251
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Tsang I, Atkinson JA, Rawsthorne S, Cockram J, Leigh F. Root hairs: an underexplored target for sustainable cereal crop production. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5484-5500. [PMID: 38894654 PMCID: PMC11427827 DOI: 10.1093/jxb/erae275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/17/2024] [Indexed: 06/21/2024]
Abstract
To meet the demands of a rising human population, plant breeders will need to develop improved crop varieties that maximize yield in the face of increasing pressure on crop production. Historically, the optimization of crop root architecture has represented a challenging breeding target due to the inaccessibility of the root systems. Root hairs, single cell projections from the root epidermis, are perhaps the most overlooked component of root architecture traits. Root hairs play a central role in facilitating water, nutrient uptake, and soil cohesion. Current root hair architectures may be suboptimal under future agricultural production regimes, coupled with an increasingly variable climate. Here, we review the genetic control of root hair development in the world's three most important crops-rice, maize, and wheat-and highlight conservation of gene function between monocots and the model dicot species Arabidopsis. Advances in genomic techniques including gene editing combined with traditional plant breeding methods have the potential to overcome many inherent issues associated with the design of improved root hair architectures. Ultimately, this will enable detailed characterization of the effects of contrasting root hair morphology strategies on crop yield and resilience, and the development of new varieties better adapted to deliver future food security.
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Affiliation(s)
- Ian Tsang
- NIAB, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK
- University of Nottingham, Plant Sciences Building, Sutton Bonnington Campus, Nottingham LE12 5RD, UK
| | - Jonathan A Atkinson
- University of Nottingham, Plant Sciences Building, Sutton Bonnington Campus, Nottingham LE12 5RD, UK
| | - Stephen Rawsthorne
- The Morley Agricultural Foundation, Morley Business Centre, Deopham Road, Morley St Botolph, Wymondham NR18 9DF, UK
| | - James Cockram
- NIAB, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK
| | - Fiona Leigh
- NIAB, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK
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252
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de Carvalho ND, Rofatto HK, de Senna Villar K, Magnelli RF, Silva Junior PI, Mendonça RZ. Proteins with Anti-apoptotic Action in the Hemolymph of Caterpillars of the Megalopygidae Family Acts by Maintaining the Structure of the Cellular Cytoskeleton. Mol Biotechnol 2024:10.1007/s12033-024-01271-x. [PMID: 39333334 DOI: 10.1007/s12033-024-01271-x] [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: 01/26/2024] [Accepted: 08/26/2024] [Indexed: 09/29/2024]
Abstract
Brazil has a very large biological variety, which is an almost inexhaustible source of substances of pharmacological and biotechnological interest. Several studies have demonstrated the presence of bioactive peptides in insect hemolymph and their potential use as therapeutic agents. However, few data are available regarding molecules extracted from insects with anti-apoptotic action. The objective of this work was to identify the presence of proteins from the hemolymph of caterpillars of the Megalopygidae family with pharmacological and biotechnological interest. This study provides preliminary and innovative information on a new substance that inhibits cellular apoptopsis and stabilizes the tested cells, impacting the cytoskeleton, maintaining cellular structure and its functions. To this, two species of Megalopygidae family were studied, Podalia sp. and Megalopyge albicolis. Cytotoxicity tests on Vero and Sf-9 cells revealed that the hemolymph of both caterpillars was cytotoxic only at concentrations greater than 5%v/v. In the anti-apoptotic activity assays, it was verified that the supplementation of cell cultures with only 1% of hemolymph v/v is sufficient to inhibit cell death by apoptosis induced by different inducers such as terbutyl, actinomycin D, hydrogen peroxide, or even by nutrient depletion. For this study, cells were stained with trypan blue, crystal violet, and fluorescent markers to cytoskeleton (actin and tubulin), mitochondria membrane electric potential (JC-1), and apoptosis marker (acridine orange and ethidium). The protein responsible for anti-apoptotic action was isolated through gel filtration chromatography, using an AKTA purifier high-resolution liquid chromatography system. The hemolymph was fractionated into 3 pools for Podalia sp. and 6 pools for M. abicolis. In the antiapoptotic tests, semi-purified hemolymph from both caterpillars showed anti-apoptotic effect in VERO and SF-9 cells, pre-treated with only 1% v/v of hemolymph and induced to death by different and apoptotic inductors. Was observed that the molecule with anti-apoptotic effect is present in pool 3 in both hemolymphs. This protector effect blocked and attenuated the disruption of the cytoskeleton (actin filaments), being that the protective effect also was observed on the integrity of the mitochondrial membrane of SF-9 cells pre-treated with both hemolymphs and treated with the apoptosis inducer Terbutil at concentrations of 25 to 100 µM. By acting on the mitochondrial pathway of death by apoptosis, and by maintaining the structure of the cytoskeleton and cellular functions, pathway that can cause disorders and diseases neurodegenerative, the substances present in the hemolymph of these and other caterpillars could be good candidates in studies for the treatment of neurodegenerative diseases such as Parkinson's disease and Alzheimer's.
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Affiliation(s)
| | | | | | | | - P I Silva Junior
- Laboratory for Applied Toxinology (LETA), Center of Toxins, Immune-Response and Cell Signaling (CeTICS/CEPID), Butantan Institute, São Paulo, Brazil.
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253
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Wu X, Xu M, Yang JR, Lu J. Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster. Nat Commun 2024; 15:8329. [PMID: 39333102 PMCID: PMC11437122 DOI: 10.1038/s41467-024-52660-4] [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: 09/26/2023] [Accepted: 09/17/2024] [Indexed: 09/29/2024] Open
Abstract
Accuracy and efficiency are fundamental to mRNA translation. Codon usage bias is widespread across species. Despite the long-standing association between optimized codon usage and improved translation, our understanding of its evolutionary basis and functional effects remains limited. Drosophila is widely used to study codon usage bias, but genome-scale experimental data are scarce. Using high-resolution mass spectrometry data from Drosophila melanogaster, we show that optimal codons have lower translation errors than nonoptimal codons after accounting for these biases. Genomic-scale analysis of ribosome profiling data shows that optimal codons are translated more rapidly than nonoptimal codons. Although we find no long-term selection favoring synonymous mutations in D. melanogaster after diverging from D. simulans, we identify signatures of positive selection driving codon optimization in the D. melanogaster population. These findings expand our understanding of the functional consequences of codon optimization and serve as a foundation for future investigations.
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Affiliation(s)
- Xinkai Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Mengze Xu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Jian-Rong Yang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China.
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254
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Di Rocco G, Trivisonno A, Trivisonno G, Toietta G. Dissecting human adipose tissue heterogeneity using single-cell omics technologies. Stem Cell Res Ther 2024; 15:322. [PMID: 39334440 PMCID: PMC11437900 DOI: 10.1186/s13287-024-03931-w] [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: 07/04/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Single-cell omics technologies that profile genes (genomic and epigenomic) and determine the abundance of mRNA (transcriptomic), protein (proteomic and secretomic), lipids (lipidomic), and extracellular matrix (matrisomic) support the dissection of adipose tissue heterogeneity at unprecedented resolution in a temporally and spatially defined manner. In particular, cell omics technologies may provide innovative biomarkers for the identification of rare specific progenitor cell subpopulations, assess transcriptional and proteomic changes affecting cell proliferation and immunomodulatory potential, and accurately define the lineage hierarchy and differentiation status of progenitor cells. Unraveling adipose tissue complexity may also provide for the precise assessment of a dysfunctional state, which has been associated with cancer, as cancer-associated adipocytes play an important role in shaping the tumor microenvironment supporting tumor progression and metastasis, obesity, metabolic syndrome, and type 2 diabetes mellitus. The information collected by single-cell omics has relevant implications for regenerative medicine because adipose tissue is an accessible source of multipotent cells; alternative cell-free approaches, including the use of adipose tissue stromal cell-conditioned medium, extracellular vesicles, or decellularized extracellular matrix, are clinically valid options. Subcutaneous white adipose tissue, which is generally harvested via liposuction, is highly heterogeneous because of intrinsic biological variability and extrinsic inconsistencies in the harvesting and processing procedures. The current limited understanding of adipose tissue heterogeneity impinges on the definition of quality standards appropriate for clinical translation, which requires consistency and uniformity of the administered product. We review the methods used for dissecting adipose tissue heterogeneity and provide an overview of advances in omics technology that may contribute to the exploration of heterogeneity and dynamics of adipose tissue at the single-cell level.
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Affiliation(s)
- Giuliana Di Rocco
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Angelo Trivisonno
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168, Rome, Italy
| | | | - Gabriele Toietta
- Tumor Immunology and Immunotherapy Unit, IRCCS Regina Elena National Cancer Institute, Via E. Chianesi, 53, 00144, Rome, Italy.
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255
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Vijatovic D, Toma FA, Harrington ZPM, Sommer C, Hauschild R, Trevisan AJ, Chapman P, Julseth MJ, Brenner-Morton S, Gabitto MI, Dasen JS, Bikoff JB, Sweeney LB. Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.20.614050. [PMID: 39345366 PMCID: PMC11430061 DOI: 10.1101/2024.09.20.614050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Vertebrates exhibit a wide range of motor behaviors, ranging from swimming to complex limb-based movements. Here we take advantage of frog metamorphosis, which captures a swim-to-limb-based movement transformation during the development of a single organism, to explore changes in the underlying spinal circuits. We find that the tadpole spinal cord contains small and largely homogeneous populations of motor neurons (MNs) and V1 interneurons (V1s) at early escape swimming stages. These neuronal populations only modestly increase in number and subtype heterogeneity with the emergence of free swimming. In contrast, during frog metamorphosis and the emergence of limb movement, there is a dramatic expansion of MN and V1 interneuron number and transcriptional heterogeneity, culminating in cohorts of neurons that exhibit striking molecular similarity to mammalian motor circuits. CRISPR/Cas9-mediated gene disruption of the limb MN and V1 determinants FoxP1 and Engrailed-1, respectively, results in severe but selective deficits in tail and limb function. Our work thus demonstrates that neural diversity scales exponentially with increasing behavioral complexity and illustrates striking evolutionary conservation in the molecular organization and function of motor circuits across species.
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256
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Granata I, Maddalena L, Manzo M, Guarracino MR, Giordano M. HELP: A computational framework for labelling and predicting human common and context-specific essential genes. PLoS Comput Biol 2024; 20:e1012076. [PMID: 39331694 DOI: 10.1371/journal.pcbi.1012076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 08/19/2024] [Indexed: 09/29/2024] Open
Abstract
Machine learning-based approaches are particularly suitable for identifying essential genes as they allow the generation of predictive models trained on features from multi-source data. Gene essentiality is neither binary nor static but determined by the context. The databases for essential gene annotation do not permit the personalisation of the context, and their update can be slower than the publication of new experimental data. We propose HELP (Human Gene Essentiality Labelling & Prediction), a computational framework for labelling and predicting essential genes. Its double scope allows for identifying genes based on dependency or not on experimental data. The effectiveness of the labelling method was demonstrated by comparing it with other approaches in overlapping the reference sets of essential gene annotations, where HELP demonstrated the best compromise between false and true positive rates. The gene attributes, including multi-omics and network embedding features, lead to high-performance prediction of essential genes while confirming the existence of essentiality nuances.
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Affiliation(s)
- Ilaria Granata
- Institute for High-Performance Computing and Networking, National Research Council, Naples, Italy
| | - Lucia Maddalena
- Institute for High-Performance Computing and Networking, National Research Council, Naples, Italy
| | - Mario Manzo
- Information Technology Services, University of Naples "L'Orientale", Naples, Italy
| | - Mario Rosario Guarracino
- Laboratory of Algorithms and Technologies for Network Analysis, National Research University Higher School of Economics, Nizhny Novgorod, Russia
- Department of Economics and Law, University of Cassino and Southern Lazio, Cassino, Frosinone, Italy
| | - Maurizio Giordano
- Institute for High-Performance Computing and Networking, National Research Council, Naples, Italy
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257
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Peña-Ponton C, Diez-Rodriguez B, Perez-Bello P, Becker C, McIntyre LM, van der Putten WH, De Paoli E, Heer K, Opgenoorth L, Verhoeven KJF. High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive transposable element superfamilies in the clonal Lombardy poplar. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5839-5856. [PMID: 38836523 PMCID: PMC11427840 DOI: 10.1093/jxb/erae262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 06/04/2024] [Indexed: 06/06/2024]
Abstract
DNA methylation is environment-sensitive and can mediate stress responses. In trees, changes in the environment might cumulatively shape the methylome landscape over time. However, because high-resolution methylome studies usually focus on single environmental cues, the stress-specificity and long-term stability of methylation responses remain unclear. Here, we studied the methylome plasticity of a Populus nigra cv. 'Italica' clone widely distributed across Europe. Adult trees from different geographic locations were clonally propagated in a common garden experiment and exposed to cold, heat, drought, herbivory, rust infection, and salicylic acid treatments. Whole-genome bisulfite sequencing revealed stress-induced and naturally occurring DNA methylation variants. In CG/CHG contexts, the same genomic regions were often affected by multiple stresses, suggesting a generic methylome response. Moreover, these variants showed striking overlap with naturally occurring methylation variants between trees from different locations. Drought treatment triggered CHH hypermethylation of transposable elements, affecting entire superfamilies near drought-responsive genes. Thus, we revealed genomic hotspots of methylation change that are not stress-specific and that contribute to natural DNA methylation variation, and identified stress-specific hypermethylation of entire transposon superfamilies with possible functional consequences. Our results underscore the importance of studying multiple stressors in a single experiment for recognizing general versus stress-specific methylome responses.
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Affiliation(s)
- Cristian Peña-Ponton
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Barbara Diez-Rodriguez
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch Strasse 8, D-35043 Marburg, Germany
- Eva Mayr-Stihl professorship of Forest Genetics, Albert-Ludwigs-Universität Freiburg, Bertoldstraße 17, 79098 Freiburg i. Br., Germany
- Natural Resources and Climate Area, CARTIF Technology Centre, 47151 Boecillo, Valladolid, Spain
| | - Paloma Perez-Bello
- IGA Technology Services Srl. Via Jacopo Linussio 51, 33100 Udine UD, Italy
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
| | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32611, USA
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
- Department of Nematology, Wageningen University & Research, Wageningen 6700 ES, The Netherlands
| | - Emanuele De Paoli
- Department of Agri-Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Katrin Heer
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch Strasse 8, D-35043 Marburg, Germany
- Eva Mayr-Stihl professorship of Forest Genetics, Albert-Ludwigs-Universität Freiburg, Bertoldstraße 17, 79098 Freiburg i. Br., Germany
| | - Lars Opgenoorth
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch Strasse 8, D-35043 Marburg, Germany
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
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258
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Kumar S, Singh A, Bist CMS, Sharma M. Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability. Brief Funct Genomics 2024; 23:607-623. [PMID: 38679487 DOI: 10.1093/bfgp/elae017] [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: 02/08/2024] [Revised: 04/03/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Genetic variability is essential for the development of new crop varieties with economically beneficial traits. The traits can be inherited from wild relatives or induced through mutagenesis. Novel genetic elements can then be identified and new gene functions can be predicted. In this study, forward and reverse genetics approaches were described, in addition to their applications in modern crop improvement programs and functional genomics. By using heritable phenotypes and linked genetic markers, forward genetics searches for genes by using traditional genetic mapping and allele frequency estimation. Despite recent advances in sequencing technology, omics and computation, genetic redundancy remains a major challenge in forward genetics. By analyzing close-related genes, we will be able to dissect their functional redundancy and predict possible traits and gene activity patterns. In addition to these predictions, sophisticated reverse gene editing tools can be used to verify them, including TILLING, targeted insertional mutagenesis, gene silencing, gene targeting and genome editing. By using gene knock-down, knock-up and knock-out strategies, these tools are able to detect genetic changes in cells. In addition, epigenome analysis and editing enable the development of novel traits in existing crop cultivars without affecting their genetic makeup by increasing epiallelic variants. Our understanding of gene functions and molecular dynamics of various biological phenomena has been revised by all of these findings. The study also identifies novel genetic targets in crop species to improve yields and stress tolerances through conventional and non-conventional methods. In this article, genetic techniques and functional genomics are specifically discussed and assessed for their potential in crop improvement.
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Affiliation(s)
- Surender Kumar
- Department of Biotechnology, College of Horticulture, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
| | - Anupama Singh
- Department of Biotechnology, College of Horticulture, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
| | - Chander Mohan Singh Bist
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla-171001, Himachal Pradesh, India
| | - Munish Sharma
- Department of Plant Sciences, Central University of Himachal Pradesh, Dharamshala-176215, Himachal Pradesh, India
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259
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Hong CKY, Wu Y, Erickson AA, Li J, Federico AJ, Cohen BA. Massively parallel characterization of insulator activity across the genome. Nat Commun 2024; 15:8350. [PMID: 39333469 PMCID: PMC11436800 DOI: 10.1038/s41467-024-52599-6] [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: 01/09/2024] [Accepted: 09/15/2024] [Indexed: 09/29/2024] Open
Abstract
A key question in regulatory genomics is whether cis-regulatory elements (CREs) are modular elements that can function anywhere in the genome, or whether they are adapted to certain genomic locations. To distinguish between these possibilities we develop MPIRE (Massively Parallel Integrated Regulatory Elements), a technology for recurrently assaying CREs at thousands of defined locations across the genome in parallel. MPIRE allows us to separate the intrinsic activity of CREs from the effects of their genomic environments. We apply MPIRE to assay three insulator sequences at thousands of genomic locations and find that each insulator functions in locations with distinguishable properties. All three insulators can block enhancers, but each insulator blocks specific enhancers at specific locations. However, only ALOXE3 appears to block heterochromatin silencing. We conclude that insulator function is highly context dependent and that MPIRE is a robust method for revealing the context dependencies of CREs.
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Affiliation(s)
- Clarice K Y Hong
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
| | - Yawei Wu
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
| | - Alyssa A Erickson
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
| | - Jie Li
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
| | - Arnold J Federico
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
| | - Barak A Cohen
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA.
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA.
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260
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Uribe-Salazar JM, Kaya G, Weyenberg KB, Radke B, Hino KK, Soto DC, Shiu JL, Zhang W, Ingamells C, Haghani NK, Xu E, Rosas J, Simó S, Miesfeld J, Glaser T, Baraban SC, Jao LEC, Dennis MY. Zebrafish models of human-duplicated SRGAP2 reveal novel functions in microglia and visual system development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.11.612570. [PMID: 39314374 PMCID: PMC11418993 DOI: 10.1101/2024.09.11.612570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
SRGAP2C has been implicated in contributing to altered brain features in the evolution of humans. However, the significance of SRGAP2 duplication beyond neocortex development has not been elucidated due to the embryonic lethality of complete Srgap2 knockout in mice. Using zebrafish, we show that srgap2 knockout results in viable offspring that phenocopy "humanized" SRGAP2C larvae. Morphometric, behavioral, and transcriptome analyses collectively suggest srgap2 impacts axonal guidance, synaptogenesis, and seizure susceptibility. Beyond neurons, Srgap2 functions in controlling membrane dynamics and maturation of microglial cells, possibly leading to altered axonogenesis in the developing retina and increased sensitivity to broad and fine visual cues. Comparing relevant transcriptomes between human and nonhuman primates suggests that SRGAP2C similarly impacts microglia and vision in modern humans. Our functional characterization of conserved ortholog Srgap2 and human SRGAP2C in zebrafish uncovered novel gene functions and highlights the strength of cross-species analysis in understanding the development of human-specific features.
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261
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Chaturvedi P, Belmont AS. Nuclear speckle biology: At the cross-roads of discovery and functional analysis. Curr Opin Cell Biol 2024; 91:102438. [PMID: 39340981 DOI: 10.1016/j.ceb.2024.102438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 08/16/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024]
Affiliation(s)
- Pankaj Chaturvedi
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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262
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Jing X, Zhang N, Zhou X, Chen P, Gong J, Zhang K, Wu X, Cai W, Ye BC, Hao P, Zhao GP, Yang S, Li X. Creating a bacterium that forms eukaryotic nucleosome core particles. Nat Commun 2024; 15:8283. [PMID: 39333491 PMCID: PMC11436726 DOI: 10.1038/s41467-024-52484-2] [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: 06/15/2024] [Accepted: 09/10/2024] [Indexed: 09/29/2024] Open
Abstract
The nucleosome is one of the hallmarks of eukaryotes, a dynamic platform that supports many critical functions in eukaryotic cells. Here, we engineer the in vivo assembly of the nucleosome core in the model bacterium Escherichia coli. We show that bacterial chromosome DNA and eukaryotic histones can assemble in vivo to form nucleosome complexes with many features resembling those found in eukaryotes. The formation of nucleosomes in E. coli was visualized with atomic force microscopy and using tripartite split green fluorescent protein. Under a condition that moderate histones expression was induced at 1 µM IPTG, the nucleosome-forming bacterium is viable and has sustained growth for at least 110 divisions in longer-term growth experiments. It exhibits stable nucleosome formation, a consistent transcriptome across passages, and reduced growth fitness under stress conditions. In particular, the nucleosome arrays in E. coli genic regions have profiles resembling those in eukaryotic cells. The observed compatibility between the eukaryotic nucleosome and the bacterial chromosome machinery may reflect a prerequisite for bacteria-archaea union, providing insight into eukaryogenesis and the origin of the nucleosome.
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Grants
- This work was supported in part by the National Natural Science Foundation of China (32393971 awarded to X.J., 92451303 and 32270719 awarded to X.L., 32200093 awarded to P.C.), the National Key R&D Program of China (2023ZD04073 awarded to X.L.), the National Science and Technology Major Projects (2018YFA0903700 awarded to X.J., 2019YFA0904600 awarded to Yan Zhu), and the Strategic Projects of the Chinese Academy of Sciences (XDA24010403 awarded to X.L.). We thank Fan Gong at the National Facility for Protein Science in Shanghai (NFPS), Shanghai Advanced Research Institute, CAS, for technical support with AFM experiments, and Yuan Yuan Gao, Shanshan Wang, Lianyan Jing, and Xiaoyan Xu at the core facility of the Center for Excellence in Molecular Plant Sciences (CEMPS) for assistance with LC-MS/MS experiments.
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Affiliation(s)
- Xinyun Jing
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Niubing Zhang
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiaojuan Zhou
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ping Chen
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jie Gong
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kaixiang Zhang
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xueting Wu
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenjuan Cai
- Core Facility Center, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bang-Ce Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Pei Hao
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Guo-Ping Zhao
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Lauretta ML, Jarmolowicz A, Amor DJ, Best S, Morgan AT. An Investigation of Barriers and Enablers for Genetics in Speech-Language Pathology Explored Through a Case Study of Childhood Apraxia of Speech. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2024; 67:3437-3451. [PMID: 37713535 DOI: 10.1044/2023_jslhr-22-00714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
PURPOSE Advancements in genetic testing and analysis have allowed improved identification of the genetic basis of childhood apraxia of speech, a rare speech presentation. This study aimed to understand speech-language pathologists' (SLPs') consideration of incorporation of genetics in clinical practice using a theory-informed qualitative approach. METHOD Semistructured interviews were conducted with 12 pediatric SLPs using a behavior change theory (Theoretical Domains Framework [TDF]) within a case study describing a child with complex co-occurring features, including childhood apraxia of speech. Interviews focused on three stages of the patient journey (prereferral, referral, and postreferral). Interviews were analyzed to identify barriers and enablers to considering incorporation of genetics in current clinical practice. Barriers and enablers were grouped and mapped onto a contextually relevant TDF-coded analysis framework. RESULTS Barriers were identified across several TDF domains, through all stages of the patient journey. Lack of confidence, relevance, and level of experience were most common prereferral, and connection to and awareness of genetics services and contextual factors were barriers in the referral stage. Perception of professional role, knowledge, and beliefs about effects on families were barriers postreferral. Associated enablers were also identified, including seeing value in genetic diagnosis, support from other health care professionals, supervision, and relationships with genetics services. CONCLUSIONS Results of this qualitative study highlight barriers and enablers to incorporating genetics into speech-language pathology clinical practice. These findings will assist in the development of theory-informed implementation strategies to support SLPs into the future. SUPPLEMENTAL MATERIAL https://doi.org/10.23641/asha.24112800.
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Affiliation(s)
| | - Anna Jarmolowicz
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - David J Amor
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
- Royal Children's Hospital, Parkville, Victoria, Australia
| | - Stephanie Best
- Australian Genomics, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Health Services Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Victorian Comprehensive Cancer Centre Alliance, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Angela T Morgan
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
- Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, St. Lucia, Australia
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264
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Vaishalli PM, Das R, Cheema HS, Ghosh S, Chandana M, Anand A, Murmu KC, Padmanaban G, Ravindran B, Arun Nagaraj V. Plasmodium berghei HMGB1 controls the host immune responses and splenic clearance by regulating the expression of pir genes. J Biol Chem 2024:107829. [PMID: 39341498 DOI: 10.1016/j.jbc.2024.107829] [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: 08/14/2024] [Revised: 09/11/2024] [Accepted: 09/12/2024] [Indexed: 10/01/2024] Open
Abstract
High mobility group box (HMGB) proteins belong to high mobility group (HMG) superfamily of non-histone nuclear proteins that are involved in chromatin remodeling, regulation of gene expression and DNA repair. When extracellular, HMGBs serve as alarmins inducing inflammation and this is attributed to the proinflammatory activity of box B. Here, we show that Plasmodium HMGB1 has key amino acid changes in box B resulting in the loss of TNF-α stimulatory activity. Site-directed mutagenesis of the critical amino acids in box B with respect to mouse HMGB1 renders recombinant Plasmodium berghei (Pb) HMGB1 capable of inducing TNF-α release. Targeted deletion of PbHMGB1 and a detailed in vivo phenotyping show that PbHMGB1 knockout (KO) parasites can undergo asexual stage development. Interestingly, Balb/c mice-infected with PbHMGB1KO parasites display a protective phenotype with subsequent clearance of blood parasitemia, and develop long-lasting protective immunity against the challenges performed with Pb wildtype parasites. The characterization of splenic responses show prominent germinal centres leading to effective humoral responses and enhanced T follicular helper cells. There is also a complete protection from experimental cerebral malaria in CBA/CaJ mice susceptible for cerebral pathogenesis with subsequent parasite clearance. Transcriptomic studies suggest the involvement of PbHMGB1 in pir expression. Our findings highlight the gene regulatory function of parasite HMGB1 and its in vivo significance in modulating the host immune responses. Further, clearance of asexual stages in PbHMGB1KO-infected mice underscores the important role of parasite HMGB1 in host immune evasion. These findings have implications in developing attenuated blood-stage vaccine for malaria.
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Affiliation(s)
- Pradeep Mini Vaishalli
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar - 751023, Odisha, India; Regional Centre for Biotechnology, Faridabad - 121001, Haryana, India
| | - Rahul Das
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar - 751023, Odisha, India; Regional Centre for Biotechnology, Faridabad - 121001, Haryana, India
| | - Harveer Singh Cheema
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar - 751023, Odisha, India; Meerut College, Meerut - 250003, Uttar Pradesh, India
| | - Sourav Ghosh
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar - 751023, Odisha, India; Regional Centre for Biotechnology, Faridabad - 121001, Haryana, India
| | - Manjunatha Chandana
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar - 751023, Odisha, India
| | - Aditya Anand
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar - 751023, Odisha, India; Regional Centre for Biotechnology, Faridabad - 121001, Haryana, India
| | | | - Govindarajan Padmanaban
- Department of Biochemistry, Indian Institute of Science, Bangalore - 560012, Karnataka, India
| | - Balachandran Ravindran
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar - 751023, Odisha, India
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De-Paula RB, Bacolla A, Syed A, Tainer JA. Enriched G4 forming repeats in the human genome are associated with robust well-coordinated transcription and reduced cancer transcriptome variation. J Biol Chem 2024:107822. [PMID: 39341500 DOI: 10.1016/j.jbc.2024.107822] [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: 05/24/2024] [Revised: 09/01/2024] [Accepted: 09/21/2024] [Indexed: 10/01/2024] Open
Abstract
Non-B DNA G-quadruplex (G4) structures with guanine (G) runs of 2-4 repeats can trigger opposing experimental transcriptional impacts. Here, we employed bioinformatic algorithms to comprehensively assess correlations of steady-state RNA transcript levels with all putative G4 sequence (pG4) locations genome-wide in three mammalian genomes and in normal and tumor human tissues. The human pG4-containing gene set displays higher expression levels than the set without pG4, supporting and extending some prior observations. pG4 enrichment at transcription start sites (TSS) in human, but not chimpanzee and mouse genomes, suggests possible positive selection pressure for pG4 at human TSS, potentially driving genome rewiring and gene expression divergence between human and chimpanzee. Comprehensive bioinformatic analyses revealed lower pG4-containing gene set variability in humans and among different pG4 genes in tumors. As G4 stabilizers are under therapeutic consideration for cancer and pathogens, such distinctions between human normal and tumor G4s along with other species merit attention. Furthermore, in germline and cancer sequences, the most mutagenic pG4 mapped to regions promoting alternative DNA structures. Overall findings establish high pG4 at TSS as a human genome attribute statistically associated with robust well-coordinated transcription and reduced cancer transcriptome variation with implications for biology, model organisms, and medicine.
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Affiliation(s)
- Ruth B De-Paula
- Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Aleem Syed
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Bhat AA, Afzal M, Moglad E, Thapa R, Ali H, Almalki WH, Kazmi I, Alzarea SI, Gupta G, Subramaniyan V. lncRNAs as prognostic markers and therapeutic targets in cuproptosis-mediated cancer. Clin Exp Med 2024; 24:226. [PMID: 39325172 PMCID: PMC11427524 DOI: 10.1007/s10238-024-01491-0] [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: 08/11/2024] [Accepted: 09/16/2024] [Indexed: 09/27/2024]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as crucial regulators in various cellular processes, including cancer progression and stress response. Recent studies have demonstrated that copper accumulation induces a unique form of cell death known as cuproptosis, with lncRNAs playing a key role in regulating cuproptosis-associated pathways. These lncRNAs may trigger cell-specific responses to copper stress, presenting new opportunities as prognostic markers and therapeutic targets. This paper delves into the role of lncRNAs in cuproptosis-mediated cancer, underscoring their potential as biomarkers and targets for innovative therapeutic strategies. A thorough review of scientific literature was conducted, utilizing databases such as PubMed, Google Scholar, and ScienceDirect, with search terms like 'lncRNAs,' 'cuproptosis,' and 'cancer.' Studies were selected based on their relevance to lncRNA regulation of cuproptosis pathways and their implications for cancer prognosis and treatment. The review highlights the significant contribution of lncRNAs in regulating cuproptosis-related genes and pathways, impacting copper metabolism, mitochondrial stress responses, and apoptotic signaling. Specific lncRNAs are potential prognostic markers in breast, lung, liver, ovarian, pancreatic, and gastric cancers. The objective of this article is to explore the role of lncRNAs as potential prognostic markers and therapeutic targets in cancers mediated by cuproptosis.
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Affiliation(s)
- Asif Ahmad Bhat
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, 21442, Jeddah, Saudi Arabia
| | - Ehssan Moglad
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, 11942, Al Kharj, Saudi Arabia
| | - Riya Thapa
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Haider Ali
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
- Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, 72341, Sakaka, Aljouf, Saudi Arabia
| | - Gaurav Gupta
- Centre for Research Impact & Outcome, Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, 140401, India
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Vetriselvan Subramaniyan
- Pharmacology Unit, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia.
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267
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Ewerling A, May-Simera HL. Evolutionary trajectory for nuclear functions of ciliary transport complex proteins. Microbiol Mol Biol Rev 2024; 88:e0000624. [PMID: 38995044 PMCID: PMC11426024 DOI: 10.1128/mmbr.00006-24] [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: 07/13/2024] Open
Abstract
SUMMARYCilia and the nucleus were two defining features of the last eukaryotic common ancestor. In early eukaryotic evolution, these structures evolved through the diversification of a common membrane-coating ancestor, the protocoatomer. While in cilia, the descendants of this protein complex evolved into parts of the intraflagellar transport complexes and BBSome, the nucleus gained its selectivity by recruiting protocoatomer-like proteins to the nuclear envelope to form the selective nuclear pore complexes. Recent studies show a growing number of proteins shared between the proteomes of the respective organelles, and it is currently unknown how ciliary transport proteins could acquire nuclear functions and vice versa. The nuclear functions of ciliary proteins are still observable today and remain relevant for the understanding of the disease mechanisms behind ciliopathies. In this work, we review the evolutionary history of cilia and nucleus and their respective defining proteins and integrate current knowledge into theories for early eukaryotic evolution. We postulate a scenario where both compartments co-evolved and that fits current models of eukaryotic evolution, explaining how ciliary proteins and nucleoporins acquired their dual functions.
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Affiliation(s)
- Alexander Ewerling
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
| | - Helen Louise May-Simera
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
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268
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Qiu GH, Fu M, Zheng X, Huang C. Protection of the genome and the central exome by peripheral non-coding DNA against DNA damage in health, ageing and age-related diseases. Biol Rev Camb Philos Soc 2024. [PMID: 39327815 DOI: 10.1111/brv.13151] [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: 09/26/2023] [Revised: 09/15/2024] [Accepted: 09/18/2024] [Indexed: 09/28/2024]
Abstract
DNA in eukaryotic genomes is under constant assault from both exogenous and endogenous sources, leading to DNA damage, which is considered a major molecular driver of ageing. Fortunately, the genome and the central exome are safeguarded against these attacks by abundant peripheral non-coding DNA. Non-coding DNA codes for small non-coding RNAs that inactivate foreign nucleic acids in the cytoplasm and physically blocks these attacks in the nucleus. Damage to non-coding DNA produced during such blockage is removed in the form of extrachromosomal circular DNA (eccDNA) through nucleic pore complexes. Consequently, non-coding DNA serves as a line of defence for the exome against DNA damage. The total amount of non-coding DNA/heterochromatin declines with age, resulting in a decrease in both physical blockage and eccDNA exclusion, and thus an increase in the accumulation of DNA damage in the nucleus during ageing and in age-related diseases. Here, we summarize recent evidence supporting a protective role of non-coding DNA in healthy and pathological states and argue that DNA damage is the proximate cause of ageing and age-related genetic diseases. Strategies aimed at strengthening the protective role of non-coding DNA/heterochromatin could potentially offer better systematic protection for the dynamic genome and the exome against diverse assaults, reduce the burden of DNA damage to the exome, and thus slow ageing, counteract age-related genetic diseases and promote a healthier life for individuals.
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Affiliation(s)
- Guo-Hua Qiu
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
| | - Mingjun Fu
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
| | - Xintian Zheng
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
| | - Cuiqin Huang
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
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269
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Ribeiro JC, Rodrigues BC, Bernardino RL, Alves MG, Oliveira PF. The interactome of cystic fibrosis transmembrane conductance regulator and its role in male fertility: A critical review. J Cell Physiol 2024:e31422. [PMID: 39324358 DOI: 10.1002/jcp.31422] [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: 06/12/2024] [Revised: 08/06/2024] [Accepted: 08/13/2024] [Indexed: 09/27/2024]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is a cyclic adenosine monophosphate (cAMP)-regulated chloride and bicarbonate ion channel found in many human cells. Its unique biochemical characteristics and role as a member of the adenosine triphosphate (ATP)-binding cassette transporters superfamily are pivotal for the transport of several substrates across cellular membranes. CFTR is known to interact, physically and functionally, with several other cellular proteins. Hence, its properties are essential for moving various substances across cell membranes and ensuring correct cell functioning. Genetic mutations or environmental factors may disrupt CFTR's function resulting in different possible phenotypes due to gene variations that affect not only CFTR's function, localization, and processing within cells, but also those of its interactors. This has been reported as an underlying cause of various diseases, including cystic fibrosis. The severe clinical implications of cystic fibrosis have driven intense research into the role of CFTR in lung function but its significance to fertility, particularly in men, has been comparatively understudied. However, ongoing and more recent research into CFTR and its interacting proteins in the testis or specific testicular cells is beginning to shed light on this field. Herein, we provide a comprehensive and up-to-date overview of the CFTR, its interactome, and its crucial role in male reproduction, highlighting recent discoveries and advancements in understanding the molecular mechanisms involved. The comprehension of these complex interactions may pave the way for potential therapeutic approaches to improve fertility of men suffering from alterations in the function of CFTR.
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Affiliation(s)
- João C Ribeiro
- Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), University of Porto, Porto, Portugal
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Bernardo C Rodrigues
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Raquel L Bernardino
- Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), University of Porto, Porto, Portugal
| | - Marco G Alves
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), Aveiro, Portugal
| | - Pedro F Oliveira
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, Aveiro, Portugal
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Aswani BS, Hegde M, Vishwa R, Alqahtani MS, Abbas M, Almubarak HA, Sethi G, Kunnumakkara AB. Tackling exosome and nuclear receptor interaction: an emerging paradigm in the treatment of chronic diseases. Mil Med Res 2024; 11:67. [PMID: 39327610 PMCID: PMC11426102 DOI: 10.1186/s40779-024-00564-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 08/06/2024] [Indexed: 09/28/2024] Open
Abstract
Nuclear receptors (NRs) function as crucial transcription factors in orchestrating essential functions within the realms of development, host defense, and homeostasis of body. NRs have garnered increased attention due to their potential as therapeutic targets, with drugs directed at NRs demonstrating significant efficacy in impeding chronic disease progression. Consequently, these pharmacological agents hold promise for the treatment and management of various diseases. Accumulating evidence emphasizes the regulatory role of exosome-derived microRNAs (miRNAs) in chronic inflammation, disease progression, and therapy resistance, primarily by modulating transcription factors, particularly NRs. By exploiting inflammatory pathways such as protein kinase B (Akt)/mammalian target of rapamycin (mTOR), nuclear factor kappa-B (NF-κB), signal transducer and activator of transcription 3 (STAT3), and Wnt/β-catenin signaling, exosomes and NRs play a pivotal role in the panorama of development, physiology, and pathology. The internalization of exosomes modulates NRs and initiates diverse autocrine or paracrine signaling cascades, influencing various processes in recipient cells such as survival, proliferation, differentiation, metabolism, and cellular defense mechanisms. This comprehensive review meticulously examines the involvement of exosome-mediated NR regulation in the pathogenesis of chronic ailments, including atherosclerosis, cancer, diabetes, liver diseases, and respiratory conditions. Additionally, it elucidates the molecular intricacies of exosome-mediated communication between host and recipient cells via NRs, leading to immunomodulation. Furthermore, it outlines the implications of exosome-modulated NR pathways in the prophylaxis of chronic inflammation, delineates current limitations, and provides insights into future perspectives. This review also presents existing evidence on the role of exosomes and their components in the emergence of therapeutic resistance.
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Affiliation(s)
- Babu Santha Aswani
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, 781039, Assam, India
| | - Mangala Hegde
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, 781039, Assam, India
| | - Ravichandran Vishwa
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, 781039, Assam, India
| | - Mohammed S Alqahtani
- Radiological Sciences Department, College of Applied Medical Sciences, King Khalid University, 61421, Abha, Saudi Arabia
- BioImaging Unit, Space Research Centre, Michael Atiyah Building, University of Leicester, Leicester, LE1 7RH, UK
| | - Mohamed Abbas
- Electrical Engineering Department, College of Engineering, King Khalid University, 61421, Abha, Saudi Arabia
| | - Hassan Ali Almubarak
- Division of Radiology, Department of Medicine, College of Medicine and Surgery, King Khalid University, 61421, Abha, Saudi Arabia
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117699, Singapore.
| | - Ajaikumar B Kunnumakkara
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, 781039, Assam, India.
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Campos-Sánchez JC, Meseguer J, Guardiola FA. Fish microglia: Beyond the resident macrophages of the central nervous system - A review of their morphofunctional characteristics. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 162:105274. [PMID: 39341477 DOI: 10.1016/j.dci.2024.105274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 09/25/2024] [Accepted: 09/25/2024] [Indexed: 10/01/2024]
Abstract
From classical to modern literature on microglia, the importance of the potential and variability of these immune cells in vertebrates has been pointed out. Recent aspects such as relationships and interactions between microglia and neurons in both normal and injured neural tissues, as well as their nexus with other organs and with the microbiota, or how these cells are modulated during development and adulthood are current topics of major interest. State-of-the-art research methodologies, including microscopy and potent in vivo imaging techniques, genomic and proteomic methods, current culture conditions together with the easy maintenance and manipulation of some fish embryos and adult specimens such as zebrafish (Danio rerio), have emerged and adapted to the phylogenetic position of some fish species. Furthermore, these advancements have facilitated the development of successful protocols aimed at addressing significant hypotheses and unresolved questions regarding vertebrate glia. The present review aims to analyse the available information on fish microglia, mainly the most recent one concerning teleosts, to establish an overview of their structural and immune functional features as a basis for their potentialities, heterogeneity, diversification, involvement, and relationships with neurons under normal and pathological conditions.
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Affiliation(s)
- Jose Carlos Campos-Sánchez
- Immunobiology for Aquaculture Group, Department of Cell Biology and Histology, Faculty of Biology, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", University of Murcia, 30100, Murcia, Spain
| | - José Meseguer
- Immunobiology for Aquaculture Group, Department of Cell Biology and Histology, Faculty of Biology, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", University of Murcia, 30100, Murcia, Spain
| | - Francisco A Guardiola
- Immunobiology for Aquaculture Group, Department of Cell Biology and Histology, Faculty of Biology, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", University of Murcia, 30100, Murcia, Spain.
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272
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Samanta P, Ghosh R, Pakhira S, Mondal M, Biswas S, Sarkar R, Bhowmik A, Saha P, Hajra S. Ribosome biogenesis and ribosomal proteins in cancer stem cells: a new therapeutic prospect. Mol Biol Rep 2024; 51:1016. [PMID: 39325314 DOI: 10.1007/s11033-024-09963-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: 08/13/2024] [Accepted: 09/20/2024] [Indexed: 09/27/2024]
Abstract
Ribosome has been considered as the fundamental macromolecular machine involved in protein synthesis in both prokaryotic and eukaryotic cells. This protein synthesis machinery consists of several rRNAs and numerous proteins. All of these factors are synthesized, translocated and assembled in a tightly regulated process known as ribosome biogenesis. Any impairment in this process causes development of several diseases like cancer. According to growing evidences, cancer cells display alteration of several ribosomal proteins. Besides, most of them are considered as key molecules involved in ribosome biogenesis, suggesting a correlation between those proteins and formation of ribosomes. Albeit, defective ribosome biogenesis in several cancers has gained prime importance, regulation of this process in cancer stem cells (CSCs) are still unrecognized. In this article, we aim to summarize the alteration of ribosome biogenesis and ribosomal proteins in CSCs. Moreover, we want to highlight the relation of ribosome biogenesis with hypoxia and drug resistance in CSCs based on the existing evidences. Lastly, this review wants to pay attention about the promising anti-cancer drugs which have potential to inhibit ribosome biogenesis in cancer cells as well as CSCs.
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Affiliation(s)
- Priya Samanta
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Rituparna Ghosh
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Shampa Pakhira
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Mrinmoyee Mondal
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Souradeep Biswas
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Rupali Sarkar
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Arijit Bhowmik
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Prosenjit Saha
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Subhadip Hajra
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India.
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273
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Gao AYL, Inglebert Y, Shi R, Ilie A, Popic J, Mustian J, Sonenberg N, Orlowski J, McKinney RA. Impaired hippocampal plasticity associated with loss of recycling endosomal SLC9A6/NHE6 is ameliorated by the TrkB agonist 7,8-dihydroxyflavone. Biochim Biophys Acta Mol Basis Dis 2024:167529. [PMID: 39341363 DOI: 10.1016/j.bbadis.2024.167529] [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: 05/05/2024] [Revised: 08/31/2024] [Accepted: 09/24/2024] [Indexed: 10/01/2024]
Abstract
Proper maintenance of intracellular vesicular pH is essential for cargo trafficking during synaptic function and plasticity. Mutations in the SLC9A6 gene encoding the recycling endosomal pH regulator (Na+, K+)/H+ exchanger isoform 6 (NHE6) are causal for Christianson syndrome (CS), a severe form of X-linked intellectual disability. NHE6 expression is also downregulated in other neurodevelopmental and neurodegenerative disorders, such as autism spectrum disorder and Alzheimer's disease, suggesting its dysfunction could contribute more broadly to the pathophysiology of other neurological conditions. To understand how ablation of NHE6 function leads to severe learning impairments, we assessed synaptic structure, function, and cellular mechanisms of learning in a novel line of Nhe6 knockout (KO) mice expressing a plasma membrane-tethered green fluorescent protein within hippocampal neurons. We uncovered significant reductions in dendritic spines density, AMPA receptor (AMPAR) expression, and AMPAR-mediated neurotransmission in CA1 pyramidal neurons. The neurons also failed to undergo functional and structural enhancement during long-term potentiation (LTP). Significantly, the selective TrkB agonist 7,8-dihydroxyflavone restored spine density as well as functional and structural LTP in KO neurons. TrkB activation thus may act as a potential clinical intervention to ameliorate cognitive deficits in CS and other neurodegenerative disorders.
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Affiliation(s)
- Andy Y L Gao
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Canada
| | - Yanis Inglebert
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Canada
| | - Roy Shi
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Canada
| | - Alina Ilie
- Department of Physiology, McGill University, Montreal, Canada
| | - Jelena Popic
- Department of Biochemistry, McGill University, Montreal, Canada
| | - Jamie Mustian
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal, Canada
| | - John Orlowski
- Department of Physiology, McGill University, Montreal, Canada
| | - R Anne McKinney
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Canada.
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274
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Ye Y, Cao Z. Glucose Metabolism and Glucose Transporters in Head and Neck Squamous Cell Carcinoma. Cancer Invest 2024:1-18. [PMID: 39324504 DOI: 10.1080/07357907.2024.2407424] [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: 05/11/2024] [Accepted: 09/18/2024] [Indexed: 09/27/2024]
Abstract
Head and neck squamous cell carcinoma ranks seventh globally in malignancy prevalence, with persistent high mortality rates despite treatment advancements. Glucose, pivotal in cancer metabolism via the Warburg effect, enters cells via glucose transporters, notably GLUT proteins. Glycolysis, aerobic oxidation, and the pentose phosphate pathway in glucose metabolism significantly impact HNSCC progression. HNSCC exhibits elevated expression of glucose metabolism enzymes and GLUT proteins, correlating with prognosis. Heterogeneity in HNSCC yields varied metabolic profiles, influenced by factors like HPV status and disease stage. This review highlights glucose metabolism's role and potential as therapeutic targets and cancer imaging tracers in HNSCC.
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Affiliation(s)
- Yanyan Ye
- Department of Otolaryngology, Shulan (Hangzhou) Hospital, affiliated to Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Zaizai Cao
- Department of Otolaryngology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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275
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Haase AD, Ketting RF, Lai EC, van Rij RP, Siomi M, Svoboda P, van Wolfswinkel JC, Wu PH. PIWI-interacting RNAs: who, what, when, where, why, and how. EMBO J 2024:10.1038/s44318-024-00253-8. [PMID: 39327528 DOI: 10.1038/s44318-024-00253-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 09/16/2024] [Indexed: 09/28/2024] Open
Affiliation(s)
- Astrid D Haase
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Rene F Ketting
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, USA
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mikiko Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Petr Svoboda
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Pei-Hsuan Wu
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.
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276
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Smith P, Carroll B. Senescence in the ageing skin: a new focus on mTORC1 and the lysosome. FEBS J 2024. [PMID: 39325694 DOI: 10.1111/febs.17281] [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: 04/10/2024] [Revised: 07/23/2024] [Accepted: 09/09/2024] [Indexed: 09/28/2024]
Abstract
Ageing is defined as the progressive loss of tissue function and regenerative capacity and is caused by both intrinsic factors i.e. the natural accumulation of damage, and extrinsic factors i.e. damage from environmental stressors. Cellular senescence, in brief, is an irreversible exit from the cell cycle that occurs primarily in response to excessive cellular damage, such as from ultraviolet (UV) exposure and oxidative stress, and it has been comprehensively demonstrated to contribute to tissue and organismal ageing. In this review, we will focus on the skin, an organ which acts as an essential protective barrier against injury, insults, and infection. We will explore the evidence for the existence and contribution of cellular senescence to skin ageing. We discuss the known molecular mechanisms driving senescence in the skin, with a focus on the dysregulation of the master growth regulator, mechanistic Target of Rapamycin Complex 1 (mTORC1). We explore the interplay of dysregulated mTORC1 with lysosomes and how they contribute to senescence phenotypes.
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277
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Ribeiro AF, Fitas AL, Pires MO, Matoso P, Ligeiro D, Sobral D, Penha-Gonçalves C, Demengeot J, Caramalho Í, Limbert C. Whole Exome Sequencing in Children With Type 1 Diabetes Before Age 6 Years Reveals Insights Into Disease Heterogeneity. J Diabetes Res 2024; 2024:3076895. [PMID: 39364395 PMCID: PMC11449554 DOI: 10.1155/2024/3076895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/04/2024] [Accepted: 08/24/2024] [Indexed: 10/05/2024] Open
Abstract
Aims: This study is aimed at comparing whole exome sequencing (WES) data with the clinical presentation in children with type 1 diabetes onset ≤ 5 years of age (EOT1D). Methods: WES was performed in 99 unrelated children with EOT1D with subsequent analysis to identify potentially deleterious rare variants in MODY genes. High-resolution HLA class II haplotyping, SNP genotyping, and T1D-genetic risk score (T1D-GRS) were also evaluated. Results: Eight of the ninety-nine EOT1D participants carried a potentially deleterious rare variant in a MODY gene. Rare variants affected five genes: GCK (n = 1), HNF1B (n = 2), HNF4A (n = 1), PDX1 (n = 2), and RFX6 (n = 2). At diagnosis, these children had a mean age of 3.0 years, a mean HbA1c of 10.5%, a detectable C-peptide in 5/8, and a positive islet autoantibody in 6/7. Children with MODY variants tend to exhibit a lower number of pancreatic autoantibodies and a lower fasting C-peptide compared to EOT1D without MODY rare variants. They also carried at least one high-risk DR3-DQ2 or DR4-DQ8 haplotype and exhibited a T1D-GRS similar to the other individuals in the EOT1D cohort, but higher than healthy controls. Conclusions: WES found potentially deleterious rare variants in MODY genes in 8.1% of EOT1D, occurring in the context of a T1D genetic background. Such genetic variants may contribute to disease precipitation by a β-cell dysfunction mechanism. This supports the concept of different endotypes of T1D, and WES at T1D onset may be a prerequisite for the implementation of precision therapies in children with autoimmune diabetes.
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Affiliation(s)
- Andreia Fiúza Ribeiro
- Pediatric Endocrinology UnitHospital de Dona EstefâniaSão José Local Health Unit, Lisbon, Portugal
- Pediatric DepartmentHospital Prof. Doutor Fernando FonsecaAmadora Sintra Local Health Unit, Amadora, Portugal
| | - Ana Laura Fitas
- Pediatric Endocrinology UnitHospital de Dona EstefâniaSão José Local Health Unit, Lisbon, Portugal
- Comprehensive Health Research Centre (CHRC)NOVA Medical SchoolUniversidade NOVA de Lisboa, Lisbon, Portugal
| | - Marcela Oliveira Pires
- Pediatric Endocrinology UnitHospital de Dona EstefâniaSão José Local Health Unit, Lisbon, Portugal
- Pediatric DepartmentHospital de São Francisco XavierLisboa Ocidental Local Health Unit, Lisbon, Portugal
| | - Paula Matoso
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Dário Ligeiro
- Blood and Transplantation Center of LisbonInstituto Português do Sangue e da Transplantação, Lisbon, Portugal
- Immunosurgery UnitChampalimaud Foundation, Lisbon, Portugal
| | | | | | | | - Íris Caramalho
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Faculty of SciencesUniversity of Lisbon, Lisbon, Portugal
| | - Catarina Limbert
- Pediatric Endocrinology UnitHospital de Dona EstefâniaSão José Local Health Unit, Lisbon, Portugal
- Comprehensive Health Research Centre (CHRC)NOVA Medical SchoolUniversidade NOVA de Lisboa, Lisbon, Portugal
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278
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Irene B, Andrea D, Pia CM, Gianluca C, Gianluca DG, Evelina S, Marco C, Francesco B, Andrea L, Alessandro P, Silvia M, Giovanni C, Paola G. An inherited TBX3 alteration in a prenatal case of ulnar-mammary syndrome: Clinical assessment and functional characterization in Drosophila melanogaster. J Cell Physiol 2024:e31440. [PMID: 39320041 DOI: 10.1002/jcp.31440] [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: 03/11/2024] [Revised: 09/03/2024] [Accepted: 09/09/2024] [Indexed: 09/26/2024]
Abstract
Ulnar mammary syndrome (UMS) results from heterozygous variants in the TBX3 gene and impacts limb, tooth, hair, apocrine gland, and genitalia development. The expressivity of UMS is highly variable with no established genotype-phenotype correlations. TBX3 belongs to the Tbx gene family, which encodes transcription factors characterized by the presence of a T-box DNA-binding domain. We describe a fetus exhibiting severe upper limb defects and harboring the novel TBX3:c.400 C > T (p.P134S) variant inherited from the mother who remained clinically misdiagnosed until prenatal diagnosis. Literature revision was conducted to uncover the TBX3 clinical and mutational spectrum. Moreover, we generated a Drosophila humanized model for TBX3 to study the developmental consequences of the p.P134S as well as of other variants targeting different regions of the protein. Phenotypic analysis in flies, coupled with in silico modeling on the TBX3 variants, suggested that the c.400 C > T is UMS-causing and impacts TBX3 localization. Comparative analyses of the fly phenotypes caused by the expression of all variants, demonstrated that missense changes in the T-box domain affect more significantly TBX3 activity than variants outside this domain. To improve the clinicians' recognition of UMS, we estimated the frequency of the main clinical features of the disease. Core features often present pre-pubertally include defects of the ulna and/or of ulnar ray, hypoplastic nipples and/or areolas and, less frequently, genitalia anomalies in young males. These results enhance our understanding of the molecular basis and the clinical spectrum of UMS, shedding light on the functional consequences of TBX3 variants in a developmental context.
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Affiliation(s)
- Bottillo Irene
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - D'Alessandro Andrea
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Rome, Italy
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Ciccone Maria Pia
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Cestra Gianluca
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Rome, Italy
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR), Rome, Italy
- Fondazione Santa Lucia IRCCS, c/o CERC, Rome, Italy
| | - Di Giacomo Gianluca
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Silvestri Evelina
- Unit of Fetal and Neonatal Pathology, Division of Pathology, San Camillo-Forlanini Hospital, Rome, Italy
| | - Castori Marco
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Brancati Francesco
- Human Genetics Laboratory, Department of Life, Health and Environmental Sciences, University of L'Aquila, Italy
- San Raffaele Roma IRCCS, Rome, Italy
| | - Lenzi Andrea
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Paiardini Alessandro
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Majore Silvia
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Cenci Giovanni
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Rome, Italy
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Grammatico Paola
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
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279
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Zhang Y, Sun D, Han W, Yang Z, Lu Y, Zhang X, Wang Y, Zhang C, Liu N, Hou H. SMARCA4 mutations and expression in lung adenocarcinoma: prognostic significance and impact on the immunotherapy response. FEBS Open Bio 2024. [PMID: 39322625 DOI: 10.1002/2211-5463.13899] [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: 05/30/2024] [Revised: 08/20/2024] [Accepted: 09/10/2024] [Indexed: 09/27/2024] Open
Abstract
The switch/sucrose non-fermenting (SWI/SNF) complex family includes important chromatin-remodeling factors that are frequently mutated in lung adenocarcinoma (LUAD). However, the role of one family member, SMARCA4, in LUAD prognosis and immunotherapy sensitivity remains unclear. In the present study, 6745 LUAD samples from the cBioPortal database were used to analyze the relationships between SMARCA4 mutations and patient prognoses and clinical characteristics. Additionally, we examined the correlation between SMARCA4 mutations and prognosis in patients treated with immunotherapy using two immune-related datasets. SMARCA4 mutations and low expression were associated with shorter survival, and mutations were associated with a high tumor mutational burden and high microsatellite instability. SMARCA4 mutations were accompanied by KRAS, KEAP1, TP53 and STK11 mutations. No significant difference was observed in the immunotherapy response between patients with and without SMARCA4 mutations. When KRAS or STK11 mutations were present, immunotherapy effectiveness was poorer; however, when both SMARCA4 and TP53 mutations were present, immunotherapy was more effective. Furthermore, low SMARCA4 expression predicted a higher immunophenoscore, and SMARCA4 expression was correlated with certain immune microenvironment features. Taken together, our results suggest that SMARCA4 mutations and low expression might be associated with poor LUAD prognosis. Additionally, immunotherapy efficacy in patients with SMARCA4 mutations depended on the co-mutant genes. Thus, SMARCA4 could be an important factor to be considered for LUAD diagnosis and treatment.
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Affiliation(s)
- Yuming Zhang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, China
| | - Dantong Sun
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weizhong Han
- Department of Respiratory Medicine, The Affiliated Hospital of Qingdao University, China
| | - Zhen Yang
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao University, China
| | - Yongzhi Lu
- Department of Oncology, Qingdao Municipal Hospital, China
| | - Xuchen Zhang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, China
| | - Yongjie Wang
- Department of Thoracic Surgery, The Affiliation Hospital of Qingdao University, China
| | - Chuantao Zhang
- Department of Oncology, The Affiliated Hospital of Qingdao University, China
| | - Ning Liu
- Department of Oncology, The Affiliated Hospital of Qingdao University, China
| | - Helei Hou
- Department of Oncology, The Affiliated Hospital of Qingdao University, China
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280
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Zhao C, Luo J, Zhang Y, Yu Y. Temperature-dependent lifespan extension is achieved in miR-80-deleted Caenorhabditis elegans by NLP-45 to modulate endoplasmic reticulum unfolded protein responses. Aging Cell 2024:e14345. [PMID: 39323014 DOI: 10.1111/acel.14345] [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: 01/02/2024] [Revised: 08/29/2024] [Accepted: 09/05/2024] [Indexed: 09/27/2024] Open
Abstract
MicroRNA plays a crucial role in post-transcriptional gene regulation and has recently emerged as a factor linked to aging, but the underlying regulatory mechanisms remain incompletely understood. In this study, we observed lifespan-extending effects in miR-80-deficient Caenorhabditis elegans at 20°C but not 25°C. At 20°C, miR-80 deletion leads to NLP-45 upregulation, which positively correlates to increased abu transcripts and extended lifespan. Supportively, we identified miR-80 binding regions in the 5' and 3' UTR of nlp-45. As the temperature rises to 25°C, wildtype increases miR-80 levels, but removal of miR-80 is accompanied by decreased nlp-45 expression, suggesting intervention from other temperature-sensitive mechanisms. These findings support the concept that microRNAs and neuropeptide-like proteins can form molecular regulatory networks involving downstream molecules to regulate lifespan, and such regulatory effects vary on environmental conditions. This study unveils the role of an axis of miR-80/NLP-45/UPRER components in regulating longevity, offering new insights on strategies of aging attenuation and health span prolongation.
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Affiliation(s)
- Chunlin Zhao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Jintao Luo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Yuqiang Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Yong Yu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
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281
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Masiero C, Aresi C, Forlino A, Tonelli F. Zebrafish Models for Skeletal and Extraskeletal Osteogenesis Imperfecta Features: Unveiling Pathophysiology and Paving the Way for Drug Discovery. Calcif Tissue Int 2024:10.1007/s00223-024-01282-5. [PMID: 39320469 DOI: 10.1007/s00223-024-01282-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 08/27/2024] [Indexed: 09/26/2024]
Abstract
In the last decades, the easy genetic manipulation, the external fertilization, the high percentage of homology with human genes and the reduced husbandry costs compared to rodents, made zebrafish a valid model for studying human diseases and for developing new therapeutical strategies. Since zebrafish shares with mammals the same bone cells and ossification types, it became widely used to dissect mechanisms and possible new therapeutic approaches in the field of common and rare bone diseases, such as osteoporosis and osteogenesis imperfecta (OI), respectively. OI is a heritable skeletal disorder caused by defects in gene encoding collagen I or proteins/enzymes necessary for collagen I synthesis and secretion. Nevertheless, OI patients can be also characterized by extraskeletal manifestations such as dentinogenesis imperfecta, muscle weakness, cardiac valve and pulmonary abnormalities and skin laxity. In this review, we provide an overview of the available zebrafish models for both dominant and recessive forms of OI. An updated description of all the main similarities and differences between zebrafish and mammal skeleton, muscle, heart and skin, will be also discussed. Finally, a list of high- and low-throughput techniques available to exploit both larvae and adult OI zebrafish models as unique tools for the discovery of new therapeutic approaches will be presented.
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Affiliation(s)
- Cecilia Masiero
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3B, 27100, Pavia, Italy
| | - Carla Aresi
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3B, 27100, Pavia, Italy
| | - Antonella Forlino
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3B, 27100, Pavia, Italy.
| | - Francesca Tonelli
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3B, 27100, Pavia, Italy
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282
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Formstone C, Aldeiri B, Davenport M, Francis-West P. Ventral body wall closure: Mechanistic insights from mouse models and translation to human pathology. Dev Dyn 2024. [PMID: 39319771 DOI: 10.1002/dvdy.735] [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: 12/19/2023] [Revised: 08/17/2024] [Accepted: 08/21/2024] [Indexed: 09/26/2024] Open
Abstract
The ventral body wall (VBW) that encloses the thoracic and abdominal cavities arises by extensive cell movements and morphogenetic changes during embryonic development. These morphogenetic processes include embryonic folding generating the primary body wall; the initial ventral cover of the embryo, followed by directed mesodermal cell migrations, contributing to the secondary body wall. Clinical anomalies in VBW development affect approximately 1 in 3000 live births. However, the cell interactions and critical cellular behaviors that control VBW development remain little understood. Here, we describe the embryonic origins of the VBW, the cellular and morphogenetic processes, and key genes, that are essential for VBW development. We also provide a clinical overview of VBW anomalies, together with environmental and genetic influences, and discuss the insight gained from over 70 mouse models that exhibit VBW defects, and their relevance, with respect to human pathology. In doing so we propose a phenotypic framework for researchers in the field which takes into account the clinical picture. We also highlight cases where there is a current paucity of mouse models for particular clinical defects and key gaps in knowledge about embryonic VBW development that need to be addressed to further understand mechanisms of human VBW pathologies.
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Affiliation(s)
- Caroline Formstone
- Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, Hatfield, UK
| | - Bashar Aldeiri
- Department of Paediatric Surgery, Chelsea and Westminster Hospital, London, UK
| | - Mark Davenport
- Department of Paediatric Surgery, King's College Hospital, London, UK
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283
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Majewski S, Klein P, Boillée S, Clarke BE, Patani R. Towards an integrated approach for understanding glia in Amyotrophic Lateral Sclerosis. Glia 2024. [PMID: 39318236 DOI: 10.1002/glia.24622] [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: 04/17/2024] [Revised: 09/03/2024] [Accepted: 09/15/2024] [Indexed: 09/26/2024]
Abstract
Substantial advances in technology are permitting a high resolution understanding of the salience of glia, and have helped us to transcend decades of predominantly neuron-centric research. In particular, recent advances in 'omic' technologies have enabled unique insights into glial biology, shedding light on the cellular and molecular aspects of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Here, we review studies using omic techniques to attempt to understand the role of glia in ALS across different model systems and post mortem tissue. We also address caveats that should be considered when interpreting such studies, and how some of these may be mitigated through either using a multi-omic approach and/or careful low throughput, high fidelity orthogonal validation with particular emphasis on functional validation. Finally, we consider emerging technologies and their potential relevance in deepening our understanding of glia in ALS.
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Affiliation(s)
- Stanislaw Majewski
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, UK
- The Francis Crick Institute, London, UK
| | - Pierre Klein
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, UK
- The Francis Crick Institute, London, UK
| | - Séverine Boillée
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, APHP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Benjamin E Clarke
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, UK
- The Francis Crick Institute, London, UK
| | - Rickie Patani
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, UK
- The Francis Crick Institute, London, UK
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284
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Hanuman Singh D, Deeksha W, Rajakumara E. Characterization of PARP1 binding to c-KIT1 G-quadruplex DNA: Insights into domain-specific interactions. Biophys Chem 2024; 315:107330. [PMID: 39342702 DOI: 10.1016/j.bpc.2024.107330] [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: 06/02/2024] [Revised: 09/10/2024] [Accepted: 09/24/2024] [Indexed: 10/01/2024]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is a nuclear enzyme involved in catalyzing Poly-(ADP-ribosyl)ation. PARP1 binds to different forms of DNA and DNA breaks and thus plays important roles in several cellular processes, including DNA damage repair, cell cycle regulation, chromatin remodeling, and maintaining genomic stability. In this study, we conducted biochemical and biophysical characterization of PARP1 binding to G-quadruplex DNA (G4-DNA). Our investigation identified ZnF1, ZnF3, and WGR as the critical domains to mediate PARP1 binding to G4-c-KIT1. Also, our results show that these domains together show cooperativity for G4-c-KIT1 recognition. Further, we establish that the presence of an oxidized (5-carboxylcytosine) base in the loop region of G4-c-KIT1 (G4-5caC-cKIT1) does not affect its recognition by PARP1. Both G4-c-KIT1 and G4-5caC-cKIT1 are potent stimulators of PARP1's catalytic activity. Our study advances the understanding of PARP1's versatile DNA binding capabilities for G4-c-KIT1 DNA irrespective of the oxidation/ modification in the DNA base. These insights into PARP1's domain-specific contributions to G4-c-KIT1 DNA recognition and catalysis expand our knowledge of its multifaceted roles in DNA repair and genome maintenance.
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Affiliation(s)
- Dagur Hanuman Singh
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Waghela Deeksha
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India.
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285
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Jann C, Giofré S, Bhattacharjee R, Lemke EA. Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids. Chem Rev 2024; 124:10281-10362. [PMID: 39120726 PMCID: PMC11441406 DOI: 10.1021/acs.chemrev.3c00878] [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: 11/29/2023] [Revised: 06/10/2024] [Accepted: 06/27/2024] [Indexed: 08/10/2024]
Abstract
Over 500 natural and synthetic amino acids have been genetically encoded in the last two decades. Incorporating these noncanonical amino acids into proteins enables many powerful applications, ranging from basic research to biotechnology, materials science, and medicine. However, major challenges remain to unleash the full potential of genetic code expansion across disciplines. Here, we provide an overview of diverse genetic code expansion methodologies and systems and their final applications in prokaryotes and eukaryotes, represented by Escherichia coli and mammalian cells as the main workhorse model systems. We highlight the power of how new technologies can be first established in simple and then transferred to more complex systems. For example, whole-genome engineering provides an excellent platform in bacteria for enabling transcript-specific genetic code expansion without off-targets in the transcriptome. In contrast, the complexity of a eukaryotic cell poses challenges that require entirely new approaches, such as striving toward establishing novel base pairs or generating orthogonally translating organelles within living cells. We connect the milestones in expanding the genetic code of living cells for encoding novel chemical functionalities to the most recent scientific discoveries, from optimizing the physicochemical properties of noncanonical amino acids to the technological advancements for their in vivo incorporation. This journey offers a glimpse into the promising developments in the years to come.
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Affiliation(s)
- Cosimo Jann
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB
Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Sabrina Giofré
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB
Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Rajanya Bhattacharjee
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB
International PhD Programme (IPP), 55128 Mainz, Germany
| | - Edward A. Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- Institute
of Molecular Biology (IMB), 55128 Mainz, Germany
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286
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Chen HH, Lin CY, Han YJ, Huang YH, Liu YH, Hsu WE, Tsai LK, Lai HJ, Tsao YP, Huang HP, Chen SL. The Innovative Role of Nuclear Receptor Interaction Protein in Orchestrating Invadosome Formation for Myoblast Fusion. J Cachexia Sarcopenia Muscle 2024. [PMID: 39323088 DOI: 10.1002/jcsm.13598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 07/24/2024] [Accepted: 08/12/2024] [Indexed: 09/27/2024] Open
Abstract
BACKGROUND Nuclear receptor interaction protein (NRIP) is versatile and engages with various proteins to execute its diverse biological function. NRIP deficiency was reported to cause small myofibre size in adult muscle regeneration, indicating a crucial role of NRIP in myoblast fusion. METHODS The colocalization and interaction of NRIP with actin were investigated by immunofluorescence and immunoprecipitation assay, respectively. The participation of NRIP in myoblast fusion was demonstrated by cell fusion assay and time-lapse microscopy. The NRIP mutants were generated for mechanism study in NRIP-null C2C12 (termed KO19) cells and muscle-specific NRIP knockout (NRIP cKO) mice. A GEO profile database was used to analyse NRIP expression in Duchenne muscular dystrophy (DMD) patients. RESULTS In this study, we found that NRIP directly and reciprocally interacted with actin both in vitro and in cells. Immunofluorescence microscopy showed that the endogenous NRIP colocalized with components of invadosome, such as actin, Tks5, and cortactin, at the tips of cells during C2C12 differentiation. The KO19 cells were generated and exhibited a significant deficit in myoblast fusion compared with wild-type C2C12 cells (3.16% vs. 33.67%, p < 0.005). Overexpressed NRIP in KO19 cells could rescue myotube formation compared with control (3.37% vs. 1.00%, p < 0.01). We further confirmed that NRIP directly participated in cell fusion by using a cell-cell fusion assay. We investigated the mechanism of invadosome formation for myoblast fusion, which depends on NRIP-actin interaction, by analysing NRIP mutants in NRIP-null cells. Loss of actin-binding of NRIP reduced invadosome (enrichment ratio, 1.00 vs. 2.54, p < 0.01) and myotube formation (21.82% vs. 35.71%, p < 0.05) in KO19 cells and forced NRIP expression in KO19 cells and muscle-specific NRIP knockout (NRIP cKO) mice increased myofibre size compared with controls (over 1500 μm2, 61.01% vs. 20.57%, p < 0.001). We also found that the NRIP mRNA level was decreased in DMD patients compared with healthy controls (18 072 vs. 28 289, p < 0.001, N = 10 for both groups). CONCLUSIONS NRIP is a novel actin-binding protein for invadosome formation to induce myoblast fusion.
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Affiliation(s)
- Hsin-Hsiung Chen
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chia-Yang Lin
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ya-Ju Han
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yun-Hsin Huang
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Hsiang Liu
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wan-En Hsu
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Li-Kai Tsai
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsing-Jung Lai
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yeou-Ping Tsao
- Department of Ophthalmology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Hsiang-Po Huang
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Show-Li Chen
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
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287
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Lin JC, Oludare A, Jung H. Connecting dots between nucleotide biosynthesis and DNA lesion repair/bypass in cancer. Biosci Rep 2024; 44:BSR20231382. [PMID: 39189649 PMCID: PMC11427732 DOI: 10.1042/bsr20231382] [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: 02/14/2024] [Revised: 08/01/2024] [Accepted: 08/15/2024] [Indexed: 08/28/2024] Open
Abstract
Purine and pyrimidine nucleotides are crucial building blocks for the survival of cells, and there are layers of pathways to make sure a stable supply of them including de novo nucleotide biosynthesis. Fast-growing cells including cancer cells have high demand for nucleotide, and they highly utilize the nucleotide biosynthesis pathways. Due to the nature of the fast-growing cells, they tend to make more errors in replication compared with the normal cells. Naturally, DNA repair and DNA lesion bypass are heavily employed in cancer cells to ensure fidelity and completion of the replication without stalling. There have been a lot of drugs targeting cancer that mimic the chemical structures of the nucleobase, nucleoside, and nucleotides, and the resistance toward those drugs is a serious problem. Herein, we have reviewed some of the representative nucleotide analog anticancer agents such as 5-fluorouracil, specifically their mechanism of action and resistance is discussed. Also, we have chosen several enzymes in nucleotide biosynthesis, DNA repair, and DNA lesion bypass, and we have discussed the known and potential roles of these enzymes in maintaining genomic fidelity and cancer chemotherapy.
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Affiliation(s)
- Jackson C Lin
- The Division of Medicinal Chemistry, School of Pharmacy, The University of Connecticut, Storrs, Connecticut 06269, U.S.A
| | - Ayobami Oludare
- The Division of Medicinal Chemistry, School of Pharmacy, The University of Connecticut, Storrs, Connecticut 06269, U.S.A
| | - Hunmin Jung
- The Division of Medicinal Chemistry, School of Pharmacy, The University of Connecticut, Storrs, Connecticut 06269, U.S.A
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288
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Sebutsoe XM, Tsotetsi NJN, Jantjies ZE, Raphela-Choma PP, Choene MS, Motadi LR. Therapeutic Strategies in Advanced Cervical Cancer Detection, Prevention and Treatment. Onco Targets Ther 2024; 17:785-801. [PMID: 39345275 PMCID: PMC11439348 DOI: 10.2147/ott.s475132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 08/08/2024] [Indexed: 10/01/2024] Open
Abstract
Cervical cancer is ranked the fourth most common cause of cancer related deaths amongst women. The situation is particularly dire in low to lower middle-income countries. It continues to affect these countries due to poor vaccine coverage and screening. Cervical cancer is mostly detected in the advanced stages leading to poor outcomes. This review focuses on the progress made to date to improve early detection and targeted therapy using both circulating RNA. Vaccine has played a major role in cervical cancer control in vaccinated young woman in mainly developed countries yet in low-income countries with challenges of 3 dose vaccination affordability, cervical cancer continues to be the second most deadly amongst women. In this review, we show the progress made in reducing cervical cancer using vaccination that in combination with other treatments that might improve survival in cervical cancer. We further show with both miRNA and siRNA that targeted therapy and specific markers might be ideal for early detection of cervical cancer in low-income countries. These markers are either upregulated or down regulated in cancer providing clue to the stage of the cancer.
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Affiliation(s)
- Xolisiwe M Sebutsoe
- Department of Biochemistry C2 Lab, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg, South Africa
| | | | - Zodwa Edith Jantjies
- Department of Biochemistry C2 Lab, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg, South Africa
| | - Portia Pheladi Raphela-Choma
- Department of Biochemistry C2 Lab, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg, South Africa
| | - Mpho S Choene
- Department of Biochemistry C2 Lab, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg, South Africa
| | - Lesetja R Motadi
- Department of Biochemistry C2 Lab, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg, South Africa
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289
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Lacoste J, Haghighi M, Haider S, Reno C, Lin ZY, Segal D, Qian WW, Xiong X, Teelucksingh T, Miglietta E, Shafqat-Abbasi H, Ryder PV, Senft R, Cimini BA, Murray RR, Nyirakanani C, Hao T, McClain GG, Roth FP, Calderwood MA, Hill DE, Vidal M, Yi SS, Sahni N, Peng J, Gingras AC, Singh S, Carpenter AE, Taipale M. Pervasive mislocalization of pathogenic coding variants underlying human disorders. Cell 2024:S0092-8674(24)01021-3. [PMID: 39353438 DOI: 10.1016/j.cell.2024.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 07/22/2024] [Accepted: 09/04/2024] [Indexed: 10/04/2024]
Abstract
Widespread sequencing has yielded thousands of missense variants predicted or confirmed as disease causing. This creates a new bottleneck: determining the functional impact of each variant-typically a painstaking, customized process undertaken one or a few genes and variants at a time. Here, we established a high-throughput imaging platform to assay the impact of coding variation on protein localization, evaluating 3,448 missense variants of over 1,000 genes and phenotypes. We discovered that mislocalization is a common consequence of coding variation, affecting about one-sixth of all pathogenic missense variants, all cellular compartments, and recessive and dominant disorders alike. Mislocalization is primarily driven by effects on protein stability and membrane insertion rather than disruptions of trafficking signals or specific interactions. Furthermore, mislocalization patterns help explain pleiotropy and disease severity and provide insights on variants of uncertain significance. Our publicly available resource extends our understanding of coding variation in human diseases.
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Affiliation(s)
- Jessica Lacoste
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Shahan Haider
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Chloe Reno
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Dmitri Segal
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Wesley Wei Qian
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xueting Xiong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Tanisha Teelucksingh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | | | - Pearl V Ryder
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Rebecca Senft
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Beth A Cimini
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ryan R Murray
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Chantal Nyirakanani
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gregory G McClain
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Frederick P Roth
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA; Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, USA; Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, USA; Interdisciplinary Life Sciences Graduate Programs (ILSGP), College of Natural Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Quantitative and Computational Biosciences Program, Baylor College of Medicine, Houston, TX, USA
| | - Jian Peng
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | | | | | - Mikko Taipale
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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290
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Attar GS, Kumar M, Bhalla V. Targeting sub-cellular organelles for boosting precision photodynamic therapy. Chem Commun (Camb) 2024. [PMID: 39320942 DOI: 10.1039/d4cc02702g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Among various cancer treatment methods, photodynamic therapy has received significant attention due to its non-invasiveness and high efficiency in inhibiting tumour growth. Recently, specific organelle targeting photosensitizers have received increasing interest due to their precise accumulation and ability to trigger organelle-mediated cell death signalling pathways, which greatly reduces the drug dosage, minimizes toxicity, avoids multidrug resistance, and prevents recurrence. In this review, recent advances and representative photosensitizers used in targeted photodynamic therapy on organelles, specifically including the endoplasmic reticulum, Golgi apparatus, mitochondria, nucleus, and lysosomes, have been comprehensively reviewed with a focus on organelle structure and organelle-mediated cell death signalling pathways. Furthermore, a perspective on future research and potential challenges in precision photodynamic therapy has been presented at the end.
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Affiliation(s)
- Gopal Singh Attar
- Department of chemistry UGC Sponsored-Centre for Advanced Studies-I, Guru Nanak Dev University, Amritsar-143005, Punjab, India.
| | - Manoj Kumar
- Department of chemistry UGC Sponsored-Centre for Advanced Studies-I, Guru Nanak Dev University, Amritsar-143005, Punjab, India.
| | - Vandana Bhalla
- Department of chemistry UGC Sponsored-Centre for Advanced Studies-I, Guru Nanak Dev University, Amritsar-143005, Punjab, India.
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291
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Manzo SG, Mazouzi A, Leemans C, van Schaik T, Neyazi N, van Ruiten MS, Rowland BD, Brummelkamp TR, van Steensel B. Chromatin protein complexes involved in gene repression in lamina-associated domains. EMBO J 2024:10.1038/s44318-024-00214-1. [PMID: 39322756 DOI: 10.1038/s44318-024-00214-1] [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: 03/26/2024] [Revised: 08/05/2024] [Accepted: 08/07/2024] [Indexed: 09/27/2024] Open
Abstract
Lamina-associated domains (LADs) are large chromatin regions that are associated with the nuclear lamina (NL) and form a repressive environment for transcription. The molecular players that mediate gene repression in LADs are currently unknown. Here, we performed FACS-based whole-genome genetic screens in human cells using LAD-integrated fluorescent reporters to identify such regulators. Surprisingly, the screen identified very few NL proteins, but revealed roles for dozens of known chromatin regulators. Among these are the negative elongation factor (NELF) complex and interacting factors involved in RNA polymerase pausing, suggesting that regulation of transcription elongation is a mechanism to repress transcription in LADs. Furthermore, the chromatin remodeler complex BAF and the activation complex Mediator can work both as activators and repressors in LADs, depending on the local context and possibly by rewiring heterochromatin. Our data indicate that the fundamental regulators of transcription and chromatin remodeling, rather than interaction with NL proteins, play a major role in transcription regulation within LADs.
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Affiliation(s)
- Stefano G Manzo
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Abdelghani Mazouzi
- Oncode Institute, Amsterdam, the Netherlands
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Christ Leemans
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Tom van Schaik
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Nadia Neyazi
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Marjon S van Ruiten
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Benjamin D Rowland
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Thijn R Brummelkamp
- Oncode Institute, Amsterdam, the Netherlands
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Oncode Institute, Amsterdam, the Netherlands.
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, the Netherlands.
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292
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Kim MS, Kim DH, Lee JS. A review of environmental epigenetics in aquatic invertebrates. MARINE POLLUTION BULLETIN 2024; 208:117011. [PMID: 39326327 DOI: 10.1016/j.marpolbul.2024.117011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/30/2024] [Accepted: 09/14/2024] [Indexed: 09/28/2024]
Abstract
Aquatic ecosystems face significant challenges due to increasing human-induced environmental stressors. Recent studies emphasize the role of epigenetic mechanisms in the stress responses and adaptations of organisms to those stressors. Epigenetics influences gene expression, enabling phenotypic plasticity and transgenerational effects. Therefore, understanding the epigenetic responses of aquatic invertebrates to environmental stressors is imperative for aquatic ecosystem research. In this study, we organize the mechanisms of epigenetics in aquatic invertebrates and explore their roles in the responses of aquatic invertebrates to environmental stressors. Furthermore, we discuss the inheritance of epigenetic changes and their influence across generations in aquatic invertebrates. A comprehensive understanding of epigenetic responses is crucial for long-term ecosystem management and conservation strategies in the face of irreversible climate change in aquatic environments. In this review, we synthesize existing knowledge about environmental epigenetics in aquatic invertebrates to provide insights and suggest directions for future research.
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Affiliation(s)
- Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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293
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Srivastava S, Cole JJ, Cohen JS, Chopra M, Smith HS, Deardorff MA, Pedapati E, Corner B, Anixt JS, Jeste S, Sahin M, Gurnett CA, Campbell CA. Survey of the Landscape of Society Practice Guidelines for Genetic Testing of Neurodevelopmental Disorders. Ann Neurol 2024. [PMID: 39319594 DOI: 10.1002/ana.27045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 09/26/2024]
Abstract
Genetic testing of patients with neurodevelopmental disabilities (NDDs) is critical for diagnosis, medical management, and access to precision therapies. Because genetic testing approaches evolve rapidly, professional society practice guidelines serve an essential role in guiding clinical care; however, several challenges exist regarding the creation and equitable implementation of these guidelines. In this scoping review, we assessed the current state of United States professional societies' guidelines pertaining to genetic testing for unexplained global developmental delay, intellectual disability, autism spectrum disorder, and cerebral palsy. We describe several identified shortcomings and argue the need for a unified, frequently updated, and easily-accessible cross-specialty society guideline. ANN NEUROL 2024.
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Affiliation(s)
- Siddharth Srivastava
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jordan J Cole
- Department of Pediatrics, University of Colorado, Children's Hospital Colorado, Aurora, CO, USA
| | - Julie S Cohen
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Maya Chopra
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hadley Stevens Smith
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Matthew A Deardorff
- Departments of Pathology and Pediatrics, Keck School of Medicine of USC, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Ernest Pedapati
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Brian Corner
- Department of Pediatrics and Genetics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Julia S Anixt
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Shafali Jeste
- Department of Neurology, Keck School of Medicine of USC, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Mustafa Sahin
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christina A Gurnett
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Colleen A Campbell
- Department of Internal Medicine, University of Iowa, Carver College of Medicine, Iowa City, IA, USA
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294
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Wu Y, Barbieri E, Kilgore RE, Moore BD, Chu W, Mollica GN, Daniele MA, Menegatti S. Peptide ligands for the affinity purification of adenovirus from HEK293 and vero cell lysates. J Chromatogr A 2024; 1736:465396. [PMID: 39342729 DOI: 10.1016/j.chroma.2024.465396] [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: 08/15/2024] [Revised: 09/09/2024] [Accepted: 09/24/2024] [Indexed: 10/01/2024]
Abstract
Adenovirus (AdVs) is the viral vector of choice in vaccines and oncolytic applications owing to its high transduction activity and inherent immunogenicity. For decades, AdV isolation has relied on ultracentrifugation and ion-exchange chromatography, which are not suitable to large-scale production and struggle to deliver sufficient purity. Immunoaffinity chromatography resins of recent introduction feature high binding capacity and selectivity, but mandate harsh elution conditions (pH 3.0), afford low yield (< 20%), and provide limited reusability. Seeking a more efficient and affordable alternative, this study introduces the first peptide affinity ligands for AdV purification. The peptides were identified via combinatorial selection and in silico design to target hexons, the most abundant proteins in the adenoviral capsid. Selected peptide ligands AEFFIWNA and TNDGPDYSSPLTGSG were conjugated on chromatographic resins and utilized to purify AdV serotype 5 from HEK293 and Vero cell lysates. The peptide-functionalized resins feature high binding capacity (> 1010 active virions per mL at the residence time of 2 min), provide high yield (> 50%) and up to 100-fold reduction of host cell proteins and DNA. Notably, the peptide ligands enable gentle elution conditions (pH 8) that prevent the "shedding" of penton and fiber proteins, thus affording intact adenovirus particles with high cell-transduction activity. The study of the peptide ligands by surface plasmon resonance and molecular docking and dynamics simulations confirmed the selective targeting of hexon proteins and elucidated the molecular-level mechanisms underlying binding and release. Collectively, these results demonstrate the strong promise of peptide ligands presented herein for the affinity purification of AdVs from cell lysates.
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Affiliation(s)
- Yuxuan Wu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
| | - Eduardo Barbieri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA; LigaTrap Technologies LLC, Raleigh, NC 27606
| | - Ryan E Kilgore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
| | - Brandyn D Moore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
| | - Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
| | - Gina N Mollica
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
| | - Michael A Daniele
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, 911 Oval Drive, Raleigh, NC 27695, USA; Department of Electrical and Computer Engineering, North Carolina State University, 890 Oval Drive, Raleigh, NC 27695, USA; North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, 911 Oval Dr, Raleigh, NC 27695, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA; Biomanufacturing Training and Education Center (BTEC), 850 Oval Drive, Raleigh, NC 27606, USA; North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, 911 Oval Dr, Raleigh, NC 27695, USA; LigaTrap Technologies LLC, Raleigh, NC 27606.
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295
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Hu H, Qin Y, Qu Z, Huang Y, Ren X, Liu M, Liu F, Gao P. The Zpr-3 Antibody Recognizes the 320-354 Region of Rho and Labels Both Rods and Green Cones in Zebrafish. Zebrafish 2024. [PMID: 39316468 DOI: 10.1089/zeb.2024.0159] [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: 09/26/2024] Open
Abstract
Retinal markers with high quality and specificity are important for the observation of pathologic changes of retinal cells during retinal development, degeneration, and regeneration. The zpr-3 antibody is widely used to label rods in zebrafish, but the exact antigen is still unknown. In this study, we provided evidence to demonstrate that the antigen gene of zpr-3 is rho, which encodes the rod opsin, and the exact epitope of zpr-3 is the 320-354 region of Rho protein. More importantly, our immunofluorescence assays indicated that zpr-3 labels both the outer segments of rods and green cones on zebrafish retinal sections, probably due to the cross-reaction with the green-cone opsin. Our work is valuable for the scientific community to interpret the experimental data involving the zpr-3 antibody.
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Affiliation(s)
- Hualei Hu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yayun Qin
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Zhen Qu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiang Ren
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Liu
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
| | - Pan Gao
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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296
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Zhang X, Li L, Li Y, Dong C, Shi J, Guo X, Sui A. The role of trimethylation on histone H3 lysine 27 (H3K27me3) in temozolomide resistance of glioma. Brain Res 2024; 1846:149252. [PMID: 39326722 DOI: 10.1016/j.brainres.2024.149252] [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: 05/16/2024] [Revised: 09/19/2024] [Accepted: 09/23/2024] [Indexed: 09/28/2024]
Abstract
Temozolomide (TMZ) is the first-line chemotherapeutic agent for malignant glioma, but its resistance limited the benefits of the treated patients. In this study, the role and significance of trimethylation of histone H3 lysine 27 (H3K27me3) in TMZ resistance were investigated. Data from twenty advanced glioma patients were collected, and their pathological samples were analyzed for H3K27me3 levels. TMZ sensitivity was compared between glioma cells U87 and TMZ-resistant cells U87TR, with H3K27me3 levels determined in both cells. The effects of H3K27me3 demethylases inhibitor GSK-J4, combined with TMZ, were assessed on the proliferation and migration of U87TR cells. The results indicated that a high level of H3K27me3 predicts longer disease free survival (DFS) and overall survival (OS) in glioma patients receiving TMZ treatment. The H3K27me3 level was lower in U87TR cells compared to U87 cells. GSK-J4 increased the H3K27me3 level in U87TR cells and decreased their resistance to TMZ. In summary, this study identified a novel marker of TMZ resistance in glioma and provided a new strategy to address this challenge. These findings are significant for improving the clinical treatment of glioma in the future.
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Affiliation(s)
- Xiaopei Zhang
- Sixth Department of Oncology, Hebei General Hospital, Shijiazhuang 050057, Hebei, China; Graduate School, Hebei North University, Zhangjiakou 075132, Hebei, China
| | - Li Li
- Sixth Department of Oncology, Hebei General Hospital, Shijiazhuang 050057, Hebei, China
| | - Yitong Li
- Sixth Department of Oncology, Hebei General Hospital, Shijiazhuang 050057, Hebei, China
| | - Changzheng Dong
- Second Department of Neurosurgery, Hebei General Hospital, Shijiazhuang 050057, Hebei, China
| | - Jian Shi
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, Hebei, China
| | - Xiaoqiang Guo
- Department of Sports Human Sciences, Hebei Sport University, Shijiazhuang 050041, Hebei, China.
| | - Aixia Sui
- Sixth Department of Oncology, Hebei General Hospital, Shijiazhuang 050057, Hebei, China.
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297
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Yang Y, Yang H, Gao Y, Yang Q, Zhu X, Miao Q, Xu X, Li Z, Zuo D. EML4-ALK G1202R and EML4-ALK L1196M mutations induce crizotinib resistance in non-small cell lung cancer cells through activating epithelial-mesenchymal transition mediated by MDM2/MEK/ERK signal axis. Cell Biol Int 2024. [PMID: 39318039 DOI: 10.1002/cbin.12249] [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: 01/14/2024] [Revised: 08/04/2024] [Accepted: 09/13/2024] [Indexed: 09/26/2024]
Abstract
Crizotinib, as the first-generation of anaplastic lymphoma kinase (ALK) inhibitor, effectively improves the survival time of ALK-positive non-small cell lung cancer (NSCLC) patients. However, its efficacy is severely limited by drug resistance caused by secondary mutations. G1202R and L1196M are classical mutation sites located in ALK kinase domain. They may hinder the binding of ALK inhibitors to the target kinase domain, resulting in drug resistance in patients. However, the exact mechanism of drug resistance mediated by these mutations remains unclear. In this study, we aimed to evaluate how G1202R and L1196M mutations mediate crizotinib resistance. To explore the resistance mechanism, we constructed EML4-ALK G1202R and L1196M mutant cell lines with A549 cells. The results showed that the mutant cells exhibited significant epithelial-mesenchymal transition (EMT) and metastasis compared to control (A549-vector) or wild type (A549-EML4-ALK) cells. Subsequently, it was found that the occurrence of EMT was correlated to the high expression of murine double minute 2 (MDM2) protein and the activation of mitogen-activated protein kinase (MEK)/extracellular signal-regulated kinase (ERK) pathway in mutant cells. Down-regulation of MDM2 inhibited the activation of MEK/ERK pathway, thus reversed the EMT process and markedly increased the inhibitory effect of crizotinib on the growth of mutant cells. Collectively, resistance of ALK-positive NSCLC cells to crizotinib is induced by G1202R and L1196M mutations through activation of the MDM2/MEK/ERK signalling axis, promoting EMT process and metastasis. These findings suggest that the combination of MDM2 inhibitors and crizotinib could be a potential therapeutic strategy.
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Affiliation(s)
- Yuying Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
| | - Huan Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
| | - Yunhui Gao
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
| | - Qian Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
| | - Xinya Zhu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
| | - Qianying Miao
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
| | - Xiaobo Xu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
| | - Zengqiang Li
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
| | - Daiying Zuo
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
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298
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Gong X, Zhao Q, Zhang H, Liu R, Wu J, Zhang N, Zou Y, Zhao W, Huo R, Cui R. The Effects of Mesenchymal Stem Cells-Derived Exosomes on Metabolic Reprogramming in Scar Formation and Wound Healing. Int J Nanomedicine 2024; 19:9871-9887. [PMID: 39345908 PMCID: PMC11438468 DOI: 10.2147/ijn.s480901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
Pathological scarring results from aberrant cutaneous wound healing due to the overactivation of biological behaviors of human skin fibroblasts, characterized by local inordinate inflammation, excessive extracellular matrix and collagen deposition. Yet, its underlying pathogenesis opinions vary, which could be caused by increased local mechanical tension, enhanced and continuous inflammation, gene mutation, as well as cellular metabolic disorder, etc. Metabolic reprogramming is the process by which the metabolic pattern of cells undergoes a systematic adjustment and transformation to adapt to the changes of the external environment and meet the needs of their growth and differentiation. Therefore, the abnormality of metabolic reprogramming in cells within wounds and scars attaches great importance to scar formation. Mesenchymal stem cells-derived exosomes (MSC-Exo) are the extracellular vesicles that play an important role in tissue repair, cancer treatment as well as immune and metabolic regulation. However, there is not a systematic work to detail the relevant studies. Herein, we gave a comprehensive summary of the existing research on three main metabolisms, including glycometabolism, lipid metabolism and amino acid metabolism, and MSC-Exo regulating metabolic reprogramming in wound healing and scar formation for further research reference.
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Affiliation(s)
- Xiangan Gong
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Qian Zhao
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Huimin Zhang
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Rui Liu
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Jie Wu
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Nanxin Zhang
- School of Clinical Medicine, Shandong Second Medical University, Weifang, People’s Republic of China
| | - Yuanxian Zou
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Wen Zhao
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Ran Huo
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People’s Republic of China
| | - Rongtao Cui
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
- School of Clinical Medicine, Shandong Second Medical University, Weifang, People’s Republic of China
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People’s Republic of China
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299
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Palermo V, Malacaria E, Semproni M, Camerini S, Casella M, Perdichizzi B, Valenzisi P, Sanchez M, Marini F, Pellicioli A, Franchitto A, Pichierri P. Switch-like phosphorylation of WRN integrates end-resection with RAD51 metabolism at collapsed replication forks. Nucleic Acids Res 2024:gkae807. [PMID: 39315694 DOI: 10.1093/nar/gkae807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/25/2024] [Accepted: 09/03/2024] [Indexed: 09/25/2024] Open
Abstract
Replication-dependent DNA double-strand breaks are harmful lesions preferentially repaired by homologous recombination (HR), a process that requires processing of DNA ends to allow RAD51-mediated strand invasion. End resection and subsequent repair are two intertwined processes, but the mechanism underlying their execution is still poorly appreciated. The WRN helicase is one of the crucial factors for end resection and is instrumental in selecting the proper repair pathway. Here, we reveal that ordered phosphorylation of WRN by the CDK1, ATM and ATR kinases defines a complex regulatory layer essential for correct long-range end resection, connecting it to repair by HR. We establish that long-range end resection requires an ATM-dependent phosphorylation of WRN at Ser1058 and that phosphorylation at Ser1141, together with dephosphorylation at the CDK1 site Ser1133, is needed for the proper metabolism of RAD51 foci and RAD51-dependent repair. Collectively, our findings suggest that regulation of WRN by multiple kinases functions as a molecular switch to allow timely execution of end resection and repair at replication-dependent DNA double-strand breaks.
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Affiliation(s)
- Valentina Palermo
- Department of Environment and Health, Mechanisms, Biomarkers and Models Section, Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Eva Malacaria
- Department of Environment and Health, Mechanisms, Biomarkers and Models Section, Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Maurizio Semproni
- Department of Environment and Health, Mechanisms, Biomarkers and Models Section, Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Serena Camerini
- FAST, Core Facilities Service, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Marialuisa Casella
- FAST, Core Facilities Service, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Benedetta Perdichizzi
- Department of Environment and Health, Mechanisms, Biomarkers and Models Section, Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Pasquale Valenzisi
- Department of Environment and Health, Mechanisms, Biomarkers and Models Section, Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Massimo Sanchez
- FAST, Core Facilities Service, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Federica Marini
- Department of Biosciences, Genomic Instability and Human Pathologies Section, Università degli Studi di Milano, Via Giovanni Celoria 26, 20133 Milan, Italy
| | - Achille Pellicioli
- Department of Biosciences, Genomic Instability and Human Pathologies Section, Università degli Studi di Milano, Via Giovanni Celoria 26, 20133 Milan, Italy
| | - Annapaola Franchitto
- Department of Environment and Health, Mechanisms, Biomarkers and Models Section, Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Pietro Pichierri
- Department of Environment and Health, Mechanisms, Biomarkers and Models Section, Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
- Istituto Nazionale di Biostrutture e Biosistemi, Viale delle Medaglie d'Oro 305, 00134 Rome, Italy
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300
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Lapraz F, Fixary-Schuster C, Noselli S. Brain bilateral asymmetry - insights from nematodes, zebrafish, and Drosophila. Trends Neurosci 2024:S0166-2236(24)00146-2. [PMID: 39322499 DOI: 10.1016/j.tins.2024.08.003] [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: 04/19/2024] [Revised: 07/16/2024] [Accepted: 08/06/2024] [Indexed: 09/27/2024]
Abstract
Chirality is a fundamental trait of living organisms, encompassing the homochirality of biological molecules and the left-right (LR) asymmetry of visceral organs and the brain. The nervous system in bilaterian organisms displays a lateralized organization characterized by the presence of asymmetrical neuronal circuits and brain functions that are predominantly localized within one hemisphere. Although body asymmetry is relatively well understood, and exhibits robust phenotypic expression and regulation via conserved molecular mechanisms across phyla, current findings indicate that the asymmetry of the nervous system displays greater phenotypic, genetic, and evolutionary variability. In this review we explore the use of nematode, zebrafish, and Drosophila genetic models to investigate neuronal circuit asymmetry. We discuss recent discoveries in the context of body-brain concordance and highlight the distinct characteristics of nervous system asymmetry and its cognitive correlates.
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