1
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Jasim SA, Farhan SH, Ahmad I, Hjazi A, Kumar A, Jawad MA, Pramanik A, Altalbawy FMA, Alsaadi SB, Abosaoda MK. Role of homeobox genes in cancer: immune system interactions, long non-coding RNAs, and tumor progression. Mol Biol Rep 2024; 51:964. [PMID: 39240390 DOI: 10.1007/s11033-024-09857-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 08/09/2024] [Indexed: 09/07/2024]
Abstract
The intricate interplay between Homeobox genes, long non-coding RNAs (lncRNAs), and the development of malignancies represents a rapidly expanding area of research. Specific discernible lncRNAs have been discovered to adeptly regulate HOX gene expression in the context of cancer, providing fresh insights into the molecular mechanisms that govern cancer development and progression. An in-depth comprehension of these intricate associations may pave the way for innovative therapeutic strategies in cancer treatment. The HOX gene family is garnering increasing attention due to its involvement in immune system regulation, interaction with long non-coding RNAs, and tumor progression. Although initially recognized for its crucial role in embryonic development, this comprehensive exploration of the world of HOX genes contributes to our understanding of their diverse functions, potentially leading to immunology, developmental biology, and cancer research discoveries. Thus, the primary objective of this review is to delve into these aspects of HOX gene biology in greater detail, shedding light on their complex functions and potential therapeutic applications.
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Affiliation(s)
| | - Shireen Hamid Farhan
- Biotechnology Department, College of Applied Science, Fallujah University, Al-Fallujah, Iraq
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, King Khalid University, Abha, Saudi Arabia
| | - Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, 11942, Al-Kharj, Saudi Arabia
| | - Ashwani Kumar
- Department of Life Sciences, School of Sciences, Jain (Deemed-to-Be) University, Bengaluru, Karnataka, 560069, India
- Department of Pharmacy, Vivekananda Global University, Jaipur, Rajasthan, 303012, India
| | | | - Atreyi Pramanik
- School of Applied and Life Sciences, Division of Research and Innovation, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Farag M A Altalbawy
- Department of Chemistry, University College of Duba, University of Tabuk, Tabuk, Saudi Arabia
| | - Salim B Alsaadi
- Department of Pharmaceutics, Al-Hadi University College, Baghdad, 10011, Iraq
| | - Munther Kadhim Abosaoda
- College of Pharmacy, the Islamic University, Najaf, Iraq
- College of Pharmacy, the Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
- College of Pharmacy, the Islamic University of Babylon, Al Diwaniyah, Iraq
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2
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Mozin E, Massouridès E, Mournetas V, Lièvre C, Bourdon A, Jackson DL, Packer JS, Seong J, Trapnell C, Le Guiner C, Adjali O, Pinset C, Mack DL, Dupont JB. Dystrophin deficiency impairs cell junction formation during embryonic myogenesis from pluripotent stem cells. iScience 2024; 27:110242. [PMID: 39040067 PMCID: PMC11261405 DOI: 10.1016/j.isci.2024.110242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 05/02/2024] [Accepted: 06/07/2024] [Indexed: 07/24/2024] Open
Abstract
Mutations in the DMD gene lead to Duchenne muscular dystrophy (DMD), a severe neuromuscular disorder affecting young boys as they acquire motor functions. DMD is typically diagnosed at 2-4 years of age, but the absence of dystrophin has negative impacts on skeletal muscles before overt symptoms appear in patients, which poses a serious challenge in current standards of care. Here, we investigated the consequences of dystrophin deficiency during skeletal muscle development. We used single-cell transcriptome profiling to characterize the myogenic trajectory of human pluripotent stem cells and showed that DMD cells bifurcate to an alternative branch when they reach the somite stage. Dystrophin deficiency was linked to marked dysregulations of cell junction proteins involved in the cell state transitions characteristic of embryonic somitogenesis. Altogether, this work demonstrates that in vitro, dystrophin deficiency has deleterious effects on cell-cell communication during myogenic development, which should be considered in future therapeutic strategies for DMD.
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Affiliation(s)
- Elise Mozin
- Nantes Université, CHU Nantes, INSERM, TARGET, F-44000 Nantes, France
| | | | | | - Clémence Lièvre
- Nantes Université, CHU Nantes, INSERM, TARGET, F-44000 Nantes, France
| | - Audrey Bourdon
- Nantes Université, CHU Nantes, INSERM, TARGET, F-44000 Nantes, France
| | - Dana L. Jackson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Jonathan S. Packer
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Juyoung Seong
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, South Korea
- Institute for Stem Cell and Regenerative Medicine, Department of Rehabilitation Medicine, University of Washington, Seattle, WA 98109, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
| | | | - Oumeya Adjali
- Nantes Université, CHU Nantes, INSERM, TARGET, F-44000 Nantes, France
| | - Christian Pinset
- Centre d’Etude des Cellules Souches, I-Stem, AFM, F-91100 Corbeil-Essonnes, France
| | - David L. Mack
- Institute for Stem Cell and Regenerative Medicine, Department of Rehabilitation Medicine, University of Washington, Seattle, WA 98109, USA
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Mok GF, Turner S, Smith EL, Mincarelli L, Lister A, Lipscombe J, Uzun V, Haerty W, Macaulay IC, Münsterberg AE. Single cell RNA-sequencing and RNA-tomography of the avian embryo extending body axis. Front Cell Dev Biol 2024; 12:1382960. [PMID: 38863942 PMCID: PMC11165230 DOI: 10.3389/fcell.2024.1382960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/29/2024] [Indexed: 06/13/2024] Open
Abstract
Introduction: Vertebrate body axis formation initiates during gastrulation and continues within the tail bud at the posterior end of the embryo. Major structures in the trunk are paired somites, which generate the musculoskeletal system, the spinal cord-forming part of the central nervous system, and the notochord, with important patterning functions. The specification of these different cell lineages by key signalling pathways and transcription factors is essential, however, a global map of cell types and expressed genes in the avian trunk is missing. Methods: Here we use high-throughput sequencing approaches to generate a molecular map of the emerging trunk and tailbud in the chick embryo. Results and Discussion: Single cell RNA-sequencing (scRNA-seq) identifies discrete cell lineages including somites, neural tube, neural crest, lateral plate mesoderm, ectoderm, endothelial and blood progenitors. In addition, RNA-seq of sequential tissue sections (RNA-tomography) provides a spatially resolved, genome-wide expression dataset for the avian tailbud and emerging body, comparable to other model systems. Combining the single cell and RNA-tomography datasets, we identify spatially restricted genes, focusing on somites and early myoblasts. Thus, this high-resolution transcriptome map incorporating cell types in the embryonic trunk can expose molecular pathways involved in body axis development.
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Affiliation(s)
- G. F. Mok
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - S. Turner
- Earlham Institute, Norwich, United Kingdom
| | - E. L. Smith
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | | | - A. Lister
- Earlham Institute, Norwich, United Kingdom
| | | | - V. Uzun
- Earlham Institute, Norwich, United Kingdom
| | - W. Haerty
- Earlham Institute, Norwich, United Kingdom
| | | | - A. E. Münsterberg
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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4
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Mozin E, Massouridès E, Mournetas V, Lièvre C, Bourdon A, Jackson DL, Packer JS, Seong J, Trapnell C, Le Guiner C, Adjali O, Pinset C, Mack DL, Dupont JB. Dystrophin deficiency impairs cell junction formation during embryonic myogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.05.569919. [PMID: 38106055 PMCID: PMC10723310 DOI: 10.1101/2023.12.05.569919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Mutations in the DMD gene lead to Duchenne muscular dystrophy, a severe X-linked neuromuscular disorder that manifests itself as young boys acquire motor functions. DMD is typically diagnosed at 2 to 4 years of age, but the absence of dystrophin negatively impacts muscle structure and function before overt symptoms appear in patients, which poses a serious challenge in the optimization of standards of care. In this report, we investigated the early consequences of dystrophin deficiency during skeletal muscle development. We used single-cell transcriptome profiling to characterize the myogenic trajectory of human pluripotent stem cells and showed that DMD cells bifurcate to an alternative branch when they reach the somite stage. Here, dystrophin deficiency was linked to marked dysregulations of cell junction protein families involved in the cell state transitions characteristic of embryonic somitogenesis. Altogether, this work demonstrates that in vitro, dystrophin deficiency has deleterious effects on cell-cell communication during myogenic development, which should be considered in future therapeutic strategies for DMD.
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Affiliation(s)
- Elise Mozin
- Nantes Université, CHU Nantes, INSERM, TARGET, F-44000 Nantes, France
| | | | | | - Clémence Lièvre
- Nantes Université, CHU Nantes, INSERM, TARGET, F-44000 Nantes, France
| | - Audrey Bourdon
- Nantes Université, CHU Nantes, INSERM, TARGET, F-44000 Nantes, France
| | - Dana L Jackson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Jonathan S Packer
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Juyoung Seong
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, South Korea
- Institute for Stem Cell and Regenerative Medicine, Department of Rehabilitation Medicine, University of Washington, Seattle, WA 98109, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
| | | | - Oumeya Adjali
- Nantes Université, CHU Nantes, INSERM, TARGET, F-44000 Nantes, France
| | - Christian Pinset
- Centre d’Etude des Cellules Souches, I-Stem, AFM, F-91100 Corbeil-Essonnes, France
| | - David L Mack
- Institute for Stem Cell and Regenerative Medicine, Department of Rehabilitation Medicine, University of Washington, Seattle, WA 98109, USA
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Kondoh H. Gastrulation: Its Principles and Variations. Results Probl Cell Differ 2024; 72:27-60. [PMID: 38509251 DOI: 10.1007/978-3-031-39027-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
As epiblast cells initiate development into various somatic cells, they undergo a large-scale reorganization, called gastrulation. The gastrulation of the epiblast cells produces three groups of cells: the endoderm layer, the collection of miscellaneous mesodermal tissues, and the ectodermal layer, which includes the neural, epidermal, and associated tissues. Most studies of gastrulation have focused on the formation of the tissues that provide the primary route for cell reorganization, that is, the primitive streak, in the chicken and mouse. In contrast, how gastrulation alters epiblast-derived cells has remained underinvestigated. This chapter highlights the regulation of cell and tissue fate via the gastrulation process. The roles and regulatory functions of neuromesodermal progenitors (NMPs) in the gastrulation process, elucidated in the last decade, are discussed in depth to resolve points of confusion. Chicken and mouse embryos, which form a primitive streak as the site of mesoderm precursor ingression, have been investigated extensively. However, primitive streak formation is an exception, even among amniotes. The roles of gastrulation processes in generating various somatic tissues will be discussed broadly.
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Affiliation(s)
- Hisato Kondoh
- Osaka University, Suita, Osaka, Japan
- Biohistory Research Hall, Takatsuki, Osaka, Japan
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6
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Masak G, Davidson LA. Constructing the pharyngula: Connecting the primary axial tissues of the head with the posterior axial tissues of the tail. Cells Dev 2023; 176:203866. [PMID: 37394035 PMCID: PMC10756936 DOI: 10.1016/j.cdev.2023.203866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/04/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023]
Abstract
The pharyngula stage of vertebrate development is characterized by stereotypical arrangement of ectoderm, mesoderm, and neural tissues from the anterior spinal cord to the posterior, yet unformed tail. While early embryologists over-emphasized the similarity between vertebrate embryos at the pharyngula stage, there is clearly a common architecture upon which subsequent developmental programs generate diverse cranial structures and epithelial appendages such as fins, limbs, gills, and tails. The pharyngula stage is preceded by two morphogenetic events: gastrulation and neurulation, which establish common shared structures despite the occurrence of cellular processes that are distinct to each of the species. Even along the body axis of a singular organism, structures with seemingly uniform phenotypic characteristics at the pharyngula stage have been established by different processes. We focus our review on the processes underlying integration of posterior axial tissue formation with the primary axial tissues that creates the structures laid out in the pharyngula. Single cell sequencing and novel gene targeting technologies have provided us with new insights into the differences between the processes that form the anterior and posterior axis, but it is still unclear how these processes are integrated to create a seamless body. We suggest that the primary and posterior axial tissues in vertebrates form through distinct mechanisms and that the transition between these mechanisms occur at different locations along the anterior-posterior axis. Filling gaps that remain in our understanding of this transition could resolve ongoing problems in organoid culture and regeneration.
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Affiliation(s)
- Geneva Masak
- Integrative Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Lance A Davidson
- Integrative Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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7
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Ibarra-Soria X, Thierion E, Mok GF, Münsterberg AE, Odom DT, Marioni JC. A transcriptional and regulatory map of mouse somite maturation. Dev Cell 2023; 58:1983-1995.e7. [PMID: 37499658 PMCID: PMC10563765 DOI: 10.1016/j.devcel.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/12/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023]
Abstract
The mammalian body plan is shaped by rhythmic segmentation of mesoderm into somites, which are transient embryonic structures that form down each side of the neural tube. We have analyzed the genome-wide transcriptional and chromatin dynamics occurring within nascent somites, from early inception of somitogenesis to the latest stages of body plan establishment. We created matched gene expression and open chromatin maps for the three leading pairs of somites at six time points during mouse embryonic development. We show that the rate of somite differentiation accelerates as development progresses. We identified a conserved maturation program followed by all somites, but somites from more developed embryos concomitantly switch on differentiation programs from derivative cell lineages soon after segmentation. Integrated analysis of the somitic transcriptional and chromatin activities identified opposing regulatory modules controlling the onset of differentiation. Our results provide a powerful, high-resolution view of the molecular genetics underlying somitic development in mammals.
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Affiliation(s)
- Ximena Ibarra-Soria
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
| | - Elodie Thierion
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Gi Fay Mok
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Andrea E Münsterberg
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; DKFZ, Division of Regulatory Genomics and Cancer Evolution B270, Im Neunheimer Feld 280, Heidelberg, 69120, Germany.
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
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