PeerJ最新文献

{"title":"The role of transcriptional and epigenetic modifications in astrogliogenesis.","authors":"Shuangping Ma, Lei Wang, Junhe Zhang, Lujing Geng, Junzheng Yang","doi":"10.7717/peerj.18151","DOIUrl":"https://doi.org/10.7717/peerj.18151","url":null,"abstract":"<p><p>Astrocytes are widely distributed and play a critical role in the central nervous system (CNS) of the human brain. During the development of CNS, astrocytes provide essential nutritional and supportive functions for neural cells and are involved in their metabolism and pathological processes. Despite the numerous studies that have reported on the regulation of astrogliogenesis at the transcriptional and epigenetic levels, there is a paucity of literature that provides a comprehensive summary of the key factors influencing this process. In this review, we analyzed the impact of transcription factors (<i>e.g.</i>, NFI, JAK/STAT, BMP, and Ngn2), DNA methylation, histone acetylation, and noncoding RNA on astrocyte behavior and the regulation of astrogliogenesis, hope it enhances our comprehension of the mechanisms underlying astrogliogenesis and offers a theoretical foundation for the treatment of patients with neurological diseases.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11418818/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and expression analyses of SWEET gene family reveal potential roles in plant development, fruit ripening and abiotic stress responses in cranberry (Vaccinium macrocarpon Ait)","authors":"Li Chen, Mingyu Cai, Jiaxin Liu, Xuxin Jiang, Jiayi Liu, Wang Zhenxing, Yunpeng Wang, Yadong Li","doi":"10.7717/peerj.17974","DOIUrl":"https://doi.org/10.7717/peerj.17974","url":null,"abstract":"The sugars will eventually be exported transporter (SWEET) family is a novel class of sugar transporters that play a crucial role in plant growth, development, and responses to stress. Cranberry (Vaccinium macrocarpon Ait.) is a nutritious berry with economic importance, but little is known about SWEET gene family functions in this small fruit. In this research, 13 VmSWEET genes belonging to four clades were identified in the cranberry genome for the first time. In the conserved domains, we observed seven phosphorylation sites and four amino acid residues that might be crucial for the binding function. The majority of VmSWEET genes in each clade shared similar gene structures and conserved motifs, showing that the VmSWEET genes were highly conserved during evolution. Chromosomal localization and duplication analyses showed that VmSWEET genes were unevenly distributed in eight chromosomes and two pairs of them displayed synteny. A total of 79 cis-acting elements were predicted in the promoter regions of VmSWEETs including elements responsive to plant hormones, light, growth and development and stress responses. qRT-PCR analysis showed that VmSWEET10.1 was highly expressed in flowers, VmSWEET16 was highly expressed in upright and runner stems, and VmSWEET3 was highly expressed in the leaves of both types of stems. In fruit, the expression of VmSWEET14 and VmSWEET16 was highest of all members during the young fruit stage and were downregulated as fruit matured. The expression of VmSWEET4 was higher during later developmental stages than earlier developmental stages. Furthermore, qRT-PCR results revealed a significant up-regulation of VmSWEET10.2, under osmotic, saline, salt-alkali, and aluminum stress conditions, suggesting it has a crucial role in mediating plant responses to various environmental stresses. Overall, these results provide new insights into the characteristics and evolution of VmSWEET genes. Moreover, the candidate VmSWEET genes involved in the growth, development and abiotic stress responses can be used for molecular breeding to improve cranberry fruit quality and abiotic stress resistance.","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical outcomes in lupus nephritis patients treated with belimumab in real-life setting: a retrospective comparative study in China","authors":"Zishan Lin, Bingjing Jiang, Wenfeng Wang, Caiming Chen, Yujia Wang, Jianxin Wan, Yanfang Xu","doi":"10.7717/peerj.18028","DOIUrl":"https://doi.org/10.7717/peerj.18028","url":null,"abstract":"Objective The use of belimumab in treating lupus nephritis (LN) patients in China is still in its early stages. This retrospective comparative study aims to delineate the disease activity, associated therapies, clinical outcomes, and adverse events among LN patients treated with belimumab, reflecting real-world experience in southeastern China. Methods From May 2020 to December 2023, 54 LN patients treated with belimumab and 42 LN patients treated with conventional therapy were enrolled. All patients had a follow-up period of more than 3 months. The general information, presenting clinical and laboratory data, and outcomes were collected and compared. Results At 3 months of belimumab treatment, compared to baseline, there was a decrease in proteinuria from 74.1% to 64.8% (p < 0.001), a reduction in hematuria from 59.3% to 37.0% (p = 0.008), and an increase in partial or complete renal response from 53.7% to 75.9% (p < 0.001). The median SLEDAI score decreased from 10 to 5 (p < 0.001), and the proportion of patients achieving low lupus disease activity state (LLDAS) increased from 11.11% to 16.67% (p < 0.001) by the 3-month evaluation. Notably, there were significant reductions in oral corticosteroid dosages, with a median decrease from 30 to 17.5 mg/day (p < 0.001) by 3 months, and the proportion of patients requiring >5 mg/day of steroids decreased from 88.89% at baseline to 79.07% at six months (p < 0.001). Compared to the conventional therapy group, the belimumab group experienced a significant reduction in median steroid dosage and increased the proportion of patients achieving remission or LLDAS. The incidence of treatment-emergent adverse events (TEAEs) was significantly lower in the belimumab group (29.6% vs 52.4%, p = 0.024). Conclusion These findings support the potential of belimumab to improve renal and serological parameters, reduce disease activity, lessen corticosteroid dependence, and decrease the risk of TEAEs, demonstrating its safety and efficacy as an adjunct therapy in LN management.","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Key regulators of vascular calcification in chronic kidney disease: Hyperphosphatemia, BMP2, and RUNX2.","authors":"Xinhua Liang, Yankun Li, Peng Wang, Huafeng Liu","doi":"10.7717/peerj.18063","DOIUrl":"10.7717/peerj.18063","url":null,"abstract":"<p><p>Vascular calcification is quite common in patients with end-stage chronic kidney disease and is a major trigger for cardiovascular complications in these patients. These complications significantly impact the survival rate and long-term prognosis of individuals with chronic kidney disease. Numerous studies have demonstrated that the development of vascular calcification involves various pathophysiological mechanisms, with the osteogenic transdifferentiation of vascular smooth muscle cells (VSMCs) being of utmost importance. High phosphate levels, bone morphogenetic protein 2 (BMP2), and runt-related transcription factor 2 (RUNX2) play crucial roles in the osteogenic transdifferentiation process of VSMCs. This article primarily reviews the molecular mechanisms by which high phosphate, BMP2, and RUNX2 regulate vascular calcification secondary to chronic kidney disease, and discusses the complex interactions among these factors and their impact on the progression of vascular calcification. The insights provided here aim to offer new perspectives for future research on the phenotypic switching and osteogenic transdifferentiation of VSMCs, as well as to aid in optimizing clinical treatment strategies for this condition, bearing significant clinical and scientific implications.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11416758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142292921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacterial co-infection in COVID-19: a call to stay vigilant","authors":"Shengbi Liu, Chao Yu, Qin Tu, Qianming Zhang, Zuowei Fu, Yifeng Huang, Chuan He, Lei Yao","doi":"10.7717/peerj.18041","DOIUrl":"https://doi.org/10.7717/peerj.18041","url":null,"abstract":"Co-infection with diverse bacteria is commonly seen in patients infected with the novel coronavirus, SARS-CoV-2. This type of co-infection significantly impacts the occurrence and development of novel coronavirus infection. Bacterial co-pathogens are typically identified in the respiratory system and blood culture, which complicates the diagnosis, treatment, and prognosis of COVID-19, and even exacerbates the severity of disease symptoms and increases mortality rates. However, the status and impact of bacterial co-infections during the COVID-19 pandemic have not been properly studied. Recently, the amount of literature on the co-infection of SARS-CoV-2 and bacteria has gradually increased, enabling a comprehensive discussion on this type of co-infection. In this study, we focus on bacterial infections in the respiratory system and blood of patients with COVID-19 because these infection types significantly affect the severity and mortality of COVID-19. Furthermore, the progression of COVID-19 has markedly elevated the antimicrobial resistance among specific bacteria, such as Klebsiella pneumoniae, in clinical settings including intensive care units (ICUs). Grasping these resistance patterns is pivotal for the optimal utilization and stewardship of antibiotics, including fluoroquinolones. Our study offers insights into these aspects and serves as a fundamental basis for devising effective therapeutic strategies. We primarily sourced our articles from PubMed, ScienceDirect, Scopus, and Google Scholar. We queried these databases using specific search terms related to COVID-19 and its co-infections with bacteria or fungi, and selectively chose relevant articles for inclusion in our review.","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative analysis of radiological outcomes among cephalomedullary nails: helical, screw and winged screw","authors":"Arman Vahabi, Ali Engin Dastan, Bunyamin Kilicli, Omar Aljasim, Huseyin Gunay, Nadir Ozkayin, Kemal Aktuglu","doi":"10.7717/peerj.18020","DOIUrl":"https://doi.org/10.7717/peerj.18020","url":null,"abstract":"Objective Cephalomedullary nails (CMN) are implants with a high success rate in the surgical treatment of trochanteric fractures. The aim of this study is to compare the radiological outcomes and mechanical complications of femoral trochanteric fractures treated with three different CMNs. Methods Intertrochanteric fractures in patients aged 50 years and older treated with CMN between January 2016 and December 2021 were reviewed retrospectively. A total of 158 cases meeting the criteria were included to final analysis. Cases were divided into three groups based on the type of nail used (helical blade: group 1, n = 54; screw: group 2, n = 53; winged screw: group 3, n = 51). Demographic characteristics, mechanical complications, reduction quality, tip-apex distances (TAD) and Cleveland zones were compared between the groups. Femoral neck shortening, varus collapse, lag sliding, changes in abductor length were compared between study groups. Factors affecting mechanical complications were also analyzed. Results Study groups were homogenic in terms of demographic characteristics, fracture type and reduction quality. Regarding mechanical complications, no statistically significant difference was found between groups. All three implants had similar outcomes on femoral neck shortening, varus collapse and lag sliding. Pooled analysis of 158 cases showed that mechanical complications increase as the quality of reduction decreases (p = 0.000) same applies when TAD alters from the desired range (p = 0.025) and with non-optimally implanted blade according to Cleveland zones (p = 0, 000). Conclusion The radiological outcomes and mechanical complications of helical blade, screw type blade and winged screw type blade proximal femoral nails are similar in selected group. Regardless of the device type, it is necessary to obtain high reduction quality, obtain TAD within described range and optimally place the blade according to Cleveland Zones to reduce the failure rate and avoid complications.","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sandy loam soil maintains better physicochemical parameters and more abundant beneficial microbiomes than clay soil in Stevia rebaudiana cultivation","authors":"Xinjuan Xu, Qingyun Luo, Ningnan Zhang, Yingxia Wu, Qichao Wei, Zhongwen Huang, Caixia Dong","doi":"10.7717/peerj.18010","DOIUrl":"https://doi.org/10.7717/peerj.18010","url":null,"abstract":"Depending on the texture of soil, different physicochemical and microbiological parameters are characterized, and these characteristics are influenced by crop cultivation. Stevia, a popular zero-calorie sweetener crop, is widely cultivated around the world on various soil textures. Sandy loam and clay soil show great differences in physicochemical and biological parameters and are often used for Stevia cultivation. To understand the effects of Stevia cultivation on soil physicochemical and biological features, we investigated the changes of physicochemical and microbiological parameters in sandy loam and clay soil following Stevia cultivation. This study was carried out through different physiological and biochemical assays and microbiomic analysis. The results indicated that the sandy loam soil had significantly lower pH and higher nutrient content in the rhizosphere and bulk soils after the Stevia cultivation. The sandy loam soil maintained higher bacterial diversity and richness than the clay soil after Stevia harvest. Beneficial bacteria such as Dongia, SWB02, Chryseolinea, Bryobacter and Devosia were enriched in the sandy loam soil; however, bacteria such as RB41, Haliangium and Ramlibacter, which are unfavorable for nutrient accumulation, predominated in clay soil. Redundancy analysis indicated that the variation in the composition of bacterial community was mainly driven by soil pH, organic matter, total nitrogen, available phosphorus, and microbial biomass phosphorus. This study provides a deeper understanding of physicochemical and microbiological changes in different soil textures after Stevia cultivation and guidance on fertilizer management for Stevia rotational cultivation.","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of hunting site strategies of the common buzzard Buteo buteo in open landscapes and along expressways","authors":"Paweł Cieśluk, Federico Morelli, Zbigniew Kasprzykowski","doi":"10.7717/peerj.18045","DOIUrl":"https://doi.org/10.7717/peerj.18045","url":null,"abstract":"Background\u0000The expansion of human activities in their many forms increases the frequency, diversity, and scale of human-wildlife interactions. One such negative form is the expansion of road infrastructure, causing road kill and traffic-related noise as well as habitat loss and fragmentation. Even so, habitats around road infrastructure are attractive foraging areas that attract certain bird species. We assessed the impact of road infrastructure on the foraging strategies of the common buzzard Buteo buteo. Methods\u0000Birds were observed during two winter seasons in two land-use types, along an expressway and an open agricultural landscape. Individual birds were tracked for a 10-min sequence as a separate sample was analysed. The material, covering 1,220 min along the expressway, and 1,100 min in the agricultural landscape, was collected. Results\u0000Time spent by buzzards on medium-height sites was higher along the expressway than in farmland. Buzzards changed their hunting sites following the mean wind speed. Also, they more often changed their sites along the expressway than in farmland. The land-use types, snow cover, and the mean wind speed mediated the number of attacks on prey. These results illustrate the high plasticity of the buzzards’ behaviour, which can adapt their hunting strategies to both foraging locations (expressway and farmland) and weather conditions. Roadsides along expressways are attractive foraging areas for this diurnal raptor, so reducing the risk of vehicle collisions with this and other birds of prey may require targeted planning efforts.","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Short- and long-term effects of concurrent aerobic and resistance training on circulating irisin levels in overweight or obese individuals: a systematic review and meta-analysis of randomized controlled trials","authors":"Yang Cheng, Jing Ma, Shumin Bo","doi":"10.7717/peerj.17958","DOIUrl":"https://doi.org/10.7717/peerj.17958","url":null,"abstract":"Background Concurrent training (CT) is emerging as a practical and effective approach to enhance body composition, cardiovascular function, and muscle mass, thereby elevating overall individual health. This study aims to systematically investigate the effects of short- and long-term concurrent aerobic and resistance training on circulating irisin levels in overweight or obese individuals. Methodology The electronic databases, including China National Knowledge Infrastructure, PubMed, Embase, Wan Fang Database, and Web of Science, were systematically searched for articles on “concurrent training” and “irisin” published from their inception to 30 November 2023. The pooled effect size was determined using standardized mean difference (SMD) and corresponding 95% confidence intervals (CIs). The study protocol received registration with the International Prospective Register of Systematic Reviews (CRD42023494163). Results All nine studies, encompassing a total of 264 participants, were randomized controlled trials and met the eligibility criteria. Results indicate that short- and long-term concurrent training moderately increased circulating irisin levels compared to the control group (SMD = 0.56, 95% CI [0.33–0.80], p = 0.00; I2 = 36.6%, heterogeneity p = 0.106). Subgroup analyses revealed that both equal to or less than 10 weeks (SMD = 0.78, 95% CI [0.18–1.37], p = 0.01; I2 = 62.3%, heterogeneity p = 0.03) and more than 10 weeks (SMD = 0.45, 95% CI [0.14–0.76], p = 0.00; I2 = 0%, heterogeneity p = 0.54) of concurrent training significantly increased circulating irisin levels in overweight or obese individuals. There were no significant between-group differences (I2 = 0%, p = 0.34). Additionally, concurrent training significantly increased irisin levels in overweight or obese participants (SMD = 1.06, 95% CI [0.34–1.78], p = 0.00; I2 = 50.6%, heterogeneity p = 0.13) and in type 2 diabetes patients (SMD = 0.70, 95% CI [0.30–1.10], p = 0.00; I2 = 0%, heterogeneity p = 0.99). However, no significant effect was observed in patients with metabolic syndrome (SMD = 0.21, 95% CI [−0.25–0.68], p = 0.37; I2 = 38.7%, heterogeneity p = 0.18). There were significant between-group differences (I2 = 53.9%, p = 0.11). Lastly, concurrent training significantly increased circulating irisin levels in overweight or obese individuals aged 45-60 years (SMD = 0.56, 95% CI [0.25–0.86], p = 0.00; I2 = 6.5%, heterogeneity p = 0.38), and a significant increase in irisin levels was observed 12 h post-intervention (SMD = 0.70, 95% CI [0.35–1.05], p = 0.00; I2 = 0%, heterogeneity p = 0.74). However, none of the above categorical variables showed significant between-group differences. Conclusions Short- and long-term concurrent training can effectively improve circulating irisin levels in overweight or obese individuals. However, the effects of short- and long-term concurrent training should consider the participants’ health status, age, and the timing of post-exercise measurements","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Similarity-based metric analysis approach for predicting osteogenic differentiation correlation coefficients and discovering the novel osteogenic-related gene FOXA1 in BMSCs.","authors":"Lingtong Sun, Juan Chen, Li Jun Li, Lingdi Li","doi":"10.7717/peerj.18068","DOIUrl":"10.7717/peerj.18068","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;As a powerful tool, bioinformatics analysis is playing an increasingly important role in many fields. Osteogenic differentiation is a complex biological process involving the fine regulation of numerous genes and signaling pathways.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Method: &lt;/strong&gt;Osteogenic differentiation-related genes are collected from the online databases. Then, we proposed two indexes Jaccard similarity and Sorensen-Dice similarity to measure the topological relevance of genes in the human PPI network. Furthermore, we selected three pathways involving osteoblast-related transcription factors, osteoblast differentiation, and RUNX2 regulation of osteoblast differentiation for investigation. Subsequently, we performed functional a enrichment analysis of these top-ranked genes to check whether these candidate genes identified by similarity-based metrics are enriched in some specific biological functions and states. we performed a permutation test to investigate the similarity score with four well-known osteogenic differentiation-related pathways including hedgehog signaling pathway, BMP signaling, ERK pathway, and Wnt signaling pathway to check whether these osteogenic differentiation-related pathways can be regulated by FOXA1. Lentiviral transfection was used to knockdown and overexpress gene FOXA1 in human bone mesenchymal stem cells (hBMSCs). Alkaline phosphatase (ALP) staining and Alizarin Red staining (ARS) were employed to investigate osteogenic differentiation of hBMSCs.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Result: &lt;/strong&gt;After data collection, human PPI network involving 19,344 genes is included in our analysis. After simplifying, we used Jaccard and Sorensen-Dice similarity to identify osteogenic differentiation-related genes and integrated into a final similarity matrix. Furthermore, we calculated the sum of similarity scores with these osteogenic differentiation-related genes for each gene and found 337 osteogenic differentiation-related genes are involved in our analysis. We selected three pathways involving osteoblast-related transcription factors, osteoblast differentiation, and RUNX2 regulation of osteoblast differentiation for investigation and performed functional enrichment analysis of these top-ranked 50 genes. The results collectively demonstrate that these candidate genes can indeed capture osteogenic differentiation-related features of hBSMCs. According to the novel analyzing method, we found that these four pathways have significantly higher similarity with FOXA1 than random noise. Moreover, knockdown FOXA1 significantly increased the ALP activity and mineral deposits. Furthermore, overexpression of FOXA1 dramatically decreased the ALP activity and mineral deposits.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;In summary, this study showed that FOXA1 is a novel significant osteogenic differentiation-related transcription factor. Moreover, our study has tightly integrated bioinformatics analysis with biological knowledge, and developed a n","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11416762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142292924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}