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Nguyen TH, Vicidomini R, Choudhury SD, Han TH, Maric D, Brody T, Serpe M. scRNA-seq data from the larval Drosophila ventral cord provides a resource for studying motor systems function and development. Dev Cell 2024; 59:1210-1230.e9. [PMID: 38569548 PMCID: PMC11078614 DOI: 10.1016/j.devcel.2024.03.016] [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: 06/27/2023] [Revised: 12/05/2023] [Accepted: 03/06/2024] [Indexed: 04/05/2024]
Abstract
The Drosophila larval ventral nerve cord (VNC) shares many similarities with the spinal cord of vertebrates and has emerged as a major model for understanding the development and function of motor systems. Here, we use high-quality scRNA-seq, validated by anatomical identification, to create a comprehensive census of larval VNC cell types. We show that the neural lineages that comprise the adult VNC are already defined, but quiescent, at the larval stage. Using fluorescence-activated cell sorting (FACS)-enriched populations, we separate all motor neuron bundles and link individual neuron clusters to morphologically characterized known subtypes. We discovered a glutamate receptor subunit required for basal neurotransmission and homeostasis at the larval neuromuscular junction. We describe larval glia and endorse the general view that glia perform consistent activities throughout development. This census represents an extensive resource and a powerful platform for future discoveries of cellular and molecular mechanisms in repair, regeneration, plasticity, homeostasis, and behavioral coordination.
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Affiliation(s)
| | | | | | | | - Dragan Maric
- Flow and Imaging Cytometry Core, NINDS, NIH, Bethesda, MD 20892, USA
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2
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Smith JJ, Kratsios P. Hox gene functions in the C. elegans nervous system: From early patterning to maintenance of neuronal identity. Semin Cell Dev Biol 2024; 152-153:58-69. [PMID: 36496326 PMCID: PMC10244487 DOI: 10.1016/j.semcdb.2022.11.012] [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: 09/13/2022] [Revised: 11/14/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
The nervous system emerges from a series of genetic programs that generate a remarkable array of neuronal cell types. Each cell type must acquire a distinct anatomical position, morphology, and function, enabling the generation of specialized circuits that drive animal behavior. How are these diverse cell types and circuits patterned along the anterior-posterior (A-P) axis of the animal body? Hox genes encode transcription factors that regulate cell fate and patterning events along the A-P axis of the nervous system. While most of our understanding of Hox-mediated control of neuronal development stems from studies in segmented animals like flies, mice, and zebrafish, important new themes are emerging from work in a non-segmented animal: the nematode Caenorhabditis elegans. Studies in C. elegans support the idea that Hox genes are needed continuously and across different life stages in the nervous system; they are not only required in dividing progenitor cells, but also in post-mitotic neurons during development and adult life. In C. elegans embryos and young larvae, Hox genes control progenitor cell specification, cell survival, and neuronal migration, consistent with their neural patterning roles in other animals. In late larvae and adults, C. elegans Hox genes control neuron type-specific identity features critical for neuronal function, thereby extending the Hox functional repertoire beyond early patterning. Here, we provide a comprehensive review of Hox studies in the C. elegans nervous system. To relate to readers outside the C. elegans community, we highlight conserved roles of Hox genes in patterning the nervous system of invertebrate and vertebrate animals. We end by calling attention to new functions in adult post-mitotic neurons for these paradigmatic regulators of cell fate.
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Affiliation(s)
- Jayson J Smith
- Department of Neurobiology, University of Chicago, 947 East 58th Street, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, 947 East 58th Street, Chicago, IL 60637, USA.
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, 947 East 58th Street, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, 947 East 58th Street, Chicago, IL 60637, USA.
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Quesnelle DC, Bendena WG, Chin-Sang ID. A Compilation of the Diverse miRNA Functions in Caenorhabditis elegans and Drosophila melanogaster Development. Int J Mol Sci 2023; 24:ijms24086963. [PMID: 37108126 PMCID: PMC10139094 DOI: 10.3390/ijms24086963] [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: 03/21/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
MicroRNAs are critical regulators of post-transcriptional gene expression in a wide range of taxa, including invertebrates, mammals, and plants. Since their discovery in the nematode, Caenorhabditis elegans, miRNA research has exploded, and they are being identified in almost every facet of development. Invertebrate model organisms, particularly C. elegans, and Drosophila melanogaster, are ideal systems for studying miRNA function, and the roles of many miRNAs are known in these animals. In this review, we compiled the functions of many of the miRNAs that are involved in the development of these invertebrate model species. We examine how gene regulation by miRNAs shapes both embryonic and larval development and show that, although many different aspects of development are regulated, several trends are apparent in the nature of their regulation.
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Affiliation(s)
| | - William G Bendena
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Ian D Chin-Sang
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
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4
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Hajirnis N, Pandey S, Mishra RK. CRISPR/Cas9 and FLP-FRT mediated regulatory dissection of the BX-C of Drosophila melanogaster. CHROMOSOME RESEARCH : AN INTERNATIONAL JOURNAL ON THE MOLECULAR, SUPRAMOLECULAR AND EVOLUTIONARY ASPECTS OF CHROMOSOME BIOLOGY 2023; 31:7. [PMID: 36719476 DOI: 10.1007/s10577-023-09716-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 02/01/2023]
Abstract
The homeotic genes or Hox define the anterior-posterior (AP) body axis formation in bilaterians and are often present on the chromosome in an order collinear to their function across the AP axis. However, there are many cases wherein the Hox are not collinear, but their expression pattern is conserved across the AP axis. The expression pattern of Hox is attributed to the cis-regulatory modules (CRMs) consisting of enhancers, initiators, or repressor elements that regulate the genes in a segment-specific manner. In the Drosophila melanogaster Hox complex, the bithorax complex (BX-C) and even the CRMs are organized in an order that is collinear to their function in the thoracic and abdominal segments. In the present study, the regulatorily inert regions were targeted using CRISPR/Cas9 to generate a series of transgenic lines with the insertion of FRT sequences. These FRT lines are repurposed to shuffle the CRMs associated with Abd-B to generate modular deletion, duplication, or inversion of multiple CRMs. The rearrangements yielded entirely novel phenotypes in the fly suggesting the requirement of such complex manipulations to address the significance of higher order arrangement of the CRMs. The functional map and the transgenic flies generated in this study are important resources to decipher the collective ability of multiple regulatory elements in the eukaryotic genome to function as complex modules.
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Affiliation(s)
- Nikhil Hajirnis
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India.,Department of Anatomy and Neurobiology, University of Maryland, Baltimore, USA
| | | | - Rakesh K Mishra
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India. .,AcSIR - Academy of Scientific and Innovative Research, Ghaziabad, India. .,Tata Institute for Genetics and Society (TIGS), Bangalore, India.
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5
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Matsuoka Y, Monteiro A. Ultrabithorax modifies a regulatory network of genes essential for butterfly eyespot development in a wing sector-specific manner. Development 2022; 149:285574. [PMID: 36341494 DOI: 10.1242/dev.200781] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022]
Abstract
Nymphalid butterfly species often have a different number of eyespots in forewings and hindwings, but how the hindwing identity gene Ultrabithorax (Ubx) drives this asymmetry is not fully understood. We examined a three-gene regulatory network for eyespot development in the hindwings of Bicyclus anynana butterflies and compared it with the same network previously described for forewings. We also examined how Ubx interacts with each of these three eyespot-essential genes. We found similar genetic interactions between the three genes in fore- and hindwings, but we discovered three regulatory differences: Antennapedia (Antp) merely enhances spalt (sal) expression in the eyespot foci in hindwings, but is not essential for sal activation, as in forewings; Ubx upregulates Antp in all hindwing eyespot foci but represses Antp outside these wing regions; and Ubx regulates sal in a wing sector-specific manner, i.e. it activates sal expression only in the sectors that have hindwing-specific eyespots. We propose a model for how the regulatory connections between these four genes evolved to produce wing- and sector-specific variation in eyespot number.
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Affiliation(s)
- Yuji Matsuoka
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Block S2, Level 1, 117543Singapore
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Block S2, Level 1, 117543Singapore
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6
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Lail SS, Arnold CR, de Almeida LGN, McKenna N, Chiriboga JA, Dufour A, Warren AL, Yates RM. Hox-driven conditional immortalization of myeloid and lymphoid progenitors: Uses, advantages, and future potential. Traffic 2022; 23:538-553. [PMID: 36117140 DOI: 10.1111/tra.12869] [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: 06/10/2022] [Revised: 08/28/2022] [Accepted: 09/12/2022] [Indexed: 01/20/2023]
Abstract
Those who study macrophage biology struggle with the decision whether to utilize primary macrophages derived directly from mice or opt for the convenience and genetic tractability of immortalized macrophage-like cell lines in in vitro studies. Particularly when it comes to studying phagocytosis and phagosomal maturation-a signature cellular process of the macrophage-many commonly used cell lines are not representative of what occurs in primary macrophages. A system developed by Mark Kamps' group, that utilizes conditionally constitutive activity of Hox transcription factors (Hoxb8 and Hoxa9) to immortalize differentiation-competent myeloid cell progenitors of mice, offers an alternative to the macrophage/macrophage-like dichotomy. In this resource, we will review the use of Hoxb8 and Hoxa9 as hematopoietic regulators to conditionally immortalize murine hematopoietic progenitor cells which retain their ability to differentiate into many functional immune cell types including macrophages, neutrophils, basophils, osteoclasts, eosinophils, dendritic cells, as well as limited potential for the generation of lymphocytes. We further demonstrate that the use of macrophages derived from Hoxb8/Hoxa9 immortalized progenitors and their similarities to bone marrow-derived macrophages. To supplement the existing data, mass spectrometry-based proteomics, flow cytometry, cytology, and in vitro phagosomal assays were conducted on macrophages derived from Hoxb8 immortalized progenitors and compared to bone marrow-derived macrophages and the macrophage-like cell line J774. We additionally propose the use of a standardized nomenclature to describe cells derived from the Hoxb8/Hoxa9 system in anticipation of their expanded use in the study of leukocyte cell biology.
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Affiliation(s)
- Shranjit S Lail
- Department of Medical Science, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Corey R Arnold
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Luiz G N de Almeida
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Neil McKenna
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jose A Chiriboga
- Department of Veterinary Clinical and Diagnostic Sciences, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Antoine Dufour
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Snyder Institute of Chronic Disease, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Amy L Warren
- Department of Veterinary Clinical and Diagnostic Sciences, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Robin Michael Yates
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.,Snyder Institute of Chronic Disease, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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7
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Feng W, Li Y, Kratsios P. Emerging Roles for Hox Proteins in the Last Steps of Neuronal Development in Worms, Flies, and Mice. Front Neurosci 2022; 15:801791. [PMID: 35185450 PMCID: PMC8855150 DOI: 10.3389/fnins.2021.801791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/31/2021] [Indexed: 12/28/2022] Open
Abstract
A remarkable diversity of cell types characterizes every animal nervous system. Previous studies provided important insights into how neurons commit to a particular fate, migrate to the right place and form precise axodendritic patterns. However, the mechanisms controlling later steps of neuronal development remain poorly understood. Hox proteins represent a conserved family of homeodomain transcription factors with well-established roles in anterior-posterior (A-P) patterning and the early steps of nervous system development, including progenitor cell specification, neuronal migration, cell survival, axon guidance and dendrite morphogenesis. This review highlights recent studies in Caenorhabditis elegans, Drosophila melanogaster and mice that suggest new roles for Hox proteins in processes occurring during later steps of neuronal development, such as synapse formation and acquisition of neuronal terminal identity features (e.g., expression of ion channels, neurotransmitter receptors, and neuropeptides). Moreover, we focus on exciting findings suggesting Hox proteins are required to maintain synaptic structures and neuronal terminal identity during post-embryonic life. Altogether, these studies, in three model systems, support the hypothesis that certain Hox proteins are continuously required, from early development throughout post-embryonic life, to build and maintain a functional nervous system, significantly expanding their functional repertoire beyond the control of early A-P patterning.
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Affiliation(s)
- Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL, United States
- University of Chicago Neuroscience Institute, Chicago, IL, United States
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL, United States
| | - Yinan Li
- Department of Neurobiology, University of Chicago, Chicago, IL, United States
- University of Chicago Neuroscience Institute, Chicago, IL, United States
- Committee on Neurobiology, University of Chicago, Chicago, IL, United States
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, United States
- University of Chicago Neuroscience Institute, Chicago, IL, United States
- *Correspondence: Paschalis Kratsios,
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8
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Wang HQ, Wang WH, Chen CZ, Guo HX, Jiang H, Yuan B, Zhang JB. Regulation of FSH Synthesis by Differentially Expressed miR-488 in Anterior Adenohypophyseal Cells. Animals (Basel) 2021; 11:ani11113262. [PMID: 34827994 PMCID: PMC8614264 DOI: 10.3390/ani11113262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/27/2021] [Accepted: 11/12/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary GnRH and FSH play an important regulatory role in the reproductive activities of mammals. At present, many artificially synthesized GnRH analogues have been used in the regulation of cattle reproduction and the clinical treatment of various reproductive diseases. This study explored the potential mechanism of miR-488 in GnRH regulation of FSH synthesis and secretion and provides a theoretical basis for the application of GnRH analogue in cattle artificial breeding. We hope to provide a research foundation for improving the processing procedures of cattle estrus control and the domestic application of hormone products. Abstract Gonadotropin-releasing hormone (GnRH), which is synthesized and released by the hypothalamus, promotes the synthesis and secretion of follicle-stimulating hormone (FSH), thereby regulating the growth and reproduction of animals. GnRH analogues have been widely used in livestock production. MiRNAs, which are endogenous non-coding RNAs, have been found to play important roles in hormone regulation and other physiological processes in recent years. However, the roles of miRNAs in GnRH-mediated regulation of FSH secretion have rarely been studied. Herein, we treated bovine anterior adenohypophyseal cells with an exogenous GnRH analogue and found that miR-488 was differentially expressed. Through a combination of TargetScan prediction and dual luciferase reporter analysis, miR-488 was confirmed to be able to target the FSHB gene. Based on this finding, we verified the expression of Fshβ and Lhβ mRNA in the rat adenohypophysis before and after exogenous GnRH treatment in vivo and in vitro. Experiments on rat anterior adenohypophyseal cells showed that overexpression of miR-488 significantly inhibited Fshβ expression and FSH synthesis, while knockdown of miR-488 had the opposite effects. Our results demonstrate that GnRH relies on miR-488 to regulate FSH synthesis, providing additional useful evidence for the significance of miRNAs in the regulation of animal reproduction.
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Affiliation(s)
| | | | | | | | | | - Bao Yuan
- Correspondence: (B.Y.); (J.-B.Z.); Tel.: +86-431-8783-6536 (B.Y.); +86-431-8783-6551 (J.-B.Z.)
| | - Jia-Bao Zhang
- Correspondence: (B.Y.); (J.-B.Z.); Tel.: +86-431-8783-6536 (B.Y.); +86-431-8783-6551 (J.-B.Z.)
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LINC00152 acts as a potential marker in gliomas and promotes tumor proliferation and invasion through the LINC00152/miR-107/RAB10 axis. J Neurooncol 2021; 154:285-299. [PMID: 34478013 DOI: 10.1007/s11060-021-03836-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/25/2021] [Indexed: 10/20/2022]
Abstract
PURPOSE Aberrant expression of long noncoding RNAs plays a pivotal role in tumorigenesis. Recently, several studies have showed that the LINC00152 gene is upregulated in a variety of tumors and plays an oncogene role; however, its underlying molecular mechanisms in glioblastoma remain unclear. In this study, we prepare to investigate the biological role and underlying molecular mechanisms of LINC00152 in glioblastoma cells. METHODS Bioinformatics analysis to identify LINC00152 expression, Cell Counting kit-8 assay and Colony formation assay were used to evaluate proliferation, Flow cytometric analysis was used to evaluate apoptosis, Cell Matrigel invasion assay and Wound healing assay was used to evaluate invasion, Western blot analysis to check protein expression level, Mouse xenograft models was used to check cell proliferation in vivo. RESULTS In this study, we found that LINC00152 was upregulated in gliomas and its expression was significantly associated with high tumor aggressiveness and poor outcomes for glioma patients. Functionally, the knockdown of LINC00152 not only inhibited malignant behaviors of glioma, such as proliferation and invasion of glioma cells and induced apoptosis in vitro but also suppressed tumorigenesis in vivo. Mechanistically, results of the bioinformatics analysis and experimental studies confirmed that LINC00152 and RAB10 as the targets of miR-107, and LINC00152 might act as a sponge for miR-107 to regulate the expression of RAB10 in glioblastoma. Additionally, silencing miR-107 reversed the effects induced by LINC00152 knockdown on glioblastoma cells both in vitro and in vivo. CONCLUSION Our data suggested that LINC00152 is a candidate prognostic marker of glioma, and that the LINC00152/MIR-107/RAB10 axis plays a pivotal role in regulation of the glioma malignancy, and therefore, targeting the axis might be an effective therapeutic strategy to treat glioma.
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10
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Gadhave K, Kumar D, Uversky VN, Giri R. A multitude of signaling pathways associated with Alzheimer's disease and their roles in AD pathogenesis and therapy. Med Res Rev 2021; 41:2689-2745. [PMID: 32783388 PMCID: PMC7876169 DOI: 10.1002/med.21719] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/13/2020] [Accepted: 07/29/2020] [Indexed: 02/06/2023]
Abstract
The exact molecular mechanisms associated with Alzheimer's disease (AD) pathology continue to represent a mystery. In the past decades, comprehensive data were generated on the involvement of different signaling pathways in the AD pathogenesis. However, the utilization of signaling pathways as potential targets for the development of drugs against AD is rather limited due to the immense complexity of the brain and intricate molecular links between these pathways. Therefore, finding a correlation and cross-talk between these signaling pathways and establishing different therapeutic targets within and between those pathways are needed for better understanding of the biological events responsible for the AD-related neurodegeneration. For example, autophagy is a conservative cellular process that shows link with many other AD-related pathways and is crucial for maintenance of the correct cellular balance by degrading AD-associated pathogenic proteins. Considering the central role of autophagy in AD and its interplay with many other pathways, the finest therapeutic strategy to fight against AD is the use of autophagy as a target. As an essential step in this direction, this comprehensive review represents recent findings on the individual AD-related signaling pathways, describes key features of these pathways and their cross-talk with autophagy, represents current drug development, and introduces some of the multitarget beneficial approaches and strategies for the therapeutic intervention of AD.
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Affiliation(s)
- Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Deepak Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
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11
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Hajirnis N, Mishra RK. Homeotic Genes: Clustering, Modularity, and Diversity. Front Cell Dev Biol 2021; 9:718308. [PMID: 34458272 PMCID: PMC8386295 DOI: 10.3389/fcell.2021.718308] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
Hox genes code for transcription factors and are evolutionarily conserved. They regulate a plethora of downstream targets to define the anterior-posterior (AP) body axis of a developing bilaterian embryo. Early work suggested a possible role of clustering and ordering of Hox to regulate their expression in a spatially restricted manner along the AP axis. However, the recent availability of many genome assemblies for different organisms uncovered several examples that defy this constraint. With recent advancements in genomics, the current review discusses the arrangement of Hox in various organisms. Further, we revisit their discovery and regulation in Drosophila melanogaster. We also review their regulation in different arthropods and vertebrates, with a significant focus on Hox expression in the crustacean Parahyale hawaiensis. It is noteworthy that subtle changes in the levels of Hox gene expression can contribute to the development of novel features in an organism. We, therefore, delve into the distinct regulation of these genes during primary axis formation, segment identity, and extra-embryonic roles such as in the formation of hair follicles or misregulation leading to cancer. Toward the end of each section, we emphasize the possibilities of several experiments involving various organisms, owing to the advancements in the field of genomics and CRISPR-based genome engineering. Overall, we present a holistic view of the functioning of Hox in the animal world.
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Affiliation(s)
- Nikhil Hajirnis
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Rakesh K. Mishra
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
- AcSIR – Academy of Scientific and Innovative Research, Ghaziabad, India
- Tata Institute for Genetics and Society (TIGS), Bangalore, India
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12
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Mika K, Cruchet S, Chai PC, Prieto-Godino LL, Auer TO, Pradervand S, Benton R. Olfactory receptor-dependent receptor repression in Drosophila. SCIENCE ADVANCES 2021; 7:eabe3745. [PMID: 34362730 PMCID: PMC8346220 DOI: 10.1126/sciadv.abe3745] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 06/17/2021] [Indexed: 06/01/2023]
Abstract
In olfactory systems across phyla, most sensory neurons express a single olfactory receptor gene selected from a large genomic repertoire. We describe previously unknown receptor gene-dependent mechanisms that ensure singular expression of receptors encoded by a tandem gene array [Ionotropic receptor 75c (Ir75c), Ir75b, and Ir75a, organized 5' to 3'] in Drosophila melanogaster Transcription from upstream genes in the cluster runs through the coding region of downstream loci and inhibits their expression in cis, most likely via transcriptional interference. Moreover, Ir75c blocks accumulation of other receptor proteins in trans through a protein-dependent, posttranscriptional mechanism. These repression mechanisms operate in endogenous neurons, in conjunction with cell type-specific gene regulatory networks, to ensure unique receptor expression. Our data provide evidence for inter-olfactory receptor regulation in invertebrates and highlight unprecedented, but potentially widespread, mechanisms for ensuring exclusive expression of chemosensory receptors, and other protein families, encoded by tandemly arranged genes.
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Affiliation(s)
- Kaan Mika
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Steeve Cruchet
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Phing Chian Chai
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Lucia L Prieto-Godino
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Thomas O Auer
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Sylvain Pradervand
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
- Lausanne Genomic Technologies Facility, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland.
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Chen H, Shan G. The physiological function of long-noncoding RNAs. Noncoding RNA Res 2020; 5:178-184. [PMID: 32959025 PMCID: PMC7494506 DOI: 10.1016/j.ncrna.2020.09.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
The physiological processes of cells and organisms are regulated by various biological macromolecules, including long-noncoding RNAs (lncRNAs), which cannot be translated into protein and are different from small-noncoding RNAs on their length. In animals, lncRNAs are involved in development, metabolism, reproduction, aging and other life events by cis or trans effects. For many functional lncRNAs, there is growing evidence that they play different roles on cellular level and organismal level. On the other hand, many annotated lncRNAs are not essential and could be transcription noises. In this minireview, we investigate the physiological function of lncRNAs in cells and focus on their functions and functional mechanisms on the organismal level. The studies on lncRNAs using different classic animal models such as worms and flies are summarized and discussed in this article.
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Affiliation(s)
- He Chen
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province, 230027, China
| | - Ge Shan
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province, 230027, China
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Guan L, Li T, Ai N, Wang W, He B, Bai Y, Yu Z, Li M, Dong S, Zhu Q, Ding XX, Zhang S, Li M, Tang G, Xia X, Zhao J, Lin S, Yao S, Zhang L, Chen G, Liu FE, Li X, Zhang H. MEIS2C and MEIS2D promote tumor progression via Wnt/β-catenin and hippo/YAP signaling in hepatocellular carcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:417. [PMID: 31623651 PMCID: PMC6796342 DOI: 10.1186/s13046-019-1417-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/09/2019] [Indexed: 01/14/2023]
Abstract
Background MEIS2 has been identified as one of the key transcription factors in the gene regulatory network in the development and pathogenesis of human cancers. Our study aims to identify the regulatory mechanisms of MEIS2 in hepatocellular carcinoma (HCC), which could be targeted to develop new therapeutic strategies. Methods The variation of MEIS2 levels were assayed in a cohort of HCC patients. The proliferation, clone-formation, migration, and invasion abilities of HCC cells were measured to analyze the effects of MEIS2C and MEIS2D (MEIS2C/D) knockdown with small hairpin RNAs in vitro and in vivo. Chromatin immunoprecipitation (ChIP) was performed to identify MEIS2 binding site. Immunoprecipitation and immunofluorescence assays were employed to detect proteins regulated by MEIS2. Results The expression of MEIS2C/D was increased in the HCC specimens when compared with the adjacent noncancerous liver (ANL) tissues. Moreover, MEIS2C/D expression negatively correlated with the prognosis of HCC patients. On the other hand, knockdown of MEIS2C/D could inhibit proliferation and diminish migration and invasion of hepatoma cells in vitro and in vivo. Mechanistically, MESI2C activated Wnt/β-catenin pathway in cooperation with Parafibromin (CDC73), while MEIS2D suppressed Hippo pathway by promoting YAP nuclear translocation via miR-1307-3p/LATS1 axis. Notably, CDC73 could directly either interact with MEIS2C/β-catenin or MEIS2D/YAP complex, depending on its tyrosine-phosphorylation status. Conclusions Our studies indicate that MEISC/D promote HCC development via Wnt/β-catenin and Hippo/YAP signaling pathways, highlighting the complex molecular network of MEIS2C/D in HCC pathogenesis. These results suggest that MEISC/D may serve as a potential novel therapeutic target for HCC.
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Affiliation(s)
- Lei Guan
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, 28, Xianning West Road, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Ting Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, 28, Xianning West Road, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Nanping Ai
- Department of Ophthalmology, Chinese PLA General Hospital, Beijing, 100853, People's Republic of China
| | - Wei Wang
- Department of Immunology, State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, China
| | - Bing He
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, 28, Xianning West Road, Xi'an, 710049, Shaanxi, People's Republic of China.,Department of Clinical Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Yanxia Bai
- Department of Otolaryngology-Head-Neck Surgery, The First Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Zhaocai Yu
- Department of Medical Oncology. Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, People's Republic of China
| | - Mingyue Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 712 Stellar-Chance Laboratories, 422 Curie Blvd, Philadelphia, PA, 19104, USA
| | - Shanshan Dong
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, 28, Xianning West Road, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Qingge Zhu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, 28, Xianning West Road, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Xiao Xiao Ding
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, 28, Xianning West Road, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Shiming Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, 28, Xianning West Road, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Ming Li
- School of Electronics and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Guangbo Tang
- Medical College, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Xiaochun Xia
- Department of Medical Technology, Xiamen Medical College, Xiamen, 361023, People's Republic of China
| | - Jing Zhao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, 28, Xianning West Road, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Song Lin
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, 28, Xianning West Road, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Shi Yao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, 28, Xianning West Road, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Lei Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, 28, Xianning West Road, Xi'an, 710049, Shaanxi, People's Republic of China.,Department of General Surgery, 967 Hospital of PLA, Dalian, 116041, People's Republic of China
| | - Geng Chen
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, 28, Xianning West Road, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Fang-E Liu
- Medical College, Xi'an Peihua University, Xi'an, People's Republic of China
| | - Xinyuan Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 712 Stellar-Chance Laboratories, 422 Curie Blvd, Philadelphia, PA, 19104, USA.
| | - Huqin Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, 28, Xianning West Road, Xi'an, 710049, Shaanxi, People's Republic of China.
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15
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Wang H, Hu H, Xiang Z, Lu C, Dai F, Tong X. Identification and characterization of a new long noncoding RNA iab-1 in the Hox cluster of silkworm, Bombyx mori identification of iab-1. J Cell Biochem 2019; 120:17283-17292. [PMID: 31106470 DOI: 10.1002/jcb.28990] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/06/2019] [Accepted: 04/11/2019] [Indexed: 02/04/2023]
Abstract
Long noncoding RNAs (lncRNAs) areinvolvedin a variety of biological processes. In silkworm, numerous lncRNAs have been predicted through deep transcriptome sequencing, but no functional role has been experimentally validated yet. Here, we characterized a new lncRNA iab-1 that was mainly encoded by the intergenic region between Bmabd-A and Bmabd-B in the Homeobox (Hox) cluster of the silkworm, Bombyx mori. More than seven alternative splicing isoforms of lncRNA iab-1 were cloned, which were subgrouped into types 1 and 2 based on the location of the 3'-ends. The iab-1 was expressed at a low level, but the expression of iab-1 peaked at several specific development stages, including 3 to 4 days during the embryonic stage, stages before fourth molting, and the sixth hour after the fourth molting, and early stages during metamorphosis. It was highly expressed in the nervus and epidermis, especially the epidermis of the posterior abdomen at the fourth instar premolting stage. The relationship between iab-1 and nearby Hox genes was analyzed at different developmental stages. Iab-1 expression was highly associated with Bmabd-A as well as Bmabd-B in the embryonic and larval stages, while this association was decreased at the metamorphic stage; iab-1 expression was highly associated with BmUbx only in the embryonic stage. Downregulation of iab-1 expression by small interfering RNA led to the death of most of the treated individuals at the larval stage, suggesting that iab-1 transcript expression might be involved in certain relevant physiological processes. The expression of Bmabd-A and Bmabd-B did not change in iab-1 downregulated individuals, indicating that the relevance between the two genes and iab-1 was not induced by iab-1 transcript. Collectively, the results showed that the newly identified iab-1 may be involved in some physiological processes, and the interaction between iab-1 and Hox genes was also preliminarily analyzed.
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Affiliation(s)
- Honglei Wang
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Hai Hu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Zhonghuai Xiang
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Cheng Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Fangyin Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Xiaoling Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
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16
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Wang A, Wang J, Liu Y, Zhou Y. Mechanisms of Long Non-Coding RNAs in the Assembly and Plasticity of Neural Circuitry. Front Neural Circuits 2017; 11:76. [PMID: 29109677 PMCID: PMC5660110 DOI: 10.3389/fncir.2017.00076] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/28/2017] [Indexed: 12/31/2022] Open
Abstract
The mechanisms underlying development processes and functional dynamics of neural circuits are far from understood. Long non-coding RNAs (lncRNAs) have emerged as essential players in defining identities of neural cells, and in modulating neural activities. In this review, we summarized latest advances concerning roles and mechanisms of lncRNAs in assembly, maintenance and plasticity of neural circuitry, as well as lncRNAs' implications in neurological disorders. We also discussed technical advances and challenges in studying functions and mechanisms of lncRNAs in neural circuitry. Finally, we proposed that lncRNA studies would advance our understanding on how neural circuits develop and function in physiology and disease conditions.
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Affiliation(s)
- Andi Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Junbao Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ying Liu
- Medical Research Institute, Wuhan University, Wuhan, China
| | - Yan Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.,Medical Research Institute, Wuhan University, Wuhan, China
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17
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Wang Q, Zhang J, Liu Y, Zhang W, Zhou J, Duan R, Pu P, Kang C, Han L. A novel cell cycle-associated lncRNA, HOXA11-AS, is transcribed from the 5-prime end of the HOXA transcript and is a biomarker of progression in glioma. Cancer Lett 2016; 373:251-9. [PMID: 26828136 DOI: 10.1016/j.canlet.2016.01.039] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/08/2016] [Accepted: 01/24/2016] [Indexed: 01/17/2023]
Abstract
The comprehensive lncRNA expression signature in glioma has not yet been fully elucidated. We performed a high-throughput microarray to detect the ncRNA expression profiles of 220 human glioma tissues. Here, we found that a novel lncRNA, HOXA11-AS, was the antisense transcript of the HOX11 gene. It was shown that HOXA11-AS was closely associated with glioma grade and poor prognosis. Multivariate Cox regression analysis revealed that HOXA11-AS was an independent prognostic factor in glioblastoma multiforme patients, and its expression was correlated with the glioma molecular subtypes of the Cancer Genome Atlas. Gene set enrichment analysis indicated that the gene sets most correlated with HOXA11-AS expression were involved in cell cycle progression. Over-expression of the HOXA11-AS transcript promoted cell proliferation in vitro, while knockdown of HOXA11-AS expression repressed cell proliferation via regulation of cell cycle progression. The growth-promoting and growth-inhibiting effects of HOXA11-AS were also demonstrated in a xenograft mouse model. Our data confirms, for the first time, that HOXA11-AS is an important long non-coding RNA that primarily serves as a prognostic factor for glioma patient survival. HOXA11-AS could serve as a biomarker for identifying glioma molecular subtypes and as therapeutic target for glioma patients.
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Affiliation(s)
- Qixue Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China; Key Laboratory of Post-trauma Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin 300052, China; Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China; Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China
| | - Junxia Zhang
- Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China; Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yanwei Liu
- Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China; Glioma Center, Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Wei Zhang
- Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China; Glioma Center, Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Junhu Zhou
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China; Key Laboratory of Post-trauma Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin 300052, China; Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China; Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China
| | - Ran Duan
- Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China; Glioma Center, Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Peiyu Pu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China; Key Laboratory of Post-trauma Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin 300052, China; Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China; Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China
| | - Chunsheng Kang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China; Key Laboratory of Post-trauma Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin 300052, China; Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China; Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China
| | - Lei Han
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China; Key Laboratory of Post-trauma Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin 300052, China; Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China; Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China.
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18
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Picao-Osorio J, Johnston J, Landgraf M, Berni J, Alonso CR. MicroRNA-encoded behavior in Drosophila. Science 2015; 350:815-20. [PMID: 26494171 PMCID: PMC4902127 DOI: 10.1126/science.aad0217] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/25/2015] [Indexed: 12/20/2022]
Abstract
The relationship between microRNA (miRNA) regulation and the specification of behavior is only beginning to be explored. We found that mutation of a single miRNA locus (miR-iab4/iab8) in Drosophila larvae affects the animal's capacity to correct its orientation if turned upside down (self-righting). One of the miRNA targets involved in this behavior is the Hox gene Ultrabithorax, whose derepression in two metameric neurons leads to self-righting defects. In vivo neural activity analysis reveals that these neurons, the self-righting node (SRN), have different activity patterns in wild type and miRNA mutants, whereas thermogenetic manipulation of SRN activity results in changes in self-righting behavior. Our work thus reveals a miRNA-encoded behavior and suggests that other miRNAs might also be involved in behavioral control in Drosophila and other species.
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Affiliation(s)
- Joao Picao-Osorio
- Sussex Neuroscience, School of Life Science, University of Sussex, Brighton BN1 9QG, UK
| | - Jamie Johnston
- Sussex Neuroscience, School of Life Science, University of Sussex, Brighton BN1 9QG, UK
| | - Matthias Landgraf
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Jimena Berni
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Claudio R Alonso
- Sussex Neuroscience, School of Life Science, University of Sussex, Brighton BN1 9QG, UK.
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19
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Abstract
Apoptosis is a cellular suicide program, which is on the one hand used to remove superfluous cells thereby promoting tissue or organ morphogenesis. On the other hand, the programmed killing of cells is also critical when potentially harmful cells emerge in a developing or adult organism thereby endangering survival. Due to its critical role apoptosis is tightly controlled, however so far, its regulation on the transcriptional level is less studied and understood. Hox genes, a highly conserved gene family encoding homeodomain transcription factors, have crucial roles in development. One of their prominent functions is to shape animal body plans by eliciting different developmental programs along the anterior-posterior axis. To this end, Hox proteins transcriptionally regulate numerous processes in a coordinated manner, including cell-type specification, differentiation, motility, proliferation as well as apoptosis. In this review, we will focus on how Hox proteins control organismal morphology and function by regulating the apoptotic machinery. We will first focus on well-established paradigms of Hox-apoptosis interactions and summarize how Hox transcription factors control morphological outputs and differentially shape tissues along the anterior-posterior axis by fine-tuning apoptosis in a healthy organism. We will then discuss the consequences when this interaction is disturbed and will conclude with some ideas and concepts emerging from these studies.
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Hox miRNA regulation within the Drosophila Bithorax complex: Patterning behavior. Mech Dev 2015; 138 Pt 2:151-159. [PMID: 26311219 DOI: 10.1016/j.mod.2015.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 08/14/2015] [Accepted: 08/17/2015] [Indexed: 01/02/2023]
Abstract
The study of Drosophila Hox genes, located in the Antennapedia complex (ANT-C) and Bithorax complex (BX-C), has provided fundamental insights into mechanisms of how the segments of the animal body plan are specified. Notably, even though the analysis of the BX-C formally began over a century ago, surprises continue to emerge regarding its regulation and function. Even simply the gene content of the BX-C has been regularly revised in past years, especially with regard to non-coding RNAs (ncRNAs), including microRNAs. In this perspective, we review the history of studies of non-coding transcription in the BX-C, and highlight recent studies of its miRNAs that provide new insights into their tissue-specific roles in Hox gene regulation. In particular, we have demonstrated unexpected importance of endogenous BX-C miRNAs to restrict the spatial accumulation of Hox proteins and their TALE cofactors in the ventral nerve cord, and link this to aberrant neural differentiation and reproductive behavior. These findings open new directions on studying Hox miRNA function, and we speculate that further understanding of their roles in insect models may provide new leads for studying the enigmatic biological functions of analogous miRNAs located in vertebrate Hox clusters.
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Following the intracellular localization of the iab-8ncRNA of the bithorax complex using the MS2-MCP-GFP system. Mech Dev 2015; 138 Pt 2:133-140. [PMID: 26277563 DOI: 10.1016/j.mod.2015.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/05/2015] [Accepted: 08/07/2015] [Indexed: 10/23/2022]
Abstract
Homeotic genes are aligned on the chromosome in the order of the segments that they specify along the antero-posterior axis of the fly. In general the genes affecting the more posterior segments repress the more anterior genes, a phenomenon known as "posterior dominance". There is however a noticeable exception to this rule in the central nervous system of Drosophila melanogaster where the posterior Abd-B gene does not repress the immediately more anterior abd-A gene. Instead, abd-A repression is accomplished by a 92 kb-long ncRNA (the iab-8ncRNA) that is transcribed from the large inter-genic region between abd-A and Abd-B. This iab-8ncRNA encodes a microRNA to repress abd-A and also a second redundant repression mechanism acting in cis and thought to be transcriptional interference with the abd-A promoter. Using in situ hybridization, a previous work suggested that the iab8ncRNA transcript forms discrete foci restricted to the nuclear periphery and that this localization may be important for its function. In order to better characterize the intra-cellular localization of the iab-8ncRNA we used the MS2-MCP system, which allows fluorescent labeling of RNA in cells and relies on the interaction between GFP-tagged MS2 coat protein (MCP-GFP) and MS2 RNA stem loops. Our results indicate that the large foci seen in previous studies correspond to the site of iab8ncRNA transcription and that the foci seen may simply be an indication of the level of transcription at the locus. We find no evidence to suggest that this localization is important for its function on abd-A repression. We discuss the idea that the iab-8ncRNA may be a relic of a more general ancient mechanism of posterior dominance during the emergence of the hox clusters that was mediated by transcriptional interference.
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22
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Cellerino A, Bally-Cuif L, Pizzorusso T. Editorial for "Regulatory RNAs in the nervous system". Front Cell Neurosci 2015; 9:38. [PMID: 25713514 PMCID: PMC4322715 DOI: 10.3389/fncel.2015.00038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 01/22/2015] [Indexed: 01/19/2023] Open
Affiliation(s)
- Alessandro Cellerino
- Scuola Normale Superiore Pisa, Italy ; Biology of Aging, Fritz Lipmann Institute for Age Research-Leibniz Institute Jena, Germany
| | - Laure Bally-Cuif
- Institute of Neurobiology A. Fessard, CNRS UPR3294 Gif-sur-Yvette, France
| | - Tommaso Pizzorusso
- Department of Neuroscience, Psychology, Drug Research and Child Health Neurofarba, University of Florence Florence, Italy ; Pisa Unit, Institute of Neuroscience, National Research Council Pisa, Italy
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23
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Singh NP, Mishra RK. Role of abd-A and Abd-B in development of abdominal epithelia breaks posterior prevalence rule. PLoS Genet 2014; 10:e1004717. [PMID: 25340649 PMCID: PMC4207640 DOI: 10.1371/journal.pgen.1004717] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 08/28/2014] [Indexed: 11/19/2022] Open
Abstract
Hox genes that determine anteroposterior body axis formation in all bilaterians are often found to have partially overlapping expression pattern. Since posterior genes dominate over anterior Hox genes in the region of co-expression, the anterior Hox genes are thought to have no function in such regions. In this study we show that two Hox genes have distinct and essential functions in the same cell. In Drosophila, the three Hox genes of the bithorax complex, Ubx, abd-A and Abd-B, show coexpression during embryonic development. Here, we show that in early pupal abdominal epithelia, Ubx does not coexpress with abd-A and Abd-B, while abd-A and Abd-B continue to coexpress in the same nuclei. The abd-A and Abd-B are expressed in both histoblast nest cells and larval epithelial cells of early pupal abdominal epithelia. Further functional studies demonstrate that abd-A is required in histoblast nest cells for their proliferation and suppression of Ubx to prevent first abdominal segment like features in posterior segments while in larval epithelial cells it is required for their elimination. We also observed that these functions of abd-A are required in its exclusive as well as the coexpression domain with that of Abd-B. The expression of Abd-B is required in histoblast nest cells for their identity while it is dispensable in the larval epithelial cells. The higher level of Abd-B in the seventh abdominal segment, that down-regulates abd-A expression, leads this segment to be absent in males or of smaller size in females. We also show that abd-A in histoblast nest cells positively regulates expression of wingless for the formation of the abdominal epithelia. Our study reveals an exception to the rule of posterior prevalence and shows that two different Hox genes have distinct functions in the same cell, which is essential for the development of abdominal epithelia. The spatially non-overlapping function of Hox genes is known to determine Antero-posterior body axis in all the bilaterians. The expression of Hox genes is found to be overlapping in several cases. According to the posterior prevalence rule, posterior Hox genes suppress the function of anterior Hox genes in the overlapping expression domains. Our findings show an exception to the rule of posterior prevalence. We show that in the overlapping expression domains of abd-A and Abd-B in early pupal abdominal epithelia, both the genes have essential roles. While abd-A is required for cell proliferation, Abd-B determines the segmental identity.
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Affiliation(s)
- Narendra Pratap Singh
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, India
| | - Rakesh Kumar Mishra
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, India
- * E-mail:
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