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The culture and application of circulating tumor cell-derived organoids. 循环肿瘤细胞衍生有机体的培养和应用。
IF 13 1区 生物学
Trends in Cell Biology Pub Date : 2024-11-09 DOI: 10.1016/j.tcb.2024.10.004
Can Pan, Xueping Wang, Chuan Yang, Kai Fu, Fang Wang, Liwu Fu
{"title":"The culture and application of circulating tumor cell-derived organoids.","authors":"Can Pan, Xueping Wang, Chuan Yang, Kai Fu, Fang Wang, Liwu Fu","doi":"10.1016/j.tcb.2024.10.004","DOIUrl":"https://doi.org/10.1016/j.tcb.2024.10.004","url":null,"abstract":"<p><p>Circulating tumor cells (CTCs), which have the heterogeneity and histological properties of the primary tumor and metastases, are shed from the primary tumor and/or metastatic lesions into the vasculature and initiate metastases at remote sites. In the clinic, CTCs are used extensively in liquid biopsies for early screening, diagnosis, treatment, and prognosis. Current research focuses on using CTC-derived models to study tumor heterogeneity and metastasis, with 3D organoids emerging as a promising tool in cancer research and precision oncology. However, isolating and enriching CTCs from blood remains challenging due to their scarcity, exacerbated by the lack of an optimized culture medium for CTC-derived organoids (CTCDOs). In this review, we summarize the origin, isolation, enrichment, culture, validation, and clinical application of CTCs and CTCDOs.</p>","PeriodicalId":56085,"journal":{"name":"Trends in Cell Biology","volume":" ","pages":""},"PeriodicalIF":13.0,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Emerging roles of palmitoylation in pyroptosis. 棕榈酰化在高温变态反应中的新作用。
IF 13 1区 生物学
Trends in Cell Biology Pub Date : 2024-11-08 DOI: 10.1016/j.tcb.2024.10.005
Na Zhang, Yuanxin Yang, Daichao Xu
{"title":"Emerging roles of palmitoylation in pyroptosis.","authors":"Na Zhang, Yuanxin Yang, Daichao Xu","doi":"10.1016/j.tcb.2024.10.005","DOIUrl":"https://doi.org/10.1016/j.tcb.2024.10.005","url":null,"abstract":"<p><p>Pyroptosis is a lytic, proinflammatory type of programmed cell death crucial for the immune response to pathogen infections and internal danger signals. Gasdermin D (GSDMD) acts as the pore-forming protein in pyroptosis following inflammasome activation. While recent research has improved our understanding of pyroptosis activation and execution, many aspects regarding the molecular mechanisms controlling inflammasome and GSDMD activation remain to be elucidated. A growing body of literature has shown that S-palmitoylation, a reversible post-translational modification (PTM) that attaches palmitate to cysteine residues, contributes to multi-layered regulation of pyroptosis. This review summarizes the emerging roles of S-palmitoylation in pyroptosis research with a focus on mechanisms that regulate NLRP3 inflammasome and GSDMD activation.</p>","PeriodicalId":56085,"journal":{"name":"Trends in Cell Biology","volume":" ","pages":""},"PeriodicalIF":13.0,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
MDM4 exon skipping upon dysfunctional ribosome assembly. 核糖体组装失调时的 MDM4 外显子跳转。
IF 13 1区 生物学
Trends in Cell Biology Pub Date : 2024-11-07 DOI: 10.1016/j.tcb.2024.10.006
Jennifer Jansen, Matthias Dobbelstein
{"title":"MDM4 exon skipping upon dysfunctional ribosome assembly.","authors":"Jennifer Jansen, Matthias Dobbelstein","doi":"10.1016/j.tcb.2024.10.006","DOIUrl":"https://doi.org/10.1016/j.tcb.2024.10.006","url":null,"abstract":"<p><p>Recent studies revealed how nucleolar stress enhances MDM4 exon skipping and activates p53 via the ribosomal protein L22 (RPL22; eL22). Tumor-associated L22 mutations lead to full-length MDM4 synthesis, overcoming tumor suppression by p53. This forum article explores how MDM4 splicing patterns integrate stress signaling to take p53-dependent cell fate decisions.</p>","PeriodicalId":56085,"journal":{"name":"Trends in Cell Biology","volume":" ","pages":""},"PeriodicalIF":13.0,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Dynamic rRNA modifications as a source of ribosome heterogeneity. 动态 rRNA 修饰是核糖体异质性的来源。
IF 13 1区 生物学
Trends in Cell Biology Pub Date : 2024-11-04 DOI: 10.1016/j.tcb.2024.10.001
Ivan Milenkovic, Eva Maria Novoa
{"title":"Dynamic rRNA modifications as a source of ribosome heterogeneity.","authors":"Ivan Milenkovic, Eva Maria Novoa","doi":"10.1016/j.tcb.2024.10.001","DOIUrl":"https://doi.org/10.1016/j.tcb.2024.10.001","url":null,"abstract":"<p><p>Ribosomal RNAs (rRNA) are the most abundant RNA molecules in almost all cell types. The general consensus in the field is that rRNA modifications are largely species-specific, with most previous works and databases solely stratifying modifications by the species of origin, without taking other levels of complexity into account. However, new evidence has emerged suggesting dynamic rRNA modifications may have additional layers of complexity and might play an important role in development and disease. In this review article, we summarize recent evidence supporting heterogeneity and dynamics in rRNA modifications in diverse biological contexts, challenging the simplistic view of 'one-species-one-rRNA-modification-pattern'. Moreover, we highlight how rRNA modification dynamics have been studied to date and how long-read sequencing methods can significantly improve our understanding of this largely unexplored yet highly abundant RNA family, across tissues, developmental stages, and diseases.</p>","PeriodicalId":56085,"journal":{"name":"Trends in Cell Biology","volume":" ","pages":""},"PeriodicalIF":13.0,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142585245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Timing is everything: advances in quantifying splicing kinetics. 时间就是一切：量化剪接动力学的进展。
IF 13 1区 生物学
Trends in Cell Biology Pub Date : 2024-11-01 Epub Date: 2024-05-21 DOI: 10.1016/j.tcb.2024.03.007
Hope E Merens, Karine Choquet, Autum R Baxter-Koenigs, L Stirling Churchman
{"title":"Timing is everything: advances in quantifying splicing kinetics.","authors":"Hope E Merens, Karine Choquet, Autum R Baxter-Koenigs, L Stirling Churchman","doi":"10.1016/j.tcb.2024.03.007","DOIUrl":"10.1016/j.tcb.2024.03.007","url":null,"abstract":"<p><p>Splicing is a highly regulated process critical for proper pre-mRNA maturation and the maintenance of a healthy cellular environment. Splicing events are impacted by ongoing transcription, neighboring splicing events, and cis and trans regulatory factors on the respective pre-mRNA transcript. Within this complex regulatory environment, splicing kinetics have the potential to influence splicing outcomes but have historically been challenging to study in vivo. In this review, we highlight recent technological advancements that have enabled measurements of global splicing kinetics and of the variability of splicing kinetics at single introns. We demonstrate how identifying features that are correlated with splicing kinetics has increased our ability to form potential models for how splicing kinetics may be regulated in vivo.</p>","PeriodicalId":56085,"journal":{"name":"Trends in Cell Biology","volume":" ","pages":"968-981"},"PeriodicalIF":13.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141081871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Cytoplasmic mtDNA clearance suppresses inflammatory immune responses. 细胞质 mtDNA 清除抑制炎症免疫反应。
IF 13 1区 生物学
Trends in Cell Biology Pub Date : 2024-11-01 Epub Date: 2024-10-07 DOI: 10.1016/j.tcb.2024.09.002
Chenghao Yan, Xu Liu, Haodong Xu, Liming Wang
{"title":"Cytoplasmic mtDNA clearance suppresses inflammatory immune responses.","authors":"Chenghao Yan, Xu Liu, Haodong Xu, Liming Wang","doi":"10.1016/j.tcb.2024.09.002","DOIUrl":"10.1016/j.tcb.2024.09.002","url":null,"abstract":"<p><p>Upon various stresses, mtDNA leaks from mitochondria into the cytoplasm, leading to cellular dysfunction and inflammation, thereby exacerbating disease progression. The autophagy-lysosome pathway has emerged as a pivotal quality control mechanism for eliminating abnormal cytoplasmic mtDNA. This article summarizes the mechanisms underlying mtDNA-triggered inflammation and how cytoplasmic mtDNA is eliminated.</p>","PeriodicalId":56085,"journal":{"name":"Trends in Cell Biology","volume":" ","pages":"897-900"},"PeriodicalIF":13.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Epithelial metabolism as a rheostat for intestinal inflammation and malignancy. 上皮代谢是肠道炎症和恶性肿瘤的调节器。
IF 13 1区 生物学
Trends in Cell Biology Pub Date : 2024-11-01 Epub Date: 2024-02-10 DOI: 10.1016/j.tcb.2024.01.004
Julian Schwärzler, Lisa Mayr, Felix Grabherr, Herbert Tilg, Timon E Adolph
{"title":"Epithelial metabolism as a rheostat for intestinal inflammation and malignancy.","authors":"Julian Schwärzler, Lisa Mayr, Felix Grabherr, Herbert Tilg, Timon E Adolph","doi":"10.1016/j.tcb.2024.01.004","DOIUrl":"10.1016/j.tcb.2024.01.004","url":null,"abstract":"<p><p>The gut epithelium protects the host from a potentially hostile environment while allowing nutrient uptake that is vital for the organism. To maintain this delicate task, the gut epithelium has evolved multilayered cellular functions ranging from mucus production to hormone release and orchestration of mucosal immunity. Here, we review the execution of intestinal epithelial metabolism in health and illustrate how perturbation of epithelial metabolism affects experimental gut inflammation and tumorigenesis. We also discuss the impact of environmental factors and host-microbe interactions on epithelial metabolism in the context of inflammatory bowel disease and colorectal cancer. Insights into epithelial metabolism hold promise to unravel mechanisms of organismal health that may be therapeutically exploited in humans in the future.</p>","PeriodicalId":56085,"journal":{"name":"Trends in Cell Biology","volume":" ","pages":"913-927"},"PeriodicalIF":13.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139716632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
ER remodeling via lipid metabolism. 通过脂质代谢重塑 ER。
IF 13 1区 生物学
Trends in Cell Biology Pub Date : 2024-11-01 Epub Date: 2024-02-23 DOI: 10.1016/j.tcb.2024.01.011
Wonyul Jang, Volker Haucke
{"title":"ER remodeling via lipid metabolism.","authors":"Wonyul Jang, Volker Haucke","doi":"10.1016/j.tcb.2024.01.011","DOIUrl":"10.1016/j.tcb.2024.01.011","url":null,"abstract":"<p><p>Unlike most other organelles found in multiple copies, the endoplasmic reticulum (ER) is a unique singular organelle within eukaryotic cells. Despite its continuous membrane structure, encompassing more than half of the cellular endomembrane system, the ER is subdivided into specialized sub-compartments, including morphological, membrane contact site (MCS), and de novo organelle biogenesis domains. In this review, we discuss recent emerging evidence indicating that, in response to nutrient stress, cells undergo a reorganization of these sub-compartmental ER domains through two main mechanisms: non-destructive remodeling of morphological ER domains via regulation of MCS and organelle hitchhiking, and destructive remodeling of specialized domains by ER-phagy. We further highlight and propose a critical role of membrane lipid metabolism in this ER remodeling during starvation.</p>","PeriodicalId":56085,"journal":{"name":"Trends in Cell Biology","volume":" ","pages":"942-954"},"PeriodicalIF":13.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139941262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
SUMO proteases: from cellular functions to disease. SUMO 蛋白酶：从细胞功能到疾病。
IF 13 1区 生物学
Trends in Cell Biology Pub Date : 2024-11-01 Epub Date: 2024-02-06 DOI: 10.1016/j.tcb.2024.01.002
Laura A Claessens, Alfred C O Vertegaal
{"title":"SUMO proteases: from cellular functions to disease.","authors":"Laura A Claessens, Alfred C O Vertegaal","doi":"10.1016/j.tcb.2024.01.002","DOIUrl":"10.1016/j.tcb.2024.01.002","url":null,"abstract":"<p><p>Posttranslational modification by small ubiquitin-like modifiers (SUMOs) is critical in regulating diverse cellular processes including gene expression, cell cycle progression, genome integrity, cellular metabolism, and inflammation and immunity. The covalent attachment of SUMOs to target proteins is highly dynamic and reversible through the concerted action of SUMO conjugating and deconjugating enzymes. In mammalian cells, sentrin-specific proteases (SENPs) are the most abundant family of deconjugating enzymes. This review highlights recent advances in our knowledge of the substrates and cellular and physiological processes controlled by SENPs. Notably, SENPs are emerging as significant players in cancer, as well as in other diseases, making them attractive targets for therapeutic intervention. Consequently, a growing amount of effort in the field is being directed towards the development of SENP inhibitors.</p>","PeriodicalId":56085,"journal":{"name":"Trends in Cell Biology","volume":" ","pages":"901-912"},"PeriodicalIF":13.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139704140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Opportunities and challenges for deep learning in cell dynamics research. 细胞动力学研究中深度学习的机遇与挑战。
IF 13 1区 生物学
Trends in Cell Biology Pub Date : 2024-11-01 Epub Date: 2023-11-28 DOI: 10.1016/j.tcb.2023.10.010
Binghao Chai, Christoforos Efstathiou, Haoran Yue, Viji M Draviam
{"title":"Opportunities and challenges for deep learning in cell dynamics research.","authors":"Binghao Chai, Christoforos Efstathiou, Haoran Yue, Viji M Draviam","doi":"10.1016/j.tcb.2023.10.010","DOIUrl":"10.1016/j.tcb.2023.10.010","url":null,"abstract":"<p><p>The growth of artificial intelligence (AI) has led to an increase in the adoption of computer vision and deep learning (DL) techniques for the evaluation of microscopy images and movies. This adoption has not only addressed hurdles in quantitative analysis of dynamic cell biological processes but has also started to support advances in drug development, precision medicine, and genome-phenome mapping. We survey existing AI-based techniques and tools, as well as open-source datasets, with a specific focus on the computational tasks of segmentation, classification, and tracking of cellular and subcellular structures and dynamics. We summarise long-standing challenges in microscopy video analysis from a computational perspective and review emerging research frontiers and innovative applications for DL-guided automation in cell dynamics research.</p>","PeriodicalId":56085,"journal":{"name":"Trends in Cell Biology","volume":" ","pages":"955-967"},"PeriodicalIF":13.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138464665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
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