{"title":"Revisiting the gene mutations and protein profile of WT 9-12: An autosomal dominant polycystic kidney disease cell line","authors":"Hwa Chia Chai, Rhubaniya Mahendran, Kien Chai Ong, Kek Heng Chua","doi":"10.1111/gtc.13129","DOIUrl":"10.1111/gtc.13129","url":null,"abstract":"<p>WT 9-12 is one of the cell lines commonly used for autosomal dominant polycystic kidney disease (ADPKD) studies. Previous studies had described the <i>PKD</i> gene mutations and polycystin expression in WT 9-12. Nonetheless, the mutations occurring in other ADPKD-associated genes have not been investigated. This study aims to revisit these mutations and protein profile of WT 9-12. Whole genome sequencing verified the presence of truncation mutation at amino acid 2556 (Q2556X) in <i>PKD1</i> gene of WT 9-12. Besides, those variations with high impacts included single nucleotide polymorphisms (rs8054182, rs117006360, and rs12925771) and insertions and deletions (InDels) (rs145602984 and rs55980345) in <i>PKD1L2</i>; InDel (rs1296698195) in <i>PKD1L3</i>; and copy number variations in <i>GANAB</i>. Protein profiles generated from the total proteins of WT 9-12 and HK-2 cells were compared using isobaric tags for relative and absolute quantitation (iTRAQ) analysis. Polycystin-1 was absent in WT 9-12. The gene ontology enrichment and reactome pathway analyses revealed that the upregulated and downregulated proteins of WT 9-12 relative to HK-2 cell line leaded to signaling pathways related to immune response and amino acid metabolism, respectively. The ADPKD-related mutations and signaling pathways associated with differentially expressed proteins in WT 9-12 may help researchers in cell line selection for their studies.</p>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141087291","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}
{"title":"Chimera RNA transcribed from integrated HPV18 genome with adjacent host genomic region promotes oncogenic gene expression through condensate formation","authors":"Kazuki Furugori, Hidefumi Suzuki, Ryota Abe, Keiko Horiuchi, Tomohiko Akiyama, Tomonori Hirose, Atsushi Toyoda, Hidehisa Takahashi","doi":"10.1111/gtc.13121","DOIUrl":"10.1111/gtc.13121","url":null,"abstract":"<p>Most cervical cancers are caused by human papillomavirus (HPV) infection. In HeLa cells, the HPV18 viral genome is integrated at chromosome 8q24.21 and activates transcription of the proto-oncogene <i>c-Myc</i>. However, the mechanism of how the integrated HPV genome and its transcribed RNAs exhibit transcription activation function has not been fully elucidated. In this study, we found that HPV18 transcripts contain an enhancer RNA-like function to activate proximal genes including <i>CCAT1-5L</i> and <i>c-Myc</i>. We showed that the human genome-integrated <i>HPV18</i> genes are activated by transcription coregulators including BRD4 and Mediator. The transcribed HPV18 RNAs form a liquid-like condensate at chromosome 8q24.21 locus, which in turn accumulates RNA polymerase II. Moreover, we focused on a relatively uncharacterized transcript from the <b>u</b>pstream <b>r</b>egion of <i><b>C</b>CAT1</i>, named <i>URC</i>. The <i>URC</i> RNA is transcribed as a chimera RNA with HPV18 and is composed of the 3′-untranslated region of the HPV18 transcript. We experimentally showed that the <i>URC</i> contributes to stabilization of HPV18 RNAs by supplying a polyadenylation site for the HPV18 transcript. Our findings suggest that integrated HPV18 at 8q24.21 locus produces HPV18-URC chimera RNA and promotes tumorigenesis through RNA-based condensate formation.</p>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140876258","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}
{"title":"Rcn1, the fission yeast homolog of human DSCR1, regulates arsenite tolerance independently from calcineurin","authors":"Teruaki Takasaki, Asuka Bamba, Yuka Kukita, Aiko Nishida, Daiki Kanbayashi, Kanako Hagihara, Ryosuke Satoh, Keiichi Ishihara, Reiko Sugiura","doi":"10.1111/gtc.13122","DOIUrl":"10.1111/gtc.13122","url":null,"abstract":"<p>Calcineurin (CN) is a conserved Ca<sup>2+</sup>/calmodulin-dependent phosphoprotein phosphatase that plays a key role in Ca<sup>2+</sup> signaling. Regulator of calcineurin 1 (RCAN1), also known as Down syndrome critical region gene 1 (DSCR1), interacts with calcineurin and inhibits calcineurin-dependent signaling in various organisms. Ppb1, the fission yeast calcineurin regulates Cl<sup>−</sup>-homeostasis, and Ppb1 deletion induces MgCl<sub>2</sub> hypersensitivity. Here, we characterize the conserved and novel roles of the fission yeast RCAN1 homolog <i>rcn1</i><sup>+</sup>. Consistent with its role as an endogenous calcineurin inhibitor, Rcn1 overproduction reproduced the calcineurin-null phenotypes, including MgCl<sub>2</sub> hypersensitivity and inhibition of calcineurin signaling upon extracellular Ca<sup>2+</sup> stimuli as evaluated by the nuclear translocation and transcriptional activation of the calcineurin substrate Prz1. Notably, overexpression of <i>rcn1</i><sup>+</sup> causes hypersensitivity to arsenite, whereas calcineurin deletion induces arsenite tolerance, showing a phenotypic discrepancy between Rcn1 overexpression and calcineurin deletion. Importantly, although Rcn1 deletion induces modest sensitivities to arsenite and MgCl<sub>2</sub> in wild-type cells, the arsenite tolerance, but not MgCl<sub>2</sub> sensitivity, associated with Ppb1 deletion was markedly suppressed by Rcn1 deletion. Collectively, our findings reveal a previously unrecognized functional collaboration between Rcn1 and calcineurin, wherein Rcn1 not only negatively regulates calcineurin in the Cl<sup>−</sup> homeostasis, but also Rcn1 mediates calcineurin signaling to modulate arsenite cytotoxicity.</p>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140876259","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}
Genes to CellsPub Date : 2024-04-29DOI: 10.1111/gtc.13117
Riko Katsuki, Mai Kanuka, Ren Ohta, Shusei Yoshida, Taku Tamura
{"title":"Turnover of EDEM1, an ERAD-enhancing factor, is mediated by multiple degradation routes","authors":"Riko Katsuki, Mai Kanuka, Ren Ohta, Shusei Yoshida, Taku Tamura","doi":"10.1111/gtc.13117","DOIUrl":"10.1111/gtc.13117","url":null,"abstract":"<p>Quality-based protein production and degradation in the endoplasmic reticulum (ER) are essential for eukaryotic cell survival. During protein maturation in the ER, misfolded or unassembled proteins are destined for disposal through a process known as ER-associated degradation (ERAD). EDEM1 is an ERAD-accelerating factor whose gene expression is upregulated by the accumulation of aberrant proteins in the ER, known as ER stress. Although the role of EDEM1 in ERAD has been studied in detail, the turnover of EDEM1 by intracellular degradation machinery, including the proteasome and autophagy, is not well understood. To clarify EDEM1 regulation in the protein level, degradation mechanism of EDEM1 was examined. Our results indicate that both ERAD and autophagy degrade EDEM1 alike misfolded degradation substrates, although each degradation machinery targets EDEM1 in different folded states of proteins. We also found that ERAD factors, including the SEL1L/Hrd1 complex, YOD1, XTP3B, ERdj3, VIMP, BAG6, and JB12, but not OS9, are involved in EDEM1 degradation in a mannose-trimming-dependent and -independent manner. Our results suggest that the ERAD accelerating factor, EDEM1, is turned over by the ERAD itself, similar to ERAD clients.</p>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/gtc.13117","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140839121","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}
Genes to CellsPub Date : 2024-04-25DOI: 10.1111/gtc.13120
Mitsuhiro Itaya, Masakazu Kataoka
{"title":"Integrated conjugal plasmid pLS20 in the Bacillus subtilis genome produced 850-kbp circular subgenomes transmissible to another B. subtilis","authors":"Mitsuhiro Itaya, Masakazu Kataoka","doi":"10.1111/gtc.13120","DOIUrl":"10.1111/gtc.13120","url":null,"abstract":"<p><i>Bacillus subtilis</i> was engineered to produce circular subgenomes that are directly transmittable to another <i>B. subtilis</i>. The conjugational plasmid pLS20 integrated into the <i>B. subtilis</i> genome supported not only subgenome replication but also transmission to another <i>B. subtilis</i> species. The subgenome system developed in this study completes a streamlined platform from the synthesis to the transmission of giant DNA by <i>B. subtilis</i>.</p>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/gtc.13120","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140801478","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}
{"title":"A zinc-finger protein Moc3 functions as a transcription activator to promote RNAi-dependent constitutive heterochromatin establishment in fission yeast","authors":"Miyuki Mori, Michiaki Sato, Shinya Takahata, Takuya Kajitani, Yota Murakami","doi":"10.1111/gtc.13116","DOIUrl":"10.1111/gtc.13116","url":null,"abstract":"<p>In fission yeast, <i>Schizosaccharomyces pombe,</i> constitutive heterochromatin defined by methylation of histone H3 lysine 9 (H3K9me) and its binding protein Swi6/HP1 localizes at the telomere, centromere, and mating-type loci. These loci contain DNA sequences called <i>dg</i> and <i>dh</i>, and the RNA interference (RNAi)-dependent system establishes and maintains heterochromatin at <i>dg/dh</i>. Bi-directional transcription at <i>dg/dh</i> induced by RNA polymerase II is critical in RNAi-dependent heterochromatin formation because the transcribed RNAs provide substrates for siRNA synthesis and a platform for assembling RNAi factors. However, a regulator of <i>dg/dh</i> transcription during the establishment of heterochromatin is not known. Here, we found that a zinc-finger protein Moc3 localizes <i>dh</i> and activates <i>dh</i>-forward transcription in its zinc-finger-dependent manner when heterochromatin structure or heterochromatin-dependent silencing is compromised. However, Moc3 does not localize at normal heterochromatin and does not activate the <i>dh</i>-forward transcription. Notably, the loss of Moc3 caused a retarded heterochromatin establishment, showing that Moc3-dependent <i>dh</i>-forward transcription is critical for RNAi-dependent heterochromatin establishment. Therefore, Moc3 is a transcriptional activator that induces RNAi to establish heterochromatin.</p>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140614086","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}
Genes to CellsPub Date : 2024-04-11DOI: 10.1111/gtc.13119
Gina Miku Oba, Ryuichiro Nakato
{"title":"Clover: An unbiased method for prioritizing differentially expressed genes using a data-driven approach","authors":"Gina Miku Oba, Ryuichiro Nakato","doi":"10.1111/gtc.13119","DOIUrl":"10.1111/gtc.13119","url":null,"abstract":"<p>Identifying key genes from a list of differentially expressed genes (DEGs) is a critical step in transcriptome analysis. However, current methods, including Gene Ontology analysis and manual annotation, essentially rely on existing knowledge, which is highly biased depending on the extent of the literature. As a result, understudied genes, some of which may be associated with important molecular mechanisms, are often ignored or remain obscure. To address this problem, we propose Clover, a data-driven scoring method to specifically highlight understudied genes. Clover aims to prioritize genes associated with important molecular mechanisms by integrating three metrics: the likelihood of appearing in the DEG list, tissue specificity, and number of publications. We applied Clover to Alzheimer's disease data and confirmed that it successfully detected known associated genes. Moreover, Clover effectively prioritized understudied but potentially druggable genes. Overall, our method offers a novel approach to gene characterization and has the potential to expand our understanding of gene functions. Clover is an open-source software written in Python3 and available on GitHub at https://github.com/G708/Clover.</p>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/gtc.13119","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140592619","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}
{"title":"ATP2B4 is an essential gene for epidermal growth factor-induced macropinocytosis in A431 cells","authors":"Shunsuke Yoshie, Masashi Kuriyama, Masashi Maekawa, Wei Xu, Takuro Niidome, Shiroh Futaki, Hisaaki Hirose","doi":"10.1111/gtc.13118","DOIUrl":"10.1111/gtc.13118","url":null,"abstract":"<p>Macropinocytosis (MPC) is a large-scale endocytosis pathway that involves actin-dependent membrane ruffle formation and subsequent ruffle closure to generate macropinosomes for the uptake of fluid-phase cargos. MPC is categorized into two types: constitutive and stimuli-induced. Constitutive MPC in macrophages relies on extracellular Ca<sup>2+</sup> sensing by a calcium-sensing receptor. However, the link between stimuli-induced MPC and Ca<sup>2+</sup> remains unclear. Here, we find that both intracellular and extracellular Ca<sup>2+</sup> are required for epidermal growth factor (EGF)-induced MPC in A431 human epidermoid carcinoma cells. Through investigation of mammalian homologs of coelomocyte uptake defective (CUP) genes, we identify <i>ATP2B4</i>, encoding for a Ca<sup>2+</sup> pump called the plasma membrane calcium ATPase 4 (PMCA4), as a Ca<sup>2+</sup>-related regulator of EGF-induced MPC. Knockout (KO) of <i>ATP2B4</i>, as well as depletion of extracellular/intracellular Ca<sup>2+</sup>, inhibited ruffle closure and macropinosome formation, without affecting ruffle formation. We demonstrate the importance of PMCA4 activity itself, independent of interactions with other proteins via its C-terminus known as a PDZ domain-binding motif. Additionally, we show that <i>ATP2B4</i>-KO reduces EGF-stimulated Ca<sup>2+</sup> oscillation during MPC. Our findings suggest that EGF-induced MPC requires <i>ATP2B4</i>-dependent Ca<sup>2+</sup> dynamics.</p>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140592620","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}
Genes to CellsPub Date : 2024-03-29DOI: 10.1111/gtc.13114
Rieko Ohki, Koji Itahana, Tomoo Iwakuma
{"title":"“The 10th International MDM2 Workshop”: Opening up new avenues for MDM2 and p53 research, the First International MDM2 Workshop in Asia","authors":"Rieko Ohki, Koji Itahana, Tomoo Iwakuma","doi":"10.1111/gtc.13114","DOIUrl":"10.1111/gtc.13114","url":null,"abstract":"<p>The 10th International MDM2 Workshop was held at the National Cancer Center Research Institute (NCCRI) in Tokyo, Japan, from October 15 to 18, 2023. It attracted 166 participants from 12 countries. The meeting featured 52 talks and 41 poster presentations. In the first special session, six invited speakers gave educational and outstanding talks on breakthroughs in MDM2 research. Three keynote speakers presented emerging p53-independent functions of MDM2/MDM4, functional association of MDM2/p53 with cancer immunity, and drug discovery targeting the MDM2/MDM4-p53 pathway. Additionally, 19 invited speakers introduced their new findings. Twenty-one presenters, many of whom were young investigators, postdocs, and students, were selected from submitted abstracts and reported their exciting and unpublished results. For poster presenters, outstanding poster awards were given to the best presenters. There were many inspiring questions and discussions throughout the meeting. Social events like a welcome party, a workshop dinner, and an optional tour enabled further scientific interactions among the participants. The meeting successfully provided an exciting platform for scientific exchange. The experience gained from organizing this meeting will be handed over to the next organizers of the 11th International MDM2 Workshop.</p>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140326532","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}
{"title":"Role of Wnt5b-Ror1 signaling in the proliferation of pancreatic ductal adenocarcinoma cells","authors":"Natsuko Yamauchi, Mako Otsuka, Tomohiro Ishikawa, Yoshihiro Kakeji, Akira Kikuchi, Atsuhiro Masuda, Yuzo Kodama, Yasuhiro Minami, Koki Kamizaki","doi":"10.1111/gtc.13115","DOIUrl":"10.1111/gtc.13115","url":null,"abstract":"<p>Pancreatic ductal adenocarcinoma (PDAC) is one of the most refractory cancers with the worst prognosis. Although several molecules are known to be associated with the progression of PDAC, the molecular mechanisms underlying the progression of PDAC remain largely elusive. The Ror-family receptors, Ror1 and Ror2, which act as a receptor(s) for Wnt-family ligands, particularly Wnt5a, are involved in the progression of various types of cancers. Here, we show that higher expression of <i>Ror1</i> and <i>Wnt5b</i>, but not <i>Ror2</i>, are associated with poorer prognosis of PDAC patients, and that Ror1 and Wnt5b are expressed highly in a type of PDAC cell lines, PANC-1 cells. Knockdown of either <i>Ror1</i> or <i>Wnt5b</i> in PANC-1 cells inhibited their proliferation significantly in vitro, and knockout of <i>Ror1</i> in PANC-1 cells resulted in a significant inhibition of tumor growth in vivo. Furthermore, we show that Wnt5b-Ror1 signaling in PANC-1 cells promotes their proliferation in a cell-autonomous manner by modulating our experimental setting in vitro. Collectively, these findings indicate that Wnt5b-Ror1 signaling might play an important role in the progression of some if not all of PDAC by promoting proliferation.</p>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140293350","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}