Genes to Cells最新文献_第5页

Potential Role of Trap Clone Accumulation Areas (TCAAs) in Sustaining Pluripotency in Mouse Embryonic Stem Cells 陷阱克隆积累区（TCAAs）在维持小鼠胚胎干细胞多能性中的潜在作用

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-03-09 DOI: 10.1111/gtc.70011

Masatake Araki, Luna Ikeda, Takumi Yonemori, Kumiko Yoshinobu, Mariko Yamane, Takumi Ichikawa, Kimi Araki

{"title":"Potential Role of Trap Clone Accumulation Areas (TCAAs) in Sustaining Pluripotency in Mouse Embryonic Stem Cells","authors":"Masatake Araki, Luna Ikeda, Takumi Yonemori, Kumiko Yoshinobu, Mariko Yamane, Takumi Ichikawa, Kimi Araki","doi":"10.1111/gtc.70011","DOIUrl":"https://doi.org/10.1111/gtc.70011","url":null,"abstract":"<div>\u0000 \u0000 Analysis of gene trap clones (TCs) revealed the existence of regions where TCs accumulate in the absence of genes. These regions were designated as trap clone accumulation areas (TCAAs). To ascertain the physiological function of TCAAs, negative control regions devoid of genes and TCs (NC1 and NC11), two randomly selected known gene sets (G1 and G11), and a set of genes presumed to be involved in maintaining pluripotency in embryonic stem (ES) cells (GP) were generated and compared with TCAAs. The assay for transposase-accessible chromatin with sequencing (ATAC-Seq) results indicated that TCAAs exhibited characteristics comparable to G1, G11, and GP, suggesting an open chromatin structure. Oct4-chromatin immunoprecipitation-sequencing (ChIP-seq) demonstrated that TCAAs had markedly elevated signals compared to G1 and 11, and a comparable level to that of GP. With regard to H3K4me1 and H3K27ac, which are associated with enhancer activity, TCAAs were observed to exhibit significantly higher levels than G1 and 11 and a comparable level to that of GP. Furthermore, approximately half of the super-enhancers overlapped with TCAAs in an ES cell-specific manner. These findings suggest that TCAAs are involved in maintaining the pluripotency of mouse ES cells.\u0000 </div>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143581866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to “The Protein Kinase aPKC as Well as the Small GTPases RhoA and Cdc42 Regulates Neutrophil Chemotaxis Partly by Recruiting the ROCK Kinase to the Leading Edge” 更正“蛋白激酶aPKC以及小gtpase RhoA和Cdc42通过招募ROCK激酶到前沿来部分调节中性粒细胞趋化性”

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-03-06 DOI: 10.1111/gtc.70009

{"title":"Correction to “The Protein Kinase aPKC as Well as the Small GTPases RhoA and Cdc42 Regulates Neutrophil Chemotaxis Partly by Recruiting the ROCK Kinase to the Leading Edge”","authors":"","doi":"10.1111/gtc.70009","DOIUrl":"https://doi.org/10.1111/gtc.70009","url":null,"abstract":"Naito, A., S. Kamakura, J. Hayase, et al. 2025. “The Protein Kinase aPKC as Well as the Small GTPases RhoA and Cdc42 Regulates Neutrophil Chemotaxis Partly by Recruiting the ROCK Kinase to the Leading Edge.” Genes to Cells 30, no. 2: e70002. https://doi.org/10.1111/gtc.70002.In the “Funding” section on page 1, the text “This work was supported by Japan Society for the Promotion of Science (JP21H02698, JP21H05267, and JP22K06901).” was incorrect. This should have read: “This work was supported by Japan Society for the Promotion of Science (JP21H02698, JP21H05267, and JP22K06901) and by the fellowship from the Takeda Science Foundation.”In the “Acknowledgments” section on page 17, the text “This work was supported in part by JSPS (Japan Society for the Promotion of Science) KAKENHI Grants JP21H02698 (to H.S.), JP21H05267 (to H.S.), and JP22K06901 (to S.K.).” was incorrect. This should have read: “This work was supported in part by JSPS (Japan Society for the Promotion of Science) KAKENHI Grants JP21H02698 (to H.S.), JP21H05267 (to H.S.), and JP22K06901 (to S.K.), and by the fellowship from the Takeda Science Foundation (to A.N.).”We apologize for these errors.","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/gtc.70009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization of Mucosa-Associated Microbiota in Formalin-Fixed, Paraffin-Embedded Tissues From Southern Thai Patients With Familial Adenomatous Polyposis 来自泰国南部家族性腺瘤性息肉病患者的福尔马林固定、石蜡包埋组织中粘膜相关微生物群的特征

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-02-25 DOI: 10.1111/gtc.70008

Jukrayupat Fongmanee, Worrawit Wanitsuwan, Warapond Wanna, Komwit Surachat, Charinrat Saechan, Kanitta Srinoun, Hansuk Buncherd, Supinya Thanapongpichat, Kanet Kanjanapradit, Natta Tansila

{"title":"Characterization of Mucosa-Associated Microbiota in Formalin-Fixed, Paraffin-Embedded Tissues From Southern Thai Patients With Familial Adenomatous Polyposis","authors":"Jukrayupat Fongmanee, Worrawit Wanitsuwan, Warapond Wanna, Komwit Surachat, Charinrat Saechan, Kanitta Srinoun, Hansuk Buncherd, Supinya Thanapongpichat, Kanet Kanjanapradit, Natta Tansila","doi":"10.1111/gtc.70008","DOIUrl":"https://doi.org/10.1111/gtc.70008","url":null,"abstract":"<div>\u0000 \u0000 Familial adenomatous polyposis (FAP) is an autosomal dominant syndrome associated with germline mutations in the adenomatous polyposis coli (APC) gene. Patients eventually may develop colorectal cancer (CRC) if they are not diagnosed in the early stages. Dysbiosis is an important contributing factor to the complex events in carcinogenesis, which are poorly understood. First, 25 tissue samples from 13 patients with FAP at Songklanagarind Hospital were classified as nontumor (n = 18) or tumor tissues (n = 7). Following isolation, 5 DNA samples of insufficient quantity and quality were excluded. The 16S rRNA gene targeting the V3–V4 region was sequenced, and the sequencing data were analyzed using bioinformatics tools. The abundance of Romboutsia and Clostridium genera and Lachnospiraceae NK4A136 was significantly higher in tumor tissues than that in nonneoplastic samples. Furthermore, several bacterial genera, including Acinetobacter, Paracoccus, Brevundimonas, and Brevibacillus, were predominant or key taxa in nontumor mucosae. We found an alteration in the mucosa-associated microbiota composition of southern Thai patients that may have contributed to the tumorigenesis of FAP. These findings may improve the knowledge of the potential roles of microbes in FAP and aid the development of preventive measures for cancer development and progression through modulation of the gut microbiota.\u0000 </div>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143489929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Establishment of a Novel Caco-2-Based Cell Culture System for Human Sapovirus Propagation 建立基于 Caco-2 细胞培养的新型人类沙波病毒传播系统

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-02-25 DOI: 10.1111/gtc.70007

Yuya Fukuda, Azusa Ishikawa, Ryoka Ishiyama, Reiko Takai-Todaka, Kei Haga, Yuichi Someya, Tomomi Kimura-Someya, Kazuhiko Katayama

{"title":"Establishment of a Novel Caco-2-Based Cell Culture System for Human Sapovirus Propagation","authors":"Yuya Fukuda, Azusa Ishikawa, Ryoka Ishiyama, Reiko Takai-Todaka, Kei Haga, Yuichi Someya, Tomomi Kimura-Someya, Kazuhiko Katayama","doi":"10.1111/gtc.70007","DOIUrl":"https://doi.org/10.1111/gtc.70007","url":null,"abstract":"Human sapovirus (HuSaV), first identified in the 1970s, is a significant cause of acute gastroenteritis, particularly in young children. Despite its clinical significance, research on HuSaV has been limited due to the absence of a reliable cell culture system. In 2020, a breakthrough study reported that HuSaV GI.1 and GII.3 strains could be cultured and serially propagated using HuTu80 cells in the presence of bile acids. However, in 2024, a subsequent study reported that effective replication in HuTu80 cells requires specialized cells that have undergone over 100 passages. In this study, we sought to identify an alternative cell culture system for HuSaV. HuSaV GI.1 can replicate and be serially propagated using Caco-2 cells under bile acid supplementation. Importantly, the Caco-2 cells were freshly sourced from the American Type Culture Collection, ensuring reproducibility for laboratories worldwide. Furthermore, Caco-2MC cells were established via single-cell cloning from in-house Caco-2/Cas9 cells with 91.5% HuSaV-susceptible. HuSaV strains GI.1, GI.2, GI.3, GII.1, GII.3, and GV.1 were successfully propagated using Caco-2MC cells, with RNA copy numbers increasing up to 4.4 log10-fold within 5 days post-infection. This efficient HuSaV cell culture system represents a significant advancement in HuSaV research.","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/gtc.70007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143489927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Depletion of TRAIP Results in the Retention of PCNA on Chromatin During Mitosis Leads to Inhibiting DNA Replication Initiation TRAIP的缺失导致有丝分裂过程中PCNA在染色质上的保留，从而抑制DNA复制的起始

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-02-16 DOI: 10.1111/gtc.70006

Yasushi Shiomi, Akiyo Hayashi, Yuichiro Saito, Masato T. Kanemaki, Hideo Nishitani

{"title":"The Depletion of TRAIP Results in the Retention of PCNA on Chromatin During Mitosis Leads to Inhibiting DNA Replication Initiation","authors":"Yasushi Shiomi, Akiyo Hayashi, Yuichiro Saito, Masato T. Kanemaki, Hideo Nishitani","doi":"10.1111/gtc.70006","DOIUrl":"https://doi.org/10.1111/gtc.70006","url":null,"abstract":"<div>\u0000 \u0000 Loading PCNA onto chromatin is a pivotal step in DNA replication, cell cycle progression, and genome integrity. Conversely, unloading PCNA from chromatin is equally crucial for maintaining genome stability. Cells deficient in the PCNA unloader ATAD5-RFC exhibit elevated levels of chromatin-bound PCNA during S phase, but still show dissociation of PCNA from chromatin in mitosis. In this study, we found that depletion of TRAIP, an E3 ubiquitin ligase, results in the retention of PCNA on chromatin during mitosis. Although TRAIP-depleted cells with chromatin-bound PCNA during mitosis progressed into the subsequent G1 phase, they displayed reduced levels of Cdt1, a key replication licensing factor, and impaired S phase entry. In addition, TRAIP-depleted cells exhibited delayed S phase progression. These results suggest that TRAIP functions independently of ATAD5-RFC in removing PCNA from chromatin. Furthermore, TRAIP appears to be essential for precise pre-replication complexes (pre-RCs) formation necessary for faithful initiation of DNA replication and S phase progression.\u0000 </div>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The HAT Inhibitor ISOX-DUAL Diminishes Ischemic Areas in a Mouse Model of Oxygen-Induced Retinopathy HAT抑制剂ISOX-DUAL减少氧诱导视网膜病变小鼠模型的缺血区域

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-02-07 DOI: 10.1111/gtc.13196

Kengo Nakanishi, Yoshihiro Takamura, Yusei Nakano, Masaru Inatani, Masaya Oki

{"title":"The HAT Inhibitor ISOX-DUAL Diminishes Ischemic Areas in a Mouse Model of Oxygen-Induced Retinopathy","authors":"Kengo Nakanishi, Yoshihiro Takamura, Yusei Nakano, Masaru Inatani, Masaya Oki","doi":"10.1111/gtc.13196","DOIUrl":"https://doi.org/10.1111/gtc.13196","url":null,"abstract":"Retinal ischemic disease results in significant visual impairment due to the development of fragile and disorganized, pathologically running blood vessels in the eye. Currently, the mainstay treatment for this disease is the intravitreal administration of anti-VEGF drugs targeting vascular endothelial growth factor (VEGF), which induces angiogenesis. However, current anti-VEGF drugs do not diminish the ischemic areas that lead to angiogenesis, making fundamental treatment challenging. Since retinopathy is an acquired disease caused by hypoxic stimulation from ischemia, we paid particular attention to histone acetylases. We conducted a drug screening experiment using a mouse model of oxygen-induced retinopathy (OIR), which replicates retinal ischemic disease, through the intraperitoneal administration of 17 distinct inhibitors targeting histone acetyltransferases (HAT). The results indicated that, among the 17 inhibitors, only ISOX-DUAL decreased neovascularization and ischemic regions. Furthermore, microarray analysis was conducted on the drug-treated samples to refine genes altered by the administration of ISOX-DUAL. There were 21 genes associated with angiogenesis, including Angpt2, Hmox1, Edn1, and Serpine1, exhibited upregulation in OIR mice and downregulation following treatment with ISOX-DUAL. Furthermore, STRING analysis confirmed that the aforementioned four genes are downstream factors of hypoxia-inducible factors and are assumed to be important factors in retinal ischemic diseases.","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/gtc.13196","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143362686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Protein Kinase aPKC as Well as the Small GTPases RhoA and Cdc42 Regulates Neutrophil Chemotaxis Partly by Recruiting the ROCK Kinase to the Leading Edge 蛋白激酶aPKC以及小gtpase RhoA和Cdc42通过将ROCK激酶募集到前沿来部分调节中性粒细胞趋化性

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-02-05 DOI: 10.1111/gtc.70002

Atsushi Naito, Sachiko Kamakura, Junya Hayase, Akira Kohda, Hiroaki Niiro, Koichi Akashi, Hideki Sumimoto

{"title":"The Protein Kinase aPKC as Well as the Small GTPases RhoA and Cdc42 Regulates Neutrophil Chemotaxis Partly by Recruiting the ROCK Kinase to the Leading Edge","authors":"Atsushi Naito, Sachiko Kamakura, Junya Hayase, Akira Kohda, Hiroaki Niiro, Koichi Akashi, Hideki Sumimoto","doi":"10.1111/gtc.70002","DOIUrl":"https://doi.org/10.1111/gtc.70002","url":null,"abstract":"The small GTPases RhoA and Cdc42 and their effector proteins play crucial roles in neutrophil chemotaxis. However, endogenous localization and regulation of these proteins have remained largely unknown. Here, we show, using a trichloroacetic acid fixation method, that endogenous RhoA and Cdc42 are preferentially accumulated at the F-actin-rich leading edge (pseudopod) during chemotaxis of human neutrophil-like PLB-985 cells in response to the chemoattractant C5a. Interestingly, the enrichment of RhoA is impaired by knockdown of Cdc42, indicating a positive regulation by Cdc42. Depletion of Cdc42 or RhoA each induces the formation of multiple pseudopods, confirming their significance in cell polarization with an organized actin network at the front. The Rho-associated kinase ROCK is also recruited to the leading edge during chemotaxis in a manner dependent on not only RhoA and Cdc42 but also aPKC, a Cdc42-interacting kinase that can also bind to ROCK. ROCK promotes phosphorylation of the myosin light chain at the front, possibly regulating pseudopod contractility. Knockdown of aPKC suppresses neutrophil chemotaxis by disturbing pseudopod orientation without forming multiple protrusions. An incorrectly oriented pseudopod is also observed in ROCK-depleted cells. Thus, aPKC, as well as RhoA and Cdc42, likely regulates neutrophil chemotaxis partly by recruiting ROCK to the leading edge for correct directionality.","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/gtc.70002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143112146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Vacuolar Sts1 Degradation-Induced Cytoplasmic Proteasome Translocation Restores Cell Proliferation 液泡Sts1降解诱导的细胞质蛋白酶体易位恢复细胞增殖

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-02-04 DOI: 10.1111/gtc.70004

Noritaka Ohigashi, Shoshiro Hirayama, Hideki Yashiroda, Shigeo Murata

{"title":"Vacuolar Sts1 Degradation-Induced Cytoplasmic Proteasome Translocation Restores Cell Proliferation","authors":"Noritaka Ohigashi, Shoshiro Hirayama, Hideki Yashiroda, Shigeo Murata","doi":"10.1111/gtc.70004","DOIUrl":"https://doi.org/10.1111/gtc.70004","url":null,"abstract":"<div>\u0000 \u0000 The proteasome is a large multicatalytic complex conserved across eukaryotes that regulates multiple cellular processes through the degradation of ubiquitinated proteins. The proteasome is predominantly localized to the nucleus in proliferating cells and translocates to the cytoplasm in the stationary phase. Sts1 reportedly plays a vital role in the nuclear import of the proteasome during proliferation in yeast Saccharomyces cerevisiae. However, the mechanisms underlying cytoplasmic translocation of the proteasome in the stationary phase remain unknown. Here, we showed that the ubiquitin ligase Hul5 promotes vacuolar sequestration of Sts1 in a catalytic activity-dependent manner and thus suppresses the nuclear import of the proteasome during the stationary phase. We further demonstrated that cytoplasmic translocation of the proteasome plays a vital role in the clearance of ubiquitinated protein aggregates, mitochondrial quality control, and resuming proliferation from cellular quiescence. Our results provide insights into the mechanisms and significance of the cytoplasmic localization of proteasomes in cellular quiescence.\u0000 </div>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143111572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Regulation of Gut Starvation Responses Through Drosophila NP3253 Neurons 果蝇NP3253神经元对肠道饥饿反应的调控

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-02-04 DOI: 10.1111/gtc.70005

Quang-Dat Nguyen, Kiho Fujii, Kentaro Ishibashi, Haruka Hashiba, Wakako Ohtsubo, Haruki Kitazawa, Hiromu Tanimoto, Naoyuki Fuse, Shoichiro Kurata

{"title":"Regulation of Gut Starvation Responses Through Drosophila NP3253 Neurons","authors":"Quang-Dat Nguyen, Kiho Fujii, Kentaro Ishibashi, Haruka Hashiba, Wakako Ohtsubo, Haruki Kitazawa, Hiromu Tanimoto, Naoyuki Fuse, Shoichiro Kurata","doi":"10.1111/gtc.70005","DOIUrl":"https://doi.org/10.1111/gtc.70005","url":null,"abstract":"<div>\u0000 \u0000 The “gut–brain axis,” a bidirectional communication system between the gastrointestinal tract and the central nervous system, plays a crucial role in regulating complex physiological functions in response to nutrients, pathogens, and microbiota. However, the cellular and molecular mechanisms governing this regulation remain poorly understood. Using Drosophila melanogaster as a model organism, we previously identified NP3253 neurons, located in both the brain and gut, as key contributors to gut homeostasis during oral bacterial infection. Here, we found a novel role of NP3253 neurons in regulating starvation resistance. We observed that a subset of NP3253 neurons in the gut were activated during starvation. To investigate downstream effect, we conducted RNA-Seq analysis on the gut of adult flies with genetically silenced NP3253 neurons, comparing gene expression under starved and fed conditions. This analysis identified 26 genes differentially expressed in response to both starvation and NP3253 neuronal activity. Among these, CG12643, encoding an uncharacterized short peptide, was found to be essential for starvation resistance in the gut. Our findings demonstrate that NP3253 neurons modulate the gut gene expression in response to starvation, thereby supporting physiological adaptation to environmental stressors.\u0000 </div>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143111573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An Attention-Based Deep Neural Network Model to Detect Cis-Regulatory Elements at the Single-Cell Level From Multi-Omics Data 基于注意力的深度神经网络模型在单细胞水平上从多组学数据中检测顺式调控元件

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-02-04 DOI: 10.1111/gtc.70000

Ken Murakami, Keita Iida, Mariko Okada

{"title":"An Attention-Based Deep Neural Network Model to Detect Cis-Regulatory Elements at the Single-Cell Level From Multi-Omics Data","authors":"Ken Murakami, Keita Iida, Mariko Okada","doi":"10.1111/gtc.70000","DOIUrl":"https://doi.org/10.1111/gtc.70000","url":null,"abstract":"Cis-regulatory elements (cREs) play a crucial role in regulating gene expression and determining cell differentiation and state transitions. To capture the heterogeneous transitions of cell states associated with these processes, detecting cRE activity at the single-cell level is essential. However, current analytical methods can only capture the average behavior of cREs in cell populations, thereby obscuring cell-specific variations. To address this limitation, we proposed an attention-based deep neural network framework that integrates DNA sequences, genomic distances, and single-cell multi-omics data to detect cREs and their activities in individual cells. Our model shows higher accuracy in identifying cREs within single-cell multi-omics data from healthy human peripheral blood mononuclear cells than other existing methods. Furthermore, it clusters cells more precisely based on predicted cRE activities, enabling a finer differentiation of cell states. When applied to publicly available single-cell data from patients with glioma, the model successfully identified tumor-specific SOX2 activity. Additionally, it revealed the heterogeneous activation of the ZEB1 transcription factor, a regulator of epithelial-to-mesenchymal transition-related genes, which conventional methods struggle to detect. Overall, our model is a powerful tool for detecting cRE regulation at the single-cell level, which may contribute to revealing drug resistance mechanisms in cell sub-populations.","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/gtc.70000","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143111590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0