ultrasound provide further diagnostic clues, while genetic testing can confirm the diagnosis.

Molecular mechanism of synovial joint site specification and induction in developing vertebrate limbs

The vertebrate appendage comprises three primary segments, the stylopod, zeugopod and autopod, each separated by joints. The molecular mechanisms governing the specification of joint sites, which define segment lengths and thereby limb architecture, remain largely unknown. Existing literature suggests that reciprocal gradients of retinoic acid (RA) and fibroblast growth factor (FGF) signaling define the expression domains of the putative segment markers Meis1, Hoxa11 and Hoxa13. Barx1 is expressed in the presumptive joint sites. Our data demonstrate that RA-FGF signaling gradients define the expression domain of Barx1 in the first presumptive joint site. When misexpressed, Barx1 induces ectopic interzone-like structures, and its loss of function partially blocks interzone development. Simultaneous perturbations of RA-FGF signaling gradients result in predictable shifts of Barx1 expression domains along the proximo-distal axis and, consequently, in the formation of repositioned joints. Our data suggest that during early limb bud development in chick, Meis1 and Hoxa11 expression domains are overlapping, whereas the Barx1 expression domain resides within the Hoxa11 expression domain. However, once the interzone is formed, the expression domains are refined and the Barx1 expression domain becomes congruent with the border of these two putative segment markers.

DNA Methylation Signatures Reveal the Diversity of Processes Remodeling Hepatocellular Carcinoma Methylomes

BACKGROUND AND AIMS

DNA methylation patterns are highly rearranged in HCCs. However, diverse sources of variation are intermingled in cancer methylomes, precluding the precise characterization of underlying molecular mechanisms. We developed a computational framework (methylation signature analysis with independent component analysis [MethICA]) leveraging independent component analysis to disentangle the diverse processes contributing to DNA methylation changes in tumors.

APPROACH AND RESULTS

Applied to a collection of 738 HCCs, MethICA unraveled 13 stable methylation components preferentially active in specific chromatin states, sequence contexts, and replication timings. These included signatures of general processes associated with sex and age but also signatures related to specific driver events and molecular subgroups. Catenin beta 1 mutations were major modulators of methylation patterns in HCC, characterized by a targeted hypomethylation of transcription factor 7-bound enhancers in the vicinity of Wnt target genes as well as a widespread hypomethylation of late-replicated partially methylated domains. By contrast, demethylation of early replicated highly methylated domains was a signature of replication stress, leading to an extensive hypomethylator phenotype in cyclin-activated HCC. Inactivating mutations of the chromatin remodeler AT-rich interactive domain-containing protein 1A were associated with epigenetic silencing of differentiation-promoting transcriptional networks, also detectable in cirrhotic liver. Finally, a hypermethylation signature targeting polycomb-repressed chromatin domains was identified in the G1 molecular subgroup with progenitor features.

CONCLUSIONS

This study elucidates the diversity of processes remodeling HCC methylomes and reveals the epigenetic and transcriptional impact of driver alterations.

miR-142a-5p promoted osteoblast differentiation via targeting nuclear factor IA

miR-142a-5p plays critical roles in multiple biological processes and diseases, such as inflammation and tumorigenesis. However, it remains to be explored if and how miR-142a-5p contributes to osteoblast differentiation. In this study, our results showed that miR-142a-5p was highly expressed in bone tissue of mice and increased during osteogenesis in preosteoblast MC3T3-E1 cells. Supplementing miR-142a-5p activity using miR-142a-5p agomir promoted osteogenic differentiation in stromal cell line ST2 and preosteoblastic line MC3T3-E1. Conversely, miR-142a-5p antagomir, an inhibitor of endogenous miR-142a-5p, could reduce osteoblast differentiation in ST2 and MC3T3-E1 cells. Nuclear factor IA (NFIA), a site-specific transcriptional factor, was demonstrated to be directly targeted by miR-142a-5p. Overexpression of NFIA inhibited miR-142a-5p-mediated osteoblast differentiation in ST2 cells. Furthermore, mechanism explorations revealed that Wnt/β-catenin signaling transcriptionally regulated the expression of miR-142a-5p during osteogenic differentiation. β-catenin binds to the T-cell factor/lymphoid enhancer factor binding motif within the promoter of miR-142 and positively regulates its transcriptional activity. Our findings suggested that miR-142a-5p promoted osteoblast differentiation via targeting NFIA.

Genome-Wide Differentially Methylated Region Analysis to Reveal Epigenetic Differences of Articular Cartilage in Kashin-Beck Disease and Osteoarthritis

Kashin-Beck disease (KBD) is a degenerative osteoarticular disorder, and displays the significant differences with osteoarthritis (OA) regarding the etiology and molecular changes in articular cartilage. However, the underlying dysfunctions of molecular mechanisms in KBD and OA remain unclear. Here, we primarily performed the various genome-wide differential methylation analyses to reveal the distinct differentially methylated regions (DMRs) in conjunction with corresponding differentially methylated genes (DMGs), and enriched functional pathways in KBD and OA. We identified a total of 131 DMRs in KBD vs. Control, and 58 DMRs in OA vs. Controls, and the results demonstrate that many interesting DMRs are linked to DMGs, such as SMOC2 and HOXD3, which are all key genes to regulate cartilage/skeletal physiologic and pathologic process, and are further enriched in skeletal system and limb-associated pathways. Our DMR analysis indicates that KBD-associated DMRs has higher proportion than OA-associated DMRs in gene body regions. KBD-associated DMGs were enriched in wounding and coagulation-related functional pathways that may be stimulated by trace elements. The identified molecular features provide novel clues for understanding the pathogenetic and therapeutic studies of both KBD and OA.

Biological and Clinical Significance of GATA3 Detected from TCGA Database and FFPE Sample in Bladder Cancer Patients

Purpose

The purpose of the present study was to investigate the biological and clinical significance of GATA binding protein 3 (GATA3) in bladder cancer patients.

Patients and Methods

For the detection of the correlation between GATA3 expression and bladder cancer, we downloaded the mRNA expression data from the Cancer Genome Atlas (TCGA) database and conducted immunohistochemistry staining on formalin-fixed paraffin-embedded (FFPE) sample tissues. Then, bladder cancer cell lines were utilized to investigate the potential functions of GATA3 by cell apoptosis, proliferation and cycle assays.

Results

The mRNA data from TCGA database and bladder cancer cell lines suggested that GATA3 mRNA expression was significantly higher compared with normal tissues and cells. Conversely, the Western blot assay revealed that the expression of GATA3 was significantly lower in bladder cancer than normal urothelial cell line. Additionally, we found that over-expression of GATA3 was significantly associated with tumor subtype (P = 0.001 in TCGA; P = 0.004 in FFPE tissues), earlier clinical stage (P < 0.001 in TCGA; P < 0.001 in FFPE) and lower grade tumor (P = 0.057 in TCGA; P = 0.002 in FFPE). Kaplan-Meier analysis and multivariate Cox regression analysis indicated that age (P < 0.001 in both cohort), clinical stage (P = 0.028 in TCGA; P = 0.011 in FFPE), recurrence (P < 0.001) and low GATA3 in TCGA cohort (P = 0.035) but high GATA3 in FFPE cohort (P = 0.033) were independent risk factors for overall survival in patients. The assay to detect potential functions of GATA3 indicated that this biomarker could arrest the cell cycle of G2/M and S phase in T24 cells, and inhibit bladder cancer cells proliferation.

Conclusion

Collectively, our findings identified that GATA3 served as an important prognosis biomarker for bladder cancer patients. However, the mechanism of GATA3 in bladder cancer deserves further studies.

Identification of genetic loci associated with growth traits at weaning in yak through a genome-wide association study

A multilocus GWAS was performed to explore the genetic architecture of four growth traits in yak. In total, 354 female yaks for which measurements of body weight (BW), withers height (WH), body length (BL) and chest girth (CG) at weaning were available underwent genotyping with the Illumina BovineHD BeadChip (770K). After quality control, we retained 98 688 SNPs and 354 animals for GWAS analysis. We identified seven, 18, seven and nine SNPs (corresponding to seven, 17, seven and eight candidate genes) associated with BW, WH, BL and CG at weaning respectively. Interestingly, most of these candidate genes were reported to be involved in growth-related processes such as muscle formation, lipid deposition, feed efficiency, carcass composition and development of the central and peripheral nervous system. Our results offer novel insight into the molecular architecture underpinning yak growth traits. Further functional analyses are thus warranted to explore the molecular mechanisms whereby these genes affect these traits of interest.

Lgr5 and Col22a1 Mark Progenitor Cells in the Lineage toward Juvenile Articular Chondrocytes

The synovial joint forms from a pool of progenitor cells in the future region of the joint, the interzone. Expression of Gdf5 and Wnt9a has been used to mark the earliest cellular processes in the formation of the interzone and the progenitor cells. However, lineage specification and progression toward the different tissues of the joint are not well understood. Here, by lineage-tracing studies we identify a population of Lgr5+ interzone cells that contribute to the formation of cruciate ligaments, synovial membrane, and articular chondrocytes of the joint. This finding is supported by single-cell transcriptome analyses. We show that Col22a1, a marker of early articular chondrocytes, is co-expressed with Lgr5+ cells prior to cavitation as an important lineage marker specifying the progression toward articular chondrocytes. Lgr5+ cells contribute to the repair of a joint defect with the re-establishment of a Col22a1-expressing superficial layer.

Mechanisms of synovial joint and articular cartilage development

Articular cartilage is formed at the end of epiphyses in the synovial joint cavity and permanently contributes to the smooth movement of synovial joints. Most skeletal elements develop from transient cartilage by a biological process known as endochondral ossification. Accumulating evidence indicates that articular and growth plate cartilage are derived from different cell sources and that different molecules and signaling pathways regulate these two kinds of cartilage. As the first sign of joint development, the interzone emerges at the presumptive joint site within a pre-cartilage tissue. After that, joint cavitation occurs in the center of the interzone, and the cells in the interzone and its surroundings gradually form articular cartilage and the synovial joint. During joint development, the interzone cells continuously migrate out to the epiphyseal cartilage and the surrounding cells influx into the joint region. These complicated phenomena are regulated by various molecules and signaling pathways, including GDF5, Wnt, IHH, PTHrP, BMP, TGF-β, and FGF. Here, we summarize current literature and discuss the molecular mechanisms underlying joint formation and articular development.