Hexiao Wang, Claudia Canasto-Chibuque, Jun Hyun Kim, Marcel Hohl, Christina Leslie, Jorge S. Reis-Filho, John H.J. Petrini
{"title":"Chronic interferon-stimulated gene transcription promotes oncogene-induced breast cancer","authors":"Hexiao Wang, Claudia Canasto-Chibuque, Jun Hyun Kim, Marcel Hohl, Christina Leslie, Jorge S. Reis-Filho, John H.J. Petrini","doi":"10.1101/gad.351455.123","DOIUrl":"https://doi.org/10.1101/gad.351455.123","url":null,"abstract":"The MRE11 complex (comprising MRE11, RAD50, and NBS1) is integral to the maintenance of genome stability. We previously showed that a hypomorphic <em>Mre11</em> mutant mouse strain (<em>Mre11</em><sup><em>ATLD1/ATLD1</em></sup>) was highly susceptible to oncogene-induced breast cancer. Here we used a mammary organoid system to examine which MRE11-dependent responses are tumor-suppressive. We found that <em>Mre11</em><sup><em>ATLD1/ATLD1</em></sup> organoids exhibited an elevated interferon-stimulated gene (ISG) signature and sustained changes in chromatin accessibility. This <em>Mre11</em><sup><em>ATLD1/ATLD1</em></sup> phenotype depended on DNA binding of a nuclear innate immune sensor, IFI205. Ablation of <em>Ifi205</em> in <em>Mre11</em><sup><em>ATLD1/ATLD1</em></sup> organoids restored baseline and oncogene-induced chromatin accessibility patterns to those observed in WT. Implantation of <em>Mre11</em><sup><em>ATLD1/ATLD1</em></sup> organoids and activation of the oncogene led to aggressive metastatic breast cancer. This outcome was reversed in implanted <em>Ifi205</em><sup>−/−</sup> <em>Mre11</em><sup><em>ATLD1/ATLD1</em></sup> organoids. These data reveal a connection between innate immune signaling and tumor development in the mammary epithelium. Given the abundance of aberrant DNA structures that arise in the context of genome instability syndromes, the data further suggest that cancer predisposition in those contexts may be partially attributable to chronic innate immune transcriptional programs.","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":"194 1","pages":""},"PeriodicalIF":10.5,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142490358","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}
{"title":"Circadian de(regulation) in physiology: implications for disease and treatment","authors":"Leonardo Vinicius Monteiro de Assis, Achim Kramer","doi":"10.1101/gad.352180.124","DOIUrl":"https://doi.org/10.1101/gad.352180.124","url":null,"abstract":"Time plays a crucial role in the regulation of physiological processes. Without a temporal control system, animals would be unprepared for cyclic environmental changes, negatively impacting their survival. Experimental studies have demonstrated the essential role of the circadian system in the temporal coordination of physiological processes. Translating these findings to humans has been challenging. Increasing evidence suggests that modern lifestyle factors such as diet, sedentarism, light exposure, and social jet lag can stress the human circadian system, contributing to misalignment; i.e., loss of phase coherence across tissues. An increasing body of evidence supports the negative impact of circadian disruption on several human health parameters. This review aims to provide a comprehensive overview of how circadian disruption influences various physiological processes, its long-term health consequences, and its association with various diseases. To illustrate the relevant consequences of circadian disruption, we focused on describing the many physiological consequences faced by shift workers, a population known to experience high levels of circadian disruption. We also discuss the emerging field of circadian medicine, its founding principles, and its potential impact on human health.","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":"106 1","pages":""},"PeriodicalIF":10.5,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142448383","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}
Sarmistha Banerjee, Sulagna Sanyal, Suchita Hodawadekar, Sarah Naiyer, Nasreen Bano, Anupam Banerjee, Joshua Rhoades, Dawei Dong, David Allman, Michael L Atchison
{"title":"YY1 knockout in pro-B cells impairs lineage commitment, enabling unusual hematopoietic lineage plasticity.","authors":"Sarmistha Banerjee, Sulagna Sanyal, Suchita Hodawadekar, Sarah Naiyer, Nasreen Bano, Anupam Banerjee, Joshua Rhoades, Dawei Dong, David Allman, Michael L Atchison","doi":"10.1101/gad.351734.124","DOIUrl":"10.1101/gad.351734.124","url":null,"abstract":"<p><p>During B-cell development, cells progress through multiple developmental stages, with the pro-B-cell stage defining commitment to the B-cell lineage. YY1 is a ubiquitous transcription factor that is capable of both activation and repression functions. We found here that knockout of YY1 at the pro-B-cell stage eliminates B lineage commitment. YY1 knockout pro-B cells can generate T lineage cells in vitro using the OP9-DL4 feeder system and in vivo after injection into sublethally irradiated Rag1<sup>-/-</sup> mice. These T lineage-like cells lose their B lineage transcript profile and gain a T-cell lineage profile. Single-cell RNA-seq experiments showed that as YY1 knockout pro-B cells transition into T lineage cells in vitro, various cell clusters adopt transcript profiles representing a multiplicity of hematopoietic lineages, indicating unusual lineage plasticity. In addition, YY1 KO pro-B cells in vivo can give rise to other hematopoietic lineages in vivo. Evaluation of RNA-seq, scRNA-seq, ChIP-seq, and scATAC-seq data indicates that YY1 controls numerous chromatin-modifying proteins leading to increased accessibility of alternative lineage genes in YY1 knockout pro-B cells. Given the ubiquitous nature of YY1 and its dual activation and repression functions, YY1 may regulate commitment in multiple cell lineages.</p>","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":" ","pages":"887-914"},"PeriodicalIF":7.5,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11535188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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 area postrema: a critical mediator of brain-body interactions.","authors":"Daniëlle van de Lisdonk, Bo Li","doi":"10.1101/gad.352276.124","DOIUrl":"10.1101/gad.352276.124","url":null,"abstract":"<p><p>The dorsal vagal complex contains three structures: the area postrema, the nucleus tractus solitarii, and the dorsal motor nucleus of the vagus. These structures are tightly linked, both anatomically and functionally, and have important yet distinct roles in not only conveying peripheral bodily signals to the rest of the brain but in the generation of behavioral and physiological responses. Reports on the new discoveries in these structures were highlights of the symposium. In this outlook, we focus on the roles of the area postrema in mediating brain-body interactions and its potential utility as a therapeutic target, especially in cancer cachexia.</p>","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":" ","pages":"793-797"},"PeriodicalIF":7.5,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11535157/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Cancer neuroscience at the brain-body interface.","authors":"Jeremy C Borniger","doi":"10.1101/gad.352288.124","DOIUrl":"10.1101/gad.352288.124","url":null,"abstract":"<p><p>Our approaches toward understanding cancer have evolved beyond cell-intrinsic and local microenvironmental changes within the tumor to encompass how the cancer interfaces with the entire host organism. The nervous system is uniquely situated at the interface between the brain and body, constantly receiving and sending signals back and forth to maintain homeostasis and respond to salient stimuli. It is becoming clear that various cancers disrupt this dialog between the brain and body via both neuronal and humoral routes, leading to aberrant brain activity and accelerated disease. In this outlook, I discuss this view of cancer as a homeostatic challenge, emphasize cutting-edge work, and provide outstanding questions that need to be answered to move the field forward.</p>","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":" ","pages":"787-792"},"PeriodicalIF":7.5,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11535155/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"What a wonderful world!","authors":"Claire Magnon","doi":"10.1101/gad.352278.124","DOIUrl":"10.1101/gad.352278.124","url":null,"abstract":"<p><p>The world of cancer science is moving toward a paradigm shift in making connections with neuroscience. After decades of research on genetic instability and mutations or on the tumor microenvironment, emerging evidence suggests that a malignant tumor is able to hijack and use the brain and its network of peripheral and central neurons as disrupters of homeostasis in the body. Whole-body homeostasis requires brain-body circuits to maintain survival and health via the processes of interoception, immunoception, and nociception. It is now likely that cancer disturbs physiological brain-body communication in making bidirectional brain tumor connections.</p>","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":" ","pages":"802-804"},"PeriodicalIF":7.5,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11535159/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Harnessing brain-body communication to understand cancer.","authors":"Erica K Sloan","doi":"10.1101/gad.352292.124","DOIUrl":"10.1101/gad.352292.124","url":null,"abstract":"<p><p>Solid tumors that arise in the body interact with neurons, which influences cancer progression and treatment response. Here, we discuss key questions in the field, including defining the nature of interactions between tumors and neural circuits and defining how neural signals shape the tumor microenvironment. This information will allow us to optimally target neural signaling to improve outcomes for cancer patients.</p>","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":" ","pages":"820-822"},"PeriodicalIF":7.5,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11535151/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Consolidating roles of neuroimmune reflexes: specificity of afferent, central, and efferent signals in homeostatic immune networks.","authors":"Kevin J Tracey","doi":"10.1101/gad.352287.124","DOIUrl":"10.1101/gad.352287.124","url":null,"abstract":"<p><p>Neural reflexes occupy a central role in physiological homeostasis. The vagus nerve is a major conduit for transmitting afferent and efferent signals in homeostatic reflex arcs between the body and the brain. Recent advances in neuroscience, immunology, and physiology have revealed important vagus nerve mechanisms in suppressing inflammation and treating rheumatoid arthritis and other autoimmune conditions. Numerous clinical trials indicate that there is significant benefit to vagus nerve stimulation therapy. Although many questions are still unanswered, it will be important, even necessary, to pursue answers that will be useful in guiding interventions to modulate immunological and physiological homeostasis.</p>","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":" ","pages":"805-807"},"PeriodicalIF":7.5,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11535154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Julia M. Rogers, Claudia A. Mimoso, Benjamin J.E. Martin, Alexandre P. Martin, Jon C. Aster, Karen Adelman, Stephen C. Blacklow
{"title":"Notch induces transcription by stimulating release of paused RNA polymerase II","authors":"Julia M. Rogers, Claudia A. Mimoso, Benjamin J.E. Martin, Alexandre P. Martin, Jon C. Aster, Karen Adelman, Stephen C. Blacklow","doi":"10.1101/gad.352108.124","DOIUrl":"https://doi.org/10.1101/gad.352108.124","url":null,"abstract":"Notch proteins undergo ligand-induced proteolysis to release a nuclear effector that influences a wide range of cellular processes by regulating transcription. Despite years of study, however, how Notch induces the transcription of its target genes remains unclear. Here, we comprehensively examine the response to human Notch1 across a time course of activation using high-resolution genomic assays of chromatin accessibility and nascent RNA production. Our data reveal that Notch induces target gene transcription primarily by releasing paused RNA polymerase II (RNAPII). Moreover, in contrast to prevailing models suggesting that Notch acts by promoting chromatin accessibility, we found that open chromatin was established at Notch-responsive regulatory elements prior to Notch signal induction through SWI/SNF-mediated remodeling. Together, these studies show that the nuclear response to Notch signaling is dictated by the pre-existing chromatin state and RNAPII distribution at the time of signal activation.","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":"30 1","pages":""},"PeriodicalIF":10.5,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142443874","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}
Michael Cross, Andrew Dillin, Thales Papagiannakopoulos
{"title":"Bridging brain and body in cancer.","authors":"Michael Cross, Andrew Dillin, Thales Papagiannakopoulos","doi":"10.1101/gad.352300.124","DOIUrl":"10.1101/gad.352300.124","url":null,"abstract":"<p><p>Recent work has highlighted the central role the brain-body axis plays in not only maintaining organismal homeostasis but also coordinating the body's response to immune and inflammatory insults. Here, we discuss how science is poised to address the many ways that our brain is directly involved with disease. In particular, we feel that combining cutting-edge tools in neuroscience with translationally relevant models of cancer will be critical to understanding how the brain and tumors communicate and modulate each other's behavior.</p>","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":" ","pages":"814-816"},"PeriodicalIF":7.5,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11535152/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}