Pub Date : 2024-05-22DOI: 10.1016/j.gendis.2024.101337
Recent studies have explored the spatial transcriptomics patterns of Alzheimer's disease (AD) brain by spatial sequencing in mouse models, enabling the identification of unique genome-wide transcriptomic features associated with different spatial regions and pathological status. However, the dynamics of gene interactions that occur during amyloid-β accumulation remain largely unknown. In this study, we performed analyses on ligand-receptor communication, transcription factor regulatory network, and spot-specific network to reveal the dependence and the dynamics of gene associations/interactions on spatial regions and pathological status with mouse and human brains. We first used a spatial transcriptomics dataset of the AppNL-G-F knock-in AD and wild-type mouse model. We revealed 17 ligand-receptor pairs with opposite tendencies throughout the amyloid-β accumulation process and showed the specific ligand-receptor interactions across the hippocampus layers at different extents of pathological changes. We then identified nerve function related transcription factors in the hippocampus and entorhinal cortex, as well as genes with different transcriptomic association degrees in AD versus wild-type mice. Finally, another independent spatial transcriptomics dataset from different AD mouse models and human single-nuclei RNA-seq data/AlzData database were used for validation. This is the first study to identify various gene associations throughout amyloid-β accumulation based on spatial transcriptomics, establishing the foundations to reveal advanced and in-depth AD etiology from a novel perspective based on the comprehensive analyses of gene interactions that are spatio-temporal dependent.
{"title":"Gene interactions analysis of brain spatial transcriptome for Alzheimer's disease","authors":"","doi":"10.1016/j.gendis.2024.101337","DOIUrl":"10.1016/j.gendis.2024.101337","url":null,"abstract":"<div><p>Recent studies have explored the spatial transcriptomics patterns of Alzheimer's disease (AD) brain by spatial sequencing in mouse models, enabling the identification of unique genome-wide transcriptomic features associated with different spatial regions and pathological status. However, the dynamics of gene interactions that occur during amyloid-β accumulation remain largely unknown. In this study, we performed analyses on ligand-receptor communication, transcription factor regulatory network, and spot-specific network to reveal the dependence and the dynamics of gene associations/interactions on spatial regions and pathological status with mouse and human brains. We first used a spatial transcriptomics dataset of the <em>App</em><sup><em>NL-G-F</em></sup> knock-in AD and wild-type mouse model. We revealed 17 ligand-receptor pairs with opposite tendencies throughout the amyloid-β accumulation process and showed the specific ligand-receptor interactions across the hippocampus layers at different extents of pathological changes. We then identified nerve function related transcription factors in the hippocampus and entorhinal cortex, as well as genes with different transcriptomic association degrees in AD versus wild-type mice. Finally, another independent spatial transcriptomics dataset from different AD mouse models and human single-nuclei RNA-seq data/AlzData database were used for validation. This is the first study to identify various gene associations throughout amyloid-β accumulation based on spatial transcriptomics, establishing the foundations to reveal advanced and in-depth AD etiology from a novel perspective based on the comprehensive analyses of gene interactions that are spatio-temporal dependent.</p></div>","PeriodicalId":12689,"journal":{"name":"Genes & Diseases","volume":"11 6","pages":"Article 101337"},"PeriodicalIF":6.9,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S235230422400134X/pdfft?md5=1fbf3a2d47134eb845118f0f1e520f08&pid=1-s2.0-S235230422400134X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141131079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-20DOI: 10.1016/j.gendis.2024.101330
Resistance to sorafenib, an effective first-line treatment for advanced hepatocellular carcinoma (HCC), greatly compromised the prognosis of patients. The extracellular matrix is one of the most abundant components of the tumor microenvironment. Beyond acting as a physical barrier, it remains unclear whether cell interactions and signal transduction mediated by the extracellular matrix contribute to sorafenib resistance. With the analysis of primary HCC organoid RNA-seq data combined with in vivo and in vitro experiments validation, we discovered that fibronectin extra domain A (FN-EDA) derived from cancer-associated fibroblasts played a critical role in sorafenib resistance. Mechanistically, FN-EDA stimulates the up-regulation of the key one-carbon metabolism enzyme SHMT1 in HCC cells via the TLR4/NF-κB signaling pathway, thereby countering the oxidative stress induced by sorafenib. Moreover, we reinforced the clinical significance of our discoveries by conducting in vivo assays with an immunodeficiency subcutaneous xenograft tumor model, which was established using primary cancer-associated fibroblasts derived from clinical HCC tissues, and through the analysis of HCC samples obtained from The Cancer Genome Atlas (TCGA) database. Our findings suggest that targeting the FN-EDA/SHMT1 pathway could be a potential strategy to improve sorafenib responsiveness in HCC patients.
{"title":"Cancer-associated fibroblasts derived fibronectin extra domain A promotes sorafenib resistance in hepatocellular carcinoma cells by activating SHMT1","authors":"","doi":"10.1016/j.gendis.2024.101330","DOIUrl":"10.1016/j.gendis.2024.101330","url":null,"abstract":"<div><p>Resistance to sorafenib, an effective first-line treatment for advanced hepatocellular carcinoma (HCC), greatly compromised the prognosis of patients. The extracellular matrix is one of the most abundant components of the tumor microenvironment. Beyond acting as a physical barrier, it remains unclear whether cell interactions and signal transduction mediated by the extracellular matrix contribute to sorafenib resistance. With the analysis of primary HCC organoid RNA-seq data combined with <em>in vivo</em> and <em>in vitro</em> experiments validation, we discovered that fibronectin extra domain A (FN-EDA) derived from cancer-associated fibroblasts played a critical role in sorafenib resistance. Mechanistically, FN-EDA stimulates the up-regulation of the key one-carbon metabolism enzyme SHMT1 in HCC cells via the TLR4/NF-κB signaling pathway, thereby countering the oxidative stress induced by sorafenib. Moreover, we reinforced the clinical significance of our discoveries by conducting <em>in vivo</em> assays with an immunodeficiency subcutaneous xenograft tumor model, which was established using primary cancer-associated fibroblasts derived from clinical HCC tissues, and through the analysis of HCC samples obtained from The Cancer Genome Atlas (TCGA) database. Our findings suggest that targeting the FN-EDA/SHMT1 pathway could be a potential strategy to improve sorafenib responsiveness in HCC patients.</p></div>","PeriodicalId":12689,"journal":{"name":"Genes & Diseases","volume":"11 6","pages":"Article 101330"},"PeriodicalIF":6.9,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2352304224001272/pdfft?md5=6730558c8014bf0d03ae3760faddee2e&pid=1-s2.0-S2352304224001272-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141131633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-09DOI: 10.1016/j.gendis.2024.101317
Nan Wang, Xiaoyu Shen, Huakun Huang, Runhan Zhao, Habu Jiwa, Zongxin Li, Pei Li, Jixing Ye, Qiang Zhou
Amyloid precursor protein (APP), especially Swedish mutant APP (APPswe), is recognized as a significant pathogenic protein in Alzheimer's disease, but limited research has been conducted on the correlation between APPswe and the osteogenic differentiation of mesenchymal stem cells (MSCs). The effects of APPswe and its intracellular and extracellular segments on the osteogenic differentiation of bone morphogenetic protein 2 (BMP2)-induced MSCs were analyzed in this study. Our analysis of an existing database revealed that APP was positively correlated with the osteogenic differentiation of MSCs but negatively correlated with their proliferation and migration. Furthermore, APPswe promoted BMP2-induced osteogenic differentiation of MSCs, while APPswe-C (APPswe without an intracellular segment) had the opposite effect; thus, the intracellular domain of APPswe may be a key factor in promoting the osteogenic differentiation of MSCs. Additionally, both APPswe and APPswe-C inhibited the proliferation and migration of MSCs. Furthermore, the intracellular domain of APPswe inhibited the activity of the Notch pathway by regulating the expression of the Notch intracellular domain to promote the osteogenic differentiation of MSCs. Finally, APPswe-treated primary rat bone marrow MSCs exhibited the most favorable bone repair effect when a GelMA hydrogel loaded with BMP2 was used for experiments, while APPswe-C had the opposite effect. These findings demonstrate that APPswe promotes the osteogenic differentiation of MSCs by regulating the Notch pathway, but its extracellular segment blocks the self-renewal, proliferation, and migration of MSCs, ultimately leading to a gradual decrease in the storage capacity of MSCs and affecting long-term bone formation.
{"title":"The bidirectional effects of APPswe on the osteogenic differentiation of MSCs in bone homeostasis by regulating Notch signaling","authors":"Nan Wang, Xiaoyu Shen, Huakun Huang, Runhan Zhao, Habu Jiwa, Zongxin Li, Pei Li, Jixing Ye, Qiang Zhou","doi":"10.1016/j.gendis.2024.101317","DOIUrl":"https://doi.org/10.1016/j.gendis.2024.101317","url":null,"abstract":"Amyloid precursor protein (APP), especially Swedish mutant APP (APPswe), is recognized as a significant pathogenic protein in Alzheimer's disease, but limited research has been conducted on the correlation between APPswe and the osteogenic differentiation of mesenchymal stem cells (MSCs). The effects of APPswe and its intracellular and extracellular segments on the osteogenic differentiation of bone morphogenetic protein 2 (BMP2)-induced MSCs were analyzed in this study. Our analysis of an existing database revealed that APP was positively correlated with the osteogenic differentiation of MSCs but negatively correlated with their proliferation and migration. Furthermore, APPswe promoted BMP2-induced osteogenic differentiation of MSCs, while APPswe-C (APPswe without an intracellular segment) had the opposite effect; thus, the intracellular domain of APPswe may be a key factor in promoting the osteogenic differentiation of MSCs. Additionally, both APPswe and APPswe-C inhibited the proliferation and migration of MSCs. Furthermore, the intracellular domain of APPswe inhibited the activity of the Notch pathway by regulating the expression of the Notch intracellular domain to promote the osteogenic differentiation of MSCs. Finally, APPswe-treated primary rat bone marrow MSCs exhibited the most favorable bone repair effect when a GelMA hydrogel loaded with BMP2 was used for experiments, while APPswe-C had the opposite effect. These findings demonstrate that APPswe promotes the osteogenic differentiation of MSCs by regulating the Notch pathway, but its extracellular segment blocks the self-renewal, proliferation, and migration of MSCs, ultimately leading to a gradual decrease in the storage capacity of MSCs and affecting long-term bone formation.","PeriodicalId":12689,"journal":{"name":"Genes & Diseases","volume":"10 1","pages":""},"PeriodicalIF":6.8,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140941600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-08DOI: 10.1016/j.gendis.2024.101321
Yuelei Hu, Guifang Du, Chao Li, Rui Wang, Juan Liu, Yunfang Wang, Jiahong Dong
Hepatocyte proliferation is essential for recovering liver function after injury. In liver surgery, the mechanical stimulation induced by hemodynamic changes triggers vascular endothelial cells (VECs) to secrete large amounts of cytokines that enhance hepatocyte proliferation and play a pivotal role in liver regeneration. Piezo1, a critical mechanosensory ion channel, can detect and convert mechanical forces into chemical signals, importing external stimuli into cells and triggering downstream biological effects. However, the precise role of Piezo1 in VECs, especially in terms of mediating liver regeneration, remains unclear. Here, we report on a potential mechanism by which early changes in hepatic portal hemodynamics activate Piezo1 in VECs to promote hepatocyte proliferation during the process of liver regeneration induced by portal vein ligation in rats. In this liver regeneration model, hepatocyte proliferation is mainly distributed in zone 1 and zone 2 of liver lobules at 24–48 h after surgery, while only a small number of Ki67-positive hepatocytes were observed in zone 3. Activation of Piezo1 promotes increased secretion of epiregulin and amphiregulin from VECs via the PKC/ERK1/2 axis, further activating epidermal growth factor receptor (EGFR) and ERK1/2 signals in hepatocytes and promoting proliferation. In addition, cytokines secreted by Piezo1-activated VECs can induce hepatocytes to undergo epithelial–mesenchymal transition. In the liver lobules, the expression of EGFR in hepatocytes of zone 1 and zone 2 is significantly higher than that in zone 3. The EGFR inhibitor gefitinib inhibits liver regeneration by suppressing the proliferation of hepatocytes in the middle zone. Thus, activation of Piezo1 in VECs promotes hepatocyte proliferation, suggesting mechanical stimulation regulates hepatocyte proliferation in zone 1 and zone 2 during portal vein ligation-induced liver regeneration. These data provide a theoretical basis for the regulation of liver regeneration through chemical signals mediated by mechanical stimulation.
{"title":"EGFR-mediated crosstalk between vascular endothelial cells and hepatocytes promotes Piezo1-dependent liver regeneration","authors":"Yuelei Hu, Guifang Du, Chao Li, Rui Wang, Juan Liu, Yunfang Wang, Jiahong Dong","doi":"10.1016/j.gendis.2024.101321","DOIUrl":"https://doi.org/10.1016/j.gendis.2024.101321","url":null,"abstract":"Hepatocyte proliferation is essential for recovering liver function after injury. In liver surgery, the mechanical stimulation induced by hemodynamic changes triggers vascular endothelial cells (VECs) to secrete large amounts of cytokines that enhance hepatocyte proliferation and play a pivotal role in liver regeneration. Piezo1, a critical mechanosensory ion channel, can detect and convert mechanical forces into chemical signals, importing external stimuli into cells and triggering downstream biological effects. However, the precise role of Piezo1 in VECs, especially in terms of mediating liver regeneration, remains unclear. Here, we report on a potential mechanism by which early changes in hepatic portal hemodynamics activate Piezo1 in VECs to promote hepatocyte proliferation during the process of liver regeneration induced by portal vein ligation in rats. In this liver regeneration model, hepatocyte proliferation is mainly distributed in zone 1 and zone 2 of liver lobules at 24–48 h after surgery, while only a small number of Ki67-positive hepatocytes were observed in zone 3. Activation of Piezo1 promotes increased secretion of epiregulin and amphiregulin from VECs via the PKC/ERK1/2 axis, further activating epidermal growth factor receptor (EGFR) and ERK1/2 signals in hepatocytes and promoting proliferation. In addition, cytokines secreted by Piezo1-activated VECs can induce hepatocytes to undergo epithelial–mesenchymal transition. In the liver lobules, the expression of EGFR in hepatocytes of zone 1 and zone 2 is significantly higher than that in zone 3. The EGFR inhibitor gefitinib inhibits liver regeneration by suppressing the proliferation of hepatocytes in the middle zone. Thus, activation of Piezo1 in VECs promotes hepatocyte proliferation, suggesting mechanical stimulation regulates hepatocyte proliferation in zone 1 and zone 2 during portal vein ligation-induced liver regeneration. These data provide a theoretical basis for the regulation of liver regeneration through chemical signals mediated by mechanical stimulation.","PeriodicalId":12689,"journal":{"name":"Genes & Diseases","volume":"122 1","pages":""},"PeriodicalIF":6.8,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140941444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-07DOI: 10.1016/j.gendis.2024.101316
Yang Liu , Feifei Song , Xianhuang Zeng , Siqi Yang , Zixu Zhai , Ze Wang , Wajeeha Naz , Tanzeel Yousaf , Junwei Sun , Yangjun Zhang , Ying Zhou , Mingxiong Guo , Yun-Bo Shi , Geng Tian , Guihong Sun
{"title":"The AKT1-mTOR signaling cascade is crucial for SOX3 to promote hepatocarcinogenesis","authors":"Yang Liu , Feifei Song , Xianhuang Zeng , Siqi Yang , Zixu Zhai , Ze Wang , Wajeeha Naz , Tanzeel Yousaf , Junwei Sun , Yangjun Zhang , Ying Zhou , Mingxiong Guo , Yun-Bo Shi , Geng Tian , Guihong Sun","doi":"10.1016/j.gendis.2024.101316","DOIUrl":"10.1016/j.gendis.2024.101316","url":null,"abstract":"","PeriodicalId":12689,"journal":{"name":"Genes & Diseases","volume":"12 2","pages":"Article 101316"},"PeriodicalIF":6.9,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140941541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-07DOI: 10.1016/j.gendis.2024.101319
Yue Weng , Xiangyu Yan , Biying Chen , Zhouliang Bian , Yunhui Ge , Hong Lu , Shufang He , Jian Wu , Yong Chen , Ming Lei , Yanjie Zhang
{"title":"PinX1 suppresses cancer progression by inhibiting telomerase activity in cervical squamous cell carcinoma and endocervical adenocarcinoma","authors":"Yue Weng , Xiangyu Yan , Biying Chen , Zhouliang Bian , Yunhui Ge , Hong Lu , Shufang He , Jian Wu , Yong Chen , Ming Lei , Yanjie Zhang","doi":"10.1016/j.gendis.2024.101319","DOIUrl":"10.1016/j.gendis.2024.101319","url":null,"abstract":"","PeriodicalId":12689,"journal":{"name":"Genes & Diseases","volume":"12 2","pages":"Article 101319"},"PeriodicalIF":6.9,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140941638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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