1
|
Kim T, Choi SY, Bae HW, Kim HS, Jeon H, Oh H, Ahn SH, Lee J, Suh YG, Cho YH, Kim SH. Design, synthesis, and evaluation of N 1,N 3-dialkyldioxonaphthoimidazoliums as antibacterial agents against methicillin-resistant Staphylococcus aureus. Eur J Med Chem 2024; 272:116454. [PMID: 38704937 DOI: 10.1016/j.ejmech.2024.116454] [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: 02/20/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024]
Abstract
Increasing antibiotic resistance of bacterial pathogens poses a serious threat to human health worldwide. Methicillin-resistant Staphylococcus aureus (MRSA) is among the most deleterious bacterial pathogens owing to its multidrug resistance, necessitating the development of new antibacterial agents against it. We previously identified a novel dioxonaphthoimidazolium agent, c5, with moderate antibacterial activity against MRSA from an anticancer clinical candidate, YM155. In this study, we aimed to design and synthesize several novel cationic amphiphilic N1,N3-dialkyldioxonaphthoimidazolium bromides with enhanced lipophilicity of the two side chains in the imidazolium scaffold and improved antibacterial activities compared to those of c5 against gram-positive bacteria in vitro and in vivo. Our new antibacterial lead, N1,N3-n-octylbenzyldioxonaphthoimidazolium bromide (11), exhibited highly potent antibacterial activities against various gram-positive bacterial strains (MICs: 0.19-0.39 μg/mL), including MRSA, methicillin-sensitive S. aureus, and Bacillus subtilis. Moreover, antibacterial mechanism of 11 against MRSA based on the generation of reactive oxygen species (ROS) was evaluated. Although compound 11 exhibited cytotoxic effects in vitro and lacked a therapeutic index against the HEK293 and HDFa mammalian cell lines, it exhibited low toxicity in the Drosophila animal model. Remarkably, 11 exhibited better in vivo antibacterial efficacy than c5 and the clinically used antibiotic, vancomycin, in SA3-infected Drosophila model. Moreover, the development of bacterial resistance to 11 was not observed after 16 consecutive passages. Therefore, rational design of antibacterial cationic amphiphiles based on ROS-generating pharmacophores with optimized lipophilicity can facilitate the identification of potent antibacterial agents against drug-resistant infections.
Collapse
Affiliation(s)
- Taewoo Kim
- College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, 120 Haeryong-ro, Pocheon-si, Gyeonggi-do 11160, Republic of Korea
| | - Shin-Yae Choi
- Program of Biopharmaceutical Science, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, 335 Pangyo-ro, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
| | - Hee-Won Bae
- Program of Biopharmaceutical Science, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, 335 Pangyo-ro, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
| | - Hyun Su Kim
- College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, 120 Haeryong-ro, Pocheon-si, Gyeonggi-do 11160, Republic of Korea
| | - Hoon Jeon
- College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, 120 Haeryong-ro, Pocheon-si, Gyeonggi-do 11160, Republic of Korea
| | - Haejun Oh
- College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, 120 Haeryong-ro, Pocheon-si, Gyeonggi-do 11160, Republic of Korea
| | - Sung-Hoon Ahn
- College of Pharmacy, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Jongkook Lee
- College of Pharmacy, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Young-Ger Suh
- College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, 120 Haeryong-ro, Pocheon-si, Gyeonggi-do 11160, Republic of Korea
| | - You-Hee Cho
- Program of Biopharmaceutical Science, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, 335 Pangyo-ro, Seongnam-si, Gyeonggi-do 13488, Republic of Korea.
| | - Seok-Ho Kim
- College of Pharmacy, Kangwon National University, Chuncheon 24341, Republic of Korea.
| |
Collapse
|
2
|
Jans K, Lüersen K, von Frieling J, Roeder T, Rimbach G. Dietary lithium stimulates female fecundity in Drosophila melanogaster. Biofactors 2024; 50:326-346. [PMID: 37706424 DOI: 10.1002/biof.2007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/28/2023] [Indexed: 09/15/2023]
Abstract
The trace element lithium exerts a versatile bioactivity in humans, to some extend overlapping with in vivo findings in the model organism Drosophila melanogaster. A potentially essential function of lithium in reproduction has been suggested since the 1980s and multiple studies have since been published postulating a regulatory role of lithium in female gametogenesis. However, the impact of lithium on fruit fly egg production has not been at the center of attention to date. In the present study, we report that dietary lithium (0.1-5.0 mM LiCl) substantially improved life time egg production in D. melanogaster w1118 females, with a maximum increase of plus 45% when supplementing 1.0 mM LiCl. This phenomenon was not observed in the insulin receptor mutant InRE19, indicating a potential involvement of insulin-like signaling in the lithium-mediated fecundity boost. Analysis of the whole-body and ovarian transcriptome revealed that dietary lithium affects the mRNA levels of genes encoding proteins related to processes of follicular maturation. To the best of our knowledge, this is the first report on dietary lithium acting as an in vivo fecundity stimulant in D. melanogaster, further supporting the suggested benefit of the trace element in female reproduction.
Collapse
Affiliation(s)
- Katharina Jans
- Division of Food Science, Institute of Human Nutrition and Food Science, University of Kiel, Kiel, Germany
| | - Kai Lüersen
- Division of Food Science, Institute of Human Nutrition and Food Science, University of Kiel, Kiel, Germany
| | - Jakob von Frieling
- Division of Molecular Physiology, Institute of Zoology, University of Kiel, Kiel, Germany
| | - Thomas Roeder
- Division of Molecular Physiology, Institute of Zoology, University of Kiel, Kiel, Germany
| | - Gerald Rimbach
- Division of Food Science, Institute of Human Nutrition and Food Science, University of Kiel, Kiel, Germany
| |
Collapse
|
3
|
Sutton DC, Andrews JC, Dolezal DM, Park YJ, Li H, Eberl DF, Yamamoto S, Groves AK. Comparative exploration of mammalian deafness gene homologues in the Drosophila auditory organ shows genetic correlation between insect and vertebrate hearing. PLoS One 2024; 19:e0297846. [PMID: 38412189 PMCID: PMC10898740 DOI: 10.1371/journal.pone.0297846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/13/2024] [Indexed: 02/29/2024] Open
Abstract
Johnston's organ, the Drosophila auditory organ, is anatomically very different from the mammalian organ of Corti. However, recent evidence indicates significant cellular and molecular similarities exist between vertebrate and invertebrate hearing, suggesting that Drosophila may be a useful platform to determine the function of the many mammalian deafness genes whose underlying biological mechanisms are poorly characterized. Our goal was a comprehensive screen of all known orthologues of mammalian deafness genes in the fruit fly to better understand conservation of hearing mechanisms between the insect and the fly and ultimately gain insight into human hereditary deafness. We used bioinformatic comparisons to screen previously reported human and mouse deafness genes and found that 156 of them have orthologues in Drosophila melanogaster. We used fluorescent imaging of T2A-GAL4 gene trap and GFP or YFP fluorescent protein trap lines for 54 of the Drosophila genes and found 38 to be expressed in different cell types in Johnston's organ. We phenotypically characterized the function of strong loss-of-function mutants in three genes expressed in Johnston's organ (Cad99C, Msp-300, and Koi) using a courtship assay and electrophysiological recordings of sound-evoked potentials. Cad99C and Koi were found to have significant courtship defects. However, when we tested these genes for electrophysiological defects in hearing response, we did not see a significant difference suggesting the courtship defects were not caused by hearing deficiencies. Furthermore, we used a UAS/RNAi approach to test the function of seven genes and found two additional genes, CG5921 and Myo10a, that gave a statistically significant delay in courtship but not in sound-evoked potentials. Our results suggest that many mammalian deafness genes have Drosophila homologues expressed in the Johnston's organ, but that their requirement for hearing may not necessarily be the same as in mammals.
Collapse
Affiliation(s)
- Daniel C. Sutton
- Graduate Program in Genetics & Genomics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jonathan C. Andrews
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
| | - Dylan M. Dolezal
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Ye Jin Park
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, Texas, United States of America
- Huffington Center on Aging, One Baylor Plaza, Houston, Texas, United States of America
| | - Hongjie Li
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, Texas, United States of America
- Huffington Center on Aging, One Baylor Plaza, Houston, Texas, United States of America
| | - Daniel F. Eberl
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Shinya Yamamoto
- Graduate Program in Genetics & Genomics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
| | - Andrew K. Groves
- Graduate Program in Genetics & Genomics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
| |
Collapse
|
4
|
Yu Y, Chen D, Farmer SM, Xu S, Rios B, Solbach A, Ye X, Ye L, Zhang S. Endolysosomal trafficking controls yolk granule biogenesis in vitellogenic Drosophila oocytes. PLoS Genet 2024; 20:e1011152. [PMID: 38315726 PMCID: PMC10898735 DOI: 10.1371/journal.pgen.1011152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 02/27/2024] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
Endocytosis and endolysosomal trafficking are essential for almost all aspects of physiological functions of eukaryotic cells. As our understanding on these membrane trafficking events are mostly from studies in yeast and cultured mammalian cells, one challenge is to systematically evaluate the findings from these cell-based studies in multicellular organisms under physiological settings. One potentially valuable in vivo system to address this challenge is the vitellogenic oocyte in Drosophila, which undergoes extensive endocytosis by Yolkless (Yl), a low-density lipoprotein receptor (LDLR), to uptake extracellular lipoproteins into oocytes and package them into a specialized lysosome, the yolk granule, for storage and usage during later development. However, by now there is still a lack of sufficient understanding on the molecular and cellular processes that control yolk granule biogenesis. Here, by creating genome-tagging lines for Yl receptor and analyzing its distribution in vitellogenic oocytes, we observed a close association of different endosomal structures with distinct phosphoinositides and actin cytoskeleton dynamics. We further showed that Rab5 and Rab11, but surprisingly not Rab4 and Rab7, are essential for yolk granules biogenesis. Instead, we uncovered evidence for a potential role of Rab7 in actin regulation and observed a notable overlap of Rab4 and Rab7, two Rab GTPases that have long been proposed to have distinct spatial distribution and functional roles during endolysosomal trafficking. Through a small-scale RNA interference (RNAi) screen on a set of reported Rab5 effectors, we showed that yolk granule biogenesis largely follows the canonical endolysosomal trafficking and maturation processes. Further, the data suggest that the RAVE/V-ATPase complexes function upstream of or in parallel with Rab7, and are involved in earlier stages of endosomal trafficking events. Together, our study provides s novel insights into endolysosomal pathways and establishes vitellogenic oocyte in Drosophila as an excellent in vivo model for dissecting the highly complex membrane trafficking events in metazoan.
Collapse
Affiliation(s)
- Yue Yu
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
- Program in Neuroscience, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (MD Anderson UTHealth GSBS), Houston, Texas, United States of America
| | - Dongsheng Chen
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
- The College of Life Sciences, Anhui Normal University, #1 Beijing East Road, Wuhu, Anhui, People’s Republic of China
| | - Stephen M. Farmer
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
- Program in Neuroscience, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (MD Anderson UTHealth GSBS), Houston, Texas, United States of America
- Program in Biochemistry and Cell Biology, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (MD Anderson UTHealth GSBS), Houston, Texas, United States of America
| | - Shiyu Xu
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
| | - Beatriz Rios
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
- Program in Neuroscience, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (MD Anderson UTHealth GSBS), Houston, Texas, United States of America
| | - Amanda Solbach
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
- Program in Neuroscience, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (MD Anderson UTHealth GSBS), Houston, Texas, United States of America
- Programs in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (MD Anderson UTHealth GSBS), Houston, Texas, United States of America
| | - Xin Ye
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
| | - Lili Ye
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
| | - Sheng Zhang
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
- Program in Neuroscience, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (MD Anderson UTHealth GSBS), Houston, Texas, United States of America
- Programs in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (MD Anderson UTHealth GSBS), Houston, Texas, United States of America
- Department of Neurobiology and Anatomy, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
| |
Collapse
|
5
|
Na D, Lim DH, Hong JS, Lee HM, Cho D, Yu MS, Shaker B, Ren J, Lee B, Song JG, Oh Y, Lee K, Oh KS, Lee MY, Choi MS, Choi HS, Kim YH, Bui JM, Lee K, Kim HW, Lee YS, Gsponer J. A multi-layered network model identifies Akt1 as a common modulator of neurodegeneration. Mol Syst Biol 2023; 19:e11801. [PMID: 37984409 DOI: 10.15252/msb.202311801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023] Open
Abstract
The accumulation of misfolded and aggregated proteins is a hallmark of neurodegenerative proteinopathies. Although multiple genetic loci have been associated with specific neurodegenerative diseases (NDs), molecular mechanisms that may have a broader relevance for most or all proteinopathies remain poorly resolved. In this study, we developed a multi-layered network expansion (MLnet) model to predict protein modifiers that are common to a group of diseases and, therefore, may have broader pathophysiological relevance for that group. When applied to the four NDs Alzheimer's disease (AD), Huntington's disease, and spinocerebellar ataxia types 1 and 3, we predicted multiple members of the insulin pathway, including PDK1, Akt1, InR, and sgg (GSK-3β), as common modifiers. We validated these modifiers with the help of four Drosophila ND models. Further evaluation of Akt1 in human cell-based ND models revealed that activation of Akt1 signaling by the small molecule SC79 increased cell viability in all models. Moreover, treatment of AD model mice with SC79 enhanced their long-term memory and ameliorated dysregulated anxiety levels, which are commonly affected in AD patients. These findings validate MLnet as a valuable tool to uncover molecular pathways and proteins involved in the pathophysiology of entire disease groups and identify potential therapeutic targets that have relevance across disease boundaries. MLnet can be used for any group of diseases and is available as a web tool at http://ssbio.cau.ac.kr/software/mlnet.
Collapse
Affiliation(s)
- Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Do-Hwan Lim
- College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
- School of Systems Biomedical Science, Soongsil University, Seoul, Republic of Korea
| | - Jae-Sang Hong
- College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Daeahn Cho
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Myeong-Sang Yu
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Bilal Shaker
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Jun Ren
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Bomi Lee
- College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Jae Gwang Song
- College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Yuna Oh
- Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Kyungeun Lee
- Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Kwang-Seok Oh
- Information-based Drug Research Center, Korea Research Institute of Chemical Technology, Deajeon, Republic of Korea
| | - Mi Young Lee
- Information-based Drug Research Center, Korea Research Institute of Chemical Technology, Deajeon, Republic of Korea
| | - Min-Seok Choi
- College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Han Saem Choi
- College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Yang-Hee Kim
- College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Jennifer M Bui
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hyung Wook Kim
- College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Young Sik Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jörg Gsponer
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
6
|
Akagi K, Koizumi K, Kadowaki M, Kitajima I, Saito S. New Possibilities for Evaluating the Development of Age-Related Pathologies Using the Dynamical Network Biomarkers Theory. Cells 2023; 12:2297. [PMID: 37759519 PMCID: PMC10528308 DOI: 10.3390/cells12182297] [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: 08/20/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Aging is the slowest process in a living organism. During this process, mortality rate increases exponentially due to the accumulation of damage at the cellular level. Cellular senescence is a well-established hallmark of aging, as well as a promising target for preventing aging and age-related diseases. However, mapping the senescent cells in tissues is extremely challenging, as their low abundance, lack of specific markers, and variability arise from heterogeneity. Hence, methodologies for identifying or predicting the development of senescent cells are necessary for achieving healthy aging. A new wave of bioinformatic methodologies based on mathematics/physics theories have been proposed to be applied to aging biology, which is altering the way we approach our understand of aging. Here, we discuss the dynamical network biomarkers (DNB) theory, which allows for the prediction of state transition in complex systems such as living organisms, as well as usage of Raman spectroscopy that offers a non-invasive and label-free imaging, and provide a perspective on potential applications for the study of aging.
Collapse
Affiliation(s)
- Kazutaka Akagi
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Keiichi Koizumi
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Division of Presymptomatic Disease, Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Makoto Kadowaki
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Isao Kitajima
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Shigeru Saito
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| |
Collapse
|
7
|
Dowling DK, Wolff JN. Evolutionary genetics of the mitochondrial genome: insights from Drosophila. Genetics 2023:7160843. [PMID: 37171259 DOI: 10.1093/genetics/iyad036] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 02/05/2023] [Indexed: 05/13/2023] Open
Abstract
Mitochondria are key to energy conversion in virtually all eukaryotes. Intriguingly, despite billions of years of evolution inside the eukaryote, mitochondria have retained their own small set of genes involved in the regulation of oxidative phosphorylation (OXPHOS) and protein translation. Although there was a long-standing assumption that the genetic variation found within the mitochondria would be selectively neutral, research over the past 3 decades has challenged this assumption. This research has provided novel insight into the genetic and evolutionary forces that shape mitochondrial evolution and broader implications for evolutionary ecological processes. Many of the seminal studies in this field, from the inception of the research field to current studies, have been conducted using Drosophila flies, thus establishing the species as a model system for studies in mitochondrial evolutionary biology. In this review, we comprehensively review these studies, from those focusing on genetic processes shaping evolution within the mitochondrial genome, to those examining the evolutionary implications of interactions between genes spanning mitochondrial and nuclear genomes, and to those investigating the dynamics of mitochondrial heteroplasmy. We synthesize the contribution of these studies to shaping our understanding of the evolutionary and ecological implications of mitochondrial genetic variation.
Collapse
Affiliation(s)
- Damian K Dowling
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Jonci N Wolff
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| |
Collapse
|
8
|
Collins QP, Grunsted MJ, Arcila D, Xiong Y, Padash Barmchi M. Transcriptomic analysis provides insight into the mechanism of IKKβ-mediated suppression of HPV18E6-induced cellular abnormalities. G3 (BETHESDA, MD.) 2023; 13:jkad020. [PMID: 36722216 PMCID: PMC10085804 DOI: 10.1093/g3journal/jkad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 09/12/2022] [Accepted: 01/07/2023] [Indexed: 02/02/2023]
Abstract
High-risk human papillomaviruses (HPVs) 16 and 18 are responsible for more than 70% of cervical cancers and majority of other HPV-associated cancers world-wide. Current treatments for these cancers have limited efficacy, which in turn has resulted in disease recurrence and poor survival rates in advanced disease stages. Hence, there is a significant need for development of novel molecularly-targeted therapeutics. This can only be achieved through improved understanding of disease mechanism. Recently, we developed a Drosophila model of HPV18E6 plus human E3 ubiquitin ligase (hUBE3A) and demonstrated that the E6-induced cellular abnormalities are conserved between humans and flies. Subsequently, we demonstrated that reduced level and activity of IKKβ, a regulator of NF-κB, suppresses the cellular abnormalities induced by E6 oncoprotein and that the interaction of IKKβ and E6 is conserved in human cells. In this study, we performed transcriptomic analysis to identify differentially expressed genes that play a role in IKKβ-mediated suppression of E6-induced defects. Transcriptome analysis identified 215 genes whose expression was altered due to reduced levels of IKKβ. Of these 215 genes, 151 genes showed annotations. These analyses were followed by functional genetic interaction screen using RNAi, overexpression, and mutant fly strains for identified genes. The screen identified several genes including genes involved in Hippo and Toll pathways as well as junctional complexes whose downregulation or upregulation resulted in alterations of E6-induced defects. Subsequently, RT-PCR analysis was performed for validation of altered gene expression level for a few representative genes. Our results indicate an involvement for Hippo and Toll pathways in IKKβ-mediated suppression of E6 + hUBE3A-induced cellular abnormalities. Therefore, this study enhances our understanding of the mechanisms underlying HPV-induced cancer and can potentially lead to identification of novel drug targets for cancers associated with HPV.
Collapse
Affiliation(s)
- Quincy P Collins
- Department of Biology, University of Oklahoma, Norman, OK 73019, USA
| | | | - Dahiana Arcila
- Department of Biology, University of Oklahoma, Norman, OK 73019, USA
- Department of Ichthyology, Sam Noble Oklahoma Museum of Natural History, Norman, OK 73019, USA
| | - Yi Xiong
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | | |
Collapse
|
9
|
Fischer FP, Karge RA, Weber YG, Koch H, Wolking S, Voigt A. Drosophila melanogaster as a versatile model organism to study genetic epilepsies: An overview. Front Mol Neurosci 2023; 16:1116000. [PMID: 36873106 PMCID: PMC9978166 DOI: 10.3389/fnmol.2023.1116000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/23/2023] [Indexed: 02/18/2023] Open
Abstract
Epilepsy is one of the most prevalent neurological disorders, affecting more than 45 million people worldwide. Recent advances in genetic techniques, such as next-generation sequencing, have driven genetic discovery and increased our understanding of the molecular and cellular mechanisms behind many epilepsy syndromes. These insights prompt the development of personalized therapies tailored to the genetic characteristics of an individual patient. However, the surging number of novel genetic variants renders the interpretation of pathogenetic consequences and of potential therapeutic implications ever more challenging. Model organisms can help explore these aspects in vivo. In the last decades, rodent models have significantly contributed to our understanding of genetic epilepsies but their establishment is laborious, expensive, and time-consuming. Additional model organisms to investigate disease variants on a large scale would be desirable. The fruit fly Drosophila melanogaster has been used as a model organism in epilepsy research since the discovery of "bang-sensitive" mutants more than half a century ago. These flies respond to mechanical stimulation, such as a brief vortex, with stereotypic seizures and paralysis. Furthermore, the identification of seizure-suppressor mutations allows to pinpoint novel therapeutic targets. Gene editing techniques, such as CRISPR/Cas9, are a convenient way to generate flies carrying disease-associated variants. These flies can be screened for phenotypic and behavioral abnormalities, shifting of seizure thresholds, and response to anti-seizure medications and other substances. Moreover, modification of neuronal activity and seizure induction can be achieved using optogenetic tools. In combination with calcium and fluorescent imaging, functional alterations caused by mutations in epilepsy genes can be traced. Here, we review Drosophila as a versatile model organism to study genetic epilepsies, especially as 81% of human epilepsy genes have an orthologous gene in Drosophila. Furthermore, we discuss newly established analysis techniques that might be used to further unravel the pathophysiological aspects of genetic epilepsies.
Collapse
Affiliation(s)
- Florian P Fischer
- Department of Epileptology and Neurology, RWTH Aachen University, Aachen, Germany
| | - Robin A Karge
- Department of Epileptology and Neurology, RWTH Aachen University, Aachen, Germany
| | - Yvonne G Weber
- Department of Epileptology and Neurology, RWTH Aachen University, Aachen, Germany.,Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Henner Koch
- Department of Epileptology and Neurology, RWTH Aachen University, Aachen, Germany
| | - Stefan Wolking
- Department of Epileptology and Neurology, RWTH Aachen University, Aachen, Germany
| | - Aaron Voigt
- Department of Neurology, RWTH Aachen University, Aachen, Germany.,JARA-BRAIN Institute Molecular Neuroscience and Neuroimaging, Forschungszentrum Jülich GmbH and RWTH Aachen University, Aachen, Germany
| |
Collapse
|
10
|
Hashemi L, Ormsbee ME, Patel PJ, Nielson JA, Ahlander J, Padash Barmchi M. A Drosophila model of HPV16-induced cancer reveals conserved disease mechanism. PLoS One 2022; 17:e0278058. [PMID: 36508448 PMCID: PMC9744332 DOI: 10.1371/journal.pone.0278058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/09/2022] [Indexed: 12/14/2022] Open
Abstract
High-risk human papillomaviruses (HR-HPVs) cause almost all cervical cancers and a significant number of vaginal, vulvar, penile, anal, and oropharyngeal cancers. HPV16 and 18 are the most prevalent types among HR-HPVs and together cause more than 70% of all cervical cancers. Low vaccination rate and lack of molecularly-targeted therapeutics for primary therapy have led to a slow reduction in cervical cancer incidence and high mortality rate. Hence, creating new models of HPV-induced cancer that can facilitate understanding of the disease mechanism and identification of key cellular targets of HPV oncogenes are important for development of new interventions. Here in this study, we used the tissue-specific expression technique, Gal4-UAS, to establish the first Drosophila model of HPV16-induced cancer. Using this technique, we expressed HPV16 oncogenes E5, E6, E7 and the human E3 ligase (hUBE3A) specifically in the epithelia of Drosophila eye, which allows simple phenotype scoring without affecting the viability of the organism. We found that, as in human cells, hUBE3A is essential for cellular abnormalities caused by HPV16 oncogenes in flies. Several proteins targeted for degradation by HPV16 oncoproteins in human cells were also reduced in the Drosophila epithelial cells. Cell polarity and adhesion were compromised, resulting in impaired epithelial integrity. Cells did not differentiate to the specific cell types of ommatidia, but instead were transformed into neuron-like cells. These cells extended axon-like structures to connect to each other and exhibited malignant behavior, migrating away to distant sites. Our findings suggest that given the high conservation of genes and signaling pathways between humans and flies, the Drosophila model of HPV16- induced cancer could serve as an excellent model for understanding the disease mechanism and discovery of novel molecularly-targeted therapeutics.
Collapse
Affiliation(s)
- Lydia Hashemi
- Department of Biology, University of Oklahoma, Norman, OK, United States of America
| | - McKenzi E. Ormsbee
- Department of Biology, University of Oklahoma, Norman, OK, United States of America
| | - Prashant J. Patel
- Department of Biology, University of Oklahoma, Norman, OK, United States of America
| | - Jacquelyn A. Nielson
- Stead Family Department of Pediatrics, University of Iowa, Iowa City, IA, United States of America
| | - Joseph Ahlander
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK, United States of America
| | - Mojgan Padash Barmchi
- Department of Biology, University of Oklahoma, Norman, OK, United States of America
- * E-mail:
| |
Collapse
|
11
|
Pratomo AR, Salim E, Hori A, Kuraishi T. Drosophila as an Animal Model for Testing Plant-Based Immunomodulators. Int J Mol Sci 2022; 23:ijms232314801. [PMID: 36499123 PMCID: PMC9735809 DOI: 10.3390/ijms232314801] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/02/2022] Open
Abstract
Allopathic medicines play a key role in the prevention and treatment of diseases. However, long-term consumption of these medicines may cause serious undesirable effects that harm human health. Plant-based medicines have emerged as alternatives to allopathic medicines because of their rare side effects. They contain several compounds that have the potential to improve health and treat diseases in humans, including their function as immunomodulators to treat immune-related diseases. Thus, the discovery of potent and safe immunomodulators from plants is gaining considerable research interest. Recently, Drosophila has gained prominence as a model organism in evaluating the efficacy of plant and plant-derived substances. Drosophila melanogaster "fruit fly" is a well-known, high-throughput model organism that has been used to study different biological aspects of development and diseases for more than 110 years. Most developmental and cell signaling pathways and 75% of human disease-related genes are conserved between humans and Drosophila. Using Drosophila, one can easily examine the pharmacological effects of plants/plant-derived components by employing a variety of tests in flies, such as survival, anti-inflammatory, antioxidant, and cell death tests. This review focused on D. melanogaster's potential for identifying immunomodulatory features associated with plants/plant-derived components.
Collapse
Affiliation(s)
- Andre Rizky Pratomo
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Emil Salim
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
- Department of Pharmacology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan 20155, Indonesia
- Correspondence: (E.S.); (T.K.)
| | - Aki Hori
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Takayuki Kuraishi
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
- AMED-PRIME, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
- JST-FOREST, Japan Science and Technology Agency, Tokyo 102-0081, Japan
- Correspondence: (E.S.); (T.K.)
| |
Collapse
|
12
|
Odenthal J, Dittrich S, Ludwig V, Merz T, Reitmeier K, Reusch B, Höhne M, Cosgun ZC, Hohenadel M, Putnik J, Göbel H, Rinschen MM, Altmüller J, Koehler S, Schermer B, Benzing T, Beck BB, Brinkkötter PT, Habbig S, Bartram MP. Modeling of ACTN4-Based Podocytopathy Using Drosophila Nephrocytes. Kidney Int Rep 2022; 8:317-329. [PMID: 36815115 PMCID: PMC9939316 DOI: 10.1016/j.ekir.2022.10.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/17/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Introduction Genetic disorders are among the most prevalent causes leading to progressive glomerular disease and, ultimately, end-stage renal disease (ESRD) in children and adolescents. Identification of underlying genetic causes is indispensable for targeted treatment strategies and counseling of affected patients and their families. Methods Here, we report on a boy who presented at 4 years of age with proteinuria and biopsy-proven focal segmental glomerulosclerosis (FSGS) that was temporarily responsive to treatment with ciclosporin A. Molecular genetic testing identified a novel mutation in alpha-actinin-4 (p.M240T). We describe a feasible and efficient experimental approach to test its pathogenicity by combining in silico, in vitro, and in vivo analyses. Results The de novo p.M240T mutation led to decreased alpha-actinin-4 stability as well as protein mislocalization and actin cytoskeleton rearrangements. Transgenic expression of wild-type human alpha-actinin-4 in Drosophila melanogaster nephrocytes was able to ameliorate phenotypes associated with the knockdown of endogenous actinin. In contrast, p.M240T, as well as other established disease variants p.W59R and p.K255E, failed to rescue these phenotypes, underlining the pathogenicity of the novel alpha-actinin-4 variant. Conclusion Our data highlight that the newly identified alpha-actinin-4 mutation indeed encodes for a disease-causing variant of the protein and promote the Drosophila model as a simple and convenient tool to study monogenic kidney disease in vivo.
Collapse
Affiliation(s)
- Johanna Odenthal
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Sebastian Dittrich
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Vivian Ludwig
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Tim Merz
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Katrin Reitmeier
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Björn Reusch
- Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany,Institute of Human Genetics, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Zülfü C. Cosgun
- Department of Pediatrics, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Maximilian Hohenadel
- Department of Pediatrics, Division of Pediatric Nephrology, University of Bonn, Bonn, Germany
| | - Jovana Putnik
- Mother and Child Health Care Institute of Serbia “Dr Vukan Čupić,” Department of Nephrology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Heike Göbel
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Markus M. Rinschen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark,Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark,III Medical Clinic, University Hospital Hamburg Eppendorf, Hamburg, Germany
| | - Janine Altmüller
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine, Berlin, Germany,Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Sybille Koehler
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Bodo B. Beck
- Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany,Institute of Human Genetics, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Paul T. Brinkkötter
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany,Correspondence: Paul T. Brinkkoetter, Department II of Internal Medicine, Faculty of Medicine, University of Cologne, University Hospital Cologne, Kerpener Street 62, Cologne 50935, Germany.
| | - Sandra Habbig
- Department of Pediatrics, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Malte P. Bartram
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| |
Collapse
|
13
|
Benoit I, Di Curzio D, Civetta A, Douville RN. Drosophila as a Model for Human Viral Neuroinfections. Cells 2022; 11:cells11172685. [PMID: 36078091 PMCID: PMC9454636 DOI: 10.3390/cells11172685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
The study of human neurological infection faces many technical and ethical challenges. While not as common as mammalian models, the use of Drosophila (fruit fly) in the investigation of virus–host dynamics is a powerful research tool. In this review, we focus on the benefits and caveats of using Drosophila as a model for neurological infections and neuroimmunity. Through the examination of in vitro, in vivo and transgenic systems, we highlight select examples to illustrate the use of flies for the study of exogenous and endogenous viruses associated with neurological disease. In each case, phenotypes in Drosophila are compared to those in human conditions. In addition, we discuss antiviral drug screening in flies and how investigating virus–host interactions may lead to novel antiviral drug targets. Together, we highlight standardized and reproducible readouts of fly behaviour, motor function and neurodegeneration that permit an accurate assessment of neurological outcomes for the study of viral infection in fly models. Adoption of Drosophila as a valuable model system for neurological infections has and will continue to guide the discovery of many novel virus–host interactions.
Collapse
Affiliation(s)
- Ilena Benoit
- Department of Biology, University of Winnipeg, 599 Portage Avenue, Winnipeg, MB R3B 2G3, Canada
- Division of Neurodegenerative Disorders, St. Boniface Hospital Albrechtsen Research Centre, 351 Taché Ave, Winnipeg, MB R2H 2A6, Canada
| | - Domenico Di Curzio
- Division of Neurodegenerative Disorders, St. Boniface Hospital Albrechtsen Research Centre, 351 Taché Ave, Winnipeg, MB R2H 2A6, Canada
| | - Alberto Civetta
- Department of Biology, University of Winnipeg, 599 Portage Avenue, Winnipeg, MB R3B 2G3, Canada
| | - Renée N. Douville
- Department of Biology, University of Winnipeg, 599 Portage Avenue, Winnipeg, MB R3B 2G3, Canada
- Division of Neurodegenerative Disorders, St. Boniface Hospital Albrechtsen Research Centre, 351 Taché Ave, Winnipeg, MB R2H 2A6, Canada
- Correspondence:
| |
Collapse
|
14
|
|
15
|
Identification of additional dye tracers for measuring solid food intake and food preference via consumption-excretion in Drosophila. Sci Rep 2022; 12:6201. [PMID: 35418664 PMCID: PMC9008003 DOI: 10.1038/s41598-022-10252-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/01/2022] [Indexed: 11/08/2022] Open
Abstract
The Drosophila model has become a leading platform for investigating mechanisms that drive feeding behavior and the effect of diet on physiological outputs. Several methods for tracking feeding behavior in flies have been developed. One method, consumption-excretion or Con-Ex, provides flies with media labeled with dye and then quantifies the amount of dye excreted into the vial as a measure of consumption. We previously found that Blue 1 and Orange 4 work well in Con-Ex and can be used as a dye pair in food preference studies. We have expanded our development of Con-Ex by identifying two additional dyes, Orange G and Yellow 10, that detect the anticipated effects of mating status, strain, starvation and nutrient concentration. Additionally, Orange G and Yellow 10 accumulate linearly in excretion products out to 48 h and the excreted volumes of these two dyes reflect the volumes consumed. Orange G also works with Blue 1 as a dye pair in food preference studies. Finally, consumption of Blue 1, Orange 4, Orange G or Yellow 10 does not affect ethanol sedation or rapid tolerance to ethanol. Our findings establish that Orange G and Yellow 10, like Blue 1 and Orange 4, are suitable for use in Con-Ex.
Collapse
|
16
|
Disease Modeling of Rare Neurological Disorders in Zebrafish. Int J Mol Sci 2022; 23:ijms23073946. [PMID: 35409306 PMCID: PMC9000079 DOI: 10.3390/ijms23073946] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/31/2022] [Accepted: 03/31/2022] [Indexed: 02/06/2023] Open
Abstract
Rare diseases are those which affect a small number of people compared to the general population. However, many patients with a rare disease remain undiagnosed, and a large majority of rare diseases still have no form of viable treatment. Approximately 40% of rare diseases include neurologic and neurodevelopmental disorders. In order to understand the characteristics of rare neurological disorders and identify causative genes, various model organisms have been utilized extensively. In this review, the characteristics of model organisms, such as roundworms, fruit flies, and zebrafish, are examined, with an emphasis on zebrafish disease modeling in rare neurological disorders.
Collapse
|
17
|
Mombach DM, Fontoura Gomes TMFD, Silva MM, Loreto ÉLS. Molecular and biological effects of Cisplatin in Drosophila. Comp Biochem Physiol C Toxicol Pharmacol 2022; 252:109229. [PMID: 34728387 DOI: 10.1016/j.cbpc.2021.109229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 11/24/2022]
Abstract
Cisplatin is widely used in cancer treatment and is one of the best cytostatic agents available for antitumor therapy. Drosophila melanogaster has one of the best annotated genomes and one of the best characterized sets of transposable elements (TE) sequences. This model organism is useful for analyzing the mode of action of several compounds in vivo and evaluating the behavioral consequences of treatments. The aim of our study was to increase the knowledge about the effects of Cisplatin in Drosophila by joining RNA-seq and biological assays. RNA-seq was followed by analyses of differential expression of genes (DEGs) and TEs (DETEs), and of pathways and ontology terms. DETEs were confirmed by qPCR. Cisplatin was evaluated at 50 and 100 μg/mL in Drosophila culture medium for 24 h. The fly locomotor assay, survival analysis, oviposition and development were used as biological assays. Cisplatin induced DEGs in a dose-dependent fashion, and four TEs were up-regulated. Most DEGs are related to DNA damage and detoxification processes. Cisplatin increases Drosophila locomotor activity and interrupts development. Genes and processes related to the assays were also identified. This is the first study to evaluate the effects of Cisplatin in flies using RNA-seq. Gene alteration was almost limited to drug metabolism and DNA damage, and the drug did not vastly affect Drosophila on the molecular level. Contrary to the hypothesis that stress dramatically alters TEs mobilization, only four TEs were up-regulated. Our study, together with previous knowledge, asserts Drosophila as a valuable organism in the study of chemotherapy drugs.
Collapse
Affiliation(s)
- Daniela Moreira Mombach
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Mônica Medeiros Silva
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Élgion Lúcio Silva Loreto
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil.
| |
Collapse
|
18
|
Camilleri-Robles C, Amador R, Klein CC, Guigó R, Corominas M, Ruiz-Romero M. Genomic and functional conservation of lncRNAs: lessons from flies. Mamm Genome 2022; 33:328-342. [PMID: 35098341 PMCID: PMC9114055 DOI: 10.1007/s00335-021-09939-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/09/2021] [Indexed: 12/18/2022]
Abstract
Over the last decade, the increasing interest in long non-coding RNAs (lncRNAs) has led to the discovery of these transcripts in multiple organisms. LncRNAs tend to be specifically, and often lowly, expressed in certain tissues, cell types and biological contexts. Although lncRNAs participate in the regulation of a wide variety of biological processes, including development and disease, most of their functions and mechanisms of action remain unknown. Poor conservation of the DNA sequences encoding for these transcripts makes the identification of lncRNAs orthologues among different species very challenging, especially between evolutionarily distant species such as flies and humans or mice. However, the functions of lncRNAs are unexpectedly preserved among different species supporting the idea that conservation occurs beyond DNA sequences and reinforcing the potential of characterising lncRNAs in animal models. In this review, we describe the features and roles of lncRNAs in the fruit fly Drosophila melanogaster, focusing on genomic and functional comparisons with human and mouse lncRNAs. We also discuss the current state of advances and limitations in the study of lncRNA conservation and future perspectives.
Collapse
|
19
|
Eleftherianos I, Tafesh-Edwards G. Virus Infection of the Brain: Lessons from Drosophila for Illuminating Virus Disease and Nervous System Function. Neuroscience 2022; 484:80-82. [PMID: 34995715 DOI: 10.1016/j.neuroscience.2021.12.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 10/19/2022]
Abstract
Recent studies using genomic and functional approaches in the fruit fly Drosophila melanogaster have revealed the effects of viral infection on nervous system homeostasis. An established connection between viral infection and brain function is critical due to its significant contribution to several areas of biomedical research, particularly the molecular pathogenesis of neurotropic viruses, the neurobiology of viral disease, and understanding the genetic basis and pathophysiology of viral tropism.
Collapse
Affiliation(s)
- Ioannis Eleftherianos
- Infection and Innate Immunity Lab, Department of Biological Sciences, Science and Engineering Hall, 800 22nd St NW, The George Washington University, Washington, DC 20052, USA.
| | - Ghada Tafesh-Edwards
- Infection and Innate Immunity Lab, Department of Biological Sciences, Science and Engineering Hall, 800 22nd St NW, The George Washington University, Washington, DC 20052, USA
| |
Collapse
|
20
|
Klaitong P, Smith DR. Roles of Non-Structural Protein 4A in Flavivirus Infection. Viruses 2021; 13:v13102077. [PMID: 34696510 PMCID: PMC8538649 DOI: 10.3390/v13102077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Infections with viruses in the genus Flavivirus are a worldwide public health problem. These enveloped, positive sense single stranded RNA viruses use a small complement of only 10 encoded proteins and the RNA genome itself to remodel host cells to achieve conditions favoring viral replication. A consequence of the limited viral armamentarium is that each protein exerts multiple cellular effects, in addition to any direct role in viral replication. The viruses encode four non-structural (NS) small transmembrane proteins (NS2A, NS2B, NS4A and NS4B) which collectively remain rather poorly characterized. NS4A is a 16kDa membrane associated protein and recent studies have shown that this protein plays multiple roles, including in membrane remodeling, antagonism of the host cell interferon response, and in the induction of autophagy, in addition to playing a role in viral replication. Perhaps most importantly, NS4A has been implicated as playing a critical role in fetal developmental defects seen as a consequence of Zika virus infection during pregnancy. This review provides a comprehensive overview of the multiple roles of this small but pivotal protein in mediating the pathobiology of flaviviral infections.
Collapse
|
21
|
Bellen HJ, Hubbard EJA, Lehmann R, Madhani HD, Solnica-Krezel L, Southard-Smith EM. Model organism databases are in jeopardy. Development 2021; 148:dev200193. [PMID: 35231122 PMCID: PMC10656462 DOI: 10.1242/dev.200193] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Hugo J. Bellen
- Department of Molecular and Human Genetics, Duncan Neurological Research Institute at Texas Children Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | - E. J. A. Hubbard
- Department of Cell Biology, Skirball Institute, NYU Grossman School of Medicine, New York 10016, USA
| | - Ruth Lehmann
- Whitehead Institute, Department of Biology at MIT, Cambridge, MA 02142, USA
| | - Hiten D. Madhani
- Department of Biophysics and Biochemistry, UCSF, San Francisco, CA 94158, USA
| | - Lila Solnica-Krezel
- Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | | |
Collapse
|
22
|
Salim S, Banu A, Alwa A, Gowda SBM, Mohammad F. The gut-microbiota-brain axis in autism: what Drosophila models can offer? J Neurodev Disord 2021; 13:37. [PMID: 34525941 PMCID: PMC8442445 DOI: 10.1186/s11689-021-09378-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/06/2021] [Indexed: 12/28/2022] Open
Abstract
The idea that alterations in gut-microbiome-brain axis (GUMBA)-mediated communication play a crucial role in human brain disorders like autism remains a topic of intensive research in various labs. Gastrointestinal issues are a common comorbidity in patients with autism spectrum disorder (ASD). Although gut microbiome and microbial metabolites have been implicated in the etiology of ASD, the underlying molecular mechanism remains largely unknown. In this review, we have summarized recent findings in human and animal models highlighting the role of the gut-brain axis in ASD. We have discussed genetic and neurobehavioral characteristics of Drosophila as an animal model to study the role of GUMBA in ASD. The utility of Drosophila fruit flies as an amenable genetic tool, combined with axenic and gnotobiotic approaches, and availability of transgenic flies may reveal mechanistic insight into gut-microbiota-brain interactions and the impact of its alteration on behaviors relevant to neurological disorders like ASD.
Collapse
Affiliation(s)
- Safa Salim
- Division of Biological and Biomedical Sciences (BBS), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha, 34110, Qatar
| | - Ayesha Banu
- Division of Biological and Biomedical Sciences (BBS), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha, 34110, Qatar
| | - Amira Alwa
- Division of Biological and Biomedical Sciences (BBS), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha, 34110, Qatar
| | - Swetha B M Gowda
- Division of Biological and Biomedical Sciences (BBS), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha, 34110, Qatar
| | - Farhan Mohammad
- Division of Biological and Biomedical Sciences (BBS), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha, 34110, Qatar.
| |
Collapse
|
23
|
Ganguly P, Madonsela L, Chao JT, Loewen CJR, O’Connor TP, Verheyen EM, Allan DW. A scalable Drosophila assay for clinical interpretation of human PTEN variants in suppression of PI3K/AKT induced cellular proliferation. PLoS Genet 2021; 17:e1009774. [PMID: 34492006 PMCID: PMC8448351 DOI: 10.1371/journal.pgen.1009774] [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: 03/30/2021] [Revised: 09/17/2021] [Accepted: 08/10/2021] [Indexed: 12/28/2022] Open
Abstract
Gene variant discovery is becoming routine, but it remains difficult to usefully interpret the functional consequence or disease relevance of most variants. To fill this interpretation gap, experimental assays of variant function are becoming common place. Yet, it remains challenging to make these assays reproducible, scalable to high numbers of variants, and capable of assessing defined gene-disease mechanism for clinical interpretation aligned to the ClinGen Sequence Variant Interpretation (SVI) Working Group guidelines for 'well-established assays'. Drosophila melanogaster offers great potential as an assay platform, but was untested for high numbers of human variants adherent to these guidelines. Here, we wished to test the utility of Drosophila as a platform for scalable well-established assays. We took a genetic interaction approach to test the function of ~100 human PTEN variants in cancer-relevant suppression of PI3K/AKT signaling in cellular growth and proliferation. We validated the assay using biochemically characterized PTEN mutants as well as 23 total known pathogenic and benign PTEN variants, all of which the assay correctly assigned into predicted functional categories. Additionally, function calls for these variants correlated very well with our recent published data from a human cell line. Finally, using these pathogenic and benign variants to calibrate the assay, we could set readout thresholds for clinical interpretation of the pathogenicity of 70 other PTEN variants. Overall, we demonstrate that Drosophila offers a powerful assay platform for clinical variant interpretation, that can be used in conjunction with other well-established assays, to increase confidence in the accurate assessment of variant function and pathogenicity.
Collapse
Affiliation(s)
- Payel Ganguly
- Department of Cellular and Physiological Sciences, Life Sciences Institute, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Landiso Madonsela
- Department of Molecular Biology and Biochemistry, Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jesse T. Chao
- Department of Cellular and Physiological Sciences, Life Sciences Institute, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher J. R. Loewen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Timothy P. O’Connor
- Department of Cellular and Physiological Sciences, Life Sciences Institute, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Esther M. Verheyen
- Department of Molecular Biology and Biochemistry, Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Douglas W. Allan
- Department of Cellular and Physiological Sciences, Life Sciences Institute, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
24
|
Redolfi N, García-Casas P, Fornetto C, Sonda S, Pizzo P, Pendin D. Lighting Up Ca 2+ Dynamics in Animal Models. Cells 2021; 10:2133. [PMID: 34440902 PMCID: PMC8392631 DOI: 10.3390/cells10082133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/08/2021] [Accepted: 08/16/2021] [Indexed: 12/11/2022] Open
Abstract
Calcium (Ca2+) signaling coordinates are crucial processes in brain physiology. Particularly, fundamental aspects of neuronal function such as synaptic transmission and neuronal plasticity are regulated by Ca2+, and neuronal survival itself relies on Ca2+-dependent cascades. Indeed, impaired Ca2+ homeostasis has been reported in aging as well as in the onset and progression of neurodegeneration. Understanding the physiology of brain function and the key processes leading to its derangement is a core challenge for neuroscience. In this context, Ca2+ imaging represents a powerful tool, effectively fostered by the continuous amelioration of Ca2+ sensors in parallel with the improvement of imaging instrumentation. In this review, we explore the potentiality of the most used animal models employed for Ca2+ imaging, highlighting their application in brain research to explore the pathogenesis of neurodegenerative diseases.
Collapse
Affiliation(s)
- Nelly Redolfi
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
| | - Paloma García-Casas
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
| | - Chiara Fornetto
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
| | - Sonia Sonda
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
| | - Paola Pizzo
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
- Neuroscience Institute, National Research Council (CNR), 35131 Padua, Italy
| | - Diana Pendin
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
- Neuroscience Institute, National Research Council (CNR), 35131 Padua, Italy
| |
Collapse
|
25
|
Yadav V, Tolwinski N, Saunders TE. Spatiotemporal sensitivity of mesoderm specification to FGFR signalling in the Drosophila embryo. Sci Rep 2021; 11:14091. [PMID: 34238963 PMCID: PMC8266908 DOI: 10.1038/s41598-021-93512-1] [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: 03/29/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
Development of the Drosophila embryonic mesoderm is controlled through both internal and external inputs to the mesoderm. One such factor is Heartless (Htl), a Fibroblast Growth Factor Receptor (FGFR) expressed in the mesoderm. Although Htl has been extensively studied, the dynamics of its action are poorly understood after the initial phases of mesoderm formation and spreading. To begin to address this challenge, we have developed an optogenetic version of the FGFR Heartless in Drosophila (Opto-htl). Opto-htl enables us to activate the FGFR pathway in selective spatial (~ 35 μm section from one of the lateral sides of the embryo) and temporal domains (ranging from 40 min to 14 h) during embryogenesis. Importantly, the effects can be tuned by the intensity of light-activation, making this approach significantly more flexible than other genetic approaches. We performed controlled perturbations to the FGFR pathway to define the contribution of Htl signalling to the formation of the developing embryonic heart and somatic muscles. We find a direct correlation between Htl signalling dosage and number of Tinman-positive heart cells specified. Opto-htl activation favours the specification of Tinman positive cardioblasts and eliminates Eve-positive DA1 muscles. This effect is seen to increase progressively with increasing light intensity. Therefore, fine tuning of phenotypic responses to varied Htl signalling dosage can be achieved more conveniently than with other genetic approaches. Overall, Opto-htl is a powerful new tool for dissecting the role of FGFR signalling during development.
Collapse
Affiliation(s)
- V. Yadav
- grid.4280.e0000 0001 2180 6431Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - N. Tolwinski
- grid.4280.e0000 0001 2180 6431Yale-NUS, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - T. E. Saunders
- grid.4280.e0000 0001 2180 6431Mechanobiology Institute, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore ,grid.185448.40000 0004 0637 0221Institute of Molecular and Cell Biology, A*Star, Singapore, Singapore ,grid.7372.10000 0000 8809 1613Warwick Medical School, University of Warwick, Coventry, UK
| |
Collapse
|
26
|
Vitorović J, Joković N, Radulović N, Mihajilov-Krstev T, Cvetković VJ, Jovanović N, Mitrović T, Aleksić A, Stanković N, Bernstein N. Antioxidant Activity of Hemp ( Cannabis sativa L.) Seed Oil in Drosophila melanogaster Larvae under Non-Stress and H 2O 2-Induced Oxidative Stress Conditions. Antioxidants (Basel) 2021; 10:antiox10060830. [PMID: 34067432 PMCID: PMC8224776 DOI: 10.3390/antiox10060830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/11/2021] [Accepted: 05/18/2021] [Indexed: 12/26/2022] Open
Abstract
The oil extracted from hemp seeds has significant nutritional and biological properties due to the unique composition of polyunsaturated fatty acids and various antioxidant compounds. The potential of this oil for the prevention of oxidative stress and for the treatment of oxidative-stress-induced ailments is of increasing interest. Most studies of hemp seed oil were conducted in-vitro, meaning we lack information about effects and activity in vivo. In the present study, we evaluated the hypothesis that hemp seed oil at different concentrations improves the oxidative state of D. melanogaster, under non-stress as well as hydrogen-peroxide-induced stress. We analyzed the effects of hemp seed oil on oxidative stress markers and on the life cycle of D.melanogaster under non-stress and hydrogen-peroxide-induced stress conditions. D.melanogaster larvae were exposed to hemp seed oil concentrations ranging from 12.5 to 125 μL/mL. The results revealed that under non-stress conditions, oil concentrations up to 62.5 µL/mL did not induce negative effects on the life cycle of D. melanogaster and maintained the redox status of the larval cells at similar levels to the control level. Under oxidative stress conditions, biochemical parameters were significantly affected and only two oil concentrations, 18.7 and 31.2 µL/mL, provided protection against hydrogen peroxide stress effects. A higher oil concentration (125 μL/mL) exerted negative effects on the oxidative status and increased larval mortality. The tested oil was characterized chemically by NMR, transesterification, and silylation, followed by GC-MS analyses, and was shown to contain polyunsaturated fatty acid triglycerides and low levels of tocopherols. The high levels of linoleic and linolenic acids in the oil are suggested to be responsible for the observed in vivo antioxidant effects. Taken together, the results show that hemp seed oil is effective for reducing oxidative stress at the cellular level, thus supporting the hypothesis. The obtained results point to the potential of hemp seed oil for the prevention and treatment of conditions caused by the action of reactive oxygen species.
Collapse
Affiliation(s)
- Jelena Vitorović
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, 18000 Niš, Serbia; (J.V.); (N.J.); (T.M.-K.); (V.J.C.); (N.J.); (T.M.); (A.A.)
| | - Nataša Joković
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, 18000 Niš, Serbia; (J.V.); (N.J.); (T.M.-K.); (V.J.C.); (N.J.); (T.M.); (A.A.)
| | - Niko Radulović
- Department of Chemistry, Faculty of Sciences and Mathematics, University of Niš, 18000 Niš, Serbia;
| | - Tatjana Mihajilov-Krstev
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, 18000 Niš, Serbia; (J.V.); (N.J.); (T.M.-K.); (V.J.C.); (N.J.); (T.M.); (A.A.)
| | - Vladimir J. Cvetković
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, 18000 Niš, Serbia; (J.V.); (N.J.); (T.M.-K.); (V.J.C.); (N.J.); (T.M.); (A.A.)
| | - Nikola Jovanović
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, 18000 Niš, Serbia; (J.V.); (N.J.); (T.M.-K.); (V.J.C.); (N.J.); (T.M.); (A.A.)
| | - Tatjana Mitrović
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, 18000 Niš, Serbia; (J.V.); (N.J.); (T.M.-K.); (V.J.C.); (N.J.); (T.M.); (A.A.)
| | - Ana Aleksić
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, 18000 Niš, Serbia; (J.V.); (N.J.); (T.M.-K.); (V.J.C.); (N.J.); (T.M.); (A.A.)
| | | | - Nirit Bernstein
- Institute of Soil Water and Environmental Sciences, Volcani Center, Rishon LeZion 15159, Israel
- Correspondence:
| |
Collapse
|
27
|
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: 40] [Impact Index Per Article: 13.3] [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.
Collapse
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
| |
Collapse
|
28
|
Schneider J, Imler JL. Sensing and signalling viral infection in drosophila. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 117:103985. [PMID: 33358662 DOI: 10.1016/j.dci.2020.103985] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
The fruitfly Drosophila melanogaster is a valuable model to unravel mechanisms of innate immunity, in particular in the context of viral infections. RNA interference, and more specifically the small interfering RNA pathway, is a major component of antiviral immunity in drosophila. In addition, the contribution of inducible transcriptional responses to the control of viruses in drosophila and other invertebrates is increasingly recognized. In particular, the recent discovery of a STING-IKKβ-Relish signalling cassette in drosophila has confirmed that NF-κB transcription factors play an important role in the control of viral infections, in addition to bacterial and fungal infections. Here, we review recent developments in the field, which begin to shed light on the mechanisms involved in sensing of viral infections and in signalling leading to production of antiviral effectors.
Collapse
Affiliation(s)
- Juliette Schneider
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Jean-Luc Imler
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France; Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou 511436, China.
| |
Collapse
|
29
|
Sundararajan V, Venkatasubbu GD, Sheik Mohideen S. Investigation of therapeutic potential of cerium oxide nanoparticles in Alzheimer's disease using transgenic Drosophila. 3 Biotech 2021; 11:159. [PMID: 33758737 PMCID: PMC7937010 DOI: 10.1007/s13205-021-02706-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/23/2021] [Indexed: 12/15/2022] Open
Abstract
In the current study, the therapeutic potential of cerium oxide nanoparticles (nCeO2) was investigated in a human tau (htau) model of Alzheimer's disease (AD), using Drosophila melanogaster as an in vivo model. nCeO2 synthesised via the hydroxide-mediated approach were characterised using Fourier transform infrared (FTIR), transmission electron microscopy (TEM), X-ray diffraction (XRD) analyses and Raman spectroscopy. Characterisation studies confirmed the formation of pure cubic-structured nCeO2 and showed that the particles were spherically shaped, with an average size between 20 and 25 nm. The synthesised nCeO2 were then administered as part of the diet to transgenic Drosophila for one month, at 0.1 and 1 mM concentrations, and its effect on the biochemical levels of superoxide dismutase (SOD), acetylcholinesterase (AChE), and the climbing activity of flies were studied in a pan-neuronal model (elav; htau) of AD. Using an eye-specific model of htau expression (GMR; htau), the effect of nCeO2 on htau and autophagy-related (ATG) gene expression was also studied. Dietary administration of nCeO2 at a concentration of 1 mM restored the activity of SOD similar to that of control, but both concentrations of nCeO2 failed to modulate the level of AChE, and did not elicit any significant improvements in the climbing activity of elav; htau flies. Moreover, nCeO2 at a concentration of 1 mM significantly affected the climbing activity of elav; htau flies. nCeO2 also elicited a significant decrease in htau gene expression at both concentrations and increased the mRNA expression of key autophagy genes ATG1 and ATG18. The results therefore indicate that nCeO2 aids in replenishing the levels of SOD and tau clearance via the activation of autophagy.
Collapse
Affiliation(s)
- Vignesh Sundararajan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203 India
| | - G. Devanand Venkatasubbu
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203 India
| | - Sahabudeen Sheik Mohideen
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203 India
| |
Collapse
|
30
|
Little AG, Pamenter ME, Sitaraman D, Templeman NM, Willmore WG, Hedrick MS, Moyes CD. WITHDRAWN: Utilizing comparative models in biomedical research. Comp Biochem Physiol A Mol Integr Physiol 2021; 256:110938. [PMID: 33737041 DOI: 10.1016/j.cbpa.2021.110938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The Publisher regrets that this article is an accidental duplication of an article that has already been published in Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, Volume 255, 2021, 110593, https://doi.org/10.1016/j.cbpb.2021.110593. The duplicate article has therefore been withdrawn.
The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
Collapse
Affiliation(s)
| | | | - Divya Sitaraman
- Department of Psychology, California State University, East Bay, Hayward, CA, USA
| | | | | | - Michael S Hedrick
- Department of Biological Sciences, California State University, East Bay, Hayward, CA, USA.
| | | |
Collapse
|
31
|
Little AG, Pamenter ME, Sitaraman D, Templeman NM, Willmore WG, Hedrick MS, Moyes CD. Utilizing comparative models in biomedical research. Comp Biochem Physiol B Biochem Mol Biol 2021; 255:110593. [PMID: 33779562 DOI: 10.1016/j.cbpb.2021.110593] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review serves as an introduction to a Special Issue of Comparative Biochemistry and Physiology, focused on using non-human models to study biomedical physiology. The concept of a model differs across disciplines. For example, several models are used primarily to gain an understanding of specific human pathologies and disease states, whereas other models may be focused on gaining insight into developmental or evolutionary mechanisms. It is often the case that animals initially used to gain knowledge of some unique biochemical or physiological process finds foothold in the biomedical community and becomes an established model. The choice of a particular model for biomedical research is an ongoing process and model validation must keep pace with existing and emerging technologies. While the importance of non-mammalian models, such as Caenorhabditis elegans, Drosophila melanogaster, Danio rerio and Xenopus laevis, is well known, we also seek to bring attention to emerging alternative models of both invertebrates and vertebrates, which are less established but of interest to the comparative biochemistry and physiology community.
Collapse
Affiliation(s)
| | | | - Divya Sitaraman
- Department of Psychology, California State University, East Bay, Hayward, CA, USA
| | | | | | - Michael S Hedrick
- Department of Biological Sciences, California State University, East Bay, Hayward, CA, USA
| | | |
Collapse
|
32
|
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: 27] [Impact Index Per Article: 9.0] [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.
Collapse
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
| |
Collapse
|
33
|
Nweke EE, Thimiri Govinda Raj DB. Development of insect cell line using CRISPR technology. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 180:1-20. [PMID: 33934833 DOI: 10.1016/bs.pmbts.2021.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In this chapter, we delineated the methods of CRISPR technology that has been used for the development of engineered insect cell line. We elaborated on how CRISPR/Cas9 genome editing in Drosophila melanogaster, Bombyx mori, Spodoptera frugiperda (Sf9 and Sf21), and Mosquitoes enabled the use of model or non-model insect system in various biological and medical applications. Also, the application of synthetic baculovirus genome along with CRISPR/Cas9 vector system to enable genome editing of insect cell systems for treatment of communicable and non-communicable diseases.
Collapse
Affiliation(s)
| | - Deepak B Thimiri Govinda Raj
- Synthetic Nanobiotechnology and Biomachines Group, ERA Synthetic Biology, Centre for Synthetic Biology and Precision Medicine, CSIR, Pretoria, South Africa.
| |
Collapse
|
34
|
Wei T, Ji X, Xue J, Gao Y, Zhu X, Xiao G. Cyanidin-3-O-glucoside represses tumor growth and invasion in vivo by suppressing autophagy via inhibition of the JNK signaling pathways. Food Funct 2020; 12:387-396. [PMID: 33326533 DOI: 10.1039/d0fo02107e] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Black bean seed coat extract (BBSCE) contains a high amount of bioactive compounds which can reduce the risk of cancers, but the underlying mechanism remains poorly understood in vivo. Here using a Drosophila model of a malignant tumor, wherein the activated oncogene Raf (RafGOF) cooperates with loss-of-function mutations in the conserved tumor suppressor scribble (scrib-/-), we investigated the antitumor mechanism of BBSCE and its main active component cyanidin-3-O-glucoside (C3G) in vivo. The results showed that supplementation of either BBSCE or C3G inhibited the tumor growth and invasion of RafGOFscrib-/- and extended their survival in a dose dependent manner. Strikingly, the activation of both autonomous and non-autonomous autophagy in tumor flies was significantly reduced by C3G treatment. A further study indicated that C3G exhibited an antitumor effect in vivo by blocking autophagy both in tumor cells and in its microenvironment by inhibiting the JNK pathway. Interestingly, the efficacy of chloroquine (CQ, an autophagy inhibitor used as an antitumor agent) combined with C3G is much better than either C3G or CQ treatment alone. C3G may be combined with CQ to treat cancers and to provide a theoretical basis for functional food or natural medicine development.
Collapse
Affiliation(s)
- Tian Wei
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China.
| | - Xiaowen Ji
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China.
| | - Jinsong Xue
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China.
| | - Yan Gao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China.
| | - Xiaomei Zhu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Guiran Xiao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China.
| |
Collapse
|
35
|
An Unbiased Drug Screen for Seizure Suppressors in Duplication 15q Syndrome Reveals 5-HT 1A and Dopamine Pathway Activation as Potential Therapies. Biol Psychiatry 2020; 88:698-709. [PMID: 32507391 PMCID: PMC7554174 DOI: 10.1016/j.biopsych.2020.03.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/06/2020] [Accepted: 04/02/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Duplication 15q (Dup15q) syndrome is a rare neurogenetic disorder characterized by autism and pharmacoresistant epilepsy. Most individuals with isodicentric duplications have been on multiple medications to control seizures. We recently developed a model of Dup15q in Drosophila by elevating levels of fly Dube3a in glial cells using repo-GAL4, not neurons. In contrast to other Dup15q models, these flies develop seizures that worsen with age. METHODS We screened repo>Dube3a flies for approved compounds that can suppress seizures. Flies 3 to 5 days old were exposed to compounds in the fly food during development. Flies were tested using a bang sensitivity assay for seizure recovery time. At least 40 animals were tested per experiment, with separate testing for male and female flies. Studies of K+ content in glial cells of the fly brain were also performed using a fluorescent K+ indicator. RESULTS We identified 17 of 1280 compounds in the Prestwick Chemical Library that could suppress seizures. Eight compounds were validated in secondary screening. Four of these compounds regulated either serotonergic or dopaminergic signaling, and subsequent experiments confirmed that seizure suppression occurred primarily through stimulation of serotonin receptor 5-HT1A. Additional studies of K+ levels showed that Dube3a regulation of the Na+/K+ exchanger ATPα (adenosine triphosphatase α) in glia may be modulated by serotonin/dopamine signaling, causing seizure suppression. CONCLUSIONS Based on these pharmacological and genetic studies, we present an argument for the use of 5-HT1A agonists in the treatment of Dup15q epilepsy.
Collapse
|
36
|
Pridie C, Ueda K, Simmonds AJ. Rosy Beginnings: Studying Peroxisomes in Drosophila. Front Cell Dev Biol 2020; 8:835. [PMID: 32984330 PMCID: PMC7477296 DOI: 10.3389/fcell.2020.00835] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/04/2020] [Indexed: 12/19/2022] Open
Abstract
Research using the fruit fly Drosophila melanogaster has traditionally focused on understanding how mutations affecting gene regulation or function affect processes linked to animal development. Accordingly, flies have become an essential foundation of modern medical research through repeated contributions to our fundamental understanding of how their homologs of human genes function. Peroxisomes are organelles that metabolize lipids and reactive oxygen species like peroxides. However, despite clear linkage of mutations in human genes affecting peroxisomes to developmental defects, for many years fly models were conspicuously absent from the study of peroxisomes. Now, the few early studies linking the Rosy eye color phenotype to peroxisomes in flies have been joined by a growing body of research establishing novel roles for peroxisomes during the development or function of specific tissues or cell types. Similarly, unique properties of cultured fly Schneider 2 cells have advanced our understanding of how peroxisomes move on the cytoskeleton. Here, we profile how those past and more recent Drosophila studies started to link specific effects of peroxisome dysfunction to organ development and highlight the utility of flies as a model for human peroxisomal diseases. We also identify key differences in the function and proliferation of fly peroxisomes compared to yeast or mammals. Finally, we discuss the future of the fly model system for peroxisome research including new techniques that should support identification of additional tissue specific regulation of and roles for peroxisomes.
Collapse
Affiliation(s)
- C Pridie
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Kazuki Ueda
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
37
|
Torres-Zelada EF, Weake VM. The Gcn5 complexes in Drosophila as a model for metazoa. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194610. [PMID: 32735945 DOI: 10.1016/j.bbagrm.2020.194610] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 01/14/2023]
Abstract
The histone acetyltransferase Gcn5 is conserved throughout eukaryotes where it functions as part of large multi-subunit transcriptional coactivator complexes that stimulate gene expression. Here, we describe how studies in the model insect Drosophila melanogaster have provided insight into the essential roles played by Gcn5 in the development of multicellular organisms. We outline the composition and activity of the four different Gcn5 complexes in Drosophila: the Spt-Ada-Gcn5 Acetyltransferase (SAGA), Ada2a-containing (ATAC), Ada2/Gcn5/Ada3 transcription activator (ADA), and Chiffon Histone Acetyltransferase (CHAT) complexes. Whereas the SAGA and ADA complexes are also present in the yeast Saccharomyces cerevisiae, ATAC has only been identified in other metazoa such as humans, and the CHAT complex appears to be unique to insects. Each of these Gcn5 complexes is nucleated by unique Ada2 homologs or splice isoforms that share conserved N-terminal domains, and differ only in their C-terminal domains. We describe the common and specialized developmental functions of each Gcn5 complex based on phenotypic analysis of mutant flies. In addition, we outline how gene expression studies in mutant flies have shed light on the different biological roles of each complex. Together, these studies highlight the key role that Drosophila has played in understanding the expanded biological function of Gcn5 in multicellular eukaryotes.
Collapse
Affiliation(s)
| | - Vikki M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
| |
Collapse
|
38
|
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.
Collapse
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
| |
Collapse
|
39
|
Diez-Hermano S, Ganfornina MD, Vegas-Lozano E, Sanchez D. Machine Learning Representation of Loss of Eye Regularity in a Drosophila Neurodegenerative Model. Front Neurosci 2020; 14:516. [PMID: 32581679 PMCID: PMC7287026 DOI: 10.3389/fnins.2020.00516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/27/2020] [Indexed: 12/14/2022] Open
Abstract
The fruit fly compound eye is a premier experimental system for modeling human neurodegenerative diseases. The disruption of the retinal geometry has been historically assessed using time-consuming and poorly reliable techniques such as histology or pseudopupil manual counting. Recent semiautomated quantification approaches rely either on manual region-of-interest delimitation or engineered features to estimate the extent of degeneration. This work presents a fully automated classification pipeline of bright-field images based on orientated gradient descriptors and machine learning techniques. An initial region-of-interest extraction is performed, applying morphological kernels and Euclidean distance-to-centroid thresholding. Image classification algorithms are trained on these regions (support vector machine, decision trees, random forest, and convolutional neural network), and their performance is evaluated on independent, unseen datasets. The combinations of oriented gradient + gaussian kernel Support Vector Machine [0.97 accuracy and 0.98 area under the curve (AUC)] and fine-tuned pre-trained convolutional neural network (0.98 accuracy and 0.99 AUC) yielded the best results overall. The proposed method provides a robust quantification framework that can be generalized to address the loss of regularity in biological patterns similar to the Drosophila eye surface and speeds up the processing of large sample batches.
Collapse
Affiliation(s)
- Sergio Diez-Hermano
- Instituto de Biologia y Genetica Molecular-Departamento de Bioquimica y Biologia Molecular y Fisiologia, Universidad de Valladolid-CSIC, Valladolid, Spain.,Departamento de Biodiversidad, Ecologia y Evolucion, Unidad de Biomatematicas, Universidad Complutense, Madrid, Spain
| | - Maria D Ganfornina
- Instituto de Biologia y Genetica Molecular-Departamento de Bioquimica y Biologia Molecular y Fisiologia, Universidad de Valladolid-CSIC, Valladolid, Spain
| | - Esteban Vegas-Lozano
- Departamento de Genetica, Microbiologia y Estadistica, Universidad de Barcelona, Barcelona, Spain
| | - Diego Sanchez
- Instituto de Biologia y Genetica Molecular-Departamento de Bioquimica y Biologia Molecular y Fisiologia, Universidad de Valladolid-CSIC, Valladolid, Spain
| |
Collapse
|
40
|
Yusuff T, Jensen M, Yennawar S, Pizzo L, Karthikeyan S, Gould DJ, Sarker A, Gedvilaite E, Matsui Y, Iyer J, Lai ZC, Girirajan S. Drosophila models of pathogenic copy-number variant genes show global and non-neuronal defects during development. PLoS Genet 2020; 16:e1008792. [PMID: 32579612 PMCID: PMC7313740 DOI: 10.1371/journal.pgen.1008792] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/23/2020] [Indexed: 11/25/2022] Open
Abstract
While rare pathogenic copy-number variants (CNVs) are associated with both neuronal and non-neuronal phenotypes, functional studies evaluating these regions have focused on the molecular basis of neuronal defects. We report a systematic functional analysis of non-neuronal defects for homologs of 59 genes within ten pathogenic CNVs and 20 neurodevelopmental genes in Drosophila melanogaster. Using wing-specific knockdown of 136 RNA interference lines, we identified qualitative and quantitative phenotypes in 72/79 homologs, including 21 lines with severe wing defects and six lines with lethality. In fact, we found that 10/31 homologs of CNV genes also showed complete or partial lethality at larval or pupal stages with ubiquitous knockdown. Comparisons between eye and wing-specific knockdown of 37/45 homologs showed both neuronal and non-neuronal defects, but with no correlation in the severity of defects. We further observed disruptions in cell proliferation and apoptosis in larval wing discs for 23/27 homologs, and altered Wnt, Hedgehog and Notch signaling for 9/14 homologs, including AATF/Aatf, PPP4C/Pp4-19C, and KIF11/Klp61F. These findings were further supported by tissue-specific differences in expression patterns of human CNV genes, as well as connectivity of CNV genes to signaling pathway genes in brain, heart and kidney-specific networks. Our findings suggest that multiple genes within each CNV differentially affect both global and tissue-specific developmental processes within conserved pathways, and that their roles are not restricted to neuronal functions. Rare copy-number variants (CNVs), or large deletions and duplications in the genome, are associated with both neuronal and non-neuronal clinical features. Previous functional studies for these disorders have primarily focused on understanding the cellular mechanisms for neurological and behavioral phenotypes. To understand how genes within these CNVs contribute to developmental defects in non-neuronal tissues, we assessed 79 homologs of CNV and known neurodevelopmental genes in Drosophila models. We found that most homologs showed developmental defects when knocked down in the adult fly wing, ranging from mild size changes to severe wrinkled wings or lethality. Although a majority of tested homologs showed defects when knocked down specifically in wings or eyes, we found no correlation in the severity of the observed defects in these two tissues. A subset of the homologs showed disruptions in cellular processes in the developing fly wing, including alterations in cell proliferation, apoptosis, and cellular signaling pathways. Furthermore, human CNV genes also showed differences in gene expression patterns and interactions with signaling pathway genes across multiple human tissues. Our findings suggest that genes within CNV disorders affect global developmental processes in both neuronal and non-neuronal tissues.
Collapse
Affiliation(s)
- Tanzeen Yusuff
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Matthew Jensen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Sneha Yennawar
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Lucilla Pizzo
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Siddharth Karthikeyan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Dagny J. Gould
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Avik Sarker
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Erika Gedvilaite
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Yurika Matsui
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Janani Iyer
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Zhi-Chun Lai
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
41
|
Yamakawa-Kobayashi K, Ohhara Y, Kawashima T, Ohishi Y, Kayashima Y. Loss of CNDP causes a shorter lifespan and higher sensitivity to oxidative stress in Drosophila melanogaster. Biomed Res 2020; 41:131-138. [PMID: 32522930 DOI: 10.2220/biomedres.41.131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Increasing oxidative stress seems to be the result of an imbalance between free radical production and antioxidant defenses. During the course of aging, oxidative stress causes tissue/cellular damage, which is implicated in numerous age-related diseases. Carnosinase (CN or CNDP) is dipeptidase, which is associated with carnosine and/or glutathione (GSH) metabolism, those are the most abundant naturally occurring endogenous dipeptide and tripeptides with antioxidant and free radical scavenger properties. In the present study, we generated Drosophila cndp (dcndp) mutant flies using the CRISPR/Cas9 system to study the roles of dcndp in vivo. We demonstrate that dcndp mutant flies exhibit shorter lifespan and increased sensitivity to paraquat or hydrogen peroxide (H2O2) induced oxidative stress. These results suggest that dcndp maintains homeostatic conditions, protecting cells and tissues against the harmful effects of oxidative stress in the course of aging.
Collapse
Affiliation(s)
- Kimiko Yamakawa-Kobayashi
- Laboratory of Human Genetics, School of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka
| | - Yuya Ohhara
- Laboratory of Human Genetics, School of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka
| | - Takumi Kawashima
- Laboratory of Human Genetics, School of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka
| | - Yoshitatsu Ohishi
- Laboratory of Human Genetics, School of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka
| | | |
Collapse
|
42
|
Thurmond J, Goodman JL, Strelets VB, Attrill H, Gramates LS, Marygold SJ, Matthews BB, Millburn G, Antonazzo G, Trovisco V, Kaufman TC, Calvi BR. FlyBase 2.0: the next generation. Nucleic Acids Res 2020; 47:D759-D765. [PMID: 30364959 PMCID: PMC6323960 DOI: 10.1093/nar/gky1003] [Citation(s) in RCA: 488] [Impact Index Per Article: 122.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 10/09/2018] [Indexed: 01/01/2023] Open
Abstract
FlyBase (flybase.org) is a knowledge base that supports the community of researchers that use the fruit fly, Drosophila melanogaster, as a model organism. The FlyBase team curates and organizes a diverse array of genetic, molecular, genomic, and developmental information about Drosophila. At the beginning of 2018, ‘FlyBase 2.0’ was released with a significantly improved user interface and new tools. Among these important changes are a new organization of search results into interactive lists or tables (hitlists), enhanced reference lists, and new protein domain graphics. An important new data class called ‘experimental tools’ consolidates information on useful fly strains and other resources related to a specific gene, which significantly enhances the ability of the Drosophila researcher to design and carry out experiments. With the release of FlyBase 2.0, there has also been a restructuring of backend architecture and a continued development of application programming interfaces (APIs) for programmatic access to FlyBase data. In this review, we describe these major new features and functionalities of the FlyBase 2.0 site and how they support the use of Drosophila as a model organism for biological discovery and translational research.
Collapse
Affiliation(s)
- Jim Thurmond
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Joshua L Goodman
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Victor B Strelets
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Helen Attrill
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - L Sian Gramates
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Steven J Marygold
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Beverley B Matthews
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Gillian Millburn
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Giulia Antonazzo
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Vitor Trovisco
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Thomas C Kaufman
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | | |
Collapse
|
43
|
Rahit KMTH, Tarailo-Graovac M. Genetic Modifiers and Rare Mendelian Disease. Genes (Basel) 2020; 11:E239. [PMID: 32106447 PMCID: PMC7140819 DOI: 10.3390/genes11030239] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/21/2020] [Indexed: 12/11/2022] Open
Abstract
Despite advances in high-throughput sequencing that have revolutionized the discovery of gene defects in rare Mendelian diseases, there are still gaps in translating individual genome variation to observed phenotypic outcomes. While we continue to improve genomics approaches to identify primary disease-causing variants, it is evident that no genetic variant acts alone. In other words, some other variants in the genome (genetic modifiers) may alleviate (suppress) or exacerbate (enhance) the severity of the disease, resulting in the variability of phenotypic outcomes. Thus, to truly understand the disease, we need to consider how the disease-causing variants interact with the rest of the genome in an individual. Here, we review the current state-of-the-field in the identification of genetic modifiers in rare Mendelian diseases and discuss the potential for future approaches that could bridge the existing gap.
Collapse
Affiliation(s)
- K. M. Tahsin Hassan Rahit
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| |
Collapse
|
44
|
Singh MD, Jensen M, Lasser M, Huber E, Yusuff T, Pizzo L, Lifschutz B, Desai I, Kubina A, Yennawar S, Kim S, Iyer J, Rincon-Limas DE, Lowery LA, Girirajan S. NCBP2 modulates neurodevelopmental defects of the 3q29 deletion in Drosophila and Xenopus laevis models. PLoS Genet 2020; 16:e1008590. [PMID: 32053595 PMCID: PMC7043793 DOI: 10.1371/journal.pgen.1008590] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/26/2020] [Accepted: 12/30/2019] [Indexed: 12/12/2022] Open
Abstract
The 1.6 Mbp deletion on chromosome 3q29 is associated with a range of neurodevelopmental disorders, including schizophrenia, autism, microcephaly, and intellectual disability. Despite its importance towards neurodevelopment, the role of individual genes, genetic interactions, and disrupted biological mechanisms underlying the deletion have not been thoroughly characterized. Here, we used quantitative methods to assay Drosophila melanogaster and Xenopus laevis models with tissue-specific individual and pairwise knockdown of 14 homologs of genes within the 3q29 region. We identified developmental, cellular, and neuronal phenotypes for multiple homologs of 3q29 genes, potentially due to altered apoptosis and cell cycle mechanisms during development. Using the fly eye, we screened for 314 pairwise knockdowns of homologs of 3q29 genes and identified 44 interactions between pairs of homologs and 34 interactions with other neurodevelopmental genes. Interestingly, NCBP2 homologs in Drosophila (Cbp20) and X. laevis (ncbp2) enhanced the phenotypes of homologs of the other 3q29 genes, leading to significant increases in apoptosis that disrupted cellular organization and brain morphology. These cellular and neuronal defects were rescued with overexpression of the apoptosis inhibitors Diap1 and xiap in both models, suggesting that apoptosis is one of several potential biological mechanisms disrupted by the deletion. NCBP2 was also highly connected to other 3q29 genes in a human brain-specific interaction network, providing support for the relevance of our results towards the human deletion. Overall, our study suggests that NCBP2-mediated genetic interactions within the 3q29 region disrupt apoptosis and cell cycle mechanisms during development. Rare copy-number variants, or large deletions and duplications in the genome, are associated with a wide range of neurodevelopmental disorders. The 3q29 deletion confers an increased risk for schizophrenia and autism. To understand the conserved biological mechanisms that are disrupted by this deletion, we systematically tested 14 individual homologs and 314 pairwise interactions of 3q29 genes for neuronal, cellular, and developmental phenotypes in Drosophila melanogaster and Xenopus laevis models. We found that multiple homologs of genes within the deletion region contribute towards developmental defects, such as larval lethality and disrupted cellular organization. Interestingly, we found that NCBP2 acts as a key modifier gene within the region, enhancing the developmental phenotypes of each of the homologs for other 3q29 genes and leading to disruptions in apoptosis and cell cycle pathways. Our results suggest that multiple genes within the 3q29 region interact with each other through shared mechanisms and jointly contribute to neurodevelopmental defects.
Collapse
Affiliation(s)
- Mayanglambam Dhruba Singh
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Matthew Jensen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Micaela Lasser
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Emily Huber
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Tanzeen Yusuff
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Lucilla Pizzo
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Brian Lifschutz
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Inshya Desai
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Alexis Kubina
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Sneha Yennawar
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Sydney Kim
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Janani Iyer
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Diego E Rincon-Limas
- Department of Neurology, McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Laura Anne Lowery
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
- Department of Medicine, Boston University Medical Center, Boston, Massachusetts, United States of America
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| |
Collapse
|
45
|
Graves HK, Jangam S, Tan KL, Pignata A, Seto ES, Yamamoto S, Wangler MF. A Genetic Screen for Genes That Impact Peroxisomes in Drosophila Identifies Candidate Genes for Human Disease. G3 (BETHESDA, MD.) 2020; 10:69-77. [PMID: 31767637 PMCID: PMC6945042 DOI: 10.1534/g3.119.400803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/11/2019] [Indexed: 02/06/2023]
Abstract
Peroxisomes are subcellular organelles that are essential for proper function of eukaryotic cells. In addition to being the sites of a variety of oxidative reactions, they are crucial regulators of lipid metabolism. Peroxisome loss or dysfunction leads to multi-system diseases in humans that strongly affect the nervous system. In order to identify previously unidentified genes and mechanisms that impact peroxisomes, we conducted a genetic screen on a collection of lethal mutations on the X chromosome in Drosophila Using the number, size and morphology of GFP tagged peroxisomes as a readout, we screened for mutations that altered peroxisomes based on clonal analysis and confocal microscopy. From this screen, we identified eighteen genes that cause increases in peroxisome number or altered morphology when mutated. We examined the human homologs of these genes and found that they are involved in a diverse array of cellular processes. Interestingly, the human homologs from the X-chromosome collection are under selective constraint in human populations and are good candidate genes particularly for dominant genetic disease. This in vivo screening approach for peroxisome defects allows identification of novel genes that impact peroxisomes in vivo in a multicellular organism and is a valuable platform to discover genes potentially involved in dominant disease that could affect peroxisomes.
Collapse
Affiliation(s)
| | | | - Kai Li Tan
- Department of Molecular and Human Genetics
| | | | | | - Shinya Yamamoto
- Department of Molecular and Human Genetics,
- Department of Neuroscience
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, and
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX 77030
| | - Michael F Wangler
- Department of Molecular and Human Genetics,
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, and
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX 77030
| |
Collapse
|
46
|
Antioxidant Therapy in Parkinson's Disease: Insights from Drosophila melanogaster. Antioxidants (Basel) 2020; 9:antiox9010052. [PMID: 31936094 PMCID: PMC7023233 DOI: 10.3390/antiox9010052] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/03/2020] [Accepted: 01/04/2020] [Indexed: 12/20/2022] Open
Abstract
Reactive oxygen species (ROS) play an important role as endogenous mediators in several cellular signalling pathways. However, at high concentrations they can also exert deleterious effects by reacting with many macromolecules including DNA, proteins and lipids. The precise balance between ROS production and their removal via numerous enzymatic and nonenzymatic molecules is of fundamental importance for cell survival. Accordingly, many neurodegenerative disorders, including Parkinson’s disease (PD), are associated with excessive levels of ROS, which induce oxidative damage. With the aim of coping with the progression of PD, antioxidant compounds are currently receiving increasing attention as potential co-adjuvant molecules in the treatment of these diseases, and many studies have been performed to evaluate the purported protective effects of several antioxidant molecules. In the present review, we present and discuss the relevance of the use of Drosophila melanogaster as an animal model with which to evaluate the therapeutic potential of natural and synthetic antioxidants. The conservation of most of the PD-related genes between humans and D. melanogaster, along with the animal’s rapid life cycle and the versatility of genetic tools, makes fruit flies an ideal experimental system for rapid screening of antioxidant-based treatments.
Collapse
|
47
|
Abstract
Drosophila melanogaster, colloquially known as the fruit fly, is one of the most commonly used model organisms in scientific research. Although the final architecture of a fly and a human differs greatly, most of the fundamental biological mechanisms and pathways controlling development and survival are conserved through evolution between the two species. For this reason, Drosophila has been productively used as a model organism for over a century, to study a diverse range of biological processes, including development, learning, behavior and aging. Ca2+ signaling comprises complex pathways that impact on virtually every aspect of cellular physiology. Within such a complex field of study, Drosophila offers the advantages of consolidated molecular and genetic techniques, lack of genetic redundancy and a completely annotated genome since 2000. These and other characteristics provided the basis for the identification of many genes encoding Ca2+ signaling molecules and the disclosure of conserved Ca2+ signaling pathways. In this review, we will analyze the applications of Ca2+ imaging in the fruit fly model, highlighting in particular their impact on the study of normal brain function and pathogenesis of neurodegenerative diseases.
Collapse
|
48
|
Robles-Murguia M, Rao D, Finkelstein D, Xu B, Fan Y, Demontis F. Muscle-derived Dpp regulates feeding initiation via endocrine modulation of brain dopamine biosynthesis. Genes Dev 2019; 34:37-52. [PMID: 31831628 PMCID: PMC6938663 DOI: 10.1101/gad.329110.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 11/08/2019] [Indexed: 12/26/2022]
Abstract
In this study, Robles-Murguia et al. set out to examine whether muscle-secreted hormones regulate feeding. Using Drosophila as a model system combined with several in vivo and in vitro experiments, the authors identify Decapentaplegic (Dpp) as a myokine that can signal from the muscle to the brain to control feeding by altering dopamine synthesis through transcriptional regulation of tyrosine hydroxylase (TH). In animals, the brain regulates feeding behavior in response to local energy demands of peripheral tissues, which secrete orexigenic and anorexigenic hormones. Although skeletal muscle is a key peripheral tissue, it remains unknown whether muscle-secreted hormones regulate feeding. In Drosophila, we found that decapentaplegic (dpp), the homolog of human bone morphogenetic proteins BMP2 and BMP4, is a muscle-secreted factor (a myokine) that is induced by nutrient sensing and that circulates and signals to the brain. Muscle-restricted dpp RNAi promotes foraging and feeding initiation, whereas dpp overexpression reduces it. This regulation of feeding by muscle-derived Dpp stems from modulation of brain tyrosine hydroxylase (TH) expression and dopamine biosynthesis. Consistently, Dpp receptor signaling in dopaminergic neurons regulates TH expression and feeding initiation via the downstream transcriptional repressor Schnurri. Moreover, pharmacologic modulation of TH activity rescues the changes in feeding initiation due to modulation of dpp expression in muscle. These findings indicate that muscle-to-brain endocrine signaling mediated by the myokine Dpp regulates feeding behavior.
Collapse
Affiliation(s)
- Maricela Robles-Murguia
- Division of Developmental Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Deepti Rao
- Division of Developmental Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Fabio Demontis
- Division of Developmental Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| |
Collapse
|
49
|
Cox RL, Hofley CM, Tatapudy P, Patel RK, Dayani Y, Betcher M, LaRocque JR. Functional conservation of RecQ helicase BLM between humans and Drosophila melanogaster. Sci Rep 2019; 9:17527. [PMID: 31772289 PMCID: PMC6879748 DOI: 10.1038/s41598-019-54101-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/09/2019] [Indexed: 12/02/2022] Open
Abstract
RecQ helicases are a family of proteins involved in maintaining genome integrity with functions in DNA repair, recombination, and replication. The human RecQ helicase family consists of five helicases: BLM, WRN, RECQL, RECQL4, and RECQL5. Inherited mutations in RecQ helicases result in Bloom Syndrome (BLM mutation), Werner Syndrome (WRN mutation), Rothmund-Thomson Syndrome (RECQL4 mutation), and other genetic diseases, including cancer. The RecQ helicase family is evolutionarily conserved, as Drosophila melanogaster have three family members: DmBlm, DmRecQL4, and DmRecQL5 and DmWRNexo, which contains a conserved exonuclease domain. DmBlm has functional similarities to human BLM (hBLM) as mutants demonstrate increased sensitivity to ionizing radiation (IR) and a decrease in DNA double-strand break (DSB) repair. To determine the extent of functional conservation of RecQ helicases, hBLM was expressed in Drosophila using the GAL4 > UASp system to determine if GAL4 > UASp::hBLM can rescue DmBlm mutant sensitivity to IR. hBLM was able to rescue female DmBlm mutant sensitivity to IR, supporting functional conservation. This functional conservation is specific to BLM, as human GAL4 > UASp::RECQL was not able to rescue DmBlm mutant sensitivity to IR. These results demonstrate the conserved role of BLM in maintaining the genome while reinforcing the applicability of using Drosophila as a model system to study Bloom Syndrome.
Collapse
Affiliation(s)
- Rebecca L Cox
- Department of Human Science, Georgetown University Medical Center, Washington, DC, 20057, USA
| | - Carolyn M Hofley
- Department of Human Science, Georgetown University Medical Center, Washington, DC, 20057, USA
| | - Pallavi Tatapudy
- Department of Human Science, Georgetown University Medical Center, Washington, DC, 20057, USA
| | - Romil K Patel
- Department of Human Science, Georgetown University Medical Center, Washington, DC, 20057, USA
| | - Yaron Dayani
- Department of Human Science, Georgetown University Medical Center, Washington, DC, 20057, USA
| | - Madison Betcher
- Department of Human Science, Georgetown University Medical Center, Washington, DC, 20057, USA
| | - Jeannine R LaRocque
- Department of Human Science, Georgetown University Medical Center, Washington, DC, 20057, USA.
| |
Collapse
|
50
|
The conserved mitochondrial genomes of Drosophila mercatorum (Diptera: Drosophilidae) with different reproductive modes and phylogenetic implications. Int J Biol Macromol 2019; 138:912-918. [PMID: 31362022 DOI: 10.1016/j.ijbiomac.2019.07.184] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/26/2019] [Accepted: 07/26/2019] [Indexed: 11/23/2022]
Abstract
Fruit flies (Drosophilidae: Drosophila) are commonly found in daily life and have long been used as model organisms in biology researches. Drosophila mercatorum is one important member of the Drosophila genus and has been used to study centrosome assembly of cells. In this study, we sequenced and analyzed the mitochondrial genome (mitogenome) of D. mercatorum, finding that it contains the typical structure of 37 genes and a control region. The arrangement of mitochondrial genes is in accordance with that in other Drosophila species, which is considered the ancestral organization of insects' mitogenomes. Phylogenetic analyses were performed based on 23 species of Drosophila. Our results supported two monophyletic subgenera, Drosophila and Sophophora, except for D. willistoni which was presented as an early offshoot of Drosophila. The topology ((D. yakuba + D. erecta) + D. melanogaster) was supported. We further compared the mitogenomes of parthenogenesis and sexual reproduction strains of D. mercatorum. However, only one synonymous mutation in COI gene was identified, indicating mitogenomic evolution is not strongly correlated with the different reproductive modes of this species. Taken together, our results demonstrate that mitogenome is an effective molecular marker that can be further used in phylogenetic studies of Drosophila and other organisms.
Collapse
|