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      Novel lncRNA LncMSTRG.11341.25 Promotes Osteogenic Differentiation of Human Bone Marrow Stem Cells via the miR-939-5p/PAX8 Axis

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          Abstract

          Human bone marrow stem cells (hBMSCs) play an important role during the fracture healing phase. Previous clinical studies by our research group found that fracture healing time was obviously delayed in patients who underwent splenectomy, for combined traumatic fractures and splenic rupture, which is most likely related to the dysregulation of immune inflammatory function of the body after splenectomy. A large number of studies have reported that the inflammatory factor interleukin-1β plays an important role in the multi-directional differentiation ability and immune regulation of BMSC, but its specific regulatory mechanism needs to be further studied. Recently, long noncoding RNAs (lncRNAs) have attracted remarkable attention owing to their close relationship with stem cell osteogenesis and potential role in various bone diseases. In this study, we explored the molecular mechanism of a novel lncRNA, LncMSTRG.11341.25 (LncMSTRG25), in terms of its effects on osteogenic differentiation of hBMSCs. Our results reveal significant up-regulation of LncMSTRG25, osteogenic differentiation markers during the osteogenic differentiation of hBMSCs, and decreased expression of miR-939-5p with an increase in differentiation time. LncMSTRG25 knockdown significantly inhibited the osteogenic ability of hBMSCs. When we knocked down PAX8 alone, we found that the osteogenic ability of hBMSCs was also significantly reduced. The interaction between LncMSTRG25 and PAX8 was verified using the RNA immunoprecipitation assay, RNA pull-down assays, silver staining, and the dual-luciferase reporter. The results show that LncMSTRG25 can function as a sponge to adsorb miR-939-5p, inducing the osteogenic differentiation of hBMSCs by activating PAX8. These findings deepen our understanding of the regulatory role of lncRNA–miRNA–mRNA networks in the immune microenvironment of bone marrow, and highlight the important role played by the spleen as an immune organ in fracture healing.

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          HISAT: a fast spliced aligner with low memory requirements.

          HISAT (hierarchical indexing for spliced alignment of transcripts) is a highly efficient system for aligning reads from RNA sequencing experiments. HISAT uses an indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini (FM) index, employing two types of indexes for alignment: a whole-genome FM index to anchor each alignment and numerous local FM indexes for very rapid extensions of these alignments. HISAT's hierarchical index for the human genome contains 48,000 local FM indexes, each representing a genomic region of ∼64,000 bp. Tests on real and simulated data sets showed that HISAT is the fastest system currently available, with equal or better accuracy than any other method. Despite its large number of indexes, HISAT requires only 4.3 gigabytes of memory. HISAT supports genomes of any size, including those larger than 4 billion bases.
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            ViennaRNA Package 2.0

            Background Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely used as a basis to explain experimental findings. Based on carefully measured thermodynamic parameters, exact dynamic programming algorithms can be used to compute ground states, base pairing probabilities, as well as thermodynamic properties. Results The ViennaRNA Package has been a widely used compilation of RNA secondary structure related computer programs for nearly two decades. Major changes in the structure of the standard energy model, the Turner 2004 parameters, the pervasive use of multi-core CPUs, and an increasing number of algorithmic variants prompted a major technical overhaul of both the underlying RNAlib and the interactive user programs. New features include an expanded repertoire of tools to assess RNA-RNA interactions and restricted ensembles of structures, additional output information such as centroid structures and maximum expected accuracy structures derived from base pairing probabilities, or z-scores for locally stable secondary structures, and support for input in fasta format. Updates were implemented without compromising the computational efficiency of the core algorithms and ensuring compatibility with earlier versions. Conclusions The ViennaRNA Package 2.0, supporting concurrent computations via OpenMP, can be downloaded from http://www.tbi.univie.ac.at/RNA.
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              Endogenous microRNA sponges: evidence and controversy.

              The competitive endogenous RNA (ceRNA) hypothesis proposes that transcripts with shared microRNA (miRNA) binding sites compete for post-transcriptional control. This hypothesis has gained substantial attention as a unifying function for long non-coding RNAs, pseudogene transcripts and circular RNAs, as well as an alternative function for messenger RNAs. Empirical evidence supporting the hypothesis is accumulating but not without attracting scepticism. Recent studies that model transcriptome-wide binding-site abundance suggest that physiological changes in expression of most individual transcripts will not compromise miRNA activity. In this Review, we critically evaluate the evidence for and against the ceRNA hypothesis to assess the impact of endogenous miRNA-sponge interactions.
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                Author and article information

                Journal
                Research (Wash D C)
                Research (Wash D C)
                RESEARCH
                Research
                AAAS
                2639-5274
                06 February 2025
                2025
                : 8
                : 0601
                Affiliations
                [ 1 ]Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430022, China.
                [ 2 ]Department of Orthopaedics, Shengjing Hospital of China Medical University , Shenyang 110004, Liaoning, China.
                [ 3 ] Department of Orthopedics, Wuxi Ninth People’s Hospital Affiliated to Soochow University , Wuxi 214000, Jiangsu, China.
                [ 4 ]Department of Orthopedic, The First Affiliated Hospital of Zhengzhou University , Zhengzhou 450052, China.
                Author notes
                Author information
                https://orcid.org/0009-0008-9983-3825
                Article
                0601
                10.34133/research.0601
                11798881
                39916798
                7230d272-9afd-4629-bd7b-b80c4f513f32
                Copyright © 2025 Feifei Ni et al.

                Exclusive licensee Science and Technology Review Publishing House. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License (CC BY 4.0).

                History
                : 12 November 2024
                : 09 January 2025
                : 11 January 2025
                : 06 February 2025
                Page count
                Figures: 9, Tables: 0, References: 49, Pages: 0
                Funding
                Funded by: National Natural Science Foundation of China, FundRef http://dx.doi.org/10.13039/501100001809;
                Award ID: 81672166
                Award Recipient : hong wang
                Categories
                Research Article
                Health Science

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