201
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Langdon QK, Groh JS, Aguillon SM, Powell DL, Gunn T, Payne C, Baczenas JJ, Donny A, Dodge TO, Du K, Schartl M, Ríos-Cárdenas O, Gutiérrez-Rodríguez C, Morris M, Schumer M. Swordtail fish hybrids reveal that genome evolution is surprisingly predictable after initial hybridization. PLoS Biol 2024; 22:e3002742. [PMID: 39186811 DOI: 10.1371/journal.pbio.3002742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 07/09/2024] [Indexed: 08/28/2024] Open
Abstract
Over the past 2 decades, biologists have come to appreciate that hybridization, or genetic exchange between distinct lineages, is remarkably common-not just in particular lineages but in taxonomic groups across the tree of life. As a result, the genomes of many modern species harbor regions inherited from related species. This observation has raised fundamental questions about the degree to which the genomic outcomes of hybridization are repeatable and the degree to which natural selection drives such repeatability. However, a lack of appropriate systems to answer these questions has limited empirical progress in this area. Here, we leverage independently formed hybrid populations between the swordtail fish Xiphophorus birchmanni and X. cortezi to address this fundamental question. We find that local ancestry in one hybrid population is remarkably predictive of local ancestry in another, demographically independent hybrid population. Applying newly developed methods, we can attribute much of this repeatability to strong selection in the earliest generations after initial hybridization. We complement these analyses with time-series data that demonstrates that ancestry at regions under selection has remained stable over the past approximately 40 generations of evolution. Finally, we compare our results to the well-studied X. birchmanni × X. malinche hybrid populations and conclude that deeper evolutionary divergence has resulted in stronger selection and higher repeatability in patterns of local ancestry in hybrids between X. birchmanni and X. cortezi.
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Affiliation(s)
- Quinn K Langdon
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
| | - Jeffrey S Groh
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
| | - Stepfanie M Aguillon
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, United States of America
| | - Daniel L Powell
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Theresa Gunn
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
| | - Cheyenne Payne
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
| | - John J Baczenas
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Alex Donny
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
| | - Tristram O Dodge
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
| | - Kang Du
- Xiphophorus Genetic Stock Center, Texas State University San Marcos, San Marcos, United States of America
| | - Manfred Schartl
- Xiphophorus Genetic Stock Center, Texas State University San Marcos, San Marcos, United States of America
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Oscar Ríos-Cárdenas
- Red de Biología Evolutiva, Instituto de Ecología, A.C., Xalapa, Veracruz, Mexico
| | | | - Molly Morris
- Department of Biological Sciences, Ohio University, Athens, Ohio, United States of America
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico
- Freeman Hrabowski Fellow, Howard Hughes Medical Institute, Stanford, California, United States of America
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202
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Li M, Fang Q, Xiao P, Yin Z, Mei G, Wang C, Xiang Y, Zhao X, Qu L, Xu T, Zhang J, Liu K, Li X, Dong H, Xiao R, Zhou R. KHSRP ameliorates acute liver failure by regulating pre-mRNA splicing through its interaction with SF3B1. Cell Death Dis 2024; 15:618. [PMID: 39187547 PMCID: PMC11347664 DOI: 10.1038/s41419-024-06886-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 06/27/2024] [Accepted: 07/02/2024] [Indexed: 08/28/2024]
Abstract
Acute liver failure (ALF) is characterized by the rapidly progressive deterioration of hepatic function, which, without effective medical intervention, results in high mortality and morbidity. Here, using proteomic and transcriptomic analyses in murine ALF models, we found that the expression of multiple splicing factors was downregulated in ALF. Notably, we found that KH-type splicing regulatory protein (KHSRP) has a protective effect in ALF. Knockdown of KHSRP resulted in dramatic splicing defects, such as intron retention, and led to the exacerbation of liver injury in ALF. Moreover, we demonstrated that KHSRP directly interacts with splicing factor 3b subunit 1 (SF3B1) and enhances the binding of SF3B1 to the intronic branch sites, thereby promoting pre-mRNA splicing. Using splicing inhibitors, we found that Khsrp protects against ALF by regulating pre-mRNA splicing in vivo. Overall, our findings demonstrate that KHSRP is an important splicing activator and promotes the expression of genes associated with ALF progression by interacting with SF3B1; thus, KHSRP could be a possible target for therapeutic intervention in ALF.
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Affiliation(s)
- Mingxuan Li
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Qian Fang
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Pingping Xiao
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Zhinang Yin
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Guangbo Mei
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Cheng Wang
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Ying Xiang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Xuejun Zhao
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Lihua Qu
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Tian Xu
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Jiaxi Zhang
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Kejun Liu
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Xiaoqing Li
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Huifen Dong
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Ruijing Xiao
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China.
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China.
| | - Rui Zhou
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China.
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China.
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203
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Shibai A, Furusawa C. Development of specialized devices for microbial experimental evolution. Dev Growth Differ 2024. [PMID: 39187274 DOI: 10.1111/dgd.12940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 08/06/2024] [Accepted: 08/11/2024] [Indexed: 08/28/2024]
Abstract
Experimental evolution of microbial cells provides valuable information on evolutionary dynamics, such as mutations that contribute to fitness gain under given selection pressures. Although experimental evolution is a promising tool in evolutionary biology and bioengineering, long-term culture experiments under multiple environmental conditions often impose an excessive workload on researchers. Therefore, the development of automated systems significantly contributes to the advancement of experimental evolutionary research. This review presents several specialized devices designed for experimental evolution studies, such as an automated system for high-throughput culture experiments, a culture device that generate a temperature gradient, and an automated ultraviolet (UV) irradiation culture device. The ongoing development of such specialized devices is poised to continually expand new frontiers in experimental evolution research.
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Affiliation(s)
- Atsushi Shibai
- Center for Biosystems Dynamics Research, RIKEN, Suita, Japan
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research, RIKEN, Suita, Japan
- Universal Biology Institute, The University of Tokyo, Tokyo, Japan
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204
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Xuan P, Wang W, Cui H, Wang S, Nakaguchi T, Zhang T. Mask-Guided Target Node Feature Learning and Dynamic Detailed Feature Enhancement for lncRNA-Disease Association Prediction. J Chem Inf Model 2024; 64:6662-6675. [PMID: 39112431 DOI: 10.1021/acs.jcim.4c00652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Identifying new relevant long noncoding RNAs (lncRNAs) for various human diseases can facilitate the exploration of the causes and progression of these diseases. Recently, several graph inference methods have been proposed to predict disease-related lncRNAs by exploiting the topological structure and node attributes within graphs. However, these methods did not prioritize the target lncRNA and disease nodes over auxiliary nodes like miRNA nodes, potentially limiting their ability to fully utilize the features of the target nodes. We propose a new method, mask-guided target node feature learning and dynamic detailed feature enhancement for lncRNA-disease association prediction (MDLD), to enhance node feature learning for improved lncRNA-disease association prediction. First, we designed a heterogeneous graph masked transformer autoencoder to guide feature learning, focusing more on the features of target lncRNA (disease) nodes. The target nodes were increasingly masked as training progressed, which helps develop a more robust prediction model. Second, we developed a graph convolutional network with dynamic residuals (GCNDR) to learn and integrate the heterogeneous topology and features of all lncRNA, disease, and miRNA nodes. GCNDR employs an interlayer residual strategy and a residual evolution strategy to mitigate oversmoothing caused by multilayer graph convolution. The interlayer residual strategy estimates the importance of node features learned in the previous GCN encoding layer for nodes in the current encoding layer. Additionally, since there are dependencies in the importance of features of individual lncRNA (disease, miRNA) nodes across multiple encoding layers, a gated recurrent unit-based strategy is proposed to encode these dependencies. Finally, we designed a perspective-level attention mechanism to obtain more informative features of lncRNA and disease node pairs from the perspectives of mask-enhanced and dynamic-enhanced node features. Cross-validation experimental results demonstrated that MDLD outperformed 10 other state-of-the-art prediction methods. Ablation experiments and case studies on candidate lncRNAs for three diseases further proved the technical contributions of MDLD and its capability to discover disease-related lncRNAs.
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Affiliation(s)
- Ping Xuan
- Department of Computer Science and Technology, Shantou University, Shantou 515063, China
- School of Mathematical Science, Heilongjiang University, Harbin 150080, China
| | - Wei Wang
- Department of Computer Science and Technology, Shantou University, Shantou 515063, China
| | - Hui Cui
- Department of Computer Science and Information Technology, La Trobe University, Melbourne 3083, Australia
| | - Shuai Wang
- School of Information Science and Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Toshiya Nakaguchi
- Center for Frontier Medical Engineering, Chiba University, Chiba 2638522, Japan
| | - Tiangang Zhang
- School of Mathematical Science, Heilongjiang University, Harbin 150080, China
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205
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Hertzler JI, Teng J, Bernard AR, Stone MC, Kline HL, Mahata G, Kumar N, Rolls MM. Voltage-gated calcium channels act upstream of adenylyl cyclase Ac78C to promote timely initiation of dendrite regeneration. PLoS Genet 2024; 20:e1011388. [PMID: 39186815 DOI: 10.1371/journal.pgen.1011388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 08/06/2024] [Indexed: 08/28/2024] Open
Abstract
Most neurons are not replaced after injury and thus possess robust intrinsic mechanisms for repair after damage. Axon injury triggers a calcium wave, and calcium and cAMP can augment axon regeneration. In comparison to axon regeneration, dendrite regeneration is poorly understood. To test whether calcium and cAMP might also be involved in dendrite injury signaling, we tracked the responses of Drosophila dendritic arborization neurons to laser severing of axons and dendrites. We found that calcium and subsequently cAMP accumulate in the cell body after both dendrite and axon injury. Two voltage-gated calcium channels (VGCCs), L-Type and T-Type, are required for the calcium influx in response to dendrite injury and play a role in rapid initiation of dendrite regeneration. The AC8 family adenylyl cyclase, Ac78C, is required for cAMP production after dendrite injury and timely initiation of regeneration. Injury-induced cAMP production is sensitive to VGCC reduction, placing calcium upstream of cAMP generation. We propose that two VGCCs initiate global calcium influx in response to dendrite injury followed by production of cAMP by Ac78C. This signaling pathway promotes timely initiation of dendrite regrowth several hours after dendrite damage.
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Affiliation(s)
- J Ian Hertzler
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jiajing Teng
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Annabelle R Bernard
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Michelle C Stone
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Hannah L Kline
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Gibarni Mahata
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Nitish Kumar
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Melissa M Rolls
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences The Pennsylvania State University, University Park, Pennsylvania, United States of America
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206
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Abbasi-Malati Z, Khanicheragh P, Narmi MT, Mardi N, Khosrowshahi ND, Hiradfar A, Rezabakhsh A, Sadeghsoltani F, Rashidi S, Chegeni SA, Roozbahani G, Rahbarghazi R. Tumoroids, a valid preclinical screening platform for monitoring cancer angiogenesis. Stem Cell Res Ther 2024; 15:267. [PMID: 39183337 PMCID: PMC11346257 DOI: 10.1186/s13287-024-03880-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 08/06/2024] [Indexed: 08/27/2024] Open
Abstract
In recent years, biologists and clinicians have witnessed prominent advances in in vitro 3D culture techniques related to biomimetic human/animal tissue analogs. Numerous data have confirmed that unicellular and multicellular (tumoroids) tumor spheroids with dense native cells in certain matrices are sensitive and valid analytical tools for drug screening, cancer cell dynamic growth, behavior, etc. in laboratory settings. Angiogenesis/vascularization is a very critical biological phenomenon to support oxygen and nutrients to tumor cells within the deep layer of solid masses. It has been shown that endothelial cell (EC)-incorporated or -free spheroid/tumoroid systems provide a relatively reliable biological platform for monitoring the formation of nascent blood vessels in micron/micrometer scales. Besides, the paracrine angiogenic activity of cells within the spheroid/tumoroid systems can be monitored after being treated with different therapeutic approaches. Here, we aimed to collect recent advances and findings related to the monitoring of cancer angiogenesis using unicellular and multicellular tumor spheroids. Vascularized spheroids/tumoroids can help us in the elucidation of mechanisms related to cancer formation, development, and metastasis by monitoring the main influencing factors.
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Affiliation(s)
- Zahra Abbasi-Malati
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parisa Khanicheragh
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Narges Mardi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nafiseh Didar Khosrowshahi
- Stem Cell and Tissue Engineering Research Laboratory, Sahand University of Technology, Tabriz, 51335-1996, Iran
| | - Amirataollah Hiradfar
- Pediatric Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Aysa Rezabakhsh
- Cardiovascular Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Somayyeh Rashidi
- Department of Medical Biotechnology, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | | | - Golbarg Roozbahani
- Department of Plant, Cell and Molecular Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Reza Rahbarghazi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
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207
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Gotoh H, Ohtsu I, Umino T, Yamasaki YY, Minakuchi Y, Ito T, Toyoda A, Kitano J. Induction of male-like mandibles in XX individuals of a stag beetle by gene knockdown of a feminizer gene transformer. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024. [PMID: 39188022 DOI: 10.1002/jez.b.23274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 08/06/2024] [Accepted: 08/14/2024] [Indexed: 08/28/2024]
Abstract
Males and females share most of the genome, but many animals show different phenotypes between the sexes, known as sexual dimorphism. Many insect species show extreme sexual dimorphism, including beetles with "weapon traits" represented by extremely developed horns and mandibles. Existing studies of sex-specific development of beetle weapon traits suggest that sex-specific gene expression plays an important role. On the other hand, contributions of the Y-chromosome, which may potentially carry genes necessary for male development, to weapon trait expression have not been examined. In holometabolous insects, including beetles, the feminizing gene transformer (tra) is roughly conserved in its feminizing function. Only females express a functional isoform of Tra, which causes female differentiation. Knocking down tra in females leads to male tissue differentiation, enabling us to analyze male phenotypes in individuals lacking a Y-chromosome (XX-males). In this study, we investigate whether the Y-chromosome is necessary for stag beetles to express male-specific weapon traits by comparing tra-knockdown-induced XX-males with natural XY males. We show that XX-males could express weapons (enlarged mandibles) as in XY-males. These results suggest that the Y-chromosome does not have a major role in weapon trait expression in this species.
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Affiliation(s)
- Hiroki Gotoh
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Itsuki Ohtsu
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Taichi Umino
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Nagano, Japan
| | - Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Yohei Minakuchi
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Takehiko Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
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208
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Ghaffari-Bohlouli P, Jafari H, Nie L, Kakkar A, Shavandi A. Enzymes in Addressing Hypoxia for Biomaterials Engineering. Adv Healthc Mater 2024:e2401713. [PMID: 39183514 DOI: 10.1002/adhm.202401713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 08/05/2024] [Indexed: 08/27/2024]
Abstract
Oxygen is essential for normal cellular functions. Hypoxia impacts various cellular processes, such as metabolism, growth, proliferation, angiogenesis, metastasis, tumorigenesis, microbial infection, and immune response, mediated by hypoxia-inducible factors (HIFs). Hypoxia contributes to the progression and development of cancer, cardiovascular diseases, metabolic disorders, kidney diseases, and infections. The potential alleviation of hypoxia has been explored through the enzymatic in situ decomposition of hydrogen peroxide, leading to the generation of oxygen. However, challenges such as limited stability restrict the effectiveness of enzymes such as catalase in biomedical and in vivo applications. To overcome these limitations, targeted delivery of the enzymes has been proposed. This review offers a critical comparison of i) current approaches to enhance the in vivo stability of catalase; and ii) the structure, mechanism of action, and kinetics of catalase and catalase-like nanozymes.
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Affiliation(s)
- Pejman Ghaffari-Bohlouli
- 3BIO-BioMatter, École Polytechnique de Bruxelles, Université Libre de Bruxelles, Avenue F.D. Roosevelt, 50-CP 165/61, Brussels, 1050, Belgium
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, H3A 0B8, Canada
| | - Hafez Jafari
- 3BIO-BioMatter, École Polytechnique de Bruxelles, Université Libre de Bruxelles, Avenue F.D. Roosevelt, 50-CP 165/61, Brussels, 1050, Belgium
| | - Lei Nie
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Ashok Kakkar
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, H3A 0B8, Canada
| | - Amin Shavandi
- 3BIO-BioMatter, École Polytechnique de Bruxelles, Université Libre de Bruxelles, Avenue F.D. Roosevelt, 50-CP 165/61, Brussels, 1050, Belgium
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209
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Zhao S, Zhang Y, Bao S, Jiang L, Li Q, Kong Y, Cao J. A novel HMGA2/MPC-1/mTOR signaling pathway promotes cell growth via facilitating Cr (VI)-induced glycolysis. Chem Biol Interact 2024; 399:111141. [PMID: 38992767 DOI: 10.1016/j.cbi.2024.111141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/25/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
Mitochondrial Pyruvate Carrier 1 (MPC1) is localized on mitochondrial outer membrane to mediate the transport of pyruvate from cytosol to mitochondria. It is also well known to act as a tumor suppressor. Hexavalent chromium (Cr (VI)) contamination poses a global challenge due to its high toxicity and carcinogenesis. This research was intended to probe the potential mechanism of MPC1 in the effect of Cr (VI)-induced carcinogenesis. First, Cr (VI)-treatments decreased the expression of MPC1 in vitro and in vivo. Overexpression of MPC1 inhibited Cr (VI)-induced glycolysis and migration in A549 cells. Then, high mobility group A2 (HMGA2) protein strongly suppressed the transcription of MPC1 by binding to its promoter, and HMGA2/MPC1 axis played an important role in oxidative phosphorylation (OXPHOS), glycolysis and cell migration. Furthermore, endoplasmic reticulum (ER) stress made a great effect on the interaction between HMGA2 and MPC1. Finally, the mammalian target of the rapamycin (mTOR) was determined to mediate MPC1-regulated OXPHOS, aerobic glycolysis and cell migration. Collectively, our data revealed a novel HMGA2/MPC-1/mTOR signaling pathway to promote cell growth via facilitating the metabolism reprogramming from OXPHOS to aerobic glycolysis, which might be a potential therapy for cancers.
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Affiliation(s)
- Siyang Zhao
- Department of Occupational and Environmental Health, Dalian Medical University, No. 9 W. Lvshun South Road, Dalian, 116044, China; Institute of Plant Resources, Dalian Minzu University, No.18 Liaohe West Road, Dalian, 116600, China
| | - Yahui Zhang
- Department of Occupational and Environmental Health, Dalian Medical University, No. 9 W. Lvshun South Road, Dalian, 116044, China
| | - Shibo Bao
- Department of Occupational and Environmental Health, Dalian Medical University, No. 9 W. Lvshun South Road, Dalian, 116044, China
| | - Liping Jiang
- Department of Occupational and Environmental Health, Dalian Medical University, No. 9 W. Lvshun South Road, Dalian, 116044, China
| | - Qiujuan Li
- Department of Occupational and Environmental Health, Dalian Medical University, No. 9 W. Lvshun South Road, Dalian, 116044, China
| | - Ying Kong
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, 116044, China.
| | - Jun Cao
- Department of Occupational and Environmental Health, Dalian Medical University, No. 9 W. Lvshun South Road, Dalian, 116044, China.
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210
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Tarannum R, Mun G, Quddos F, Swanger SA, Steward O, Farris S. Dendritically localized RNAs are packaged as diversely composed ribonucleoprotein particles with heterogeneous copy number states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.13.603387. [PMID: 39071419 PMCID: PMC11275876 DOI: 10.1101/2024.07.13.603387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Localization of mRNAs to dendrites is a fundamental mechanism by which neurons achieve spatiotemporal control of gene expression. Translationally repressed neuronal mRNA transport granules, also referred to as ribonucleoprotein particles (RNPs), have been shown to be trafficked as single or low copy number RNPs and as larger complexes with multiple copies and/or species of mRNAs. However, there is little evidence of either population in intact neuronal circuits. Using single molecule fluorescence in situ hybridization studies in the dendrites of adult rat and mouse hippocampus, we provide evidence that supports the existence of multi-transcript RNPs with the constituents varying in amounts for each RNA species. By competing-off fluorescently labeled probe with serial increases of unlabeled probe, we detected stepwise decreases in Arc RNP number and fluorescence intensity, suggesting Arc RNAs localize to dendrites in both low- and multiple-copy number RNPs. When probing for multiple mRNAs, we find that localized RNPs are heterogeneous in size and colocalization patterns that vary per RNA. Further, localized RNAs that are targeted by the same trans-acting element (FMRP) display greater levels of colocalization compared to an RNA not targeted by FMRP. Simultaneous visualization of a dozen FMRP-targeted mRNA species using highly multiplexed imaging demonstrates that dendritic RNAs are mostly trafficked as heteromeric cargoes of multiple types of RNAs (at least one or more RNAs). Moreover, the composition of these RNA cargoes, as assessed by colocalization, correlates with the abundance of the transcripts even after accounting for the expected differences in colocalization based on expression. Collectively, these results suggest that dendritic RNPs are packaged as heterogeneous co-assemblies of different mRNAs and that RNP contents may be driven, at least partially, by highly abundant dendritic RNAs; a model that favors efficiency over fine-tuned control for sustaining long-distance trafficking of thousands of messenger molecules.
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211
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Kametani H, Tong Y, Shimada A, Takeda H, Sushida T, Akiyama M, Kawanishi T. Twisted cell flow facilitates three-dimensional somite morphogenesis in zebrafish. Cells Dev 2024:203969. [PMID: 39191372 DOI: 10.1016/j.cdev.2024.203969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 07/05/2024] [Accepted: 08/23/2024] [Indexed: 08/29/2024]
Abstract
Tissue elongation is a fundamental morphogenetic process to construct complex embryonic structures. In zebrafish, somites rapidly elongate in both dorsal and ventral directions and transform their cuboidal shape into a V-shape within a few hours of development. Despite its significance, the cellular behaviors that directly lead to somite elongation have not been examined at single-cell resolution. Here we described the motion and shapes of all cells composing the dorsal half of the somite in three-dimensional space using lightsheet microscopy. We identified two types of cell movement-in horizontal and dorsal directions-that occur simultaneously within individual cells, creating a complex, twisted flow of cells during somite elongation. Chemical inhibition of Sdf1 signaling disrupted the collective movement in both directions and inhibited somite elongation, suggesting that Sdf1 signaling is crucial for the cell flow. Furthermore, three-dimensional computational modeling suggested that horizontal cell rotation accelerates the perpendicular elongation of the somite along the dorsoventral axis. Together, our study offers novel insights into the role of collective cell migration in tissue morphogenesis, which proceeds dynamically in the three-dimensional space of the embryo.
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Affiliation(s)
- Harunobu Kametani
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Yue Tong
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Atsuko Shimada
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo 113-0033, Japan; Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan.
| | - Takamichi Sushida
- Faculty of Informatics, University of Fukuchiyama, Kyoto 620-0886, Japan.
| | - Masakazu Akiyama
- Department of Mathematics, Faculty of Science, Academic Assembly, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan.
| | - Toru Kawanishi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo 113-0033, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
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212
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Xu M, Zhang Q, Shi H, Wu Z, Zhou W, Lin F, Kou Y, Tao Z. A repressive H3K36me2 reader mediates Polycomb silencing. Nat Commun 2024; 15:7287. [PMID: 39179589 PMCID: PMC11343894 DOI: 10.1038/s41467-024-51789-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 08/16/2024] [Indexed: 08/26/2024] Open
Abstract
In animals, evolutionarily conserved Polycomb repressive complex 2 (PRC2) catalyzes histone H3 lysine 27 trimethylation (H3K27me3) and PRC1 functions in recruitment and transcriptional repression. However, the mechanisms underlying H3K27me3-mediated stable transcriptional silencing are largely unknown, as PRC1 subunits are poorly characterized in fungi. Here, we report that in the filamentous fungus Magnaporthe oryzae, the N-terminal chromodomain and C-terminal MRG domain of Eaf3 play key roles in facultative heterochromatin formation and transcriptional silencing. Eaf3 physically interacts with Ash1, Eed, and Sin3, encoding an H3K36 methyltransferase, the core subunit of PRC2, and a histone deacetylation co-suppressor, respectively. Eaf3 co-localizes with a set of repressive Ash1-H3K36me2 and H3K27me3 loci and mediates their transcriptional silencing. Furthermore, Eaf3 acts as a histone reader for the repressive H3K36me2 and H3K27me3 marks. Eaf3-occupied regions are associated with increased nucleosome occupancy, contributing to transcriptional silencing in M. oryzae. Together, these findings reveal that Eaf3 is a repressive H3K36me2 reader and plays a vital role in Polycomb gene silencing and the formation of facultative heterochromatin in fungi.
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Affiliation(s)
- Mengting Xu
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Qi Zhang
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Huanbin Shi
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, China
| | - Zhongling Wu
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Wei Zhou
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Fucheng Lin
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yanjun Kou
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, China.
| | - Zeng Tao
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
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213
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Breton G, Barham L, Mudenda G, Soodyall H, Schlebusch CM, Jakobsson M. BaTwa populations from Zambia retain ancestry of past hunter-gatherer groups. Nat Commun 2024; 15:7307. [PMID: 39181874 PMCID: PMC11344834 DOI: 10.1038/s41467-024-50733-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/19/2024] [Indexed: 08/27/2024] Open
Abstract
Sub-equatorial Africa is today inhabited predominantly by Bantu-speaking groups of Western African descent who brought agriculture to the Luangwa valley in eastern Zambia ~2000 years ago. Before their arrival the area was inhabited by hunter-gatherers, who in many cases were subsequently replaced, displaced or assimilated. In Zambia, we know little about the genetic affinities of these hunter-gatherers. We examine ancestry of two isolated communities in Zambia, known as BaTwa and possible descendants of recent hunter-gatherers. We genotype over two million genome-wide SNPs from two BaTwa populations (total of 80 individuals) and from three comparative farming populations to: (i) determine if the BaTwa carry genetic links to past hunter-gatherer-groups, and (ii) characterise the genetic affinities of past Zambian hunter-gatherer-groups. The BaTwa populations do harbour a hunter-gatherer-like genetic ancestry and Western African ancestry. The hunter-gatherer component is a unique local signature, intermediate between current-day Khoe-San ancestry from southern Africa and central African rainforest hunter-gatherer ancestry.
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Affiliation(s)
- Gwenna Breton
- Department of Organismal Biology, Human Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
- Department of Clinical Genetics and Genomics, Centre for Medical Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden.
| | - Lawrence Barham
- Department of Archaeology, Classics & Egyptology, University of Liverpool, Liverpool, UK
| | - George Mudenda
- Livingstone Museum, Livingstone, Zambia
- National Museums Board, Lusaka, Zambia
| | - Himla Soodyall
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa
- Academy of Science of South Africa, Pretoria, South Africa
| | - Carina M Schlebusch
- Department of Organismal Biology, Human Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
- SciLifeLab, Uppsala, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.
- SciLifeLab, Uppsala, Sweden.
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214
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Sharma A, Dsilva GJ, Deshpande G, Galande S. Exploring the versatility of zygotic genome regulators: A comparative and functional analysis. Cell Rep 2024; 43:114680. [PMID: 39182225 DOI: 10.1016/j.celrep.2024.114680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/30/2024] [Accepted: 08/08/2024] [Indexed: 08/27/2024] Open
Abstract
The activation of the zygotic genome constitutes an essential process during early embryogenesis that determines the overall progression of embryonic development. Zygotic genome activation (ZGA) is tightly regulated, involving a delicate interplay of activators and repressors, to precisely control the timing and spatial pattern of gene expression. While regulators of ZGA vary across species, they accomplish comparable outcomes. Recent studies have shed light on the unanticipated roles of ZGA components both during and after ZGA. Moreover, different ZGA regulators seem to have acquired unique functional modalities to manifest their regulatory potential. In this review, we explore these observations to assess whether these are simply anecdotal or contribute to a broader regulatory framework that employs a versatile means to arrive at the conserved outcome.
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Affiliation(s)
- Ankita Sharma
- Department of Biology, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pune 411008, India; Center of Excellence in Epigenetics, Department of Life Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR 201314, India
| | - Greg Jude Dsilva
- Department of Biology, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pune 411008, India; Center of Excellence in Epigenetics, Department of Life Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR 201314, India
| | - Girish Deshpande
- Department of Biology, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pune 411008, India; Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA.
| | - Sanjeev Galande
- Department of Biology, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pune 411008, India; Center of Excellence in Epigenetics, Department of Life Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR 201314, India.
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215
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Oud MS, de Leeuw N, Smeets DFCM, Ramos L, van der Heijden GW, Timmermans RGJ, van de Vorst M, Hofste T, Kempers MJE, Stokman MF, D'Hauwers KWM, Faas BHW, Westra D. Innovative all-in-one exome sequencing strategy for diagnostic genetic testing in male infertility: Validation and 10-month experience. Andrology 2024. [PMID: 39180390 DOI: 10.1111/andr.13742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/16/2024] [Accepted: 08/10/2024] [Indexed: 08/26/2024]
Abstract
BACKGROUND Current guidelines indicate that patients with extreme oligozoospermia or azoospermia should be tested for chromosomal imbalances, azoospermia factor (AZF) deletions and/or CFTR variants. For other sperm abnormalities, no genetic diagnostics are recommended. OBJECTIVES To determine whether exome sequencing (ES) with combined copy number variant (CNV) and single nucleotide variant (SNV) analysis is a reliable first-tier method to replace current methods (validation study), and to evaluate the diagnostic yield after 10 months of implementation (evaluation study). MATERIALS AND METHODS In the validation study, ES was performed on DNA of patients already diagnosed with AZF deletions (n = 17), (non-)mosaic sex chromosomal aneuploidies or structural chromosomal anomalies (n = 37), CFTR variants (n = 26), or variants in known infertility genes (n = 4), and 90 controls. The data were analyzed using our standard diagnostic pipeline, with a bioinformatic filter for 130 male infertility genes. In the evaluation study, results of 292 clinical exomes were included. RESULTS All previously reported variants in the validation cohort, including clinically relevant Y-chromosomal microdeletions, were correctly identified and reliably detected. In the evaluation study, we identified one or more clinically relevant genetic anomalies in 67 of 292 of all cases (22.9%): these included aberrations that could have been detected with current methods in 30 of 67 patients (10.2% of total), (possible) (mono)genetic causes in the male infertility gene panel in 28 of 67 patients (9.6%), and carriership of cystic fibrosis in nine of 67 patients (3.1%). CONCLUSION ES is a reliable first-tier method to detect the most common genetic causes of male infertility and, as additional genetic causes can be detected, in our evaluation cohort the diagnostic yield almost doubled (10.2%-19.8%, excluding CF carriers). A genetic diagnosis provides answers on the cause of infertility and helps the professionals in the counseling for treatment, possible co-morbidities and risk for offspring and/or family members. Karyotyping will still remain necessary for detecting balanced translocations or low-grade chromosomal mosaicism.
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Affiliation(s)
- Manon S Oud
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Dominique F C M Smeets
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Liliana Ramos
- Department of Obstetrics and Gynaecology, Radboud university medical center, Nijmegen, The Netherlands
| | | | - Raoul G J Timmermans
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Maartje van de Vorst
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Tom Hofste
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Marlies J E Kempers
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Marijn F Stokman
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | | | - Brigitte H W Faas
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Dineke Westra
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
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216
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Colicino-Murbach E, Hathaway C, Dungrawala H. Replication fork stalling in late S-phase elicits nascent strand degradation by DNA mismatch repair. Nucleic Acids Res 2024:gkae721. [PMID: 39180395 DOI: 10.1093/nar/gkae721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 07/03/2024] [Accepted: 08/06/2024] [Indexed: 08/26/2024] Open
Abstract
Eukaryotic chromosomal replication occurs in a segmented, temporal manner wherein open euchromatin and compact heterochromatin replicate during early and late S-phase respectively. Using single molecule DNA fiber analyses coupled with cell synchronization, we find that newly synthesized strands remain stable at perturbed forks in early S-phase. Unexpectedly, stalled forks are susceptible to nucleolytic digestion during late replication resulting in defective fork restart. This inherent vulnerability to nascent strand degradation is dependent on fork reversal enzymes and resection nucleases MRE11, DNA2 and EXO1. Inducing chromatin compaction elicits digestion of nascent DNA in response to fork stalling due to reduced association of RAD51 with nascent DNA. Furthermore, RAD51 occupancy at stalled forks in late S-phase is diminished indicating that densely packed chromatin limits RAD51 accessibility to mediate replication fork protection. Genetic analyses reveal that susceptibility of late replicating forks to nascent DNA digestion is dependent on EXO1 via DNA mismatch repair (MMR) and that the BRCA2-mediated replication fork protection blocks MMR from degrading nascent DNA. Overall, our findings illustrate differential regulation of fork protection between early and late replication and demonstrate nascent strand degradation as a critical determinant of heterochromatin instability in response to replication stress.
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Affiliation(s)
| | - Caitlin Hathaway
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA
| | - Huzefa Dungrawala
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA
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217
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Wang J, Zhou T. Unveiling gut microbiota's role: Bidirectional regulation of drug transport for improved safety. Med Res Rev 2024. [PMID: 39180410 DOI: 10.1002/med.22077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 07/20/2024] [Accepted: 08/04/2024] [Indexed: 08/26/2024]
Abstract
Drug safety is a paramount concern in the field of drug development, with researchers increasingly focusing on the bidirectional regulation of gut microbiota in this context. The gut microbiota plays a crucial role in maintaining drug safety. It can influence drug transport processes in the body through various mechanisms, thereby modulating their efficacy and toxicity. The main mechanisms include: (1) The gut microbiota directly interacts with drugs, altering their chemical structure to reduce toxicity and enhance efficacy, thereby impacting drug transport mechanisms, drugs can also change the structure and abundance of gut bacteria; (2) bidirectional regulation of intestinal barrier permeability by gut microbiota, promoting the absorption of nontoxic drugs and inhibiting the absorption of toxic components; (3) bidirectional regulation of the expression and activity of transport proteins by gut microbiota, selectively promoting the absorption of effective components or inhibiting the absorption of toxic components. This bidirectional regulatory role enables the gut microbiota to play a key role in maintaining drug balance in the body and reducing adverse reactions. Understanding these regulatory mechanisms sheds light on novel approaches to minimize toxic side effects, enhance drug efficacy, and ultimately improve drug safety. This review systematically examines the bidirectional regulation of gut microbiota in drug transportation from the aforementioned aspects, emphasizing their significance in ensuring drug safety. Furthermore, it offers a prospective outlook from the standpoint of enhancing therapeutic efficacy and reducing drug toxicity, underscoring the importance of further exploration in this research domain. It aims to provide more effective strategies for drug development and treatment.
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Affiliation(s)
- Jinyi Wang
- Department of Pharmaceutical Analysis, School of Pharmacy, Second Military Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Tingting Zhou
- Department of Pharmaceutical Analysis, School of Pharmacy, Second Military Medical University, Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, China
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218
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Sizovs A, Melkus G, Rucevskis P, Silina S, Lace L, Celms E, Viksna J. A technique for preserving network structure in randomized Hi-C data. J Bioinform Comput Biol 2024:2440001. [PMID: 39183696 DOI: 10.1142/s0219720024400018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Chromatin interaction data are frequently analyzed as a network to study several aspects of chromatin structure. Hi-C experiments are costly and there is a need to create simulated networks for quality assessment or result validation purposes. Existing tools do not maintain network properties during randomization. We propose an algorithm to modify an existing chromatin interaction graph while preserving the graphs most basic topological features - node degrees and interaction length distribution. The algorithm is implemented in Python and its open-source code as well as the data to reproduce the results are available on Github.
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Affiliation(s)
- Andrejs Sizovs
- Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia
| | - Gatis Melkus
- Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia
| | - Peteris Rucevskis
- Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia
| | - Sandra Silina
- Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia
| | - Lelde Lace
- Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia
| | - Edgars Celms
- Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia
| | - Juris Viksna
- Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia
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219
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Jang JW, Capaldi E, Smith T, Verma P, Varga J, Ho KJ. Trimethylamine N-oxide: a meta-organismal axis linking the gut and fibrosis. Mol Med 2024; 30:128. [PMID: 39180015 PMCID: PMC11344357 DOI: 10.1186/s10020-024-00895-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 08/08/2024] [Indexed: 08/26/2024] Open
Abstract
BACKGROUND Tissue fibrosis is a common pathway to failure in many organ systems and is the cellular and molecular driver of myriad chronic diseases that are incompletely understood and lack effective treatment. Recent studies suggest that gut microbe-dependent metabolites might be involved in the initiation and progression of fibrosis in multiple organ systems. MAIN BODY OF THE MANUSCRIPT In a meta-organismal pathway that begins in the gut, gut microbiota convert dietary precursors such as choline, phosphatidylcholine, and L-carnitine into trimethylamine (TMA), which is absorbed and subsequently converted to trimethylamine N-oxide (TMAO) via the host enzyme flavin-containing monooxygenase 3 (FMO3) in the liver. Chronic exposure to elevated TMAO appears to be associated with vascular injury and enhanced fibrosis propensity in diverse conditions, including chronic kidney disease, heart failure, metabolic dysfunction-associated steatotic liver disease, and systemic sclerosis. CONCLUSION Despite the high prevalence of fibrosis, little is known to date about the role of gut dysbiosis and of microbe-dependent metabolites in its pathogenesis. This review summarizes recent important advances in the understanding of the complex metabolism and functional role of TMAO in pathologic fibrosis and highlights unanswered questions.
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Affiliation(s)
- Jae Woong Jang
- Department of Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 650, Chicago, IL, 60611, USA
| | - Emma Capaldi
- Department of Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 650, Chicago, IL, 60611, USA
| | - Tracy Smith
- Department of Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 650, Chicago, IL, 60611, USA
| | - Priyanka Verma
- Department of Internal Medicine, University of Michigan, 1500 East Medical Center Drive, Floor 3, Reception A, Ann Arbor, MI, 48109, USA
| | - John Varga
- Department of Internal Medicine, University of Michigan, 1500 East Medical Center Drive, Floor 3, Reception A, Ann Arbor, MI, 48109, USA
| | - Karen J Ho
- Department of Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 650, Chicago, IL, 60611, USA.
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220
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Templeton CW, Laimins LA. HPV induced R-loop formation represses innate immune gene expression while activating DNA damage repair pathways. PLoS Pathog 2024; 20:e1012454. [PMID: 39178326 DOI: 10.1371/journal.ppat.1012454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 07/28/2024] [Indexed: 08/25/2024] Open
Abstract
R-loops are trimeric nucleic acid structures that form when an RNA molecule hybridizes with its complementary DNA strand, displacing the opposite strand. These structures regulate transcription as well as replication, but aberrant R-loops can form, leading to DNA breaks and genomic instability if unresolved. R-loop levels are elevated in many cancers as well as cells that maintain high-risk human papillomaviruses. We investigated how the distribution as well as function of R-loops changed between normal keratinocytes and HPV positive cells derived from a precancerous lesion of the cervix (CIN I). The levels of R-loops associated with cellular genes were found to be up to 10-fold higher in HPV positive cells than in normal keratinocytes while increases at ALU1 elements increased by up to 500-fold. The presence of enhanced R-loops resulted in altered levels of gene transcription, with equal numbers increased as decreased. While no uniform global effects on transcription due to the enhanced levels of R-loops were detected, genes in several pathways were coordinately increased or decreased in expression only in the HPV positive cells. This included the downregulation of genes in the innate immune pathway, such as DDX58, IL-6, STAT1, IFN-β, and NLRP3. All differentially expressed innate immune genes dependent on R-loops were also associated with H3K36me3 modified histones. Genes that were upregulated by the presence of R-loops in HPV positive cells included those in the DNA damage repair such as ATM, ATRX, and members of the Fanconi Anemia pathway. These genes exhibited a linkage between R-loops and H3K36me3 as well as γH2AX histone marks only in HPV positive cells. These studies identify a potential link in HPV positive cells between DNA damage repair as well as innate immune regulatory pathways with R-loops and γH2AX/H3K36me3 histone marks that may contribute to regulating important functions for HPV pathogenesis.
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Affiliation(s)
- Conor W Templeton
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Laimonis A Laimins
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
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221
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Alsina FC, Lupan BM, Lin LJ, Musso CM, Mosti F, Newman CR, Wood LM, Suzuki A, Agostino M, Moore JK, Silver DL. The RNA-binding protein EIF4A3 promotes axon development by direct control of the cytoskeleton. Cell Rep 2024; 43:114666. [PMID: 39182224 DOI: 10.1016/j.celrep.2024.114666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 02/28/2024] [Accepted: 08/06/2024] [Indexed: 08/27/2024] Open
Abstract
The exon junction complex (EJC), nucleated by EIF4A3, is indispensable for mRNA fate and function throughout eukaryotes. We discover that EIF4A3 directly controls microtubules, independent of RNA, which is critical for neural wiring. While neuronal survival in the developing mouse cerebral cortex depends upon an intact EJC, axonal tract development requires only Eif4a3. Using human cortical organoids, we show that EIF4A3 disease mutations also impair neuronal growth, highlighting conserved functions relevant for neurodevelopmental pathology. Live imaging of growing neurons shows that EIF4A3 is essential for microtubule dynamics. Employing biochemistry and competition experiments, we demonstrate that EIF4A3 directly binds to microtubules, mutually exclusive of the EJC. Finally, in vitro reconstitution assays and rescue experiments demonstrate that EIF4A3 is sufficient to promote microtubule polymerization and that EIF4A3-microtubule association is a major contributor to axon growth. This reveals a fundamental mechanism by which neurons re-utilize core gene expression machinery to directly control the cytoskeleton.
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Affiliation(s)
- Fernando C Alsina
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Bianca M Lupan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lydia J Lin
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Camila M Musso
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Federica Mosti
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Carly R Newman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lisa M Wood
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Denver, CO, USA
| | - Aussie Suzuki
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark Agostino
- Curtin Health Innovation Research Institute, Curtin Medical School, and Curtin Institute for Computation, Curtin University, Bentley, WA 6102, Australia
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Denver, CO, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Departments of Cell Biology and Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Duke Institute for Brain Sciences and Duke Regeneration Center, Duke University Medical Center, Durham, NC 27710, USA.
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222
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Vidal R, Leen E, Herold S, Müller M, Fleischhauer D, Schülein-Völk C, Papadopoulos D, Röschert I, Uhl L, Ade CP, Gallant P, Bayliss R, Eilers M, Büchel G. Association with TFIIIC limits MYCN localisation in hubs of active promoters and chromatin accumulation of non-phosphorylated RNA polymerase II. eLife 2024; 13:RP94407. [PMID: 39177021 PMCID: PMC11343564 DOI: 10.7554/elife.94407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024] Open
Abstract
MYC family oncoproteins regulate the expression of a large number of genes and broadly stimulate elongation by RNA polymerase II (RNAPII). While the factors that control the chromatin association of MYC proteins are well understood, much less is known about how interacting proteins mediate MYC's effects on transcription. Here, we show that TFIIIC, an architectural protein complex that controls the three-dimensional chromatin organisation at its target sites, binds directly to the amino-terminal transcriptional regulatory domain of MYCN. Surprisingly, TFIIIC has no discernible role in MYCN-dependent gene expression and transcription elongation. Instead, MYCN and TFIIIC preferentially bind to promoters with paused RNAPII and globally limit the accumulation of non-phosphorylated RNAPII at promoters. Consistent with its ubiquitous role in transcription, MYCN broadly participates in hubs of active promoters. Depletion of TFIIIC further increases MYCN localisation to these hubs. This increase correlates with a failure of the nuclear exosome and BRCA1, both of which are involved in nascent RNA degradation, to localise to active promoters. Our data suggest that MYCN and TFIIIC exert an censoring function in early transcription that limits promoter accumulation of inactive RNAPII and facilitates promoter-proximal degradation of nascent RNA.
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Affiliation(s)
- Raphael Vidal
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of WürzburgWürzburgGermany
- Comprehensive Cancer Center MainfrankenWürzburgGermany
| | - Eoin Leen
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeedsUnited Kingdom
| | - Steffi Herold
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of WürzburgWürzburgGermany
| | - Mareike Müller
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of WürzburgWürzburgGermany
- Mildred Scheel Early Career Center, University Hospital WürzburgWürzburgGermany
| | - Daniel Fleischhauer
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of WürzburgWürzburgGermany
| | - Christina Schülein-Völk
- Theodor Boveri Institute, Core Unit High-Content Microscopy, Biocenter, University of WürzburgWürzburgGermany
| | - Dimitrios Papadopoulos
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of WürzburgWürzburgGermany
- Mildred Scheel Early Career Center, University Hospital WürzburgWürzburgGermany
| | - Isabelle Röschert
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of WürzburgWürzburgGermany
| | - Leonie Uhl
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of WürzburgWürzburgGermany
| | - Carsten P Ade
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of WürzburgWürzburgGermany
| | - Peter Gallant
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of WürzburgWürzburgGermany
| | - Richard Bayliss
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeedsUnited Kingdom
| | - Martin Eilers
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of WürzburgWürzburgGermany
- Comprehensive Cancer Center MainfrankenWürzburgGermany
| | - Gabriele Büchel
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of WürzburgWürzburgGermany
- Comprehensive Cancer Center MainfrankenWürzburgGermany
- Mildred Scheel Early Career Center, University Hospital WürzburgWürzburgGermany
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223
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Tullius TW, Isaac RS, Dubocanin D, Ranchalis J, Churchman LS, Stergachis AB. RNA polymerases reshape chromatin architecture and couple transcription on individual fibers. Mol Cell 2024:S1097-2765(24)00667-1. [PMID: 39191261 DOI: 10.1016/j.molcel.2024.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 07/02/2024] [Accepted: 08/08/2024] [Indexed: 08/29/2024]
Abstract
RNA polymerases must initiate and pause within a complex chromatin environment, surrounded by nucleosomes and other transcriptional machinery. This environment creates a spatial arrangement along individual chromatin fibers ripe for both competition and coordination, yet these relationships remain largely unknown owing to the inherent limitations of traditional structural and sequencing methodologies. To address this, we employed long-read chromatin fiber sequencing (Fiber-seq) in Drosophila to visualize RNA polymerase (Pol) within its native chromatin context with single-molecule precision along up to 30 kb fibers. We demonstrate that Fiber-seq enables the identification of individual Pol II, nucleosome, and transcription factor footprints, revealing Pol II pausing-driven destabilization of downstream nucleosomes. Furthermore, we demonstrate pervasive direct distance-dependent transcriptional coupling between nearby Pol II genes, Pol III genes, and transcribed enhancers, modulated by local chromatin architecture. Overall, transcription initiation reshapes surrounding nucleosome architecture and couples nearby transcriptional machinery along individual chromatin fibers.
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Affiliation(s)
- Thomas W Tullius
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - R Stefan Isaac
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Danilo Dubocanin
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jane Ranchalis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
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224
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Rowan TN. Genetics and Genomics 101. Vet Clin North Am Food Anim Pract 2024:S0749-0720(24)00025-2. [PMID: 39181796 DOI: 10.1016/j.cvfa.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024] Open
Abstract
Genetic mutations, both favorable and unfavorable, are the raw material for improvement in livestock populations. The random inheritance of these mutations is essential for generating progenies with genetic potential greater than their parents. These mutations can act either in a simple manner, such that a single alteration disrupts phenotype, or in a complex manner where hundreds or thousands of mutations of small effect create a continuous distribution of phenotypes. Selection tools leverage phenotypic records, pedigrees, and genomics to estimate the genetic potential of individual animals. This more accurate accounting of genetic potential has generated enormous gains in livestock populations.
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Affiliation(s)
- Troy N Rowan
- Department of Animal Science, University of Tennessee, 2506 River Drive, Knoxville, TN 37996, USA; Department Large Animal Clinical Sciences, University of Tennessee, Knoxville, TN, USA.
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225
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Arjun OK, Sethi M, Parida D, Dash J, Kumar Das S, Prakash T, Senapati S. Comprehensive physiological and genomic characterization of a potential probiotic strain, Lactiplantibacillus plantarum ILSF15, isolated from the gut of tribes of Odisha, India. Gene 2024:148882. [PMID: 39182659 DOI: 10.1016/j.gene.2024.148882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 08/11/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
Characterizing probiotic features of organisms isolated from diverse environments can lead to the discovery of novel strains with promising functional features and health attributes. The present study attempts to characterize a novel probiotic strain isolated from the gut of the tribal population of Odisha, India. Based on 16S rRNA-based phylogeny, the strain was identified as a species of the Lactiplantibacillus genus and was named Lactiplantibacillus plantarum strain ILSF15. The current investigation focuses on elucidating this strain's genetic and physiological properties associated with probiotic attributes such as biosafety risk, host adaptation/survival traits, and beneficial functional features. The novel strain was observed, in vitro, exhibiting features such as acid/bile tolerance, adhesion to the host enteric epithelial cells, cholesterol assimilation, and pathogen exclusion, indicating its ability to survive the harsh environment of the human GIT and resist the growth of harmful microorganisms. Additionally, the L. plantarum ILSF15 strain was found to harbor genes associated with the metabolism and synthesis of various bioactive molecules, including amino acids, carbohydrates, lipids, and vitamins, highlighting the organism's ability to efficiently utilize diverse resources and contribute to the host's nutrition and health. Several genes involved in host adaptation/survival strategies and host-microbe interactions were also identified from the ILSF15 genome. Moreover, L. plantarum strains, in general, were found to have an open pangenome characterized by high genetic diversity and the absence of specific lineages associated with particular habitats, signifying its versatile nature and potential applications in probiotic and functional food industries.
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Affiliation(s)
- O K Arjun
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India
| | - Manisha Sethi
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Deepti Parida
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Jayalaxmi Dash
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Suraja Kumar Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Tulika Prakash
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India.
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226
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Liao Y, Gao Y, Chen Q, Pan M, Tsunoda M, Liu F, Zhang Y, Hu W, Li LS, Yang H, Song Y. Enantioselective toxicity effect and mechanisms of bifenthrin enantiomers on normal human hepatocytes. Food Chem Toxicol 2024; 192:114952. [PMID: 39182637 DOI: 10.1016/j.fct.2024.114952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 08/19/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
In recent decades, the toxicity of chiral pesticides to non-target organisms has attracted increasing attention. Cellular metabolic disorders are essential sensitive molecular initiating event for toxicological effects. BF is a typical chiral pesticide, and the liver is the main organ for BF accumulation. This study aimed to investigate the potential molecular mechanism of BF enantiomers' different toxic effects on L02 by a non-targeted metabolomic approach. Results revealed that the BF enantiomers exhibited different metabolic responses. In total, 51 and 36 differential metabolites were perturbed by 1S-cis-BF and 1R-cis-BF at the value of variable importance, respectively. When L02 were exposed to 1R-cis-BF, the significantly disturbed metabolic pathways were nicotinate and nicotinamide metabolism and pyrimidine metabolism. By comparison, more significantly perturbed metabolic pathways were received when the L02 were exposed to 1S-cis-BF, including glycine, serine and threonine metabolism, nicotinate and nicotinamide metabolism, arginine and proline metabolism, cysteine and methionine metabolism, glycerolipid metabolism, histidine metabolism, pyrimidine metabolism, amino sugar and nucleotide sugar metabolism and arginine biosynthesis. The results offer a new perspective in understanding the role of selective cytotoxicity of BF enantiomers, and help to evaluate the risk to human health at the enantiomeric level.
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Affiliation(s)
- Yiyi Liao
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan Engineering Research Center for Drug Screening and Evaluation, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan, China; Hainan Cancer Hospital, Haikou, 570312, Hainan, China
| | - Yuhang Gao
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan Engineering Research Center for Drug Screening and Evaluation, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan, China; 63650 Military Hospital of PLA, Luoyang, 471000, Henan, China
| | - Qigeng Chen
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan Engineering Research Center for Drug Screening and Evaluation, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Mingyu Pan
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan Engineering Research Center for Drug Screening and Evaluation, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Makoto Tsunoda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Fuping Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan Engineering Research Center for Drug Screening and Evaluation, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Yingxia Zhang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan Engineering Research Center for Drug Screening and Evaluation, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Wenting Hu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan Engineering Research Center for Drug Screening and Evaluation, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Lu-Shuang Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan Engineering Research Center for Drug Screening and Evaluation, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan, China.
| | - Haimei Yang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan Engineering Research Center for Drug Screening and Evaluation, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan, China.
| | - Yanting Song
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan Engineering Research Center for Drug Screening and Evaluation, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan, China.
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227
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Yang Z, Mameri A, Cattoglio C, Lachance C, Florez Ariza AJ, Luo J, Humbert J, Sudarshan D, Banerjea A, Galloy M, Fradet-Turcotte A, Lambert JP, Ranish JA, Côté J, Nogales E. Structural insights into the human NuA4/TIP60 acetyltransferase and chromatin remodeling complex. Science 2024; 385:eadl5816. [PMID: 39088653 DOI: 10.1126/science.adl5816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 05/25/2024] [Accepted: 06/25/2024] [Indexed: 08/03/2024]
Abstract
The human nucleosome acetyltransferase of histone H4 (NuA4)/Tat-interactive protein, 60 kilodalton (TIP60) coactivator complex, a fusion of the yeast switch/sucrose nonfermentable related 1 (SWR1) and NuA4 complexes, both incorporates the histone variant H2A.Z into nucleosomes and acetylates histones H4, H2A, and H2A.Z to regulate gene expression and maintain genome stability. Our cryo-electron microscopy studies show that, within the NuA4/TIP60 complex, the E1A binding protein P400 (EP400) subunit serves as a scaffold holding the different functional modules in specific positions, creating a distinct arrangement of the actin-related protein (ARP) module. EP400 interacts with the transformation/transcription domain-associated protein (TRRAP) subunit by using a footprint that overlaps with that of the Spt-Ada-Gcn5 acetyltransferase (SAGA) complex, preventing the formation of a hybrid complex. Loss of the TRRAP subunit leads to mislocalization of NuA4/TIP60, resulting in the redistribution of H2A.Z and its acetylation across the genome, emphasizing the dual functionality of NuA4/TIP60 as a single macromolecular assembly.
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Affiliation(s)
- Zhenlin Yang
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Amel Mameri
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Claudia Cattoglio
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Catherine Lachance
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Alfredo Jose Florez Ariza
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, WA, USA
| | - Jonathan Humbert
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Deepthi Sudarshan
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Arul Banerjea
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Maxime Galloy
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Amélie Fradet-Turcotte
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Jean-Philippe Lambert
- Endocrinology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | | | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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228
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Ealo T, Sanchez-Gaya V, Respuela P, Muñoz-San Martín M, Martin-Batista E, Haro E, Rada-Iglesias A. Cooperative insulation of regulatory domains by CTCF-dependent physical insulation and promoter competition. Nat Commun 2024; 15:7258. [PMID: 39179577 PMCID: PMC11344162 DOI: 10.1038/s41467-024-51602-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 08/10/2024] [Indexed: 08/26/2024] Open
Abstract
The specificity of gene expression during development requires the insulation of regulatory domains to avoid inappropriate enhancer-gene interactions. In vertebrates, this insulator function is mostly attributed to clusters of CTCF sites located at topologically associating domain (TAD) boundaries. However, TAD boundaries allow some physical crosstalk across regulatory domains, which is at odds with the specific and precise expression of developmental genes. Here we show that developmental genes and nearby clusters of CTCF sites cooperatively foster the robust insulation of regulatory domains. By genetically dissecting a couple of representative loci in mouse embryonic stem cells, we show that CTCF sites prevent undesirable enhancer-gene contacts (i.e. physical insulation), while developmental genes preferentially contribute to regulatory insulation through non-structural mechanisms involving promoter competition rather than enhancer blocking. Overall, our work provides important insights into the insulation of regulatory domains, which in turn might help interpreting the pathological consequences of certain structural variants.
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Affiliation(s)
- Thais Ealo
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain
| | - Victor Sanchez-Gaya
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain.
| | - Patricia Respuela
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain
| | - María Muñoz-San Martín
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain
- Service of Neurology, University Hospital Marqués de Valdecilla, Universidad de Cantabria and IDIVAL, Santander, Spain
| | | | - Endika Haro
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain.
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain.
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229
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Housman G. Advances in skeletal genomics research across tissues and cells. Curr Opin Genet Dev 2024; 88:102245. [PMID: 39180931 DOI: 10.1016/j.gde.2024.102245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/25/2024] [Accepted: 08/05/2024] [Indexed: 08/27/2024]
Abstract
Phenotypic variation within the skeleton has biological, behavioral, and biomedical functional implications for individuals and species. Thus, it is critical to understand how genomic, environmental, and mediating regulatory factors combine and interact to drive skeletal trait development and evolution. Recent research efforts to clarify these mechanisms have been made possible by expanded collections of genomic and phenotypic data from in vivo skeletal tissues, as well as the development of relevant in vitro skeletal cell culture systems. This review outlines this current work and recommends that continued exploration of this complexity should include an increased focus on how interactions between genomic and physiologically relevant contexts contribute to skeletal trait variation at population and evolutionary scales.
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Affiliation(s)
- Genevieve Housman
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
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230
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Fuller CN, Valadares Tose L, Vitorino FNL, Bhanu NV, Panczyk EM, Park MA, Garcia BA, Fernandez-Lima F. Bottom-up Histone Post-translational Modification Analysis using Liquid Chromatography, Trapped Ion Mobility Spectrometry, and Tandem Mass Spectrometry. J Proteome Res 2024. [PMID: 39177337 DOI: 10.1021/acs.jproteome.4c00177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
The amino acid position within a histone sequence and the chemical nature of post-translational modifications (PTMs) are essential for elucidating the "Histone Code". Previous work has shown that PTMs induce specific biological responses and are good candidates as biomarkers for diagnostics. Here, we evaluate the analytical advantages of trapped ion mobility (TIMS) with parallel accumulation-serial fragmentation (PASEF) and tandem mass spectrometry (MS/MS) for bottom-up proteomics of model cancer cells. The study also considered the use of nanoliquid chromatography (LC) and traditional methods: LC-TIMS-PASEF-ToF MS/MS vs nLC-TIMS-PASEF-ToF MS/MS vs nLC-MS/MS. The addition of TIMS and PASEF-MS/MS increased the number of detected peptides due to the added separation dimension. All three methods showed high reproducibility and low RSD in the MS domain (<5 ppm). While the LC, nLC and TIMS separations showed small RSD across samples, the accurate mobility (1/K0) measurements (<0.6% RSD) increased the confidence of peptide assignments. Trends were observed in the retention time and mobility concerning the number and type of PTMs (e.g., ac, me1-3) and their corresponding unmodified, propionylated peptide that aided in peptide assignment. Mobility separation permitted the annotation of coeluting structural and positional isomers and compared with nLC-MS/MS showed several advantages due to reduced chemical noise.
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Affiliation(s)
- Cassandra N Fuller
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Lilian Valadares Tose
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Francisca N L Vitorino
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Natarajan V Bhanu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Erin M Panczyk
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Melvin A Park
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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231
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Molina M, Oliveira G, Oliveira RRM, Nunes GL, Pires ES, Prous X, Ribeiro M, Vasconcelos S. Complete mitochondrial genomes of three vulnerable cave bat species and their phylogenetic relationships within the order Chiroptera. PLoS One 2024; 19:e0308741. [PMID: 39172941 PMCID: PMC11340975 DOI: 10.1371/journal.pone.0308741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 07/30/2024] [Indexed: 08/24/2024] Open
Abstract
The IUCN Red List of Threatened Species contains 175 Brazilian bat species that are threatened by extinction in some degree. From this perspective, it is essential to expand the knowledge about the genetic diversity of vulnerable bats. Genomic sequencing can be useful to generate robust and informative genetic references, increasing resolution when analyzing relationships among populations, species, or higher taxonomic levels. In this study, we sequenced and characterized in detail the first complete mitochondrial genomes of Furipterus horrens, Lonchorhina aurita, and Natalus macrourus, and investigated their phylogenetic position based on amino acid sequences of protein-coding genes (PCGs). The mitogenomes of these species are 16,516, 16,697, and 16,668 bp in length, respectively, and each comprises 13 PCGs, 22 tRNA genes, two rRNA genes, and a putative control region (CR). In the three species, genes were arranged similarly to all other previously described bat mitogenomes, and nucleotide composition was also consistent with the reported range. The length and arrangement of rrnS and rrnL were also consistent with those of other bat species, showing a positive AT-skew and a negative GC-skew. Except for trnS1, for which we did not observe the DHU arm, all other tRNAs showed the cloverleaf secondary structure in the three species. In addition, the mitogenomes showed minor differences in start and stop codons, and in all PCGs, codons ending in adenine were more common compared to those ending in guanine. We found that PCGs of the three species use multiple codons to encode each amino acid, following the previously documented pattern. Furthermore, all PCGs are under purifying selection, with atp8 experiencing the most relaxed purifying selection. Considering the phylogenetic reconstruction, F. horrens was recovered as sister to Noctilio leporinus, L. aurita and Tonatia bidens shared a node within Phyllostomidae, and N. macrourus appeared as sister to Molossidae and Vespertilionidae.
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Affiliation(s)
- Michele Molina
- Instituto Tecnológico Vale, Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Guilherme Oliveira
- Instituto Tecnológico Vale, Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | | | | | - Xavier Prous
- Gerência de Espeleologia, Vale, Nova Lima, Minas Gerais, Brazil
| | - Mariane Ribeiro
- Gerência de Espeleologia, Vale, Nova Lima, Minas Gerais, Brazil
| | - Santelmo Vasconcelos
- Instituto Tecnológico Vale, Belém, Pará, Brazil
- Programa de Pós-Graduação em Biodiversidade e Evolução, Museu Paraense Emílio Goeldi, Belém, Pará, Brazil
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232
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Bai G, Endres T, Kühbacher U, Mengoli V, Greer BH, Peacock EM, Newton MD, Stanage T, Dello Stritto MR, Lungu R, Crossley MP, Sathirachinda A, Cortez D, Boulton SJ, Cejka P, Eichman BF, Cimprich KA. HLTF resolves G4s and promotes G4-induced replication fork slowing to maintain genome stability. Mol Cell 2024; 84:3044-3060.e11. [PMID: 39142279 DOI: 10.1016/j.molcel.2024.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/29/2024] [Accepted: 07/18/2024] [Indexed: 08/16/2024]
Abstract
G-quadruplexes (G4s) form throughout the genome and influence important cellular processes. Their deregulation can challenge DNA replication fork progression and threaten genome stability. Here, we demonstrate an unexpected role for the double-stranded DNA (dsDNA) translocase helicase-like transcription factor (HLTF) in responding to G4s. We show that HLTF, which is enriched at G4s in the human genome, can directly unfold G4s in vitro and uses this ATP-dependent translocase function to suppress G4 accumulation throughout the cell cycle. Additionally, MSH2 (a component of MutS heterodimers that bind G4s) and HLTF act synergistically to suppress G4 accumulation, restrict alternative lengthening of telomeres, and promote resistance to G4-stabilizing drugs. In a discrete but complementary role, HLTF restrains DNA synthesis when G4s are stabilized by suppressing primase-polymerase (PrimPol)-dependent repriming. Together, the distinct roles of HLTF in the G4 response prevent DNA damage and potentially mutagenic replication to safeguard genome stability.
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Affiliation(s)
- Gongshi Bai
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Theresa Endres
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Ulrike Kühbacher
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Valentina Mengoli
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland
| | - Briana H Greer
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Emma M Peacock
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Matthew D Newton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Tyler Stanage
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Roxana Lungu
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Magdalena P Crossley
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Ataya Sathirachinda
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Karlene A Cimprich
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA.
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233
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Low GW, Pavlova A, Gan HM, Ko MC, Sadanandan KR, Lee YP, Amos JN, Austin L, Falk S, Dowling DK, Sunnucks P. Accelerated differentiation of neo-W nuclear-encoded mitochondrial genes between two climate-associated bird lineages signals potential co-evolution with mitogenomes. Heredity (Edinb) 2024:10.1038/s41437-024-00718-w. [PMID: 39174672 DOI: 10.1038/s41437-024-00718-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 08/11/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024] Open
Abstract
There is considerable evidence for mitochondrial-nuclear co-adaptation as a key evolutionary driver. Hypotheses regarding the roles of sex-linkage have emphasized Z-linked nuclear genes with mitochondrial function (N-mt genes), whereas it remains contentious whether the perfect co-inheritance of W genes with mitogenomes could hinder or facilitate co-adaptation. Young (neo-) sex chromosomes that possess relatively many N-mt genes compared to older chromosomes provide unprecedented hypothesis-testing opportunities. Eastern Yellow Robin (EYR) lineages in coastal and inland habitats with different climates are diverged in mitogenomes, and in a ~ 15.4 Mb nuclear region enriched with N-mt genes, in contrast with otherwise-similar nuclear genomes. This nuclear region maps to passerine chromosome 1A, previously found to be neo-sex in the inland EYR genome. To compare sex-linked Chr1A-derived genes between lineages, we assembled and annotated the coastal EYR genome. We found that: (i) the coastal lineage shares a similar neo-sex system with the inland lineage, (ii) neo-W and neo-Z N-mt genes are not more diverged between lineages than are comparable non-N-mt genes, and showed little evidence for broad positive selection, (iii) however, W-linked N-mt genes are more diverged between lineages than are their Z-linked gametologs. The latter effect was ~7 times stronger for N-mt than non-N-mt genes, suggesting that W-linked N-mt genes might have diverged between lineages under environmental selection through co-evolution with mitogenomes. Finally, we identify a candidate gene driver for divergent selection, NDUFA12. Our data represent a rare example suggesting a possible role for W-associated mitochondrial-nuclear interactions in climate-associated adaptation and lineage differentiation.
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Affiliation(s)
- Gabriel Weijie Low
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia.
- Evolution of Sensory and Physiological Systems, Max Planck Institute for Biological Intelligence, 82319, Seewiesen, Germany.
- National Parks Board, 1 Cluny Road, Singapore Botanical Gardens, Singapore, 259569, Singapore.
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220, Australia
- Patriot Biotech Sdn Bhd, 47500, Subang Jaya, Selangor, Malaysia
| | - Meng-Ching Ko
- Evolution of Sensory and Physiological Systems, Max Planck Institute for Biological Intelligence, 82319, Seewiesen, Germany
| | - Keren R Sadanandan
- Evolution of Sensory and Physiological Systems, Max Planck Institute for Biological Intelligence, 82319, Seewiesen, Germany
| | - Yin Peng Lee
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220, Australia
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3220, Australia
| | - J Nevil Amos
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
- Arthur Rylah Institute for Environmental Research, Heidelberg, VIC 3084, Australia
| | - Lana Austin
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Stephanie Falk
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia.
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234
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Lu Q, Luo L, Zeng B, Luo H, Wang X, Qiu L, Yang Y, Feng C, Zhou J, Hu Y, Huang T, Ma P, Huang T, Xie K, Yuan H, Huang S, Yang B, Zou Y, Liu Y. Prenatal chromosomal microarray analysis in a large Chinese cohort of fetuses with congenital heart defects: a single center study. Orphanet J Rare Dis 2024; 19:307. [PMID: 39175064 PMCID: PMC11342572 DOI: 10.1186/s13023-024-03317-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/08/2024] [Indexed: 08/24/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Congenital heart defect (CHD) is one of the most common birth defects. The aim of this cohort study was to evaluate the prevalence of chromosomal abnormalities and the clinical utility of chromosomal microarray analysis (CMA) in fetuses with different types of CHD, aiming to assist genetic counseling and clinical decision-making. METHODS In this study, 642 fetuses with CHD were enrolled from a single center over a six-year period (2017-2022). Both conventional karyotyping and CMA were performed simultaneously on these fetuses. RESULTS The diagnostic yield of CMA in fetuses with CHD in our study was 15.3% (98/642). Our findings revealed a significant increase in the diagnostic yield of CMA compared to karyotyping in fetuses with CHD. Among CHD subgroups, the diagnostic yields were high in complex CHD (34.9%), conotruncal defects (28.6%), right ventricular outflow tract obstructive defects (RVOTO) (25.9%), atrioventricular septal defects (AVSD) (25.0%) and left ventricular outflow tract obstructive defects (LVOTO) (24.1%), while those in other CHD (10.6%) and septal defects (10.9%) were relatively low. The overall detection rate of clinically significant chromosomal abnormalities was significantly higher in the non-isolated CHD group compared to the isolated CHD group (33.1% vs. 9.9%, P < 0.0001). Interestingly, numerical chromosomal abnormalities were more likely to occur in the non-isolated CHD group than in the isolated CHD group (20.3% vs. 2.0%, P < 0.0001). The rate of termination of pregnancy (TOP)/Still birth in the non-isolated CHD group was significantly higher than that in the isolated CHD group (40.5% vs. 20.6%, P < 0.0001). Compared to the isolated CHD group, the detection rate of clinically significant chromosomal abnormalities was significantly higher in the group of CHD with soft markers (35.6% vs. 9.9%, P < 0.0001) and in the group of CHD with additional structural anomalies (36.1% vs. 9.9%, P < 0.0001). CONCLUSIONS CMA is a reliable and high-resolution technique that should be recommended as the front-line test for prenatal diagnosis of fetuses with CHD. The prevalence of chromosomal abnormalities varies greatly among different subgroups of CHD, and special attention should be given to prenatal non-isolated cases of CHD, especially those accompanied by additional structural anomalies or soft markers.
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Affiliation(s)
- Qing Lu
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China
| | - Laipeng Luo
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China
| | - Baitao Zeng
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China
| | - Haiyan Luo
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China
| | - Xianjin Wang
- Department of Ultrasound, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China
| | - Lijuan Qiu
- Department of Ultrasound, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China
| | - Yan Yang
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China
| | - Chuanxin Feng
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China
| | - Jihui Zhou
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China
| | - Yanling Hu
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China
| | - Tingting Huang
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China
| | - Pengpeng Ma
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China
| | - Ting Huang
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China
| | - Kang Xie
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China
| | - Huizhen Yuan
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China
| | - Shuhui Huang
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China
| | - Bicheng Yang
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China.
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China.
| | - Yongyi Zou
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China.
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China.
| | - Yanqiu Liu
- Medical Genetic Center, Jiangxi Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, China.
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, No. 318, Bayi Avenue, Nanchang, China.
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235
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Lashkarboloki M, Jahanbakhshi A, Mowla SJ, Bjeije H, M Soltani B. Oncogenic roles of long non-coding RNAs in essential glioblastoma signaling pathways. J Neurogenet 2024:1-17. [PMID: 39169886 DOI: 10.1080/01677063.2024.2390403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024]
Abstract
Glioblastoma multiforme (GBM) is an aggressive and diffuse type of glioma with the lowest survival rate in patients. The recent failure of multiple treatments suggests that targeting several targets at once may be a different strategy to overcome GBM carcinogenesis. Normal function of oncogenes and tumor suppressor genes need for the preservation of regular cellular processes, so any defects in these genes' activity, operate the corresponding signaling pathways, which initiate carcinogenic processes. Long non-coding RNAs (lncRNAs) that can be found in the cytoplasm or nucleus of the cells, control the transcription and translation of genes. LncRNAs perform a variety of functions, including epigenetic alteration, protein modification and stability, transcriptional regulation, and competition for miRNA that regulate mRNA translation through sponging miRNAs. Identification of various oncogenic lncRNAs and their multiple roles in brain cancers making them potential candidates for use as glioma diagnostic, prognostic, and therapeutic targets in the future. This study highlighted multiple oncogenic lncRNAs and classified them into different signaling pathways based on the regulated target genes in glioblastoma.
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Affiliation(s)
- Mina Lashkarboloki
- Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Amin Jahanbakhshi
- Skull Base Research Center, Rasool Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Javad Mowla
- Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hassan Bjeije
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Bahram M Soltani
- Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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236
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Travaglini S, Silvestrini G, Attardi E, Fanciulli M, Scalera S, Antonelli S, Maurillo L, Palmieri R, Divona M, Ciuffreda L, Savi A, Paterno G, Ottone T, Barbieri C, Maciejewski JP, Gurnari C, Ciliberto G, Voso MT. Evolution of transcriptomic profiles in relapsed inv(16) acute myeloid leukemia. Leuk Res 2024; 145:107568. [PMID: 39180902 DOI: 10.1016/j.leukres.2024.107568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/01/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024]
Abstract
Acute myeloid leukemia (AML) with inv(16) is typically associated with a favourable prognosis. However, up to 40 % of patients will eventually experience disease relapse. Herein, we dissected the genomic and transcriptomic profile of inv(16) AML to identify potential prognostic markers and therapeutic vulnerabilities. Sequencing data from 222 diagnostic samples, including 44 relapse/refractory patients, revealed a median of 1 concomitant additional mutation, cooperating with inv(16) in leukemogenesis. Notably, the mutational landscape at diagnosis did not differ significantly between patients experiencing primary induction failure or relapse when compared to the rest of the cohort, except for an increase in the mutational burden in the relapse/refractory group. RNA-Seq of unpaired diagnostic(n=7) and relapse(n=6) samples allowed the identification of oxidative phosphorylation (OXPHOS) as one of the most significantly downregulated pathways at relapse. Considering that OXPHOS could be targeted by Venetoclax/Azacitidine combination, we explored its biological effects on an inv(16) cell-line ME-1, but there was no additional advantage in terms of cell death over Azacitidine alone. To enhance Venetoclax efficacy, we tested in vitro effects of Metformin as a potential drug able to enhance chemosensitivity of AML cells by inhibiting the mitochondrial transfer. By challenging ME-1 with this combination, we observed a significant synergistic interaction at least similar to that of Venetoclax/Azacitidine. In conclusions, we identified a downregulated expression of oxidative phosphorylation (OXPHOS) at relapse in AML with inv(16), and explored the in vitro effects of metformin as a potential drug to enhance chemosensitivity in this setting.
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Affiliation(s)
- Serena Travaglini
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy; Department of Experimental Medicine, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giorgia Silvestrini
- Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Enrico Attardi
- Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Maurizio Fanciulli
- SAFU Laboratory, Department of Research, Advanced Diagnostic and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Stefano Scalera
- Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Silvia Antonelli
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Luca Maurillo
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Raffaele Palmieri
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Mariadomenica Divona
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy; Saint Camillus International University of Health Sciences, Rome, Italy
| | - Ludovica Ciuffreda
- SAFU Laboratory, Department of Research, Advanced Diagnostic and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Arianna Savi
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | | | - Tiziana Ottone
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy; Santa Lucia Foundation, I.R.C.C.S., Neuro-Oncohematology, Rome, Italy
| | | | - Jaroslaw P Maciejewski
- Translational Hematology and Oncology Research Department, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Carmelo Gurnari
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy; Translational Hematology and Oncology Research Department, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Gennaro Ciliberto
- Scientific Direction, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Maria Teresa Voso
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy; Santa Lucia Foundation, I.R.C.C.S., Neuro-Oncohematology, Rome, Italy.
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237
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Duan X, Shan X, Uddin LQ, Chen H. The future of disentangling the heterogeneity of autism with neuroimaging studies. Biol Psychiatry 2024:S0006-3223(24)01536-1. [PMID: 39181387 DOI: 10.1016/j.biopsych.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 08/01/2024] [Accepted: 08/07/2024] [Indexed: 08/27/2024]
Abstract
Autism spectrum disorder (ASD) is a lifelong neurodevelopmental condition. Over the past decade, a considerable number of approaches have been developed to identify potential neuroimaging-based biomarkers of ASD and have uncovered specific neural mechanisms underlying behaviors associated with ASD. However, the substantial heterogeneity among those diagnosed with ASD hinders the development of biomarkers. Disentangling the heterogeneity of ASD is pivotal to improve quality of life for individuals with ASD by facilitating early diagnosis and individualized interventions for those who need support. In this Review, we discuss recent advances in neuroimaging that have facilitated the characterization of the heterogeneity of this condition from three frameworks: neurosubtyping, dimensional models, and normative models. In addition, we discuss the challenges, possible solutions, and clinical utility of these three frameworks. We argue that several factors need to be considered when parsing heterogeneity using neuroimaging, including co-occurring conditions, neurodevelopment, heredity and environment, and multi-site and multi-modality data. We close with a discussion of future directions for achieving a better understanding of the neural mechanisms underlying neurodevelopmental heterogeneity and the future of precision medicine in ASD.
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Affiliation(s)
- Xujun Duan
- Sichuan Provincial Center for Mental Health, Sichuan Provincial People's Hospital, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; MOE Key Lab for Neuroinformation, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu, 610054, PR China.
| | - Xiaolong Shan
- Sichuan Provincial Center for Mental Health, Sichuan Provincial People's Hospital, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; MOE Key Lab for Neuroinformation, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu, 610054, PR China
| | - Lucina Q Uddin
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California, United States; Department of Psychology, University of California Los Angeles, Los Angeles, California, United States
| | - Huafu Chen
- Sichuan Provincial Center for Mental Health, Sichuan Provincial People's Hospital, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; MOE Key Lab for Neuroinformation, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu, 610054, PR China.
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238
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He X, Chen W, Zhou X, Hu G, Wei J, Liu Y, Cai L, Zhang Z, Chen T. The Therapeutic Potential of Lactobacillus crispatus for Chronic Endometritis: A Comprehensive Clinical Trial and Experimental Investigation. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10349-6. [PMID: 39172215 DOI: 10.1007/s12602-024-10349-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2024] [Indexed: 08/23/2024]
Abstract
Chronic endometritis (CE) is common in patients with infertility, and it is challenging to treat with antibiotics as bacteria often acquire resistance to the antibiotics, which leads to frequent recurrence of the condition. Probiotics, especially Lactobacillus species, are known for their usefulness in treating reproductive infections. This study evaluated Lactobacillus crispatus chen 01 (L. crispatus chen 01) isolated from healthy women who were 22-30 years old and married with children. In vitro experiments showed that L. crispatus chen 01 inhibited pathogens and reduced inflammation in CE mice by downregulating inflammatory proteins (TLR, MyD88, and p65/p-p65; L + Abx vs M, P < 0.01), improving histopathological features, and inhibiting bacterial growth. It also regulated endometrial processes, such as enhancing embryo implantation (BMP2 and Wnt4, L + Abx vs M, P < 0.01) via the Wnt/β-catenin pathway, leading to increased pregnancy rates (L + Abx vs M, 100% vs 0%) in mice. In clinical trials, L. crispatus chen 01 improved progesterone levels (P = 0.0038), pregnancy rates (C vs Abx + L. c, 76.19% vs 87.18%), and pathological changes in CE patients. The findings from this study identify the administration of L. crispatus chen 01 as a promising intervention for CE that could improve pregnancy rates.
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Affiliation(s)
- Xia He
- Department of Obstetrics & Gynecology, the First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
- Department of Obstetrics & Gynecology, the Ninth Hospital in Nanchang and The Affiliated Hospital of Nanchang University, Nanchang, 330038, Jiangxi, China
| | - Weijun Chen
- Department of Reproductive Medicine, the Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, 330001, Jiangxi, China
| | - Xiaoni Zhou
- Department of Obstetrics & Gynecology, the First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Gang Hu
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Jing Wei
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Yan Liu
- Department of Reproductive Medicine, the People's Hospital of Ganzhou, Ganzhou, 341099, Jiangxi, China
| | - Liping Cai
- Department of Obstetrics & Gynecology, the First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China.
| | - Zhi Zhang
- Department of Obstetrics & Gynecology, the First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China.
| | - Tingtao Chen
- Department of Obstetrics & Gynecology, the First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China.
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, 330031, Jiangxi, China.
- School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, 330036, Jiangxi, China.
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239
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Schleifer CH, Chang SE, Amir CM, O'Hora KP, Fung H, Kang JWD, Kushan-Wells L, Daly E, Di Fabio F, Frascarelli M, Gudbrandsen M, Kates WR, Murphy D, Addington J, Anticevic A, Cadenhead KS, Cannon TD, Cornblatt BA, Keshavan M, Mathalon DH, Perkins DO, Stone W, Walker E, Woods SW, Uddin LQ, Kumar K, Hoftman GD, Bearden CE. Unique functional neuroimaging signatures of genetic versus clinical high risk for psychosis. Biol Psychiatry 2024:S0006-3223(24)01538-5. [PMID: 39181389 DOI: 10.1016/j.biopsych.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 08/05/2024] [Accepted: 08/08/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND 22q11.2 Deletion Syndrome (22qDel) is a copy number variant (CNV) associated with psychosis and other neurodevelopmental disorders. Adolescents at clinical high risk for psychosis (CHR) are identified based on the presence of subthreshold psychosis symptoms. Whether common neural substrates underlie these distinct high-risk populations is unknown. We compared functional brain measures in 22qDel and CHR cohorts and mapped results to biological pathways. METHODS We analyzed two large multi-site cohorts with resting-state functional MRI (rs-fMRI): 1) 22qDel (n=164, 47% female) and typically developing (TD) controls (n=134, 56% female); 2) CHR individuals (n=244, 41% female) and TD controls (n=151, 46% female) from the North American Prodrome Longitudinal Study-2. We computed global brain connectivity (GBC), local connectivity (LC), and brain signal variability (BSV) across cortical regions, testing case-control differences for 22qDel and CHR separately. Group difference maps were related to published brain maps using autocorrelation-preserving permutation. RESULTS BSV, LC, and GBC are significantly disrupted in 22qDel compared with TD controls (False Discovery Rate q<0.05). Spatial maps of BSV and LC differences are highly correlated with each other, unlike GBC. In CHR, only LC is significantly altered versus controls, with a different spatial pattern compared to 22qDel. Group differences map onto biological gradients, with 22qDel effects strongest in regions with high predicted blood flow and metabolism. CONCLUSION 22qDel and CHR exhibit divergent effects on fMRI temporal variability and multi-scale functional connectivity. In 22qDel, strong and convergent disruptions in BSV and LC not seen in CHR individuals suggest distinct functional brain alterations.
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Affiliation(s)
- Charles H Schleifer
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Sarah E Chang
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Carolyn M Amir
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Kathleen P O'Hora
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Hoki Fung
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Jee Won D Kang
- Department of Psychology, University of California, Los Angeles, CA, USA
| | - Leila Kushan-Wells
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Eileen Daly
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Fabio Di Fabio
- Department of Human Neurosciences, Sapienza University, Rome, Italy
| | | | - Maria Gudbrandsen
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK; Centre for Psychological Research (CREW), School of Psychology, University of Roehampton, London, UK
| | - Wendy R Kates
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Declan Murphy
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Jean Addington
- Department of Psychiatry, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Alan Anticevic
- Departments of Psychology and Psychiatry, Yale University, New Haven, CT, USA
| | | | - Tyrone D Cannon
- Departments of Psychology and Psychiatry, Yale University, New Haven, CT, USA
| | - Barbara A Cornblatt
- Department of Psychiatry, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Matcheri Keshavan
- Department of Psychiatry, Harvard Medical School at Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Daniel H Mathalon
- Department of Psychiatry, University of California, and San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Diana O Perkins
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - William Stone
- Department of Psychiatry, Harvard Medical School at Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Elaine Walker
- Department of Psychology, Emory University, Atlanta, GA, USA
| | - Scott W Woods
- Departments of Psychology and Psychiatry, Yale University, New Haven, CT, USA
| | - Lucina Q Uddin
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Kuldeep Kumar
- Centre de Recherche du CHU Sainte-Justine, University of Montreal, Montreal, Canada
| | - Gil D Hoftman
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Carrie E Bearden
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA; Department of Psychology, University of California, Los Angeles, CA, USA.
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240
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Sharma A, Soni H. Phases and correlations in active nematic granular systems. SOFT MATTER 2024; 20:6608-6617. [PMID: 39105541 DOI: 10.1039/d4sm00667d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
We investigate the statistical behavior of a system comprising fore-aft symmetric rods confined between two vertically vibrating plates using numerical simulations closely resembling the experimental setup studied by V. Narayan et al., Science, 2007, 317, 105-108. Our focus lies in studying the phase transition of the system from an isotropic phase to a nematic phase as we increase either the rod length or the rod concentration. Our simulations confirm the presence of long-range ordering in the ordered phase. Furthermore, we identify a phase characterized by a periodic ordering profile that disrupts translation symmetry. We also provide a detailed analysis of the translational and rotational diffusive dynamics of the rods. Interestingly, the translational diffusivity of the rods is found to increase with the rod concentration.
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Affiliation(s)
- Abhishek Sharma
- School of Physical Sciences (SPS), Indian Institute of Technology Mandi, Parashar Road, Tehsil Sadar, Near Kataula, Kamand, Himachal Pradesh 175005, India.
| | - Harsh Soni
- School of Physical Sciences (SPS), Indian Institute of Technology Mandi, Parashar Road, Tehsil Sadar, Near Kataula, Kamand, Himachal Pradesh 175005, India.
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241
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Palacios-Blanco I, Gómez L, Bort M, Mayerová N, Bágeľová Poláková S, Martín-Castellanos C. CDK phosphorylation of Sfr1 downregulates Rad51 function in late-meiotic homolog invasions. EMBO J 2024:10.1038/s44318-024-00205-2. [PMID: 39174851 DOI: 10.1038/s44318-024-00205-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 08/05/2024] [Accepted: 08/08/2024] [Indexed: 08/24/2024] Open
Abstract
Meiosis is the developmental program that generates gametes. To produce healthy gametes, meiotic recombination creates reciprocal exchanges between each pair of homologous chromosomes that facilitate faithful chromosome segregation. Using fission yeast and biochemical, genetic, and cytological approaches, we have studied the role of CDK (cyclin-dependent kinase) in the control of Swi5-Sfr1, a Rad51-recombinase auxiliary factor involved in homolog invasion during recombination. We show that Sfr1 is a CDK target, and its phosphorylation downregulates Swi5-Sfr1 function in the meiotic prophase. Expression of a phospho-mimetic sfr1-7D mutant inhibits Rad51 binding, its robust chromosome loading, and subsequently decreases interhomolog recombination. On the other hand, the non-phosphorylatable sfr1-7A mutant alters Rad51 dynamics at late prophase, and exacerbates chromatin segregation defects and Rad51 retention observed in dbl2 deletion mutants when combined with them. We propose Sfr1 phospho-inhibition as a novel cell-cycle-dependent mechanism, which ensures timely resolution of recombination intermediates and successful chromosome distribution into the gametes. Furthermore, the N-terminal disordered part of Sfr1, an evolutionarily conserved feature, serves as a regulatory platform coordinating this phospho-regulation, protein localization and stability, with several CDK sites and regulatory sequences being conserved.
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Affiliation(s)
- Inés Palacios-Blanco
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, Salamanca, 37007, Spain
| | - Lucía Gómez
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, Salamanca, 37007, Spain
| | - María Bort
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, Salamanca, 37007, Spain
| | - Nina Mayerová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 841 04, Slovakia
| | - Silvia Bágeľová Poláková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 841 04, Slovakia
- Centre of Biosciences SAS, Institute of Animal Biochemistry and Genetics, Bratislava, 840 05, Slovakia
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242
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Fujita T, Aoki N, Mori C, Homma KJ, Yamaguchi S. SoxC and MmpReg promote blastema formation in whole-body regeneration of fragmenting potworms Enchytraeus japonensis. Nat Commun 2024; 15:6659. [PMID: 39174502 PMCID: PMC11341731 DOI: 10.1038/s41467-024-50865-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 07/22/2024] [Indexed: 08/24/2024] Open
Abstract
Regeneration in many animals involves the formation of a blastema, which differentiates and organizes into the appropriate missing body parts. Although the mechanisms underlying blastema formation are often fundamental to regeneration biology, information on the cellular and molecular basis of blastema formation remains limited. Here, we focus on a fragmenting potworm (Enchytraeus japonensis), which can regenerate its whole body from small fragments. We find soxC and mmpReg as upregulated genes in the blastema. RNAi of soxC and mmpReg reduce the number of blastema cells, indicating that soxC and mmpReg promote blastema formation. Expression analyses show that soxC-expressing cells appear to gradually accumulate in blastema and constitute a large part of the blastema. Additionally, similar expression dynamics of SoxC orthologue genes in frog (Xenopus laevis) are found in the regeneration blastema of tadpole tail. Our findings provide insights into the cellular and molecular mechanisms underlying blastema formation across species.
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Affiliation(s)
- Toshiyuki Fujita
- Department of Biological Sciences, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Naoya Aoki
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Chihiro Mori
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Koichi J Homma
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Shinji Yamaguchi
- Department of Biological Sciences, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan.
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243
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Lu J, Zhao P, Ding X, Li H. N-acetylcysteine stimulates the proliferation and differentiation in heat-stressed skeletal muscle cells. J Therm Biol 2024; 124:103958. [PMID: 39182421 DOI: 10.1016/j.jtherbio.2024.103958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 08/13/2024] [Accepted: 08/13/2024] [Indexed: 08/27/2024]
Abstract
N-acetylcysteine (NAC) is known for its beneficial effects on health due to its antioxidant and antiapoptotic properties. This study explored the protective effects of NAC against oxidative stress in heat-stressed (HS) skeletal muscle cells and its role in promoting muscle development. NAC reduced the heat shock response by decreasing the expression of heat shock protein 70 (HSP70) in HS-induced muscle cells during proliferation and differentiation. NAC also mitigated HS-induced oxidative stress via increasing the antioxidant enzyme levels and reducing oxidant enzyme levels. Treatment with NAC at 2 mM increased cell viability from 43.68% ± 5.14%-66.69% ± 14.43% and decreased the apoptosis rate from 7.89% ± 0.53%-5.17% ± 0.11% in skeletal muscle cells. Additionally, NAC promoted the proliferation and differentiation of HS-induced skeletal muscle cells by upregulating the expression of PAX7, MYF5, MRF4 and MYHC. These findings suggest that NAC alleviates HS-induced oxidative damage in skeletal muscle cells and support muscle development.
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Affiliation(s)
- Jiawei Lu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiuhu Ding
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huixia Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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244
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Yudenko A, Bazhenov SV, Aleksenko VA, Goncharov IM, Semenov O, Remeeva A, Nazarenko VV, Kuznetsova E, Fomin VV, Konopleva MN, Al Ebrahim R, Sluchanko NN, Ryzhykau Y, Semenov YS, Kuklin A, Manukhov IV, Gushchin I. luxA Gene From Enhygromyxa salina Encodes a Functional Homodimeric Luciferase. Proteins 2024. [PMID: 39171358 DOI: 10.1002/prot.26739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/20/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024]
Abstract
Several clades of luminescent bacteria are known currently. They all contain similar lux operons, which include the genes luxA and luxB encoding a heterodimeric luciferase. The aldehyde oxygenation reaction is presumed to be catalyzed primarily by the subunit LuxA, whereas LuxB is required for efficiency and stability of the complex. Recently, genomic analysis identified a subset of bacterial species with rearranged lux operons lacking luxB. Here, we show that the product of the luxA gene from the reduced luxACDE operon of Enhygromyxa salina is luminescent upon addition of aldehydes both in vivo in Escherichia coli and in vitro. Overall, EsLuxA is much less bright compared with luciferases from Aliivibrio fischeri (AfLuxAB) and Photorhabdus luminescens (PlLuxAB), and most active with medium-chain C4-C9 aldehydes. Crystal structure of EsLuxA determined at the resolution of 2.71 Å reveals a (β/α)8 TIM-barrel fold, characteristic for other bacterial luciferases, and the protein preferentially forms a dimer in solution. The mobile loop residues 264-293, which form a β-hairpin or a coil in Vibrio harveyi LuxA, form α-helices in EsLuxA. Phylogenetic analysis shows EsLuxA and related proteins may be bacterial protoluciferases that arose prior to duplication of the luxA gene and its speciation to luxA and luxB in the previously described luminescent bacteria. Our work paves the way for the development of new bacterial luciferases that have an advantage of being encoded by a single gene.
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Affiliation(s)
- Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Sergey V Bazhenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vladimir A Aleksenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan M Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Elizaveta Kuznetsova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vadim V Fomin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Maria N Konopleva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Rahaf Al Ebrahim
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Yury Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Yury S Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexander Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Ilya V Manukhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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245
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Sekulovski N, Carleton AE, Rengarajan AA, Lin CW, Juga LL, Whorton AE, Kropp Schmidt J, Golos T, Taniguchi K. Temporally resolved single cell transcriptomics in a human model of amniogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.07.556553. [PMID: 39026707 PMCID: PMC11257495 DOI: 10.1101/2023.09.07.556553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Amniogenesis is triggered in a collection of pluripotent epiblast cells as the human embryo implants. To gain insights into the critical but poorly understood transcriptional machinery governing amnion fate determination, we examined the evolving transcriptome of a developing human pluripotent stem cell-derived amnion model at the single cell level. This analysis revealed several continuous amniotic fate progressing states with state-specific markers, which include a previously unrecognized CLDN10+ amnion progenitor state. Strikingly, we found that expression of CLDN10 is restricted to the amnion-epiblast boundary region in the human post-implantation amniotic sac model as well as in a peri-gastrula cynomolgus macaque embryo, bolstering the growing notion that, at this stage, the amnion-epiblast boundary is a site of active amniogenesis. Bioinformatic analysis of published primate peri-gastrula single cell sequencing data further confirmed that CLDN10 is expressed in cells progressing to amnion. Additionally, our loss of function analysis shows that CLDN10 promotes amniotic but suppresses primordial germ cell-like fate. Overall, this study presents a comprehensive amniogenic single cell transcriptomic resource and identifies a previously unrecognized CLDN10+ amnion progenitor population at the amnion-epiblast boundary of the primate peri-gastrula.
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246
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Abbineni PS, Baid S, Weiss MJ. A moonlighting job for α-globin in blood vessels. Blood 2024; 144:834-844. [PMID: 38848504 DOI: 10.1182/blood.2023022192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/08/2024] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
ABSTRACT Red blood cells express high levels of hemoglobin A tetramer (α2β2) to facilitate oxygen transport. Hemoglobin subunits and related proteins are also expressed at lower levels in other tissues across the animal kingdom. Physiological functions for most nonerythroid globins likely derive from their ability to catalyze reduction-oxidation (redox) reactions via electron transfer through heme-associated iron. An interesting example is illustrated by the recent discovery that α-globin without β-globin is expressed in some arteriolar endothelial cells (ECs). α-globin binds EC nitric oxide (NO) synthase (eNOS) and degrades its enzymatic product NO, a potent vasodilator. Thus, depletion of α-globin in ECs or inhibition of its association with eNOS causes arteriolar relaxation and lowering of blood pressure in mice. Some of these findings have been replicated in isolated human blood vessels, and genetic studies are tractable in populations in which α-thalassemia alleles are prevalent. Two small studies identified associations between loss of α-globin genes in humans and NO-regulated vascular responses elicited by local hypoxia-induced blood flow or thermal stimulation. In a few larger population-based studies, no associations were detected between loss of α-globin genes and blood pressure, ischemic stroke, or pulmonary hypertension. In contrast, a significant positive association between α-globin gene copy number and kidney disease was detected in an African American cohort. Further studies are required to define comprehensively the expression of α-globin in different vascular beds and ascertain their overall impact on normal and pathological vascular physiology.
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Affiliation(s)
- Prabhodh S Abbineni
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL
| | - Srishti Baid
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Mitchell J Weiss
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN
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247
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Lisowski P, Lickfett S, Rybak-Wolf A, Menacho C, Le S, Pentimalli TM, Notopoulou S, Dykstra W, Oehler D, López-Calcerrada S, Mlody B, Otto M, Wu H, Richter Y, Roth P, Anand R, Kulka LAM, Meierhofer D, Glazar P, Legnini I, Telugu NS, Hahn T, Neuendorf N, Miller DC, Böddrich A, Polzin A, Mayatepek E, Diecke S, Olzscha H, Kirstein J, Ugalde C, Petrakis S, Cambridge S, Rajewsky N, Kühn R, Wanker EE, Priller J, Metzger JJ, Prigione A. Mutant huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure. Nat Commun 2024; 15:7027. [PMID: 39174523 PMCID: PMC11341898 DOI: 10.1038/s41467-024-51216-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/01/2024] [Indexed: 08/24/2024] Open
Abstract
Expansion of the glutamine tract (poly-Q) in the protein huntingtin (HTT) causes the neurodegenerative disorder Huntington's disease (HD). Emerging evidence suggests that mutant HTT (mHTT) disrupts brain development. To gain mechanistic insights into the neurodevelopmental impact of human mHTT, we engineered male induced pluripotent stem cells to introduce a biallelic or monoallelic mutant 70Q expansion or to remove the poly-Q tract of HTT. The introduction of a 70Q mutation caused aberrant development of cerebral organoids with loss of neural progenitor organization. The early neurodevelopmental signature of mHTT highlighted the dysregulation of the protein coiled-coil-helix-coiled-coil-helix domain containing 2 (CHCHD2), a transcription factor involved in mitochondrial integrated stress response. CHCHD2 repression was associated with abnormal mitochondrial morpho-dynamics that was reverted upon overexpression of CHCHD2. Removing the poly-Q tract from HTT normalized CHCHD2 levels and corrected key mitochondrial defects. Hence, mHTT-mediated disruption of human neurodevelopment is paralleled by aberrant neurometabolic programming mediated by dysregulation of CHCHD2, which could then serve as an early interventional target for HD.
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Affiliation(s)
- Pawel Lisowski
- Quantitative Stem Cell Biology, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Psychiatry and Psychotherapy, Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité - Universitätsmedizin, Berlin, Germany
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzebiec n/Warsaw, Poland
| | - Selene Lickfett
- Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- Institute of Anatomy II, Heinrich-Heine-University, Düsseldorf, Germany
| | - Agnieszka Rybak-Wolf
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Organoid Platform, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Carmen Menacho
- Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Stephanie Le
- Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Tancredi Massimo Pentimalli
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Sofia Notopoulou
- Institute of Applied Biosciences (INAB), Centre For Research and Technology Hellas (CERTH), Thessaloniki, Greece
| | - Werner Dykstra
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht, The Netherlands
| | - Daniel Oehler
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital Düsseldorf, Cardiovascular Research Institute Düsseldorf (CARID), Düsseldorf, Germany
| | | | - Barbara Mlody
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Centogene, Rostock, Germany
| | - Maximilian Otto
- Quantitative Stem Cell Biology, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Haijia Wu
- Institute of Molecular Medicine, Medical School, Hamburg, Germany
| | | | - Philipp Roth
- Quantitative Stem Cell Biology, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Ruchika Anand
- Institute of Biochemistry and Molecular Biology I, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Linda A M Kulka
- Institute of Physiological Chemistry, Martin-Luther-University, Halle-Wittenberg, Germany
| | - David Meierhofer
- Quantitative RNA Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Petar Glazar
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Quantitative RNA Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ivano Legnini
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Human Technopole, Milan, Italy
| | - Narasimha Swamy Telugu
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Tobias Hahn
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Nancy Neuendorf
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Duncan C Miller
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Annett Böddrich
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Amin Polzin
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital Düsseldorf, Cardiovascular Research Institute Düsseldorf (CARID), Düsseldorf, Germany
| | - Ertan Mayatepek
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Sebastian Diecke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
| | - Heidi Olzscha
- Institute of Molecular Medicine, Medical School, Hamburg, Germany
- Institute of Physiological Chemistry, Martin-Luther-University, Halle-Wittenberg, Germany
| | - Janine Kirstein
- Cell Biology, University of Bremen, Bremen, Germany
- Leibniz Institute on Aging - Fritz-Lipmann Institute, Jena, Germany
| | - Cristina Ugalde
- Instituto de Investigación Hospital 12 de Octubre (i + 12), Madrid, Spain
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Spyros Petrakis
- Institute of Applied Biosciences (INAB), Centre For Research and Technology Hellas (CERTH), Thessaloniki, Greece
| | - Sidney Cambridge
- Institute of Anatomy II, Heinrich-Heine-University, Düsseldorf, Germany
- Dr. Senckenberg Anatomy, Anatomy II, Goethe-University, Frankfurt, Germany
| | - Nikolaus Rajewsky
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
- NeuroCure Cluster of Excellence, Berlin, Germany
- National Center for Tumor Diseases (NCT), German Cancer Consortium (DKTK), Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | - Ralf Kühn
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Erich E Wanker
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Josef Priller
- Department of Psychiatry and Psychotherapy, Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité - Universitätsmedizin, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Psychiatry and Psychotherapy; School of Medicine and Health, Technical University of Munich and German Center for Mental Health (DZPG), Munich, Germany
- University of Edinburgh and UK Dementia Research Institute, Edinburgh, UK
| | - Jakob J Metzger
- Quantitative Stem Cell Biology, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
| | - Alessandro Prigione
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.
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Lusk S, LaPotin S, Presnell JS, Kwan KM. Increased Netrin downstream of overactive Hedgehog signaling disrupts optic fissure formation. Dev Dyn 2024. [PMID: 39166841 DOI: 10.1002/dvdy.733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/29/2024] [Accepted: 08/02/2024] [Indexed: 08/23/2024] Open
Abstract
BACKGROUND Uveal coloboma, a developmental eye defect, is caused by failed development of the optic fissure, a ventral structure in the optic stalk and cup where axons exit the eye and vasculature enters. The Hedgehog (Hh) signaling pathway regulates optic fissure development: loss-of-function mutations in the Hh receptor ptch2 produce overactive Hh signaling and can result in coloboma. We previously proposed a model where overactive Hh signaling disrupts optic fissure formation by upregulating transcriptional targets acting both cell- and non-cell-autonomously. Here, we examine the Netrin family of secreted ligands as candidate Hh target genes. RESULTS We find multiple Netrin ligands upregulated in the zebrafish ptch2 mutant during optic fissure development. Using a gain-of-function approach to overexpress Netrin in a spatiotemporally specific manner, we find that netrin1a or netrin1b overexpression is sufficient to cause coloboma and disrupt wild-type optic fissure formation. We used loss-of-function alleles, CRISPR/Cas9 mutagenesis, and morpholino knockdown to test if loss of Netrin can rescue coloboma in the ptch2 mutant: loss of netrin genes does not rescue the ptch2 mutant phenotype. CONCLUSION These results suggest that Netrin is sufficient but not required to disrupt optic fissure formation downstream of overactive Hh signaling in the ptch2 mutant.
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Affiliation(s)
- Sarah Lusk
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Sarah LaPotin
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Jason S Presnell
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Kristen M Kwan
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
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Casacuberta-Serra S, González-Larreategui Í, Capitán-Leo D, Soucek L. MYC and KRAS cooperation: from historical challenges to therapeutic opportunities in cancer. Signal Transduct Target Ther 2024; 9:205. [PMID: 39164274 PMCID: PMC11336233 DOI: 10.1038/s41392-024-01907-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 06/05/2024] [Accepted: 06/24/2024] [Indexed: 08/22/2024] Open
Abstract
RAS and MYC rank amongst the most commonly altered oncogenes in cancer, with RAS being the most frequently mutated and MYC the most amplified. The cooperative interplay between RAS and MYC constitutes a complex and multifaceted phenomenon, profoundly influencing tumor development. Together and individually, these two oncogenes regulate most, if not all, hallmarks of cancer, including cell death escape, replicative immortality, tumor-associated angiogenesis, cell invasion and metastasis, metabolic adaptation, and immune evasion. Due to their frequent alteration and role in tumorigenesis, MYC and RAS emerge as highly appealing targets in cancer therapy. However, due to their complex nature, both oncogenes have been long considered "undruggable" and, until recently, no drugs directly targeting them had reached the clinic. This review aims to shed light on their complex partnership, with special attention to their active collaboration in fostering an immunosuppressive milieu and driving immunotherapeutic resistance in cancer. Within this review, we also present an update on the different inhibitors targeting RAS and MYC currently undergoing clinical trials, along with their clinical outcomes and the different combination strategies being explored to overcome drug resistance. This recent clinical development suggests a paradigm shift in the long-standing belief of RAS and MYC "undruggability", hinting at a new era in their therapeutic targeting.
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Affiliation(s)
| | - Íñigo González-Larreategui
- Models of cancer therapies Laboratory, Vall d'Hebron Institute of Oncology, Cellex Centre, Hospital University Vall d'Hebron Campus, Barcelona, Spain
| | - Daniel Capitán-Leo
- Models of cancer therapies Laboratory, Vall d'Hebron Institute of Oncology, Cellex Centre, Hospital University Vall d'Hebron Campus, Barcelona, Spain
| | - Laura Soucek
- Peptomyc S.L., Barcelona, Spain.
- Models of cancer therapies Laboratory, Vall d'Hebron Institute of Oncology, Cellex Centre, Hospital University Vall d'Hebron Campus, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
- Department of Biochemistry and Molecular Biology, Universitat Autonoma de Barcelona, Bellaterra, Spain.
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Zhang J, Liu H, Liu Y, Luo E, Liu S. Unlocking the potential of histone modification in regulating bone metabolism. Biochimie 2024:S0300-9084(24)00181-0. [PMID: 39154977 DOI: 10.1016/j.biochi.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/02/2024] [Accepted: 08/02/2024] [Indexed: 08/20/2024]
Abstract
Bone metabolism plays a crucial role in maintaining normal bone tissue homeostasis and function. Imbalances between bone formation and resorption can lead to osteoporosis, osteoarthritis, and other bone diseases. The dynamic and complex process of bone remodeling is driven by various factors, including epigenetics. Histone modification, one of the most important and well-studied components of epigenetic regulation, has emerged as a promising area of research in bone metabolism. Different histone proteins and modification sites exert diverse effects on osteogenesis and osteoclastogenesis. In this review, we summarize recent progress in understanding histone modifications in bone metabolism, including specific modification sites and potential regulatory enzymes. Comprehensive knowledge of histone modifications in bone metabolism could reveal new therapeutic targets and treatment strategies for bone diseases.
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Affiliation(s)
- Jiayuan Zhang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Hanghang Liu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yao Liu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - En Luo
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Shibo Liu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China.
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