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Parambath S, Selvraj NR, Venugopal P, Aradhya R. Notch Signaling: An Emerging Paradigm in the Pathogenesis of Reproductive Disorders and Diverse Pathological Conditions. Int J Mol Sci 2024; 25:5423. [PMID: 38791461 PMCID: PMC11121885 DOI: 10.3390/ijms25105423] [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: 02/01/2024] [Revised: 03/27/2024] [Accepted: 04/20/2024] [Indexed: 05/26/2024] Open
Abstract
The highly conserved Notch pathway, a pillar of juxtacrine signaling, orchestrates intricate intercellular communication, governing diverse developmental and homeostatic processes through a tightly regulated cascade of proteolytic cleavages. This pathway, culminating in the migration of the Notch intracellular domain (NICD) to the nucleus and the subsequent activation of downstream target genes, exerts a profound influence on a plethora of molecular processes, including cell cycle progression, lineage specification, cell-cell adhesion, and fate determination. Accumulating evidence underscores the pivotal role of Notch dysregulation, encompassing both gain and loss-of-function mutations, in the pathogenesis of numerous human diseases. This review delves deep into the multifaceted roles of Notch signaling in cellular dynamics, encompassing proliferation, differentiation, polarity maintenance, epithelial-mesenchymal transition (EMT), tissue regeneration/remodeling, and its intricate interplay with other signaling pathways. We then focus on the emerging landscape of Notch aberrations in gynecological pathologies predisposing individuals to infertility. By highlighting the exquisite conservation of Notch signaling in Drosophila and its power as a model organism, we pave the way for further dissection of disease mechanisms and potential therapeutic interventions through targeted modulation of this master regulatory pathway.
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Affiliation(s)
| | | | | | - Rajaguru Aradhya
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, Kerala, India; (S.P.); (N.R.S.); (P.V.)
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2
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Kałafut J, Czerwonka A, Czapla K, Przybyszewska-Podstawka A, Hermanowicz JM, Rivero-Müller A, Borkiewicz L. Regulation of Notch1 Signalling by Long Non-Coding RNAs in Cancers and Other Health Disorders. Int J Mol Sci 2023; 24:12579. [PMID: 37628760 PMCID: PMC10454443 DOI: 10.3390/ijms241612579] [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: 07/12/2023] [Revised: 07/30/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Notch1 signalling plays a multifaceted role in tissue development and homeostasis. Currently, due to the pivotal role of Notch1 signalling, the relationship between NOTCH1 expression and the development of health disorders is being intensively studied. Nevertheless, Notch1 signalling is not only controlled at the transcriptional level but also by a variety of post-translational events. First is the ligand-dependent mechanical activation of NOTCH receptors and then the intracellular crosstalk with other signalling molecules-among those are long non-coding RNAs (lncRNAs). In this review, we provide a detailed overview of the specific role of lncRNAs in the modulation of Notch1 signalling, from expression to activity, and their connection with the development of health disorders, especially cancers.
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Affiliation(s)
- Joanna Kałafut
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Arkadiusz Czerwonka
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Karolina Czapla
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Alicja Przybyszewska-Podstawka
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Justyna Magdalena Hermanowicz
- Department of Pharmacodynamics, Medical University of Bialystok, Mickiewicza 2C, 15-222 Bialystok, Poland;
- Department of Clinical Pharmacy, Medical University of Bialystok, Waszyngtona 15, 15-274 Bialystok, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Lidia Borkiewicz
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
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3
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Lampada A, Taylor V. Notch signaling as a master regulator of adult neurogenesis. Front Neurosci 2023; 17:1179011. [PMID: 37457009 PMCID: PMC10339389 DOI: 10.3389/fnins.2023.1179011] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023] Open
Abstract
Neurogenesis ceases in most regions of the mammalian brain before or shortly after birth, however, in a few restricted brain regions, the production of new neurons proceeds into adulthood. Neural stem cells (NSCs) in these neurogenic zones are integrated into niches that control their activity and fate. Most stem cells in the adult brain are mitotically inactive and these cells can remain quiescent for months or even years. One of the key questions is what are the molecular mechanisms that regulate NSC maintenance and differentiation. Notch signaling has been shown to be a critical regulator of stem cell activity and maintenance in many tissues including in the nervous system. In this mini-review we discuss the roles of Notch signaling and the functions of the different Notch receptors and ligands in regulating neurogenesis in the adult murine brain. We review the functions of Notch signaling components in controlling NSC quiescence and entry into cell cycle and neurogenesis.
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A novel variant in TLE6 is associated with embryonic developmental arrest (EDA) in familial female infertility. Sci Rep 2022; 12:17664. [PMID: 36271123 PMCID: PMC9587212 DOI: 10.1038/s41598-022-22687-y] [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: 05/07/2022] [Accepted: 10/18/2022] [Indexed: 01/18/2023] Open
Abstract
This study aims to identify genetic causes of familial female infertility characterized by embryonic developmental arrest (EDA) and repeated implantation failure (RIF) with oocyte donation IVF cycle. We used Whole-exome sequencing and Sanger validation to find causative genes in an Iranian consanguineous family that had 3 infertile daughters, 4 fertile daughters, and 2 fertile sons. All patients in this consanguineous family exhibited typical manifestations of unexplained RIF and EDA. Genetic analysis identified a homozygous missense variant (c.G1054C:p.G352R) in exon 13 of the TLE6 gene that cosegregated with the EDA phenotype in an autosomal recessive pattern. Other members of the family, the gene carriers, remain clinically asymptomatic and fertile. Our findings identify a novel nonsynonymous variant, c.G1054C:p.G352R, in the TLE6 gene within a consanguineous Iranian family with autosomal-recessive female infertility and broaden the genetic spectrum of TLE6-associated EDA.
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A dopamine-methacrylated hyaluronic acid hydrogel as an effective carrier for stem cells in skin regeneration therapy. Cell Death Dis 2022; 13:738. [PMID: 36030275 PMCID: PMC9420120 DOI: 10.1038/s41419-022-05060-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/05/2022] [Accepted: 07/01/2022] [Indexed: 01/21/2023]
Abstract
Adipose-derived stem cells (ADSCs) show potential in skin regeneration research. A previous study reported the failure of full-thickness skin self-repair in an injury area exceeding 4 cm in diameter. Stem cell therapies have shown promise in accelerating skin regeneration; however, the low survival rate of transplanted cells due to the lack of protection during and after transplantation leads to low efficacy. Hence, effective biomaterials for the delivery and retention of ADSCs are urgently needed for skin regeneration purposes. Here, we covalently crosslinked hyaluronic acid with methacrylic anhydride and then covalently crosslinked the product with dopamine to engineer dopamine-methacrylated hyaluronic acid (DA-MeHA). Our experiments suggested that the DA-MeHA hydrogel firmly adhered to the skin wound defect and promoted cell proliferation in vitro and skin defect regeneration in vivo. Mechanistic analyses revealed that the beneficial effect of the DA-MeHA hydrogel combined with ADSCs on skin defect repair may be closely related to the Notch signaling pathway. The ADSCs from the DA-MeHA hydrogel secrete high levels of growth factors and are thus highly efficacious for promoting skin wound healing. This DA-MeHA hydrogel may be used as an effective potential carrier for stem cells as it enhances the efficacy of ADSCs in skin regeneration.
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Barish S, Senturk M, Schoch K, Minogue AL, Lopergolo D, Fallerini C, Harland J, Seemann JH, Stong N, Kranz PG, Kansagra S, Mikati MA, Jasien J, El-Dairi M, Galluzzi P, Ariani F, Renieri A, Mari F, Wangler MF, Arur S, Jiang YH, Yamamoto S, Shashi V, Bellen HJ. The microRNA processor DROSHA is a candidate gene for a severe progressive neurological disorder. Hum Mol Genet 2022; 31:2934-2950. [PMID: 35405010 PMCID: PMC9433733 DOI: 10.1093/hmg/ddac085] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 03/14/2022] [Accepted: 04/05/2022] [Indexed: 11/15/2022] Open
Abstract
DROSHA encodes a ribonuclease that is a subunit of the Microprocessor complex and is involved in the first step of microRNA (miRNA) biogenesis. To date, DROSHA has not yet been associated with a Mendelian disease. Here, we describe two individuals with profound intellectual disability, epilepsy, white matter atrophy, microcephaly and dysmorphic features, who carry damaging de novo heterozygous variants in DROSHA. DROSHA is constrained for missense variants and moderately intolerant to loss-of-function (o/e = 0.24). The loss of the fruit fly ortholog drosha causes developmental arrest and death in third instar larvae, a severe reduction in brain size and loss of imaginal discs in the larva. Loss of drosha in eye clones causes small and rough eyes in adult flies. One of the identified DROSHA variants (p.Asp1219Gly) behaves as a strong loss-of-function allele in flies, while another variant (p.Arg1342Trp) is less damaging in our assays. In worms, a knock-in that mimics the p.Asp1219Gly variant at a worm equivalent residue causes loss of miRNA expression and heterochronicity, a phenotype characteristic of the loss of miRNA. Together, our data show that the DROSHA variants found in the individuals presented here are damaging based on functional studies in model organisms and likely underlie the severe phenotype involving the nervous system.
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Affiliation(s)
- Scott Barish
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Mumine Senturk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Howard Hughes Medical Institute, BCM, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda L Minogue
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Diego Lopergolo
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Chiara Fallerini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
| | - Jake Harland
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Jacob H Seemann
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Peter G Kranz
- Division of Neuroradiology, Department of Radiology, Duke Health, Durham, NC 27710, USA
| | - Sujay Kansagra
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Mohamad A Mikati
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Joan Jasien
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Mays El-Dairi
- Department of Ophthalmology, Duke Health, Durham, NC 27710, USA
| | - Paolo Galluzzi
- Department of Medical Genetics, NeuroImaging and NeuroInterventional Unit, Azienda Ospedaliera e Universitaria, Senese, Siena 53100, Italy
| | - Francesca Ariani
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Alessandra Renieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Francesca Mari
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Swathi Arur
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yong-Hui Jiang
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
- Yale School of Medicine, New Haven, CT 06510, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Howard Hughes Medical Institute, BCM, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
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Abstract
Six years ago, DMM launched a subject collection called ‘Drosophila as a Disease Model’. This collection features Review-type articles and original research that highlight the power of Drosophila research in many aspects of human disease modeling. In the ensuing years, Drosophila research has further expanded to capitalize on genome editing, development of resources, and further interest in studying rare disease mechanisms. In the current issue of DMM, we again highlight the versatility, breadth, and scope of Drosophila research in human disease modeling and translational medicine. While many researchers have embraced the power of the fly, many more could still be encouraged to appreciate the strengths of Drosophila and how such research can integrate across species in a multi-pronged approach. Only when we truly acknowledge that all models contribute to our understanding of human biology, can we take advantage of the scope of current research endeavors. Summary: This Editorial encourages us to embrace the power of the fly in studying human disease and highlights how Drosophila studies can be integrated with research in other species to further our understanding of human biology.
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Affiliation(s)
- Esther M Verheyen
- Department of Molecular Biology and Biochemistry, Centre for Cell Biology, Development and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, CanadaV5A 1S6
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8
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Lee JH. Invertebrate Model Organisms as a Platform to Investigate Rare Human Neurological Diseases. Exp Neurobiol 2022; 31:1-16. [PMID: 35256540 PMCID: PMC8907251 DOI: 10.5607/en22003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 01/16/2023] Open
Abstract
Patients suffering from rare human diseases often go through a painful journey for finding a definite molecular diagnosis prerequisite of appropriate cures. With a novel variant isolated from a single patient, determination of its pathogenicity to end such "diagnostic odyssey" requires multi-step processes involving experts in diverse areas of interest, including clinicians, bioinformaticians and research scientists. Recent efforts in building large-scale genomic databases and in silico prediction platforms have facilitated identification of potentially pathogenic variants causative of rare human diseases of a Mendelian basis. However, the functional significance of individual variants remains elusive in many cases, thus requiring incorporation of versatile and rapid model organism (MO)-based platforms for functional analyses. In this review, the current scope of rare disease research is briefly discussed. In addition, an overview of invertebrate MOs for their key features relevant to rare neurological diseases is provided, with the characteristics of two representative invertebrate MOs, Drosophila melanogaster and Caenorhabditis elegans, as well as the challenges against them. Finally, recently developed research networks integrating these MOs in collaborative research are portraited with an array of bioinformatical analyses embedded. A comprehensive survey of MO-based research activities provided in this review will help us to design a wellstructured analysis of candidate genes or potentially pathogenic variants for their roles in rare neurological diseases in future.
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Affiliation(s)
- Ji-Hye Lee
- Department of Oral Pathology & Life Science in Dentistry, School of Dentistry, Pusan National University, Yangsan 50612, Korea.,Dental Life Science Institute, Pusan National University, Yangsan 50612, Korea.,Periodontal Disease Signaling Network Research Center, Pusan National University, Yangsan 50612, Korea
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9
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Yang SA, Salazar JL, Li-Kroeger D, Yamamoto S. Functional Studies of Genetic Variants Associated with Human Diseases in Notch Signaling-Related Genes Using Drosophila. Methods Mol Biol 2022; 2472:235-276. [PMID: 35674905 PMCID: PMC9396741 DOI: 10.1007/978-1-0716-2201-8_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Rare variants in the many genes related to Notch signaling cause diverse Mendelian diseases that affect myriad organ systems. In addition, genome- and exome-wide association studies have linked common and rare variants in Notch-related genes to common diseases and phenotypic traits. Moreover, somatic mutations in these genes have been observed in many types of cancer, some of which are classified as oncogenic and others as tumor suppressive. While functional characterization of some of these variants has been performed through experimental studies, the number of "variants of unknown significance" identified in patients with diverse conditions keeps increasing as high-throughput sequencing technologies become more commonly used in the clinic. Furthermore, as disease gene discovery efforts identify rare variants in human genes that have yet to be linked to a disease, the demand for functional characterization of variants in these "genes of unknown significance" continues to increase. In this chapter, we describe a workflow to functionally characterize a rare variant in a Notch signaling related gene that was found to be associated with late-onset Alzheimer's disease. This pipeline involves informatic analysis of the variant of interest using diverse human and model organism databases, followed by in vivo experiments in the fruit fly Drosophila melanogaster. The protocol described here can be used to study variants that affect amino acids that are not conserved between human and fly. By "humanizing" the almondex gene in Drosophila with mutant alleles and heterologous genomic rescue constructs, a missense variant in TM2D3 (TM2 Domain Containing 3) was shown to be functionally damaging. This, and similar approaches, greatly facilitate functional interpretations of genetic variants in the human genome and propel personalized medicine.
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Affiliation(s)
- Sheng-An Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Jose L Salazar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - David Li-Kroeger
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA.
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
- Development, Disease Models and Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX, USA.
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Salazar JL, Yang SA, Lin YQ, Li-Kroeger D, Marcogliese PC, Deal SL, Neely GG, Yamamoto S. TM2D genes regulate Notch signaling and neuronal function in Drosophila. PLoS Genet 2021; 17:e1009962. [PMID: 34905536 PMCID: PMC8714088 DOI: 10.1371/journal.pgen.1009962] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 12/28/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
TM2 domain containing (TM2D) proteins are conserved in metazoans and encoded by three separate genes in each model organism species that has been sequenced. Rare variants in TM2D3 are associated with Alzheimer's disease (AD) and its fly ortholog almondex is required for embryonic Notch signaling. However, the functions of this gene family remain elusive. We knocked-out all three TM2D genes (almondex, CG11103/amaretto, CG10795/biscotti) in Drosophila and found that they share the same maternal-effect neurogenic defect. Triple null animals are not phenotypically worse than single nulls, suggesting these genes function together. Overexpression of the most conserved region of the TM2D proteins acts as a potent inhibitor of Notch signaling at the γ-secretase cleavage step. Lastly, Almondex is detected in the brain and its loss causes shortened lifespan accompanied by progressive motor and electrophysiological defects. The functional links between all three TM2D genes are likely to be evolutionarily conserved, suggesting that this entire gene family may be involved in AD.
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Affiliation(s)
- Jose L. Salazar
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
| | - Sheng-An Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
| | - Yong Qi Lin
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - David Li-Kroeger
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
- Department of Neurology, BCM, Houston, Texas, United States of America
- Center for Alzheimer’s and Neurodegenerative Diseases, BCM, Houston, Texas, United States of America
| | - Paul C. Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
| | - Samantha L. Deal
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
- Program in Developmental Biology, BCM, Houston, Texas, United States of America
| | - G. Gregory Neely
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
- Center for Alzheimer’s and Neurodegenerative Diseases, BCM, Houston, Texas, United States of America
- Program in Developmental Biology, BCM, Houston, Texas, United States of America
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, Texas, United States of America
- Department of Neuroscience, BCM, Houston, Texas, United States of America
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11
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Zhang F, Chen Y, Shen J, Zhang J. The Ubiquitin Conjugating Enzyme UbcD1 is Required for Notch Signaling Activation During Drosophila Wing Development. Front Genet 2021; 12:770853. [PMID: 34712275 PMCID: PMC8546230 DOI: 10.3389/fgene.2021.770853] [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: 09/05/2021] [Accepted: 09/30/2021] [Indexed: 11/13/2022] Open
Abstract
Notch signaling pathway plays crucial roles in animal development. Protein ubiquitination contributes to Notch signaling regulation by governing the stability and activity of major signaling components. Studies in Drosophila have identified multiple ubiquitin ligases and deubiquitinating enzymes that modify Notch ligand and receptor proteins. The fate of ubiquitinated substrates depend on topologies of the attached ubiquitin chains, which are determined by the ubiquitin conjugating enzymes (E2 enzymes). However, which E2 enzymes participate in Notch signal transduction remain elusive. Here, we report that the E2 enzyme UbcD1 is required for Notch signaling activation during Drosophila wing development. Mutations of UbcD1 lead to marginal nicks in the adult wing and reduction of Notch signaling targets expression in the wing imaginal disc. Genetic analysis reveal that UbcD1 functions in the signaling receiving cells prior to cleavage of the Notch protein. We provide further evidence suggesting that UbcD1 is likely involved in endocytic trafficking of Notch protein. Our results demonstrate that UbcD1 positively regulates Notch signaling and thus reveal a novel role of UbcD1 in development.
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Affiliation(s)
- Fengchao Zhang
- MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yao Chen
- MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jie Shen
- MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Junzheng Zhang
- MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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12
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Bian W, Tang M, Jiang H, Xu W, Hao W, Sui Y, Hou Y, Nie L, Zhang H, Wang C, Li N, Wang J, Qin J, Wu L, Ma X, Chen J, Wang W, Li X. Low-density-lipoprotein-receptor-related protein 1 mediates Notch pathway activation. Dev Cell 2021; 56:2902-2919.e8. [PMID: 34626540 DOI: 10.1016/j.devcel.2021.09.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/18/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022]
Abstract
The Notch signaling pathway controls cell growth, differentiation, and fate decisions, and its dysregulation has been linked to various human genetic disorders and cancers. To comprehensively understand the global organization of the Notch pathway and identify potential drug targets for Notch-related diseases, we established a protein interaction landscape for the human Notch pathway. By combining and analyzing genetic and phenotypic data with bioinformatics analysis, we greatly expanded this pathway and identified many key regulators, including low-density-lipoprotein-receptor-related protein 1 (LRP1). We demonstrated that LRP1 mediates the ubiquitination chain linkage switching of Delta ligands, which further affects ligand recycling, membrane localization, and stability. LRP1 inhibition led to Notch signaling inhibition and decreased tumorigenesis in leukemia models. Our study provides a glimpse into the Notch pathway interaction network and uncovers LRP1 as one critical regulator of the Notch pathway, as well as a possible therapeutic target for Notch-related cancers.
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Affiliation(s)
- Weixiang Bian
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, the University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
| | - Hua Jiang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Wenyan Xu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Wanyu Hao
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Science, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Yue Sui
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Yingnan Hou
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Litong Nie
- Department of Experimental Radiation Oncology, the University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
| | - Huimin Zhang
- Department of Experimental Radiation Oncology, the University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, the University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
| | - Nan Li
- Department of Experimental Radiation Oncology, the University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiadong Wang
- Institute of Systems Biomedicine, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, People's Republic of China
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Lianfeng Wu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Science, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
| | - Xianjue Ma
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
| | - Junjie Chen
- Department of Experimental Radiation Oncology, the University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA.
| | - Wenqi Wang
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697, USA.
| | - Xu Li
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China.
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13
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Tian C, Yang Y, Ke Y, Yang L, Zhong L, Wang Z, Huang H. Integrative Analyses of Genes Associated With Right Ventricular Cardiomyopathy Induced by Tricuspid Regurgitation. Front Genet 2021; 12:708275. [PMID: 34603374 PMCID: PMC8485137 DOI: 10.3389/fgene.2021.708275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/06/2021] [Indexed: 12/14/2022] Open
Abstract
Tricuspid regurgitation (TR) induces right ventricular cardiomyopathy, a common heart disease, and eventually leads to severe heart failure and serious clinical complications. Accumulating evidence shows that long non-coding RNAs (lncRNAs) are involved in the pathological process of a variety of cardiovascular diseases. However, the regulatory mechanisms and functional roles of RNA interactions in TR-induced right ventricular cardiomyopathy are still unclear. Accordingly, we performed integrative analyses of genes associated with right ventricular cardiomyopathy induced by TR to study the roles of lncRNAs in the pathogenesis of this disease. In this study, we used high-throughput sequencing data of tissue samples from nine clinical cases of right ventricular myocardial cardiomyopathy induced by TR and nine controls with normal right ventricular myocardium from the Genotype-Tissue Expression database. We identified differentially expressed lncRNAs and constructed a protein-protein interaction and lncRNA-messenger RNA (mRNA) co-expression network. Furthermore, we determined hub lncRNA-mRNA modules related to right ventricular myocardial disease induced by TR and constructed a competitive endogenous RNA network for TR-induced right ventricular myocardial disease by integrating the interaction of lncRNA-miRNA-mRNA. In addition, we analyzed the immune infiltration using integrated data and the correlation of each immune-related gene with key genes of the integrated expression matrix. The present study identified 648 differentially expressed mRNAs, 201 differentially expressed miRNAs, and 163 differentially expressed lncRNAs. Protein-protein interaction network analysis confirmed that ADRA1A, AVPR1B, OPN4, IL-1B, IL-1A, CXCL4, ADCY2, CXCL12, GNB4, CCL20, CXCL8, and CXCL1 were hub genes. CTD-2314B22.3, hsa-miR-653-5p, and KIF17ceRNA; SRGAP3-AS2, hsa-miR-539-5p, and SHANK1; CERS6-AS1, hsa-miR-497-5p, and OPN4; INTS6-AS1, hsa-miR-4262, and NEURL1B; TTN-AS1, hsa-miR-376b-3p, and TRPM5; and DLX6-AS1, hsa-miR-346, and BIRC7 axes were obtained by constructing the ceRNA networks. Through the immune infiltration analysis, we found that the proportion of CD4 and CD8 T cells was about 20%, and the proportion of fibroblasts and endothelial cells was high. Our findings provide some insights into the mechanisms of RNA interaction in TR-induced right ventricular cardiomyopathy and suggest that lncRNAs are a potential therapeutic target for treating right ventricular myocardial disease induced by TR.
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Affiliation(s)
- Chengnan Tian
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital, Guangzhou, China.,The First Affiliated Hospital, Gannan Medical University, Ganzhou, China
| | - Yanchen Yang
- Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital, Guangzhou, China.,School of Medicine, South China University of Technology, Guangzhou, China
| | - Yingjie Ke
- Nanhai Hospital of Guangdong Provincial People's Hospital, Foshan, China
| | - Liang Yang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Lishan Zhong
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Zhenzhong Wang
- Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital, Guangzhou, China.,School of Medicine, South China University of Technology, Guangzhou, China
| | - Huanlei Huang
- Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital, Guangzhou, China.,The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
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14
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Valizadeh A, Asghari S, Mansouri P, Alemi F, Majidinia M, Mahmoodpoor A, Yousefi B. The roles of signaling pathways in cardiac regeneration. Curr Med Chem 2021; 29:2142-2166. [PMID: 34521319 DOI: 10.2174/0929867328666210914115411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/05/2021] [Accepted: 07/20/2021] [Indexed: 11/22/2022]
Abstract
In recent years, knowledge of cardiac regeneration mechanisms has dramatically expanded. Regeneration can replace lost parts of organs, common among animal species. The heart is commonly considered an organ with terminal development, which has no reparability potential during post-natal life; however, some intrinsic regeneration capacity has been reported for cardiac muscle, which opens novel avenues in cardiovascular disease treatment. Different endogenous mechanisms were studied for cardiac repairing and regeneration in recent decades. Survival, proliferation, inflammation, angiogenesis, cell-cell communication, cardiomyogenesis, and anti-aging pathways are the most important mechanisms that have been studied in this regard. Several in vitro and animal model studies focused on proliferation induction for cardiac regeneration reported promising results. These studies have mainly focused on promoting proliferation signaling pathways and demonstrated various signaling pathways such as Wnt, PI3K/Akt, IGF-1, TGF-β, Hippo, and VEGF signaling cardiac regeneration. Therefore, in this review, we intended to discuss the connection between different critical signaling pathways in cardiac repair and regeneration.
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Affiliation(s)
- Amir Valizadeh
- Stem Cell and Regenerative Medicine Institute, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Samira Asghari
- Stem Cell and Regenerative Medicine Institute, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Parinaz Mansouri
- Students Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Forough Alemi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Maryam Majidinia
- Solid Tumor Research Center, Urmia University of Medical Sciences, Urmia. Iran
| | - Ata Mahmoodpoor
- Stem Cell and Regenerative Medicine Institute, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Bahman Yousefi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
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15
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Effect of NTN and Lmx1 α on the Notch Signaling Pathway during the Differentiation of Human Bone Marrow Mesenchymal Stem Cells into Dopaminergic Neuron-Like Cells. PARKINSONS DISEASE 2021; 2021:6676709. [PMID: 34373779 PMCID: PMC8349261 DOI: 10.1155/2021/6676709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 05/30/2021] [Accepted: 07/22/2021] [Indexed: 11/20/2022]
Abstract
Human bone marrow mesenchymal stem cells (h-BMSCs) have the potential to differentiate into dopaminergic neuron-like cells to treat Parkinson's disease. The Notch signaling pathway has been implicated in the regulation of cell fate decisions such as differentiation of BMSCs. This study investigated changes in the expression of Notch-related genes in the differentiation of BMSCs in vitro into dopaminergic (DA) neuron-like cells. BMSCs transfected with empty lentiviral vectors served as the control group and those transfected with NTN and Lmx1α recombinant lentiviral vectors served as the experimental group. After induction and culture of NTN and Lmx1α-transfected h-BMSCs for 21 days, the cells exhibited features of dopaminergic neuron-like cells, which were observed by transmission and scanning electron microscopy and verified by immunofluorescence of tyrosine hydroxylase (TH) and dopamine transporter (DAT). These induced cells could secrete dopamine and had basic action potentials. Expression of the neural stem cell (NSC) markers, including octamer-binding protein (Oct4), paired box gene 6 (Pax6), and sex determining region Y-box 1 (SOX1), increased on day 14 of induction and decreased on day 21 of induction during differentiation. The human Notch signaling pathway PCR array showed a differential expression of Notch-related genes during the differentiation of h-BMSCs into DA neuron-like cells in vitro relative to that in the control group. In conclusion, h-BMSCs overexpressing NTN and Lmx1α can successfully be induced to differentiate into dopaminergic neuron-like cells with a neuronal phenotype exhibiting fundamental biological functions in vitro, and NTN and Lmx1α may affect the expression of Notch-related genes during differentiation.
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16
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Baldridge D, Wangler MF, Bowman AN, Yamamoto S, Schedl T, Pak SC, Postlethwait JH, Shin J, Solnica-Krezel L, Bellen HJ, Westerfield M. Model organisms contribute to diagnosis and discovery in the undiagnosed diseases network: current state and a future vision. Orphanet J Rare Dis 2021; 16:206. [PMID: 33962631 PMCID: PMC8103593 DOI: 10.1186/s13023-021-01839-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022] Open
Abstract
Decreased sequencing costs have led to an explosion of genetic and genomic data. These data have revealed thousands of candidate human disease variants. Establishing which variants cause phenotypes and diseases, however, has remained challenging. Significant progress has been made, including advances by the National Institutes of Health (NIH)-funded Undiagnosed Diseases Network (UDN). However, 6000-13,000 additional disease genes remain to be identified. The continued discovery of rare diseases and their genetic underpinnings provides benefits to affected patients, of whom there are more than 400 million worldwide, and also advances understanding the mechanisms of more common diseases. Platforms employing model organisms enable discovery of novel gene-disease relationships, help establish variant pathogenicity, and often lead to the exploration of underlying mechanisms of pathophysiology that suggest new therapies. The Model Organism Screening Center (MOSC) of the UDN is a unique resource dedicated to utilizing informatics and functional studies in model organisms, including worm (Caenorhabditis elegans), fly (Drosophila melanogaster), and zebrafish (Danio rerio), to aid in diagnosis. The MOSC has directly contributed to the diagnosis of challenging cases, including multiple patients with complex, multi-organ phenotypes. In addition, the MOSC provides a framework for how basic scientists and clinicians can collaborate to drive diagnoses. Customized experimental plans take into account patient presentations, specific genes and variant(s), and appropriateness of each model organism for analysis. The MOSC also generates bioinformatic and experimental tools and reagents for the wider scientific community. Two elements of the MOSC that have been instrumental in its success are (1) multidisciplinary teams with expertise in variant bioinformatics and in human and model organism genetics, and (2) mechanisms for ongoing communication with clinical teams. Here we provide a position statement regarding the central role of model organisms for continued discovery of disease genes, and we advocate for the continuation and expansion of MOSC-type research entities as a Model Organisms Network (MON) to be funded through grant applications submitted to the NIH, family groups focused on specific rare diseases, other philanthropic organizations, industry partnerships, and other sources of support.
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Affiliation(s)
- Dustin Baldridge
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA.
- Department of Pediatrics, BCM, Houston, TX, 77030, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA.
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA.
| | - Angela N Bowman
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA
- Department of Neuroscience, BCM, Houston, TX, 77030, USA
| | - Tim Schedl
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Stephen C Pak
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | | | - Jimann Shin
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA
- Department of Neuroscience, BCM, Houston, TX, 77030, USA
- Howard Hughes Medical Institute, Houston, TX, 77030, USA
| | - Monte Westerfield
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97403, USA
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18
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Fang-Fang Z, You Y, Wen-Jun L. Progress in research on childhood T-cell acute lymphocytic leukemia, Notch1 signaling pathway, and its inhibitors: A review. Bosn J Basic Med Sci 2021; 21:136-144. [PMID: 32415821 PMCID: PMC7982061 DOI: 10.17305/bjbms.2020.4687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 04/25/2020] [Indexed: 02/07/2023] Open
Abstract
Childhood leukemia is cancer that seriously threatens the life of children in China. Poor sensitivity to chemotherapy and susceptibility to drug resistance are the reasons for the treatment of T-cell acute lymphocytic leukemia (T-ALL) being extremely difficult. Moreover, traditional intensive chemotherapy regimens cause great damage to children. Therefore, it is highly important to search for targeted drugs and develop a precise individualized treatment for child patients. There are activating mutations in the NOTCH1 gene in more than 50% of human T-ALLs and the Notch signaling pathway is involved in the pathogenesis of T-ALL. In this review, we summarize the progress in research on T-ALL and Notch1 signaling pathway inhibitors to provide a theoretical basis for the clinical treatment of T-ALL.
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Affiliation(s)
- Zhong Fang-Fang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Department of Pediatrics, Affiliated Hospital of Southwest Medical University, Birth Defects Clinical Medical Research Center of Sichuan Province, Luzhou, China
| | - Yang You
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Department of Pediatrics, Affiliated Hospital of Southwest Medical University, Birth Defects Clinical Medical Research Center of Sichuan Province, Luzhou, China
| | - Liu Wen-Jun
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Department of Pediatrics, Affiliated Hospital of Southwest Medical University, Birth Defects Clinical Medical Research Center of Sichuan Province, Luzhou, China
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19
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Harnish JM, Link N, Yamamoto S. Drosophila as a Model for Infectious Diseases. Int J Mol Sci 2021; 22:2724. [PMID: 33800390 PMCID: PMC7962867 DOI: 10.3390/ijms22052724] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 12/19/2022] Open
Abstract
The fruit fly, Drosophila melanogaster, has been used to understand fundamental principles of genetics and biology for over a century. Drosophila is now also considered an essential tool to study mechanisms underlying numerous human genetic diseases. In this review, we will discuss how flies can be used to deepen our knowledge of infectious disease mechanisms in vivo. Flies make effective and applicable models for studying host-pathogen interactions thanks to their highly conserved innate immune systems and cellular processes commonly hijacked by pathogens. Drosophila researchers also possess the most powerful, rapid, and versatile tools for genetic manipulation in multicellular organisms. This allows for robust experiments in which specific pathogenic proteins can be expressed either one at a time or in conjunction with each other to dissect the molecular functions of each virulent factor in a cell-type-specific manner. Well documented phenotypes allow large genetic and pharmacological screens to be performed with relative ease using huge collections of mutant and transgenic strains that are publicly available. These factors combine to make Drosophila a powerful tool for dissecting out host-pathogen interactions as well as a tool to better understand how we can treat infectious diseases that pose risks to public health, including COVID-19, caused by SARS-CoV-2.
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Affiliation(s)
- J. Michael Harnish
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; (J.M.H.); (N.L.)
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Nichole Link
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; (J.M.H.); (N.L.)
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Howard Hughes Medical Institute, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; (J.M.H.); (N.L.)
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, BCM, Houston, TX 77030, USA
- Development, Disease Models and Therapeutics Graduate Program, BCM, Houston, TX 77030, USA
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20
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Dutta D, Sharma V, Mutsuddi M, Mukherjee A. Regulation of Notch signaling by E3 ubiquitin ligases. FEBS J 2021; 289:937-954. [PMID: 33644958 DOI: 10.1111/febs.15792] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 02/07/2021] [Accepted: 02/25/2021] [Indexed: 12/11/2022]
Abstract
Notch signaling is an evolutionarily conserved pathway that is widely used for multiple cellular events during development. Activation of the Notch pathway occurs when the ligand from a neighboring cell binds to the Notch receptor and induces cleavage of the intracellular domain of Notch, which further translocates into the nucleus to activate its downstream genes. The involvement of the Notch pathway in diverse biological events is possible due to the complexity in its regulation. In order to maintain tight spatiotemporal regulation, the Notch receptor, as well as its ligand, undergoes a series of physical and biochemical modifications that, in turn, helps in proper maintenance and fine-tuning of the signaling outcome. Ubiquitination is the post-translational addition of a ubiquitin molecule to a substrate protein, and the process is regulated by E3 ubiquitin ligases. The present review describes the involvement of different E3 ubiquitin ligases that play an important role in the regulation and maintenance of proper Notch signaling and how perturbation in ubiquitination results in abnormal Notch signaling leading to a number of human diseases.
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Affiliation(s)
- Debdeep Dutta
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Vartika Sharma
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Mousumi Mutsuddi
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Ashim Mukherjee
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, India
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21
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Wu ZL, Xie QQ, Liu TC, Yang X, Zhang GZ, Zhang HH. Role of the Wnt pathway in the formation, development, and degeneration of intervertebral discs. Pathol Res Pract 2021; 220:153366. [PMID: 33647863 DOI: 10.1016/j.prp.2021.153366] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/13/2022]
Abstract
Intervertebral disc degeneration (IVDD) is an age-related degenerative disease that is the main cause of low back pain. It seriously affects the quality of life of patients and places a heavy economic burden on families and society. The Wnt pathway plays an important role in the growth, development, and degeneration of intervertebral discs (IVDs). In the embryonic stage, the Wnt pathway participates in the growth and development of IVD by promoting the transformation of progenitor cells into notochord cells and the extension of the notochord. However, the activation of the Wnt pathway after birth promotes IVD cell senescence, apoptosis, and degradation of the extracellular matrix and induces the production of inflammatory factors, thereby accelerating the IVDD process. This article reviews the relationship between the Wnt pathway and IVD, emphasizing its influence on IVD growth, development, and degeneration. Targeting this pathway may become an effective strategy for the treatment of IVDD.
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Affiliation(s)
- Zuo-Long Wu
- The Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu 730000, China; Department of Orthopaedics, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, China; Key Laboratory of Orthopaedics Disease of Gansu Province, Lanzhou, Gansu 730000, China
| | - Qi-Qi Xie
- The Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu 730000, China; Department of Orthopaedics, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, China; Key Laboratory of Orthopaedics Disease of Gansu Province, Lanzhou, Gansu 730000, China
| | - Tai-Cong Liu
- The Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu 730000, China; Department of Orthopaedics, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, China; Key Laboratory of Orthopaedics Disease of Gansu Province, Lanzhou, Gansu 730000, China
| | - Xing Yang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu 730000, China; Department of Orthopaedics, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, China; Key Laboratory of Orthopaedics Disease of Gansu Province, Lanzhou, Gansu 730000, China
| | - Guang-Zhi Zhang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu 730000, China; Department of Orthopaedics, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, China; Key Laboratory of Orthopaedics Disease of Gansu Province, Lanzhou, Gansu 730000, China
| | - Hai-Hong Zhang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu 730000, China; Department of Orthopaedics, Second Hospital of Lanzhou University, Lanzhou, Gansu 730000, China; Key Laboratory of Orthopaedics Disease of Gansu Province, Lanzhou, Gansu 730000, China.
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22
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Mizoguchi T, Fukada M, Iihama M, Song X, Fukagawa S, Kuwabara S, Omaru S, Higashijima SI, Itoh M. Transient activation of the Notch-her15.1 axis plays an important role in the maturation of V2b interneurons. Development 2020; 147:147/16/dev191312. [PMID: 32855202 DOI: 10.1242/dev.191312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022]
Abstract
In the vertebrate ventral spinal cord, p2 progenitors give rise to two interneuron subtypes: excitatory V2a interneurons and inhibitory V2b interneurons. In the differentiation of V2a and V2b cells, Notch signaling promotes V2b fate at the expense of V2a fate. Later, V2b cells extend axons along the ipsilateral side of the spinal cord and express the inhibitory transmitter GABA. Notch signaling has been reported to inhibit the axonal outgrowth of mature neurons of the central nervous system; however, it remains unknown how Notch signaling modulates V2b neurite outgrowth and maturation into GABAergic neurons. Here, we have investigated neuron-specific Notch functions regarding V2b axon growth and maturation into zebrafish GABAergic neurons. We found that continuous neuron-specific Notch activation enhanced V2b fate determination but inhibited V2b axonal outgrowth and maturation into GABAergic neurons. These results suggest that Notch signaling activation is required for V2b fate determination, whereas its downregulation at a later stage is essential for V2b maturation. Accordingly, we found that a Notch signaling downstream gene, her15.1, showed biased expression in V2 linage cells and downregulated expression during the maturation of V2b cells, and continuous expression of her15.1 repressed V2b axogenesis. Our data suggest that spatiotemporal control of Notch signaling activity is required for V2b fate determination, maturation and axogenesis.
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Affiliation(s)
- Takamasa Mizoguchi
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Michi Fukada
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Miku Iihama
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Xuehui Song
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Shun Fukagawa
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Shuhei Kuwabara
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Shuhei Omaru
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Shin-Ichi Higashijima
- National Institutes of Natural Sciences, Exploratory Research Center on Life and Living Systems, National Institute for Basic Biology, Okazaki, Aichi 444-8787, Japan.,Graduate University for Advanced Studies, Okazaki, Aichi 444-8787, Japan
| | - Motoyuki Itoh
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
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23
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Salazar JL, Yang SA, Yamamoto S. Post-Developmental Roles of Notch Signaling in the Nervous System. Biomolecules 2020; 10:biom10070985. [PMID: 32630239 PMCID: PMC7408554 DOI: 10.3390/biom10070985] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/14/2022] Open
Abstract
Since its discovery in Drosophila, the Notch signaling pathway has been studied in numerous developmental contexts in diverse multicellular organisms. The role of Notch signaling in nervous system development has been extensively investigated by numerous scientists, partially because many of the core Notch signaling components were initially identified through their dramatic ‘neurogenic’ phenotype of developing fruit fly embryos. Components of the Notch signaling pathway continue to be expressed in mature neurons and glia cells, which is suggestive of a role in the post-developmental nervous system. The Notch pathway has been, so far, implicated in learning and memory, social behavior, addiction, and other complex behaviors using genetic model organisms including Drosophila and mice. Additionally, Notch signaling has been shown to play a modulatory role in several neurodegenerative disease model animals and in mediating neural toxicity of several environmental factors. In this paper, we summarize the knowledge pertaining to the post-developmental roles of Notch signaling in the nervous system with a focus on discoveries made using the fruit fly as a model system as well as relevant studies in C elegans, mouse, rat, and cellular models. Since components of this pathway have been implicated in the pathogenesis of numerous psychiatric and neurodegenerative disorders in human, understanding the role of Notch signaling in the mature brain using model organisms will likely provide novel insights into the mechanisms underlying these diseases.
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Affiliation(s)
- Jose L. Salazar
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; (J.L.S.); (S.-A.Y.)
| | - Sheng-An Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; (J.L.S.); (S.-A.Y.)
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; (J.L.S.); (S.-A.Y.)
- Department of Neuroscience, BCM, Houston, TX 77030, USA
- Program in Developmental Biology, BCM, Houston, TX 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Correspondence: ; Tel.: +1-832-824-8119
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24
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Bertrand FE. The cross-talk of NOTCH and GSK-3 signaling in colon and other cancers. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118738. [PMID: 32389646 DOI: 10.1016/j.bbamcr.2020.118738] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/01/2020] [Accepted: 05/03/2020] [Indexed: 12/14/2022]
Abstract
The GSK-3 kinases, GSK-3α and GSK-3β, have a central role in regulating multiple cellular processes such as glycogen synthesis, insulin signaling, cell proliferation and apoptosis. GSK-3β is the most well studied, and was originally described for its role in regulating glycogen synthase. GSK-3β has been studied as a participant in the oncogenic process in a variety of cancers due to its intersection with the PTEN/PI3K/AKT and RAS/RAF/MEK/ERK pathways. Dysregulated signaling through the Notch family of receptors can also promote oncogenesis. Normal Notch receptor signaling regulates cell fate determination in stem cell pools. GSK-3β and Notch share similar targets such β-catenin and the WNT pathway. WNT and β-catenin are involved in several oncogenic processes including those of the colon. In addition, GSK-3β may directly regulate aspects of Notch signaling. This review describes how crosstalk between GSK-3β and Notch can promote oncogenesis, using colon cancer as the primary example.
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Affiliation(s)
- Fred E Bertrand
- Department of Nutrition Sciences, School of Health Professions, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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25
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Epigenetic Regulation of Notch Signaling During Drosophila Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1218:59-75. [PMID: 32060871 DOI: 10.1007/978-3-030-34436-8_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Notch signaling exerts multiple important functions in various developmental processes, including cell differentiation and cell proliferation, while mis-regulation of this pathway results in a variety of complex diseases, such as cancer and developmental defects. The simplicity of the Notch pathway in Drosophila melanogaster, in combination with the availability of powerful genetics, makes this an attractive model for studying the fundamental mechanisms of how Notch signaling is regulated and how it functions in various cellular contexts. Recently, increasing evidence for epigenetic control of Notch signaling reveals the intimate link between epigenetic regulators and Notch signaling pathway. In this chapter, we summarize the research advances of Notch and CAF-1 in Drosophila development and the epigenetic regulation mechanisms of Notch signaling activity by CAF-1 as well as other epigenetic modification machineries, which enables Notch to orchestrate different biological inputs and outputs in specific cellular contexts.
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26
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Yamamoto S. Making sense out of missense mutations: Mechanistic dissection of Notch receptors through structure-function studies in Drosophila. Dev Growth Differ 2020; 62:15-34. [PMID: 31943162 DOI: 10.1111/dgd.12640] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/15/2022]
Abstract
Notch signaling is involved in the development of almost all organ systems and is required post-developmentally to modulate tissue homeostasis. Rare variants in Notch signaling pathway genes are found in patients with rare Mendelian disorders, while unique or recurrent somatic mutations in a similar set of genes are identified in cancer. The human genome contains four genes that encode Notch receptors, NOTCH1-4, all of which are linked to genetic diseases and cancer. Although some mutations have been classified as clear loss- or gain-of-function alleles based on cellular or rodent based assay systems, the functional consequence of many variants/mutations in human Notch receptors remain unknown. In this review, I will first provide an overview of the domain structure of Notch receptors and discuss how each module is known to regulate Notch signaling activity in vivo using the Drosophila Notch receptor as an example. Next, I will introduce some interesting mutant alleles that have been isolated in the fly Notch gene over the past > 100 years of research and discuss how studies of these mutations have facilitated the understanding of Notch biology. By identifying unique alleles of the fly Notch gene through forward genetic screens, mapping their molecular lesions and characterizing their phenotypes in depth, one can begin to unravel new mechanistic insights into how different domains of Notch fine-tune signaling output. Such information can be useful in deciphering the functional consequences of rare variants/mutations in human Notch receptors, which in turn can influence disease management and therapy.
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Affiliation(s)
- Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA.,Department of Neuroscience, BCM, Houston, TX, USA.,Program in Developmental Biology, BCM, Houston, TX, USA.,Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
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27
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Das P, Salazar JL, Li-Kroeger D, Yamamoto S, Nakamura M, Sasamura T, Inaki M, Masuda W, Kitagawa M, Yamakawa T, Matsuno K. Maternal almondex, a neurogenic gene, is required for proper subcellular Notch distribution in early Drosophila embryogenesis. Dev Growth Differ 2019; 62:80-93. [PMID: 31782145 DOI: 10.1111/dgd.12639] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 10/08/2019] [Indexed: 01/03/2023]
Abstract
Notch signaling plays crucial roles in the control of cell fate and physiology through local cell-cell interactions. The core processes of Notch signal transduction are well established, but the mechanisms that fine-tune the pathway in various developmental and post-developmental contexts are less clear. Drosophila almondex, which encodes an evolutionarily conserved double-pass transmembrane protein, was identified in the 1970s as a maternal-effect gene that regulates Notch signaling in certain contexts, but its mechanistic function remains obscure. In this study, we examined the role of almondex in Notch signaling during early Drosophila embryogenesis. We found that in addition to being required for lateral inhibition in the neuroectoderm, almondex is also partially required for Notch signaling-dependent single-minded expression in the mesectoderm. Furthermore, we found that almondex is required for proper subcellular Notch receptor distribution in the neuroectoderm, specifically during mid-stage 5 development. The absence of maternal almondex during this critical window of time caused Notch to accumulate abnormally in cells in a mesh-like pattern. This phenotype did not include any obvious change in subcellular Delta ligand distribution, suggesting that it does not result from a general vesicular-trafficking defect. Considering that dynamic Notch trafficking regulates signal output to fit the specific context, we speculate that almondex may facilitate Notch activation by regulating intracellular Notch receptor distribution during early embryogenesis.
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Affiliation(s)
- Puspa Das
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Jose L Salazar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David Li-Kroeger
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Mitsutoshi Nakamura
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Takeshi Sasamura
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Mikiko Inaki
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Wataru Masuda
- Department of Pathology, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Motoo Kitagawa
- Department of Biochemistry, International University of Health and Welfare, School of Medicine, Chiba, Japan
| | - Tomoko Yamakawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Kenji Matsuno
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
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28
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Bellen HJ, Wangler MF, Yamamoto S. The fruit fly at the interface of diagnosis and pathogenic mechanisms of rare and common human diseases. Hum Mol Genet 2019; 28:R207-R214. [PMID: 31227826 PMCID: PMC6872428 DOI: 10.1093/hmg/ddz135] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 05/31/2019] [Accepted: 06/07/2019] [Indexed: 12/12/2022] Open
Abstract
Drosophila melanogaster is a unique, powerful genetic model organism for studying a broad range of biological questions. Human studies that probe the genetic causes of rare and undiagnosed diseases using massive-parallel sequencing often require complementary gene function studies to determine if and how rare variants affect gene function. These studies also provide inroads to disease mechanisms and therapeutic targets. In this review we discuss strategies for functional studies of rare human variants in Drosophila. We focus on our experience in establishing a Drosophila core of the Model Organisms Screening Center for the Undiagnosed Diseases Network (UDN) and concurrent fly studies with other large genomic rare disease research efforts such as the Centers for Mendelian Genomics. We outline four major strategies that use the latest technology in fly genetics to understand the impact of human variants on gene function. We also mention general concepts in probing disease mechanisms, therapeutics and using rare disease to understand common diseases. Drosophila is and will continue to be a fundamental genetic model to identify new disease-causing variants, pathogenic mechanisms and drugs that will impact medicine.
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Affiliation(s)
- Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine (BCM), Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX , USA
- Howard Hughes Medical Institute, Houston, TX, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX , USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine (BCM), Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX , USA
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29
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Harnish JM, Deal SL, Chao HT, Wangler MF, Yamamoto S. In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila. J Vis Exp 2019:10.3791/59658. [PMID: 31498321 PMCID: PMC7418855 DOI: 10.3791/59658] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Advances in sequencing technology have made whole-genome and whole-exome datasets more accessible for both clinical diagnosis and cutting-edge human genetics research. Although a number of in silico algorithms have been developed to predict the pathogenicity of variants identified in these datasets, functional studies are critical to determining how specific genomic variants affect protein function, especially for missense variants. In the Undiagnosed Diseases Network (UDN) and other rare disease research consortia, model organisms (MO) including Drosophila, C. elegans, zebrafish, and mice are actively used to assess the function of putative human disease-causing variants. This protocol describes a method for the functional assessment of rare human variants used in the Model Organisms Screening Center Drosophila Core of the UDN. The workflow begins with gathering human and MO information from multiple public databases, using the MARRVEL web resource to assess whether the variant is likely to contribute to a patient's condition as well as design effective experiments based on available knowledge and resources. Next, genetic tools (e.g., T2A-GAL4 and UAS-human cDNA lines) are generated to assess the functions of variants of interest in Drosophila. Upon development of these reagents, two-pronged functional assays based on rescue and overexpression experiments can be performed to assess variant function. In the rescue branch, the endogenous fly genes are "humanized" by replacing the orthologous Drosophila gene with reference or variant human transgenes. In the overexpression branch, the reference and variant human proteins are exogenously driven in a variety of tissues. In both cases, any scorable phenotype (e.g., lethality, eye morphology, electrophysiology) can be used as a read-out, irrespective of the disease of interest. Differences observed between reference and variant alleles suggest a variant-specific effect, and thus likely pathogenicity. This protocol allows rapid, in vivo assessments of putative human disease-causing variants of genes with known and unknown functions.
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Affiliation(s)
- J Michael Harnish
- Department of Molecular and Human Genetics, Baylor College of Medicine
| | - Samantha L Deal
- Program in Developmental Biology, Baylor College of Medicine
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine; Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital; Department of Neuroscience, Baylor College of Medicine
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine; Program in Developmental Biology, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine; Program in Developmental Biology, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital; Department of Neuroscience, Baylor College of Medicine;
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30
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Kanca O, Andrews JC, Lee PT, Patel C, Braddock SR, Slavotinek AM, Cohen JS, Gubbels CS, Aldinger KA, Williams J, Indaram M, Fatemi A, Yu TW, Agrawal PB, Vezina G, Simons C, Crawford J, Lau CC, Chung WK, Markello TC, Dobyns WB, Adams DR, Gahl WA, Wangler MF, Yamamoto S, Bellen HJ, Malicdan MCV, Acosta MT, Adams DR, Agrawal P, Alejandro ME, Allard P, Alvey J, Andrews A, Ashley EA, Azamian MS, Bacino CA, Bademci G, Baker E, Balasubramanyam A, Baldridge D, Bale J, Barbouth D, Batzli GF, Bayrak-Toydemir P, Beggs AH, Bejerano G, Bellen HJ, Bernstein JA, Berry GT, Bican A, Bick DP, Birch CL, Bivona S, Bohnsack J, Bonnenmann C, Bonner D, Boone BE, Bostwick BL, Botto L, Briere LC, Brokamp E, Brown DM, Brush M, Burke EA, Burrage LC, Butte MJ, Carey J, Carrasquillo O, Chang TCP, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, D'Souza P, Dasari S, Davids M, Dayal JG, Dell'Angelica EC, Dhar SU, Dorrani N, Dorset DC, Douine ED, Draper DD, Duncan L, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Estwick T, Fernandez L, Ferreira C, Fieg EL, Fisher PG, Fogel BL, Forghani I, Fresard L, Gahl WA, Godfrey RA, Goldman AM, Goldstein DB, Gourdine JPF, Grajewski A, Groden CA, Gropman AL, Haendel M, Hamid R, Hanchard NA, Hayes N, High F, Holm IA, Hom J, Huang A, Huang Y, Isasi R, Jamal F, Jiang YH, Johnston JM, Jones AL, Karaviti L, Kelley EG, Kiley D, Koeller DM, Kohane IS, Kohler JN, Krakow D, Krasnewich DM, Korrick S, Koziura M, Krier JB, Kyle JE, Lalani SR, Lam B, Lanpher BC, Lanza IR, Lau CC, Lazar J, LeBlanc K, Lee BH, Lee H, Levitt R, Levy SE, Lewis RA, Lincoln SA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Mao R, Markello TC, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, May T, McCauley J, McConkie-Rosell A, McCormack CE, McCray AT, Metz TO, Might M, Morava-Kozicz E, Moretti PM, Morimoto M, Mulvihill JJ, Murdock DR, Nath A, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CG, Papp JC, Parker NH, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Quinlan A, Raja AN, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rowley RK, Ruzhnikov M, Sacco R, Sampson JB, Samson SL, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Shakachite L, Sharma P, Shashi V, Shields K, Shin J, Signer R, Sillari CH, Silverman EK, Sinsheimer JS, Sisco K, Smith KS, Solnica-Krezel L, Spillmann RC, Stoler JM, Stong N, Sullivan JA, Sutton S, Sweetser DA, Tabor HK, Tamburro CP, Tan QKG, Tekin M, Telischi F, Thorson W, Tifft CJ, Toro C, Tran AA, Urv TK, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walley NM, Walsh CA, Walker M, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Waters KM, Webb-Robertson BJM, Wegner D, Westerfield M, Wheeler MT, Wise AL, Wolfe LA, Woods JD, Worthey EA, Yamamoto S, Yang J, Yoon AJ, Yu G, Zastrow DB, Zhao C, Zuchner S. De Novo Variants in WDR37 Are Associated with Epilepsy, Colobomas, Dysmorphism, Developmental Delay, Intellectual Disability, and Cerebellar Hypoplasia. Am J Hum Genet 2019; 105:413-424. [PMID: 31327508 PMCID: PMC6699142 DOI: 10.1016/j.ajhg.2019.06.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 06/14/2019] [Indexed: 12/16/2022] Open
Abstract
WD40 repeat-containing proteins form a large family of proteins present in all eukaryotes. Here, we identified five pediatric probands with de novo variants in WDR37, which encodes a member of the WD40 repeat protein family. Two probands shared one variant and the others have variants in nearby amino acids outside the WD40 repeats. The probands exhibited shared phenotypes of epilepsy, colobomas, facial dysmorphology reminiscent of CHARGE syndrome, developmental delay and intellectual disability, and cerebellar hypoplasia. The WDR37 protein is highly conserved in vertebrate and invertebrate model organisms and is currently not associated with a human disease. We generated a null allele of the single Drosophila ortholog to gain functional insights and replaced the coding region of the fly gene CG12333/wdr37 with GAL4. These flies are homozygous viable but display severe bang sensitivity, a phenotype associated with seizures in flies. Additionally, the mutant flies fall when climbing the walls of the vials, suggesting a defect in grip strength, and repeat the cycle of climbing and falling. Similar to wall clinging defect, mutant males often lose grip of the female abdomen during copulation. These phenotypes are rescued by using the GAL4 in the CG12333/wdr37 locus to drive the UAS-human reference WDR37 cDNA. The two variants found in three human subjects failed to rescue these phenotypes, suggesting that these alleles severely affect the function of this protein. Taken together, our data suggest that variants in WDR37 underlie a novel syndromic neurological disorder.
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31
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Deal SL, Yamamoto S. Unraveling Novel Mechanisms of Neurodegeneration Through a Large-Scale Forward Genetic Screen in Drosophila. Front Genet 2019; 9:700. [PMID: 30693015 PMCID: PMC6339878 DOI: 10.3389/fgene.2018.00700] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/13/2018] [Indexed: 01/04/2023] Open
Abstract
Neurodegeneration is characterized by progressive loss of neurons. Genetic and environmental factors both contribute to demise of neurons, leading to diverse devastating cognitive and motor disorders, including Alzheimer's and Parkinson's diseases in humans. Over the past few decades, the fruit fly, Drosophila melanogaster, has become an integral tool to understand the molecular, cellular and genetic mechanisms underlying neurodegeneration. Extensive tools and sophisticated technologies allow Drosophila geneticists to identify and study evolutionarily conserved genes that are essential for neural maintenance. In this review, we will focus on a large-scale mosaic forward genetic screen on the fly X-chromosome that led to the identification of a number of essential genes that exhibit neurodegenerative phenotypes when mutated. Most genes identified from this screen are evolutionarily conserved and many have been linked to human diseases with neurological presentations. Systematic electrophysiological and ultrastructural characterization of mutant tissue in the context of the Drosophila visual system, followed by a series of experiments to understand the mechanism of neurodegeneration in each mutant led to the discovery of novel molecular pathways that are required for neuronal integrity. Defects in mitochondrial function, lipid and iron metabolism, protein trafficking and autophagy are recurrent themes, suggesting that insults that eventually lead to neurodegeneration may converge on a set of evolutionarily conserved cellular processes. Insights from these studies have contributed to our understanding of known neurodegenerative diseases such as Leigh syndrome and Friedreich's ataxia and have also led to the identification of new human diseases. By discovering new genes required for neural maintenance in flies and working with clinicians to identify patients with deleterious variants in the orthologous human genes, Drosophila biologists can play an active role in personalized medicine.
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Affiliation(s)
- Samantha L Deal
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, United States
| | - Shinya Yamamoto
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States
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