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Gaona-López C, Martínez-Vázquez AV, Villalobos-Rocha JC, Juárez-Rendón KJ, Rivera G. Analysis of Giardia lamblia Nucleolus as Drug Target: A Review. Pharmaceuticals (Basel) 2023; 16:1168. [PMID: 37631082 PMCID: PMC10457859 DOI: 10.3390/ph16081168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Giardia lamblia (G. lamblia) is the main causative agent of diarrhea worldwide, affecting children and adults alike; in the former, it can be lethal, and in the latter a strong cause of morbidity. Despite being considered a predominant disease in low-income and developing countries, current migratory flows have caused an increase in giardiasis cases in high-income countries. Currently, there is a wide variety of chemotherapeutic treatments to combat this parasitosis, most of which have potentially serious side effects, such as genotoxic, carcinogenic, and teratogenic. The necessity to create novel treatments and discover new therapeutic targets to fight against this illness is evident. The current review centers around the controversial nucleolus of G. lamblia, providing a historical perspective that traces its apparent absence to the present evidence supporting its existence as a subnuclear compartment in this organism. Additionally, possible examples of ncRNAs and proteins ubiquitous to the nucleolus that can be used as targets of different therapeutic strategies are discussed. Finally, some examples of drugs under research that could be effective against G. lamblia are described.
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Affiliation(s)
- Carlos Gaona-López
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | | | - Juan Carlos Villalobos-Rocha
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico;
| | - Karina Janett Juárez-Rendón
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (A.V.M.-V.); (K.J.J.-R.)
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
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Bharathi JK, Anandan R, Benjamin LK, Muneer S, Prakash MAS. Recent trends and advances of RNA interference (RNAi) to improve agricultural crops and enhance their resilience to biotic and abiotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:600-618. [PMID: 36529010 DOI: 10.1016/j.plaphy.2022.11.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/04/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Over the last two decades, significant advances have been made using genetic engineering technology to modify genes from various exotic origins and introduce them into plants to induce favorable traits. RNA interference (RNAi) was discovered earlier as a natural process for controlling the expression of genes across all higher species. It aims to enhance precision and accuracy in pest/pathogen resistance, quality improvement, and manipulating the architecture of plants. However, it existed as a widely used technique recently. RNAi technologies could well be used to down-regulate any genes' expression without disrupting the expression of other genes. The use of RNA interference to silence genes in various organisms has become the preferred method for studying gene functions. The establishment of new approaches and applications for enhancing desirable characters is essential in crops by gene suppression and the refinement of knowledge of endogenous RNAi mechanisms in plants. RNAi technology in recent years has become an important and choicest method for controlling insects, pests, pathogens, and abiotic stresses like drought, salinity, and temperature. Although there are certain drawbacks in efficiency of this technology such as gene candidate selection, stability of trigger molecule, choice of target species and crops. Nevertheless, from past decade several target genes has been identified in numerous crops for their improvement towards biotic and abiotic stresses. The current review is aimed to emphasize the research done on crops under biotic and abiotic stress using RNAi technology. The review also highlights the gene regulatory pathways/gene silencing, RNA interference, RNAi knockdown, RNAi induced biotic and abiotic resistance and advancements in the understanding of RNAi technology and the functionality of various components of the RNAi machinery in crops for their improvement.
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Affiliation(s)
- Jothi Kanmani Bharathi
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Annamalai University, Annamalai Nagar, 608 002, Tamil Nadu, India
| | - Ramaswamy Anandan
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Annamalai University, Annamalai Nagar, 608 002, Tamil Nadu, India
| | - Lincy Kirubhadharsini Benjamin
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | - Sowbiya Muneer
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India.
| | - Muthu Arjuna Samy Prakash
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Annamalai University, Annamalai Nagar, 608 002, Tamil Nadu, India.
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3
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Herbert DR, Stoltzfus JDC, Rossi HL, Abraham D. Is Strongyloides stercoralis hyperinfection induced by glucocorticoids a result of both suppressed host immunity and altered parasite genetics? Mol Biochem Parasitol 2022; 251:111511. [PMID: 36007683 DOI: 10.1016/j.molbiopara.2022.111511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/01/2022] [Accepted: 08/18/2022] [Indexed: 11/19/2022]
Abstract
The gastrointestinal (GI) nematode Strongyloides stercoralis (S.s.) causes human strongyloidiasis, a potentially life-threatening disease that currently affects over 600 million people globally. The uniquely pernicious aspect of S.s. infection, as compared to all other GI nematodes, is its autoinfective larval stage (L3a) that maintains a low-grade chronic infection, allowing undetectable persistence for decades. Infected individuals who are administered glucocorticoid therapy can develop a rapid and often lethal hyperinfection syndrome within days. Hyperinfection patients often present with dramatic increases in first- and second-stage larvae and L3a in their GI tract, with L3a widely disseminating throughout host organs leading to sepsis. How glucocorticoid administration drives hyperinfection remains a critical unanswered question; specifically, it is unknown whether these steroids promote hyperinfection through eliminating essential host protective mechanisms and/or through dysregulating parasite development. This current deficiency in understanding is largely due to the previous absence of a genetically defined mouse model that would support all S.s. life-cycle stages and the lack of successful approaches for S.s. genetic manipulation. However, there are currently new possibilities through the recent demonstration that immunodeficient NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice support sub-clinical infections that can be transformed to lethal hyperinfection syndrome following glucocorticoid administration. This is coupled with advances in transcriptomics, transgenesis, and gene inactivation strategies that now allow rigorous scientific inquiry into S.s. biology. We propose that combining in vivo manipulation of host immunity and deep immunoprofiling strategies with the latest advances in S.s. transcriptomics, piggyBac transposon-mediated transgene insertion, and CRISPR/Cas-9-mediated gene inactivation will facilitate new insights into the mechanisms that could be targeted to block lethality in humans with S.s. hyperinfection.
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Affiliation(s)
- De'Broski R Herbert
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce St., Philadelphia, PA 10104, USA.
| | - Jonathan D C Stoltzfus
- Department of Biology, Millersville University of Pennsylvania, 50 E. Frederick St., Millersville, PA 17551, USA.
| | - Heather L Rossi
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce St., Philadelphia, PA 10104, USA.
| | - David Abraham
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, 1025 Walnut St., Philadelphia, PA 19107, USA.
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4
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Yokoi T, Nabe T, Ishizuka C, Hayashi K, Ito-Harashima S, Yagi T, Nakagawa Y, Miyagawa H. A luciferase reporter assay for ecdysone agonists using HEK293T cells. Biosci Biotechnol Biochem 2022; 86:1490-1496. [PMID: 35977393 DOI: 10.1093/bbb/zbac139] [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: 07/04/2022] [Accepted: 08/10/2022] [Indexed: 11/12/2022]
Abstract
Ecdysone agonists are a class of insecticides that activate the ecdysone receptor (EcR) heterodimerized with the ultraspiracle (USP). Here, we report a new luciferase reporter assay for ecdysone agonists. The assay employs mammalian HEK293T cells transiently transfected with the EcR and USP genes of Chilo suppressalis, along with the taiman (Tai) gene of Drosophila melanogaster that encodes a steroid receptor coactivator. This assay system gave results consistent with those of radioligand binding assays and showed sensitivity superior to that of the existing in vitro methods. In addition, use of the heterologous host cells precludes perturbation from intrinsic players of the ecdysone signaling, which is a potential drawback of insect cell-based methods. This reporter system is suitable for detailed structure-activity analysis of ecdysone agonists and will serve as a valuable tool for the rational design of novel insect growth regulators.
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Affiliation(s)
- Taiyo Yokoi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Taku Nabe
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Chiharu Ishizuka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Ken'ichiro Hayashi
- Department of RNA Biology and Neuroscience, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka, Japan.,Department of Ophthalmology, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi, Japan
| | - Sayoko Ito-Harashima
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, Japan
| | - Takashi Yagi
- Department of Biological Chemistry, Graduate School of Science, Osaka Metropolitan University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka, Japan
| | - Yoshiaki Nakagawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Hisashi Miyagawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
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Taubenheim J, Kortmann C, Fraune S. Function and Evolution of Nuclear Receptors in Environmental-Dependent Postembryonic Development. Front Cell Dev Biol 2021; 9:653792. [PMID: 34178983 PMCID: PMC8222990 DOI: 10.3389/fcell.2021.653792] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/06/2021] [Indexed: 12/14/2022] Open
Abstract
Nuclear receptors (NRs) fulfill key roles in the coordination of postembryonal developmental transitions in animal species. They control the metamorphosis and sexual maturation in virtually all animals and by that the two main environmental-dependent developmental decision points. Sexual maturation and metamorphosis are controlled by steroid receptors and thyroid receptors, respectively in vertebrates, while both processes are orchestrated by the ecdysone receptor (EcR) in insects. The regulation of these processes depends on environmental factors like nutrition, temperature, or photoperiods and by that NRs form evolutionary conserved mediators of phenotypic plasticity. While the mechanism of action for metamorphosis and sexual maturation are well studied in model organisms, the evolution of these systems is not entirely understood and requires further investigation. We here review the current knowledge of NR involvement in metamorphosis and sexual maturation across the animal tree of life with special attention to environmental integration and evolution of the signaling mechanism. Furthermore, we compare commonalities and differences of the different signaling systems. Finally, we identify key gaps in our knowledge of NR evolution, which, if sufficiently investigated, would lead to an importantly improved understanding of the evolution of complex signaling systems, the evolution of life history decision points, and, ultimately, speciation events in the metazoan kingdom.
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Affiliation(s)
- Jan Taubenheim
- Zoology and Organismic Interactions, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Constantin Kortmann
- Zoology and Organismic Interactions, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sebastian Fraune
- Zoology and Organismic Interactions, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Transcriptional profiles in Strongyloides stercoralis males reveal deviations from the Caenorhabditis sex determination model. Sci Rep 2021; 11:8254. [PMID: 33859232 PMCID: PMC8050236 DOI: 10.1038/s41598-021-87478-3] [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: 01/23/2021] [Accepted: 03/30/2021] [Indexed: 02/02/2023] Open
Abstract
The human and canine parasitic nematode Strongyloides stercoralis utilizes an XX/XO sex determination system, with parasitic females reproducing by mitotic parthenogenesis and free-living males and females reproducing sexually. However, the genes controlling S. stercoralis sex determination and male development are unknown. We observed precocious development of rhabditiform males in permissive hosts treated with corticosteroids, suggesting that steroid hormones can regulate male development. To examine differences in transcript abundance between free-living adult males and other developmental stages, we utilized RNA-Seq. We found two clusters of S. stercoralis-specific genes encoding predicted transmembrane proteins that are only expressed in free-living males. We additionally identified homologs of several genes important for sex determination in Caenorhabditis species, including mab-3, tra-1, fem-2, and sex-1, which may have similar functions. However, we identified three paralogs of gld-1; Ss-qki-1 transcripts were highly abundant in adult males, while Ss-qki-2 and Ss-qki-3 transcripts were highly abundant in adult females. We also identified paralogs of pumilio domain-containing proteins with sex-specific transcripts. Intriguingly, her-1 appears to have been lost in several parasite lineages, and we were unable to identify homologs of tra-2 outside of Caenorhabditis species. Together, our data suggest that different mechanisms control male development in S. stercoralis and Caenorhabditis species.
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Ito-Harashima S, Yagi T. Reporter gene assays for screening and identification of novel molting hormone- and juvenile hormone-like chemicals. JOURNAL OF PESTICIDE SCIENCE 2021; 46:29-42. [PMID: 33746544 PMCID: PMC7953021 DOI: 10.1584/jpestics.d20-079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
A reporter gene assay (RGA) is used to investigate the activity of synthetic chemicals mimicking the molting hormones (MHs) and juvenile hormones (JHs) of insects, so-called insect growth regulators (IGRs). The MH receptor, a heterodimer of the ecdysone receptor (EcR) and ultraspiracle (USP), and the JH receptor Methoprene-tolerant (Met) are ligand-dependent transcription factors. Ligand-bound EcR-USP and Met bind to specific cis-acting DNA elements, referred to as the ecdysone-responsive element (EcRE) and the JH-responsive element (JHRE), respectively, in order to transactivate target genes. Insect hormone-induced transactivation systems have been reconstituted by the introduction of reporter genes under the control of EcRE and JHRE, or two-hybrid reporter genes, into insect, mammalian, and yeast cells expressing receptor proteins. RGA is easy to use and convenient for examining the MH- and JH-like activities of synthetic chemicals and is suitable for the high-throughput screening of novel structural classes of chemicals targeting EcR-USP and Met.
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Affiliation(s)
- Sayoko Ito-Harashima
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1–1 Gakuen-cho, Naka-ku, Sakai city, Osaka 599–8531, Japan
| | - Takashi Yagi
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1–1 Gakuen-cho, Naka-ku, Sakai city, Osaka 599–8531, Japan
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Dai F, Yoo WG, Lu Y, Song JH, Lee JY, Byun Y, Pak JH, Sohn WM, Hong SJ. Sodium-bile acid co-transporter is crucial for survival of a carcinogenic liver fluke Clonorchis sinensis in the bile. PLoS Negl Trop Dis 2020; 14:e0008952. [PMID: 33284789 PMCID: PMC7746286 DOI: 10.1371/journal.pntd.0008952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 12/17/2020] [Accepted: 11/03/2020] [Indexed: 12/29/2022] Open
Abstract
The liver fluke Clonorchis sinensis inhabits the bile ducts, where bile concentration disparities across the fluke cell membrane can cause bile intoxication. Sodium-bile acid co-transporter (SBAT) plays a crucial role in bile acid recycling. The process by which SBAT imports bile acids is electrically coupled to sodium ion co-transportation. Here, we report that the SBAT of C. sinensis (CsSBAT) is involved in bile acid transportation. CsSBAT cDNA encoded a putative polypeptide of 546 amino acid residues. Furthermore, CsSBAT consisted of ten putative transmembrane domains, and its 3D structure was predicted to form panel and core domains. The CsSBAT had one bile acid- and three Na+-binding sites, enabling coordination of a symport process. CsSBAT was mainly localized in the mesenchymal tissue throughout the fluke body and sparsely localized in the basement of the tegument, intestinal epithelium, and excretory bladder wall. Bile acid permeated into the adult flukes in a short time and remained at a low concentration level. Bile acid accumulated inside the mesenchymal tissue when CsSBAT was inhibited using polyacrylic acid–tetradeoxycholic acid conjugate. The accumulated bile acid deteriorated the C. sinensis adults leading to death. CsSBAT silencing shortened the lifespan of the fluke when it was placed into bile. Taken together, we propose that CsSBAT transports bile acids in the mesenchymal tissue and coordinate with outward transporters to maintain bile acid homeostasis of C. sinensis adults, contributing to C. sinensis survival in the bile environment. Clonorchiasis is a neglected tropical disease caused by infection with the liver fluke Clonorchis sinensis. C. sinensis is a biological carcinogen causing cholangiocarcinoma in humans. Juvenile worms inhabit and grow to adults in the bile ducts. Bile acids in the bile are double-edged molecules; they promote metabolism, but differences in their concentration across the cell membrane could lead to bile intoxication. The sodium-bile acid co-transporter of C. sinensis (CsSBAT) is indispensable for maintaining its normal physiology and bile detoxification in the bile duct. However, information related to the molecular and biological characteristics of the SBAT of liver flukes is not available. Here, we cloned CsSBAT for the first time in trematodes and characterized its tertiary structure and physiological functions. The sequential and structural properties of CsSBAT were similar to the apical sodium-bile acid co-transporter found in mammalian intestines. CsSBAT shared a mesenchymal tissue distribution with Na+-taurocholate co-transporting polypeptide in the hepatocytes adjacent to the bile ducts. Bile acids accumulated in C. sinensis adults when CsSBAT was inhibited, causing their death. This information might promote further studies on the physiological functions of SBAT and other trematode bile transporters and open new avenues toward developing novel anthelminthic drugs.
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Affiliation(s)
- Fuhong Dai
- Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
- Department of Parasitology, School of Biology and Basic Medical Sciences, Medical College, Soochow University, Suzhou, Jiangsu, PR China
| | - Won Gi Yoo
- Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Yanyan Lu
- Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
- Liubei Center for Disease Control and Prevention, Liuzhou, Guangxi, PR China
| | - Jin-Ho Song
- Department of Pharmacology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Ji-Yun Lee
- Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Youngro Byun
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Jhang Ho Pak
- Department of Convergence Medicine, University of Ulsan College of Medicine and Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Woon-Mok Sohn
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, Republic of Korea
| | - Sung-Jong Hong
- Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
- * E-mail:
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Grote A, Li Y, Liu C, Voronin D, Geber A, Lustigman S, Unnasch TR, Welch L, Ghedin E. Prediction pipeline for discovery of regulatory motifs associated with Brugia malayi molting. PLoS Negl Trop Dis 2020; 14:e0008275. [PMID: 32574217 PMCID: PMC7337397 DOI: 10.1371/journal.pntd.0008275] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 07/06/2020] [Accepted: 04/07/2020] [Indexed: 11/19/2022] Open
Abstract
Filarial nematodes can cause debilitating diseases in humans. They have complicated life cycles involving an insect vector and mammalian hosts, and they go through a number of developmental molts. While whole genome sequences of parasitic worms are now available, very little is known about transcription factor (TF) binding sites and their cognate transcription factors that play a role in regulating development. To address this gap, we developed a novel motif prediction pipeline, Emotif Alpha, that integrates ten different motif discovery algorithms, multiple statistical tests, and a comparative analysis of conserved elements between the filarial worms Brugia malayi and Onchocerca volvulus, and the free-living nematode Caenorhabditis elegans. We identified stage-specific TF binding motifs in B. malayi, with a particular focus on those potentially involved in the L3-L4 molt, a stage important for the establishment of infection in the mammalian host. Using an in vitro molting system, we tested and validated three of these motifs demonstrating the accuracy of the motif prediction pipeline. Diseases caused by parasitic worms such as the filariae are among the leading causes of morbidity in the developing world. Very little is known about how development is regulated in these vector-transmitted parasites. We have developed a computational method to identify motifs that correspond to transcription factor binding sites in the genome of the parasitic worm, Brugia malayi, one of the causative agents of lymphatic filariasis. Using this approach, we were able to predict stage-specific transcription factor binding sites involved in a stage of the molting process important for the establishment of the infection. We validated the role of these motifs using an in vitro molting system.
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Affiliation(s)
- Alexandra Grote
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Yichao Li
- School of Computer Science and Electrical Engineering, Ohio University, Athens, Ohio, United States of America
| | - Canhui Liu
- Center for Global Infectious Disease Research, University of South Florida, Tampa, FL, Florida, United States of America
| | - Denis Voronin
- Laboratory of Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York, United States of America
| | - Adam Geber
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Sara Lustigman
- Laboratory of Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York, United States of America
| | - Thomas R. Unnasch
- Center for Global Infectious Disease Research, University of South Florida, Tampa, FL, Florida, United States of America
| | - Lonnie Welch
- School of Computer Science and Electrical Engineering, Ohio University, Athens, Ohio, United States of America
- * E-mail: (LW); (EG)
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
- Department of Epidemiology, School of Global Public Health, New York University, New York, New York, United States of America
- * E-mail: (LW); (EG)
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Hernandez HW, Soeung M, Zorn KM, Ashoura N, Mottin M, Andrade CH, Caffrey CR, de Siqueira-Neto JL, Ekins S. High Throughput and Computational Repurposing for Neglected Diseases. Pharm Res 2018; 36:27. [PMID: 30560386 PMCID: PMC6792295 DOI: 10.1007/s11095-018-2558-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/09/2018] [Indexed: 12/21/2022]
Abstract
Purpose Neglected tropical diseases (NTDs) represent are a heterogeneous group of communicable diseases that are found within the poorest populations of the world. There are 23 NTDs that have been prioritized by the World Health Organization, which are endemic in 149 countries and affect more than 1.4 billion people, costing these developing economies billions of dollars annually. The NTDs result from four different causative pathogens: protozoa, bacteria, helminth and virus. The majority of the diseases lack effective treatments. Therefore, new therapeutics for NTDs are desperately needed. Methods We describe various high throughput screening and computational approaches that have been performed in recent years. We have collated the molecules identified in these studies and calculated molecular properties. Results Numerous global repurposing efforts have yielded some promising compounds for various neglected tropical diseases. These compounds when analyzed as one would expect appear drug-like. Several large datasets are also now in the public domain and this enables machine learning models to be constructed that then facilitate the discovery of new molecules for these pathogens. Conclusions In the space of a few years many groups have either performed experimental or computational repurposing high throughput screens against neglected diseases. These have identified compounds which in many cases are already approved drugs. Such approaches perhaps offer a more efficient way to develop treatments which are generally not a focus for global pharmaceutical companies because of the economics or the lack of a viable market. Other diseases could perhaps benefit from these repurposing approaches. Electronic supplementary material The online version of this article (10.1007/s11095-018-2558-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Melinda Soeung
- MD Anderson Cancer Center, University of Texas, Houston, Texas, USA
| | - Kimberley M Zorn
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina, 27606, USA
| | | | - Melina Mottin
- LabMol - Laboratory for Molecular Modeling and Drug Design Faculdade de Farmacia, Universidade Federal de Goias - UFG, Goiânia, GO, 74605-170, Brazil
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design Faculdade de Farmacia, Universidade Federal de Goias - UFG, Goiânia, GO, 74605-170, Brazil
| | - Conor R Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California, 92093, USA
| | - Jair Lage de Siqueira-Neto
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California, 92093, USA
| | - Sean Ekins
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina, 27606, USA.
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11
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Liu C, Mhashilkar AS, Chabanon J, Xu S, Lustigman S, Adams JH, Unnasch TR. Development of a toolkit for piggyBac-mediated integrative transfection of the human filarial parasite Brugia malayi. PLoS Negl Trop Dis 2018; 12:e0006509. [PMID: 29782496 PMCID: PMC5983866 DOI: 10.1371/journal.pntd.0006509] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/01/2018] [Accepted: 05/08/2018] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The human filarial parasites cause diseases that are among the most important causes of morbidity in the developing world. The elimination programs targeting these infections rely on a limited number of drugs, making the identification of new chemotherapeutic agents a high priority. The study of these parasites has lagged due to the lack of reverse genetic methods. METHODOLOGY/PRINCIPAL FINDINGS We report a novel co-culture method that results in developmentally competent infective larvae of one of the human filarial parasites (Brugia malayi) and describe a method to efficiently transfect the larval stages of this parasite. We describe the production of constructs that result in integrative transfection using the piggyBac transposon system, and a selectable marker that can be used to identify transgenic parasites. We describe the production and use of dual reporter plasmids containing both a secreted luciferase selectable marker and fluorescent protein reporters that will be useful to study temporal and spatial patterns of gene expression. CONCLUSIONS/SIGNIFICANCE The methods and constructs reported here will permit the efficient production of integrated transgenic filarial parasite lines, allowing reverse genetic technologies to be applied to all life cycle stages of the parasite.
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Affiliation(s)
- Canhui Liu
- Center for Global Health Infectious Disease Research, Department of Global Health, University of South Florida, Tampa, FL, United States of America
| | - Amruta S. Mhashilkar
- Center for Global Health Infectious Disease Research, Department of Global Health, University of South Florida, Tampa, FL, United States of America
| | - Johan Chabanon
- Center for Global Health Infectious Disease Research, Department of Global Health, University of South Florida, Tampa, FL, United States of America
| | - Shulin Xu
- Center for Global Health Infectious Disease Research, Department of Global Health, University of South Florida, Tampa, FL, United States of America
| | - Sara Lustigman
- Molecular Parasitology, New York Blood Center, New York, NY, United States of America
| | - John H. Adams
- Center for Global Health Infectious Disease Research, Department of Global Health, University of South Florida, Tampa, FL, United States of America
| | - Thomas R. Unnasch
- Center for Global Health Infectious Disease Research, Department of Global Health, University of South Florida, Tampa, FL, United States of America
- * E-mail:
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12
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Wang Z, Schaffer NE, Kliewer SA, Mangelsdorf DJ. Nuclear receptors: emerging drug targets for parasitic diseases. J Clin Invest 2017; 127:1165-1171. [PMID: 28165341 PMCID: PMC5373876 DOI: 10.1172/jci88890] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Parasitic worms infect billions of people worldwide. Current treatments rely on a small group of drugs that have been used for decades. A shortcoming of these drugs is their inability to target the intractable infectious stage of the parasite. As well-known therapeutic targets in mammals, nuclear receptors have begun to be studied in parasitic worms, where they are widely distributed and play key roles in governing metabolic and developmental transcriptional networks. One such nuclear receptor is DAF-12, which is required for normal nematode development, including the all-important infectious stage. Here we review the emerging literature that implicates DAF-12 and potentially other nuclear receptors as novel anthelmintic targets.
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Affiliation(s)
| | | | | | - David J. Mangelsdorf
- Department of Pharmacology
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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ProBiS tools (algorithm, database, and web servers) for predicting and modeling of biologically interesting proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 128:24-32. [PMID: 28212856 DOI: 10.1016/j.pbiomolbio.2017.02.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 12/14/2016] [Accepted: 02/07/2017] [Indexed: 01/30/2023]
Abstract
ProBiS (Protein Binding Sites) Tools consist of algorithm, database, and web servers for prediction of binding sites and protein ligands based on the detection of structurally similar binding sites in the Protein Data Bank. In this article, we review the operations that ProBiS Tools perform, provide comments on the evolution of the tools, and give some implementation details. We review some of its applications to biologically interesting proteins. ProBiS Tools are freely available at http://probis.cmm.ki.si and http://probis.nih.gov.
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