Biology Direct最新文献

{"title":"c-Jun promotes neuroblastoma cell differentiation by inhibiting APC formation via CDC16 and reduces neuroblastoma malignancy.","authors":"Yunyun Wang, Jingjing Huang, Zhenhua Song, Shuo Zhang, Haojie Guo, Qi Leng, Na Fang, Shaoping Ji, Jian Yang","doi":"10.1186/s13062-025-00630-1","DOIUrl":"10.1186/s13062-025-00630-1","url":null,"abstract":"<p><p>Neuroblastoma is a pediatric embryonal malignancy characterized by impaired neuronal differentiation. Differentiation status in neuroblastoma strongly affects the clinical outcome, thus, enforcement of differentiation becomes a treatment strategy for this disease. However, the molecular mechanisms that control neuroblastoma differentiation are poorly understood. As an extensively studied protein of the activator protein-1 (AP-1) complex, c-Jun is involved in numerous cell regulations such as proliferation, survival and differentiation. In the current study, we demonstrated that c-Jun expression was upregulated by retinoic acid (RA) and flow cytometry assay indicated c-Jun overexpression arrested cell cycle to G1 phase, which, in turn, promoted the initiation of neuroblastoma cell differentiation. Co-immunoprecipitation (co-IP) assay showed that c-Jun competitively interacted with CDC16, a key subunit in anaphase-promoting complex (APC), resulting in reduced APC formation and inhibition of cell cycle progression. Furthermore, EdU proliferation assay and transwell experiment showed that c-Jun overexpression inhibited neuroblastoma cell proliferation and migration via interacting and sequestering CDC16. These findings identify c-Jun as a key regulator of neuroblastoma cell cycle and differentiation and may represent a promising therapeutic target to induce neuroblastoma differentiation via the interaction between c-Jun and CDC16.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"20 1","pages":"37"},"PeriodicalIF":5.7,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948754/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143728598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Circulating extracellular vesicles regulate ELAVL1 by delivering miR-133a-3p which affecting NLRP3 mRNA stability inhibiting PANoptosome formation.","authors":"Deliang Wang, Zheng Dai, Lu Jiang, Ke Liu","doi":"10.1186/s13062-025-00605-2","DOIUrl":"10.1186/s13062-025-00605-2","url":null,"abstract":"<p><strong>Background: </strong>In the quest to elucidate novel therapeutic strategies for myocardial injury, recent investigations have underscored the pivotal roles played by circulating extracellular vesicles (EVs) in intercellular communication.</p><p><strong>Method: </strong>EVs were extracted from individuals who had experienced AMI-EVs and those who were N-EVs. To assess the impact of circulating EVs on cardiomyocyte and endothelial cell proliferation, apoptosis, migration, and tube formation, a range of in vitro assays such as CCK8, EdU assays, flow cytometry, wound healing assays and angiogenesis assays were conducted. Differentially expressed miRNAs in EVs were validated using microarray analysis and real-time PCR. Through bioinformatics analysis, ELAVL1 was identified as a potential downstream target of miR-133a-3p. This finding was further confirmed by conducting dual-luciferase reporter assay and RNA co-immunoprecipitation experiments. To investigate the regulatory effects of circulating EVs from various sources on myocardial injury and PANoptosis, an animal model of ischemia-reperfusion-induced myocardial injury was established.</p><p><strong>Result: </strong>Our findings revealed that circulating EVs effectively deliver miR-133a-3p to target cells, where it binds to ELAVL1, leading to a decrease in NLRP3 mRNA stability. This reduction in NLRP3 mRNA stability subsequently inhibits the assembly of the PANoptosome, a multi-protein complex implicated in PANoptosis. As a result, we observed a significant mitigation of PANoptosis in our myocardial injury models, demonstrating the protective role of miR-133a-3p against excessive cell death.</p><p><strong>Conclusion: </strong>The present study underscores the regulatory role of circulating EV-delivered miR-133a-3p in modulating PANoptosis through ELAVL1-mediated NLRP3 mRNA stabilization. This mechanism represents a potential therapeutic target for attenuating myocardial injury by suppressing PANoptosis.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"20 1","pages":"36"},"PeriodicalIF":5.7,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948929/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143717799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prognostic and immunological implications of protein kinases in gastric cancer: a focus on hub gene ABL2 and its impact on the polarization of M2 macrophages.","authors":"Di Chen, Ju Huang, Aiming Yang, Zhifan Xiong","doi":"10.1186/s13062-025-00636-9","DOIUrl":"10.1186/s13062-025-00636-9","url":null,"abstract":"<p><strong>Background: </strong>Protein kinases are essential cellular signal modulators involved in tumorigenesis, metastasis, immune response, and drug resistance. However, the comprehensive features and clinical significance of protein kinases in gastric cancer (GC) remain inconclusive.</p><p><strong>Methods: </strong>We analyzed the transcriptional profiles of protein kinases in GC patients from the GEO and TCGA databases. Based on differentially expressed kinase genes (DE-KGs), a novel cluster was identified to assess its association with patient survival and the tumor microenvironment (TME) in GC. Subsequently, an optimal DE-KGs-based model (DE-KGsM) was determined using 101 machine-learning algorithm combinations. This model was evaluated using multi-omics data to investigate its associations with patient prognosis, clinical features, tumor microenvironment, tumor-infiltrating immune cells (TIICs), and immunotherapy response. Furthermore, scRNA-seq analysis and TIMER algorithm were applied to determine the correlation between the hub gene (ABL2) in the DE-KGsM and Macrophages. Finally, in vitro experiments were performed to explore the immune-related mechanisms of ABL2 in GC.</p><p><strong>Results: </strong>We identified two molecular subtypes of GC patients based on 64 DE-KGs expression. Significant differences were observed in overall survival and TIIC characteristics between Cluster 1 and Cluster 2. Among these 64 DE-KGs, we identified an optimal DE-KGsM that could be a prognostic indicator in GC. TIICs and TIDE analyses exhibited that GC patients in the high-DE-KGsM score group had a higher proportion of M2 macrophages and lower response rates to ICI treatment. scRNA-seq analysis indicated that ABL2 might play an indispensable role in tumor immunity. Furthermore, in vitro experiments demonstrated that ABL2 accelerated the proliferation, migration, and invasion of GC cells, as well as the polarization of M2 macrophages.</p><p><strong>Conclusions: </strong>The DE-KGsM could be a powerful predictor of GC patients' survival and might facilitate the development of personalized therapy. Furthermore, as a hub gene in the DE-KGsM, ABL2 could be an immunological biomarker that modulates the polarization of M2 macrophages, thereby promoting GC progression.</p><p><strong>Clinical trial number: </strong>Not applicable.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"20 1","pages":"35"},"PeriodicalIF":5.7,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell RNA sequencing reveals a new mechanism of endothelial cell heterogeneity and healing in diabetic foot ulcers.","authors":"Songyun Zhao, Hua Yu, Zihao Li, Wanying Chen, Kaibo Liu, Hao Dai, Gaoyi Wang, Zibing Zhang, Jiaheng Xie, Yucang He, Liqun Li","doi":"10.1186/s13062-025-00628-9","DOIUrl":"10.1186/s13062-025-00628-9","url":null,"abstract":"<p><p>Diabetic foot ulcers (DFU) are a common and severe complication among diabetic patients, posing a significant burden on patients' quality of life and healthcare systems due to their high incidence, amputation rates, and mortality. This study utilized single-cell RNA sequencing technology to deeply analyze the cellular heterogeneity of the skin on the feet ofDFU patients and the transcriptomic characteristics of endothelial cells, aiming to identify key cell populations and genes associated with the healing and progression of DFU. The study found that endothelial cells from DFU patients exhibited significant transcriptomic differences under various conditions, particularly in signaling pathways related to inflammatory responses and angiogenesis. Through trajectory analysis and cell communication research, we revealed the key role of endothelial cell subsets in the development of DFU and identified multiple important gene modules associated with the progression of DFU. Notably, the promoting effect of the SH3BGRL3 gene on endothelial cell proliferation, migration, and angiogenic capabilities under high glucose conditions was experimentally verified, providing a new potential target and theoretical basis for the treatment of DFU. This study not only enhances the understanding of the pathogenesis ofDFU but also provides a scientific basis for the development ofnew therapeutic strategies.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"20 1","pages":"34"},"PeriodicalIF":5.7,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11929994/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Doxorubicin PK/PD modeling in multiple myeloma: towards in silico trials.","authors":"Daniele Andrean, Francesco Da Ros, Mario Mazzucato, Morten Gram Pedersen, Roberto Visentin","doi":"10.1186/s13062-025-00626-x","DOIUrl":"10.1186/s13062-025-00626-x","url":null,"abstract":"<p><p>Doxorubicin (DOXO) is a well-known chemotherapy drug, which is widely used in the treatment of Multiple Myeloma (MM), a treatable but not curable type of blood cancer. Here, we propose a pharmacokinetics and pharmacodynamics (PK/PD) simulation environment, aimed at facilitating the optimization of DOXO treatment regimens in MM treatment. The resulting model has a transparent mechanistic structure, which facilitates its use and interpretation. The simulator was developed using a combination of experimental and modeling techniques, starting from in vitro PK/PD experiments conducted on MM cells. In our previous work, we carefully developed a PK model for DOXO in MM cells by fitting experimental data. We now devise a PD model from in vitro data investigating the effect of different concentrations of DOXO on cell growth and death in MM cell populations. The PK model is extended to enable a clear mechanistic link between the PK and the PD models, hence providing a complete PK/PD simulator. We show how the mathematical model can be exploited to simulate different DOXO administration protocols with different dosages, repetitions and exposure times, thus, making it possible to explore the effect of a wide range of treatment protocols easily.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"20 1","pages":"33"},"PeriodicalIF":5.7,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927236/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143676823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dualistic role of ZEB1 and ZEB2 in tumor progression.","authors":"Sergey E Parfenyev, Alexandra A Daks, Oleg Y Shuvalov, Olga A Fedorova, Nikolay B Pestov, Tatyana V Korneenko, Nickolai A Barlev","doi":"10.1186/s13062-025-00604-3","DOIUrl":"10.1186/s13062-025-00604-3","url":null,"abstract":"<p><p>It is generally accepted that ZEB1 and ZEB2 act as master regulators of the epithelial-mesenchymal transition, which arguably is the key mechanism of metastasis. Accordingly, they are deemed as negative predictors of the survival of cancer patients by promoting the emergence of secondary foci of the disease. Paradoxically, in some types of cancer types the opposite effect is observed, i.e. ZEB1 and ZEB2 are associated with better prognosis for cancer patients. In this review, we discuss the hypothesis that the tumorigenic effects of ZEB1/ZEB2 can be different in various tissues depending on the initial status of these proteins in the corresponding healthy tissues. Emerging evidence suggests that ZEB1 and ZEB2 are constitutively expressed in several healthy tissues, performing vital functions. Consequently, reducing the expression of ZEB1 and ZEB2 could negatively affect these tissues causing various diseases, including cancer. Finally, the dualistic role of ZEB1 and ZEB2 as immune modulators and their effect on tumor microenvironment is also discussed.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"20 1","pages":"32"},"PeriodicalIF":5.7,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plasma N-Glycoproteomics in monozygotic twin pairs discordant for body mass index reveals an obesity signature related to inflammation and iron metabolism.","authors":"Maheswary Muniandy, Sakari Joenväärä, Birgitta W van der Kolk, Tiialotta Tohmola, Hanna Haltia, Sina Saari, Antti Hakkarainen, Jesper Lundbom, Juho Kuula, Per-Henrik Groop, Jaakko Kaprio, Sini Heinonen, Risto Renkonen, Kirsi H Pietiläinen","doi":"10.1186/s13062-025-00609-y","DOIUrl":"10.1186/s13062-025-00609-y","url":null,"abstract":"<p><strong>Background: </strong>N-glycosylation is a complex, post-translational modification which influences protein function and is sensitive to physiological changes. Obesity is associated with alterations in protein function; however, little is known about the glycoproteome in obesity beyond observations of association with types and structures of selected glycopeptides. Most often, due to technical challenges, glycan composition and structure information are missing. Here, we combined label-free data-independent proteomics and targeted quantitative glycoproteomics to study N-glycosylation of plasma proteins in obesity. Using a monozygotic twin study design, we controlled for genetic variation and focused only on the acquired effects of obesity.</p><p><strong>Methods: </strong>Using plasma samples of 48 monozygotic twin pairs discordant for BMI (intrapair difference > 2.5 kg/m²), we identified using mass spectrometry, differential protein and glycopeptide levels between heavier and leaner co-twins. We used a within-twin paired analysis model and considered p < 0.05 as significant.</p><p><strong>Results: </strong>We identified 48 protein and 33 N-glycosylation expression differences (p < 0.05) between co-twins. These differences occurred either both in the protein expression and glycoprotein (sometimes in opposing directions) or independently from each other. Haptoglobin protein was upregulated (Fold Change = 1.10, p = 0.001) in heavier co-twins along with seven upregulated glycan compositions at N-glycosylation site Asn241. The complement protein C3 was upregulated (Fold Change = 1.08, p = 0.014) along with one upregulated glycopeptide at Asn85. Additionally, many glycopeptides were upregulated despite non-significant differences in protein-backbone plasma levels.</p><p><strong>Conclusion: </strong>Differential protein expression related to cholesterol biosynthesis and acute phase signalling as well as N-glycosylation of proteins related to iron metabolism and inflammation can be linked to acquired obesity.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"20 1","pages":"31"},"PeriodicalIF":5.7,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921541/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Macrophage-derived SPP1 exacerbate myocardial injury by interacting with fibroblasts in viral myocarditis.","authors":"Xiuyun Duan, Li Zhang, Keyu Liu, Kaiyin Guo, Yingnan You, Hailin Jia, Shan Zhou, Bo Han","doi":"10.1186/s13062-025-00621-2","DOIUrl":"10.1186/s13062-025-00621-2","url":null,"abstract":"<p><strong>Background: </strong>Viral myocarditis (VMC) is an inflammatory myocardial condition triggered by viral infections which involves pathogenic-related damage and immune-mediated damage. However, the precise immunopathogenic mechanisms underlying VMC remain elusive.</p><p><strong>Methods: </strong>We performed single-cell RNA sequencing on mouse hearts during the acute phase of CVB3-induced VMC. After manually annotating cell types, functional analyses of macrophage were performed by cell ratio changes, customized gene set module scoring and CellPhoneDB. Utilizing indirect co-culture experiments in vitro, the effects of macrophage-derived SPP1 on cardiac fibroblasts were investigated. Depletion of macrophages and inhibition of SPP1 expression in mice were carried out to study the effects of macrophage-derived SPP1 on cardiac function, inflammation levels, and myocardial injury in mice with VMC.</p><p><strong>Results: </strong>Our data revealed that macrophages are the major immune cells which infiltrate the heart during the acute phase of VMC, particularly a macrophage subpopulation which highly expresses Spp1 (Spp1⁺ macrophages) and exhibited characteristics of peripheral blood monocytes. Spp1⁺ macrophages communicate extensively with fibroblasts during VMC, and that SPP1 promotes fibroblast conversion to an inflammatory phenotype with high Ccl2/Ccl7 expression. This in turn increases monocyte chemotaxis to the heart. Besides, a partial depletion of macrophages in the early stages of VMC attenuated myocardial inflammation and myocardial injury in mice. Inhibition of SPP1 reduced cardiac macrophage infiltration, attenuated myocardial inflammation, and improved cardiac function in VMC mice.</p><p><strong>Conclusion: </strong>Our findings suggested that Spp1⁺ macrophages could self-recruit, and macrophage-derived SPP1 exacerbated myocardial immune injury by promoting high Ccl2/Ccl7 expression in fibroblasts. Our study advances understandings of VMC pathogenesis, and provides novel insight into potential immunotherapies for VMC.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"20 1","pages":"30"},"PeriodicalIF":5.7,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11907792/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of estrogen in the sex difference for the risk factors of heart failure with preserved ejection fraction.","authors":"Jun Du, Jiaqi Liu, Xiaoya Wang, Xiaowu Wang, Yu Ma, Sipan Zhang, Zilin Li, Jipeng Ma, Jincheng Liu","doi":"10.1186/s13062-025-00618-x","DOIUrl":"10.1186/s13062-025-00618-x","url":null,"abstract":"<p><p>Heart failure with preserved ejection fraction (HFpEF) is a major subtype of heart failure, primarily characterized by a normal or mildly reduced left ventricular ejection fraction along with left ventricular diastolic dysfunction. Recent studies have shown that the prevalence of HFpEF is higher in women than that in men, particularly in postmenopausal women. Concurrently, it has been observed that the incidence of risk factors contributing to HFpEF (such as obesity, hypertension, diabetes, and atrial fibrillation) also notably increases post-menopause, affecting the incidence of HFpEF. This review aimed to examine the relationship between estrogen and risk factors associated with HFpEF, clarifying the underlying mechanisms through which estrogen affects these risk factors from epidemiological and pathophysiological perspectives. This review also provides a comprehensive understanding of the association between estrogen and the risk factors for HFpEF, thus helping explore potential targets for HFpEF treatment.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"20 1","pages":"28"},"PeriodicalIF":5.7,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11895175/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143596128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differential growth and flowering capacity of tulip bulbs and the potential involvement of PHOSPHATIDYLETHANOLAMINE-BINDING PROTEINS (PEBPs).","authors":"Francesca Bellinazzo, Irene Manders, Bas Heidemann, Manuel Aguirre Bolanos, Evelien Stouten, Jacqueline Busscher, Dolores Abarca, Froukje van der Wal, Marcelo Carnier Dornelas, Gerco C Angenent, Marcel Proveniers, Harm Nijveen, Richard G H Immink","doi":"10.1186/s13062-025-00625-y","DOIUrl":"10.1186/s13062-025-00625-y","url":null,"abstract":"<p><strong>Background: </strong>Tulipa gesneriana reproduces vegetatively by the development of bulb clusters from axillary meristems in the scales of a mother bulb. While part of the daughter bulbs in a cluster develop into large, flowering bulbs, others stay small and vegetative under the same environmental conditions. This study aims to investigate how these different developmental fates are orchestrated.</p><p><strong>Results: </strong>RNA-seq analysis revealed that the overall transcriptomic landscape of the two types of daughter bulbs does not differ substantially, but follows a similar trajectory over time. Nonetheless, the expression levels of genes related to proliferation already differ at early development stages. Surprisingly, at a later stage, transcriptomic changes related to flower induction are detectable in flowering as well as non-flowering bulbs, with some quantitative differences. However, genes linked with floral organ development are differentially expressed, as well as negative regulators of flowering and more basal metabolic processes. In search for the molecular determinants of daughter bulb size and developmental fate, we investigated members of the PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN (PEBP) gene family as candidates. Tulip FLOWERING LOCUS T1 (TgFT1), TgFT2, and TgFT3 are expressed in leaves and leaf-like organs of the mother plant, and their encoded proteins interact with the TCP transcription factor TEOSINTE BRANCHED1 (TgTB1). Therefore, we suggest that these three genes act as 'bulbigens', meaning regulators of axillary meristem outgrowth and hence, daughter bulb size. Furthermore, we found that TgFT2 and TgFT4 could constitute the main florigens in tulips, because of their expression pattern and the binding of their encoding proteins to the bZIP transcription factor FD (TgFD). Moreover, Arabidopsis lines ectopically expressing TgFT2 or TgFT4 flower significantly earlier than the wild type.</p><p><strong>Conclusions: </strong>Differences in the developmental fate of tulip daughter bulbs are established early during development and are linked with differences in cell division and metabolism. The activity of members of the PEBP family, known for their role in flowering and storage organ formation in geophytes, appeared to be associated with the transcriptional switches observed during daughter bulb development. This points towards a functional role of these proteins in governing developmental trajectories underlying the mode of reproduction.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"20 1","pages":"29"},"PeriodicalIF":5.7,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11895272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143596111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}