Identification of novel genes in aging osteoblasts using next-generation sequencing and bioinformatics

Abstract

During the aging process, impaired osteoblastic function is one key factor of imbalanced bone formation and age-related bone loss. The aim of this study is to explore the differentially expressed genes in normal and aged osteoblasts and to identify genes potentially involved in age-related alteration in bone physiology. Based on next generation sequencing and bioinformatics analysis, 12 differentially expressed microRNAs and 22 differentially expressed genes were identified. Up-regulation of miR-204-5p was validated in an array of osteoporotic hip fracture in the Gene Expression Omnibus database (GSE74209). The putative targets for miR-204-5p were Kruppel-like factor 7 (KLF7) and SRY-box 11 (SOX11). Ingenuity Pathway Analysis identified SOX11, involved in osteoarthritis pathway and differentiation of osteoblasts, together with miR-204-5p, a potential upstream regulator, suggesting the critical role of miR-204-5p-SOX11 regulation in the aging process of human bones. In addition, as semaphorin 3A (SEMA3A) and ephrin type-A receptor 5 (EPHA5) were involved in nervous system related biological functions, we postulated a potential linkage between SEMA3A, EPHA5 and development of neurogenic heterotopic ossification. Our findings implicate new candidate genes in the diagnosis of geriatric musculoskeletal disorders, and provide novel insights that may contribute to the elaboration of new biomarkers for neurogenic heterotopic ossification.

Transcription Factor KLF7 Promotes Osteoclast Differentiation by Suppressing HO-1

“…Recent studies discovered that the TF SREBP2 can promote osteoclast differentiation by affecting the expression of RANKL ( Inoue and Imai, 2014 ). Through bioinformatics analysis, miR-204-5p was found as a key regulator to alter bone health condition in the elderly, while KLF7 was identified as a target gene of miR-204-5p ( Chen et al, 2017 ). Similarly, by utilizing bioinformatics approaches and ChIP assay, this study found that TF KLF7 could bind HO-1 and their expression was negatively correlated.…”

“…For example, a study manifested that the overexpression of KLF7 in bone marrow stromal stem cells can promote the regeneration of sciatic nerve ( Li et al, 2019 ). Recently, a bioinformatics study suggested that KLF7 can affect patient’s BMD, which makes it a key target of osteoporosis ( Chen et al, 2017 ). Due to the limitations of bioinformatic studies, the biological role of KLF7 in osteoporosis has not been fully elucidated yet.…”

Whole exome sequencing identifies a rare variant in DAAM2 as a potential candidate in idiopathic pulmonary ossification

“…Mitchell et al suggested that three candidate variants in ADRB2, TLR4 and CFH are associated with heterotopic ossification (48). SEMA3A was reported to play a role in neurogenic heterotopic ossification (49). However, ACVR1 and GNAS were not found in a mesenteric heterotopic ossification patient, although they were reported to have a potential connection to heterotopic ossification (50-52).…”

Aging, Bone Marrow and Next-Generation Sequencing (NGS): Recent Advances and Future Perspectives

“…However, this ability declines with advancing age, which is now known as stem cell exhaustion, identified as one of the key hallmarks of aging [4,17]. Whilst the different stem cells and immune cells all coexist within the BM niche, how their functions are altered with advancing age have been investigated separately [19]. This section summarises the changes associated with aging amongst the various cell types and the BM in general.…”

“…However, a technique that can provide us with a large amount of data at the genetic level for the identification of new pathways would be ideal for evaluating age-related changes in the BM. Next-generation sequencing (NGS) provides us with exactly that, making it among the most desirable techniques for studying changes with advancing age [18,19].…”