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Hollin T, Abel S, Banks C, Hristov B, Prudhomme J, Hales K, Florens L, Stafford Noble W, Le Roch KG. Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes. Nat Commun 2024; 15:1365. [PMID: 38355719 PMCID: PMC10866993 DOI: 10.1038/s41467-024-45519-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Ribonucleoprotein complexes are composed of RNA, RNA-dependent proteins (RDPs) and RNA-binding proteins (RBPs), and play fundamental roles in RNA regulation. However, in the human malaria parasite, Plasmodium falciparum, identification and characterization of these proteins are particularly limited. In this study, we use an unbiased proteome-wide approach, called R-DeeP, a method based on sucrose density gradient ultracentrifugation, to identify RDPs. Quantitative analysis by mass spectrometry identifies 898 RDPs, including 545 proteins not yet associated with RNA. Results are further validated using a combination of computational and molecular approaches. Overall, this method provides the first snapshot of the Plasmodium protein-protein interaction network in the presence and absence of RNA. R-DeeP also helps to reconstruct Plasmodium multiprotein complexes based on co-segregation and deciphers their RNA-dependence. One RDP candidate, PF3D7_0823200, is functionally characterized and validated as a true RBP. Using enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP-seq), we demonstrate that this protein interacts with various Plasmodium non-coding transcripts, including the var genes and ap2 transcription factors.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Charles Banks
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Borislav Hristov
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Kianna Hales
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA.
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Kirichenko A, Uemura T, Liang Y, Hasan S, Abel S, Renz P, Shamsesfandabadi P, Carpenter J, Yin Y, Thai N. Stereotactic Body Radiation Therapy (SBRT) for Hepatocellular Carcinoma (HCC) With Single Photon Emission Computed Tomography (SPECT) Functional Treatment Planning in Patients With Advanced Hepatic Cirrhosis. Adv Radiat Oncol 2024; 9:101367. [PMID: 38405302 PMCID: PMC10885583 DOI: 10.1016/j.adro.2023.101367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/19/2023] [Indexed: 02/27/2024] Open
Abstract
Purpose We report on the feasibility and outcomes of liver stereotactic body radiation therapy (SBRT) for hepatocellular carcinoma (HCC) with single-photon emission computed tomography (SPECT) functional treatment planning in patients with Child-Pugh (CP) B/C cirrhosis. Methods and Materials Liver SPECT with 99mTc-sulfur colloid was coregistered to treatment planning computed tomography (CT) for the guided avoidance of functional hepatic parenchyma during SBRT. Functional liver volumes (FLVs) obtained from SPECT were compared with anatomic liver volumes defined on the planning CT. Radiation dose constraints were adapted exclusively to FLV. Local control, toxicity, and survival were reported with at least 6 months of radiographic follow-up. Pre- and posttransplant outcomes were analyzed in a subset of patients who completed SBRT as a bridge to liver transplant. Model of End-Stage Liver Disease was used to score hepatic function before and after SBRT completion. Results With a median follow-up of 32 months, 45 patients (58 lesions) with HCC and CP-B/C cirrhosis received SBRT to a median dose of 45 Gy (3-5 fractions). FLV loss (34%, P < .001) was observed in all patients, and the functional and anatomic liver volumes matched well in a control group of noncirrhotic/non-HCC patients. Despite marked functional parenchyma retraction, the amount of FLV on SPECT exposed to the threshold irradiation was significantly less than the CT liver volumes (P < .001) because of the optimized beam placement during dosimetry planning. Twenty-three patients (51%) successfully completed orthotopic liver transplant, with a median time to transplant of 9.2 months. With 91% in-field local control, the overall 2-year survival was 65% (90% after the orthotopic liver transplant), with no incidence of radiation-induced liver disease observed within 3 to 4 months or accelerated CP class migration from B to C within the first 6 months post-SBRT. Mean Model of End-Stage Liver Disease-Na score was not significantly elevated at 3-month intervals after SBRT completion. Conclusions Functional treatment planning with 99mTc sulfur colloid SPECT/CT allows identification and avoidance of functional hepatic parenchyma in patients with CP-B/C cirrhosis, leading to low toxicity and satisfactory transplant outcomes.
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Affiliation(s)
- Alexander Kirichenko
- Division of Radiation Oncology, Allegheny Health Network Cancer Institute, Pittsburgh, Pennsylvania
| | - Tadahiro Uemura
- Division of Abdominal Transplantation and Hepato-Biliary Surgery, Allegheny General Hospital, Pittsburgh, Pennsylvania
| | - Yun Liang
- Division of Radiation Oncology, Allegheny Health Network Cancer Institute, Pittsburgh, Pennsylvania
| | | | - Steven Abel
- Division of Radiation Oncology, Allegheny Health Network Cancer Institute, Pittsburgh, Pennsylvania
| | - Paul Renz
- Division of Radiation Oncology, Allegheny Health Network Cancer Institute, Pittsburgh, Pennsylvania
| | - Parisa Shamsesfandabadi
- Division of Radiation Oncology, Allegheny Health Network Cancer Institute, Pittsburgh, Pennsylvania
| | - Jennifer Carpenter
- Division of Abdominal Transplantation and Hepato-Biliary Surgery, Allegheny General Hospital, Pittsburgh, Pennsylvania
| | - Yue Yin
- Allegheny-Singer Research Institute, Biostatistics, Allegheny Health Network, Pittsburgh, Pennsylvania
| | - Ngoc Thai
- Division of Abdominal Transplantation and Hepato-Biliary Surgery, Allegheny General Hospital, Pittsburgh, Pennsylvania
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Singh P, Vydyam P, Fang T, Estrada K, Gonzalez LM, Grande R, Kumar M, Chakravarty S, Berry V, Ranwez V, Carcy B, Depoix D, Sánchez S, Cornillot E, Abel S, Ciampossin L, Lenz T, Harb O, Sanchez-Flores A, Montero E, Le Roch KG, Lonardi S, Ben Mamoun C. Multiomics analysis reveals B. MO1 as a distinct Babesia species and provides insights into its evolution and virulence. bioRxiv 2024:2024.01.17.575932. [PMID: 38293033 PMCID: PMC10827214 DOI: 10.1101/2024.01.17.575932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Babesiosis, caused by protozoan parasites of the genus Babesia , is an emerging tick-borne disease of significance for both human and animal health. Babesia parasites infect erythrocytes of vertebrate hosts where they develop and multiply rapidly to cause the pathological symptoms associated with the disease. The identification of various Babesia species underscores the ongoing risk of new zoonotic pathogens capable of infecting humans, a concern amplified by anthropogenic activities and environmental shifts impacting the distribution and transmission dynamics of parasites, their vectors, and reservoir hosts. One such species, Babesia MO1, previously implicated in severe cases of human babesiosis in the midwestern United States, was initially considered closely related to B. divergens , the predominant agent of human babesiosis in Europe. Yet, uncertainties persist regarding whether these pathogens represent distinct variants of the same species or are entirely separate species. We show that although both B. MO1 and B. divergens share similar genome sizes, comprising three nuclear chromosomes, one linear mitochondrial chromosome, and one circular apicoplast chromosome, major differences exist in terms of genomic sequence divergence, gene functions, transcription profiles, replication rates and susceptibility to antiparasitic drugs. Furthermore, both pathogens have evolved distinct classes of multigene families, crucial for their pathogenicity and adaptation to specific mammalian hosts. Leveraging genomic information for B. MO1, B. divergens , and other members of the Babesiidae family within Apicomplexa provides valuable insights into the evolution, diversity, and virulence of these parasites. This knowledge serves as a critical tool in preemptively addressing the emergence and rapid transmission of more virulent strains.
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Baptista CG, Hosking S, Gas-Pascual E, Ciampossine L, Abel S, Hakimi MA, Jeffers V, Le Roch K, West CM, Blader IJ. Toxoplasma gondii F-Box Protein L2 Silences Feline-Restricted Genes Necessary for Sexual Commitment. bioRxiv 2023:2023.12.18.572150. [PMID: 38187549 PMCID: PMC10769283 DOI: 10.1101/2023.12.18.572150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Toxoplasma gondii is a foodborne pathogen that can cause severe and life-threatening infections in fetuses and immunocompromised patients. Felids are its only definitive hosts, and a wide range of animals, including humans, serve as intermediate hosts. When the transmissible bradyzoite stage is orally ingested by felids, they transform into merozoites that expand asexually, ultimately generating millions of gametes for the parasite sexual cycle. However, bradyzoites in intermediate hosts differentiate exclusively to disease-causing tachyzoites, which rapidly disseminate throughout the host. Though tachyzoites are well-studied, the molecular mechanisms governing transitioning between developmental stages are poorly understood. Each parasite stage can be distinguished by a characteristic transcriptional signature, with one signature being repressed during the other stages. Switching between stages requires substantial changes in the proteome, which is achieved in part by ubiquitination. F-box proteins mediate protein poly-ubiquitination by recruiting substrates to SKP1, Cullin-1, F-Box protein E3 ubiquitin ligase (SCF-E3) complexes. We have identified an F-box protein named Toxoplasma gondii F-Box Protein L2 (TgFBXL2), which localizes to distinct nuclear sites. TgFBXL2 is stably engaged in an SCF-E3 complex that is surprisingly also associated with a COP9 signalosome complex that negatively regulates SCF-E3 function. At the cellular level, TgFBXL2-depleted parasites are severely defective in centrosome replication and daughter cell development. Most remarkable, RNA seq data show that TgFBXL2 conditional depletion induces the expression of genes necessary for sexual commitment. We suggest that TgFBXL2 is a latent guardian of sexual stage development in Toxoplasma and poised to remove conflicting proteins in response to an unknown trigger of sexual development.
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Affiliation(s)
- Carlos G. Baptista
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, NY 14203 USA
| | - Sarah Hosking
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, NY 14203 USA
| | - Elisabet Gas-Pascual
- Department of Biochemistry & Molecular Biology, Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602 USA
| | - Loic Ciampossine
- Department of Molecular, Cell, and Systems Biology, University of California Riverside, Riverside, CA, 92521USA
| | - Steven Abel
- Department of Molecular, Cell, and Systems Biology, University of California Riverside, Riverside, CA, 92521USA
| | - Mohamed-Ali Hakimi
- Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences (IAB), INSERM U1209, CNRS UMR 5309, Grenoble Alpes University, Grenoble, France
| | - Victoria Jeffers
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824 USA
| | - Karine Le Roch
- Department of Molecular, Cell, and Systems Biology, University of California Riverside, Riverside, CA, 92521USA
| | - Christopher M. West
- Department of Biochemistry & Molecular Biology, Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602 USA
| | - Ira J. Blader
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, NY 14203 USA
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Chahine Z, Abel S, Hollin T, Chung JH, Barnes GL, Daub ME, Renard I, Choi JY, Pratap V, Pal A, Alba-Argomaniz M, Banks CAS, Kirkwood J, Saraf A, Camino I, Castaneda P, Cuevas MC, De Mercado-Arnanz J, Fernandez-Alvaro E, Garcia-Perez A, Ibarz N, Viera-Morilla S, Prudhomme J, Joyner CJ, Bei AK, Florens L, Ben Mamoun C, Vanderwal CD, Le Roch KG. A Potent Kalihinol Analogue Disrupts Apicoplast Function and Vesicular Trafficking in P. falciparum Malaria. bioRxiv 2023:2023.11.21.568162. [PMID: 38045341 PMCID: PMC10690269 DOI: 10.1101/2023.11.21.568162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Here we report the discovery of MED6-189, a new analogue of the kalihinol family of isocyanoterpene (ICT) natural products. MED6-189 is effective against drug-sensitive and -resistant P. falciparum strains blocking both intraerythrocytic asexual replication and sexual differentiation. This compound was also effective against P. knowlesi and P. cynomolgi. In vivo efficacy studies using a humanized mouse model of malaria confirms strong efficacy of the compound in animals with no apparent hemolytic activity or apparent toxicity. Complementary chemical biology, molecular biology, genomics and cell biological analyses revealed that MED6-189 primarily targets the parasite apicoplast and acts by inhibiting lipid biogenesis and cellular trafficking. Genetic analyses in P. falciparum revealed that a mutation in PfSec13, which encodes a component of the parasite secretory machinery, reduced susceptibility to the drug. The high potency of MED6-189 in vitro and in vivo, its broad range of efficacy, excellent therapeutic profile, and unique mode of action make it an excellent addition to the antimalarial drug pipeline.
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Affiliation(s)
- Z Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - S Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - T Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - JH Chung
- Department of Chemistry, University of California, Irvine, California, 92617, USA
| | - GL Barnes
- Department of Chemistry, University of California, Irvine, California, 92617, USA
| | - ME Daub
- Department of Chemistry, University of California, Irvine, California, 92617, USA
| | - I Renard
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - JY Choi
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - V Pratap
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - A Pal
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - M Alba-Argomaniz
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - CAS Banks
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - J Kirkwood
- Metabolomics Core Facility, University of California, Riverside, CA 92521, USA
| | - A Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - I Camino
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - P Castaneda
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - MC Cuevas
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | | | | | - A Garcia-Perez
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - N Ibarz
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - S Viera-Morilla
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - J Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - CJ Joyner
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - AK Bei
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - L Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - C Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - CD Vanderwal
- Department of Chemistry, University of California, Irvine, California, 92617, USA
| | - KG Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
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6
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Subudhi AK, Green JL, Satyam R, Salunke RP, Lenz T, Shuaib M, Isaioglou I, Abel S, Gupta M, Esau L, Mourier T, Nugmanova R, Mfarrej S, Shivapurkar R, Stead Z, Rached FB, Ostwal Y, Sougrat R, Dada A, Kadamany AF, Fischle W, Merzaban J, Knuepfer E, Ferguson DJP, Gupta I, Le Roch KG, Holder AA, Pain A. DNA-binding protein PfAP2-P regulates parasite pathogenesis during malaria parasite blood stages. Nat Microbiol 2023; 8:2154-2169. [PMID: 37884813 PMCID: PMC10627835 DOI: 10.1038/s41564-023-01497-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/11/2023] [Indexed: 10/28/2023]
Abstract
Malaria-associated pathogenesis such as parasite invasion, egress, host cell remodelling and antigenic variation requires concerted action by many proteins, but the molecular regulation is poorly understood. Here we have characterized an essential Plasmodium-specific Apicomplexan AP2 transcription factor in Plasmodium falciparum (PfAP2-P; pathogenesis) during the blood-stage development with two peaks of expression. An inducible knockout of gene function showed that PfAP2-P is essential for trophozoite development, and critical for var gene regulation, merozoite development and parasite egress. Chromatin immunoprecipitation sequencing data collected at timepoints matching the two peaks of pfap2-p expression demonstrate PfAP2-P binding to promoters of genes controlling trophozoite development, host cell remodelling, antigenic variation and pathogenicity. Single-cell RNA sequencing and fluorescence-activated cell sorting revealed de-repression of most var genes in Δpfap2-p parasites. Δpfap2-p parasites also overexpress early gametocyte marker genes, indicating a regulatory role in sexual stage conversion. We conclude that PfAP2-P is an essential upstream transcriptional regulator at two distinct stages of the intra-erythrocytic development cycle.
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Affiliation(s)
- Amit Kumar Subudhi
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Judith L Green
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, UK
| | - Rohit Satyam
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Rahul P Salunke
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Todd Lenz
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Muhammad Shuaib
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ioannis Isaioglou
- Cell Migration and Signaling Laboratory, Bioscience Program, BESE Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Mohit Gupta
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Luke Esau
- KAUST Core Labs, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Tobias Mourier
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Raushan Nugmanova
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Sara Mfarrej
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Rupali Shivapurkar
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Zenaida Stead
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Fathia Ben Rached
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Yogesh Ostwal
- Laboratory of Chromatin Biochemistry, Bioscience Program, BESE Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Rachid Sougrat
- KAUST Core Labs, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ashraf Dada
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Kingdom of Saudi Arabia
- College of Medicine, Al Faisal University, Riyadh, Saudi Arabia
| | - Abdullah Fuaad Kadamany
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Kingdom of Saudi Arabia
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Bioscience Program, BESE Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Jasmeen Merzaban
- Cell Migration and Signaling Laboratory, Bioscience Program, BESE Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ellen Knuepfer
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, UK
- Molecular and Cellular Parasitology Laboratory, Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, UK
| | - David J P Ferguson
- Nuffield Department of Clinical Laboratory Science, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
- School of Artificial Intelligence, Indian Institute of Technology Delhi, New Delhi, India
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Anthony A Holder
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, UK.
| | - Arnab Pain
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
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Shamsesfandabadi P, Ponnapalli S, Spencer K, Patel A, Yin Y, Abel S, Beriwal S, Wegner RE, Patel AK, Horne ZD. CT vs. MRI: Which is More Accurate in Grading Rectal Wall Infiltration after Hydrogel Spacer Placement for Prostate Cancer Patients? Int J Radiat Oncol Biol Phys 2023; 117:e436-e437. [PMID: 37785418 DOI: 10.1016/j.ijrobp.2023.06.1608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) The purpose of this study was to evaluate the incidence and severity of rectal wall infiltration (RWI) in prostate cancer patients after rectal hydrogel spacer implantation, a commonly used procedure to minimize rectal radiation exposure during prostate radiotherapy. The study aimed to determine correlation of RWI using computed tomography (CT) scans and magnetic resonance imaging (MRI) scans in order to determine the optimal post-placement imaging modality. MATERIALS/METHODS This retrospective study was conducted on 370 patients diagnosed with localized prostate cancer who underwent rectal hydrogel spacer placement from 2020 to 2022. CT scans were performed on all patients, with a smaller subset also undergoing MRI scans. The images were independently evaluated by three radiation oncologists to grade RWI levels using a standardized scoring system based on CT and MRI images after hydrogel placement. The levels were categorized as 0 (no RWI), 1 (focal RWI), 2 (moderate RWI), and 3 (significant RWI). RESULTS Any grade of RWI was identified in 79.8% of men with the majority (41%) being RWI grade 1. The median time for CT scans was 9 days after hydrogel spacer placement and 14.5 days for MRI scans. For the subset of patients with both CT and MRI scans after spacer (mostly SpaceOAR Vue), RWI was detected in 58.33% of patients based on CT and 61.11% of patients based on MRI. Table 1 shows the mean percentage of patients with each score of RWI for each imaging modality. MRI was more likely to lead to a designation of RWI of any grade compared to CT and more often led to detection of RWI grades 2-3. CONCLUSION Our findings demonstrate that the incidence and severity of RWI may be higher than previously reported in clinical trials and that MRI may be a more sensitive imaging modality. Caution is needed in the utilization of rectal spacer gels given the potential for complications with misplacement prior to radiation therapy. Further study is warranted to determine the potential impact of low-grade RWI on the safety of subsequent treatment.
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Affiliation(s)
- P Shamsesfandabadi
- Allegheny Health Network Cancer Institute, Department of Radiation Oncology, Pittsburgh, PA
| | - S Ponnapalli
- Drexel University College of Medicine, Philadelphia, PA
| | - K Spencer
- Drexel University College of Medicine, Philadelphia, PA
| | - A Patel
- Drexel University College of Medicine, Philadelphia, PA
| | - Y Yin
- Allegheny Health Network, Pittsburgh, PA
| | - S Abel
- Allegheny Health Network Cancer Institute, Department of Radiation Oncology, Pittsburgh, PA
| | - S Beriwal
- Allegheny Health Network Cancer Institute, Department of Radiation Oncology, Pittsburgh, PA
| | - R E Wegner
- Allegheny Health Network Cancer Institute, Department of Radiation Oncology, Pittsburgh, PA
| | - A K Patel
- Allegheny Health Network Cancer Institute, Department of Radiation Oncology, Pittsburgh, PA
| | - Z D Horne
- Allegheny Health Network Cancer Institute, Department of Radiation Oncology, Pittsburgh, PA
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8
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Zeeshan M, Rea E, Abel S, Vukušić K, Markus R, Brady D, Eze A, Rashpa R, Balestra AC, Bottrill AR, Brochet M, Guttery DS, Tolić IM, Holder AA, Le Roch KG, Tromer EC, Tewari R. Plasmodium ARK2 and EB1 drive unconventional spindle dynamics, during chromosome segregation in sexual transmission stages. Nat Commun 2023; 14:5652. [PMID: 37704606 PMCID: PMC10499817 DOI: 10.1038/s41467-023-41395-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
The Aurora family of kinases orchestrates chromosome segregation and cytokinesis during cell division, with precise spatiotemporal regulation of its catalytic activities by distinct protein scaffolds. Plasmodium spp., the causative agents of malaria, are unicellular eukaryotes with three unique and highly divergent aurora-related kinases (ARK1-3) that are essential for asexual cellular proliferation but lack most canonical scaffolds/activators. Here we investigate the role of ARK2 during sexual proliferation of the rodent malaria Plasmodium berghei, using a combination of super-resolution microscopy, mass spectrometry, and live-cell fluorescence imaging. We find that ARK2 is primarily located at spindle microtubules in the vicinity of kinetochores during both mitosis and meiosis. Interactomic and co-localisation studies reveal several putative ARK2-associated interactors including the microtubule-interacting protein EB1, together with MISFIT and Myosin-K, but no conserved eukaryotic scaffold proteins. Gene function studies indicate that ARK2 and EB1 are complementary in driving endomitotic division and thereby parasite transmission through the mosquito. This discovery underlines the flexibility of molecular networks to rewire and drive unconventional mechanisms of chromosome segregation in the malaria parasite.
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Affiliation(s)
- Mohammad Zeeshan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Edward Rea
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave., Riverside, CA, USA
| | - Kruno Vukušić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000, Zagreb, Croatia
| | - Robert Markus
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Declan Brady
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Antonius Eze
- School of Life Sciences, University of Nottingham, Nottingham, UK
- Department of Medical Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, University of Nigeria, Enugu Campus, Enugu, Nigeria
| | - Ravish Rashpa
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Andrew R Bottrill
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, UK
| | - Mathieu Brochet
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - David S Guttery
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, UK
| | - Iva M Tolić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000, Zagreb, Croatia
| | - Anthony A Holder
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, UK
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave., Riverside, CA, USA
| | - Eelco C Tromer
- Cell Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Rita Tewari
- School of Life Sciences, University of Nottingham, Nottingham, UK.
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9
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Chahine Z, Gupta M, Lenz T, Hollin T, Abel S, Banks CAS, Saraf A, Prudhomme J, Florens L, Le Roch KG. PfMORC protein regulates chromatin accessibility and transcriptional repression in the human malaria parasite, P. falciparum. bioRxiv 2023:2023.09.11.557253. [PMID: 37745554 PMCID: PMC10515874 DOI: 10.1101/2023.09.11.557253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The environmental challenges the human malaria parasite, Plasmodium falciparum, faces during its progression into its various lifecycle stages warrant the use of effective and highly regulated access to chromatin for transcriptional regulation. Microrchidia (MORC) proteins have been implicated in DNA compaction and gene silencing across plant and animal kingdoms. Accumulating evidence has shed light into the role MORC protein plays as a transcriptional switch in apicomplexan parasites. In this study, using CRISPR/Cas9 genome editing tool along with complementary molecular and genomics approaches, we demonstrate that PfMORC not only modulates chromatin structure and heterochromatin formation throughout the parasite erythrocytic cycle, but is also essential to the parasite survival. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) experiments suggest that PfMORC binds to not only sub-telomeric regions and genes involved in antigenic variation but is also most likely a key modulator of stage transition. Protein knockdown experiments followed by chromatin conformation capture (Hi-C) studies indicate that downregulation of PfMORC induces the collapse of the parasite heterochromatin structure leading to its death. All together these findings confirm that PfMORC plays a crucial role in chromatin structure and gene regulation, validating this factor as a strong candidate for novel antimalarial strategies.
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Affiliation(s)
- Z Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - M Gupta
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - T Lenz
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - T Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - S Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - CAS Banks
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - A Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - J Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - L Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - KG Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
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10
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Batugedara G, Lu XM, Hristov B, Abel S, Chahine Z, Hollin T, Williams D, Wang T, Cort A, Lenz T, Thompson TA, Prudhomme J, Tripathi AK, Xu G, Cudini J, Dogga S, Lawniczak M, Noble WS, Sinnis P, Le Roch KG. Novel insights into the role of long non-coding RNA in the human malaria parasite, Plasmodium falciparum. Nat Commun 2023; 14:5086. [PMID: 37607941 PMCID: PMC10444892 DOI: 10.1038/s41467-023-40883-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 08/10/2023] [Indexed: 08/24/2023] Open
Abstract
The complex life cycle of Plasmodium falciparum requires coordinated gene expression regulation to allow host cell invasion, transmission, and immune evasion. Increasing evidence now suggests a major role for epigenetic mechanisms in gene expression in the parasite. In eukaryotes, many lncRNAs have been identified to be pivotal regulators of genome structure and gene expression. To investigate the regulatory roles of lncRNAs in P. falciparum we explore the intergenic lncRNA distribution in nuclear and cytoplasmic subcellular locations. Using nascent RNA expression profiles, we identify a total of 1768 lncRNAs, of which 718 (~41%) are novels in P. falciparum. The subcellular localization and stage-specific expression of several putative lncRNAs are validated using RNA-FISH. Additionally, the genome-wide occupancy of several candidate nuclear lncRNAs is explored using ChIRP. The results reveal that lncRNA occupancy sites are focal and sequence-specific with a particular enrichment for several parasite-specific gene families, including those involved in pathogenesis and sexual differentiation. Genomic and phenotypic analysis of one specific lncRNA demonstrate its importance in sexual differentiation and reproduction. Our findings bring a new level of insight into the role of lncRNAs in pathogenicity, gene regulation and sexual differentiation, opening new avenues for targeted therapeutic strategies against the deadly malaria parasite.
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Affiliation(s)
- Gayani Batugedara
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Xueqing M Lu
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Borislav Hristov
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195-5065, USA
| | - Steven Abel
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Zeinab Chahine
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Thomas Hollin
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Desiree Williams
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Tina Wang
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Anthony Cort
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Todd Lenz
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Trevor A Thompson
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Jacques Prudhomme
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Abhai K Tripathi
- Department of Molecular Microbiology and Immunology and the Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Guoyue Xu
- Department of Molecular Microbiology and Immunology and the Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | | | - Sunil Dogga
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | | | | | - Photini Sinnis
- Department of Molecular Microbiology and Immunology and the Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Karine G Le Roch
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA.
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11
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Subudhi AK, Green JL, Satyam R, Lenz T, Salunke RP, Shuaib M, Isaioglou I, Abel S, Gupta M, Esau L, Mourier T, Nugmanova R, Mfarrej S, Sivapurkar R, Stead Z, Rached FB, Otswal Y, Sougrat R, Dada A, Kadamany AF, Fischle W, Merzaban J, Knuepfer E, Ferguson DJP, Gupta I, Le Roch KG, Holder AA, Pain A. PfAP2-MRP DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages. bioRxiv 2023:2023.05.23.541898. [PMID: 37293082 PMCID: PMC10245809 DOI: 10.1101/2023.05.23.541898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Malaria pathogenicity results from the parasite's ability to invade, multiply within and then egress from the host red blood cell (RBC). Infected RBCs are remodeled, expressing antigenic variant proteins (such as PfEMP1, coded by the var gene family) for immune evasion and survival. These processes require the concerted actions of many proteins, but the molecular regulation is poorly understood. We have characterized an essential Plasmodium specific Apicomplexan AP2 (ApiAP2) transcription factor in Plasmodium falciparum (PfAP2-MRP; Master Regulator of Pathogenesis) during the intraerythrocytic developmental cycle (IDC). An inducible gene knockout approach showed that PfAP2-MRP is essential for development during the trophozoite stage, and critical for var gene regulation, merozoite development and parasite egress. ChIP-seq experiments performed at 16 hour post invasion (h.p.i.) and 40 h.p.i. matching the two peaks of PfAP2-MRP expression, demonstrate binding of PfAP2-MRP to the promoters of genes controlling trophozoite development and host cell remodeling at 16 h.p.i. and antigenic variation and pathogenicity at 40 h.p.i. Using single-cell RNA-seq and fluorescence-activated cell sorting, we show de-repression of most var genes in Δpfap2-mrp parasites that express multiple PfEMP1 proteins on the surface of infected RBCs. In addition, the Δpfap2-mrp parasites overexpress several early gametocyte marker genes at both 16 and 40 h.p.i., indicating a regulatory role in the sexual stage conversion. Using the Chromosomes Conformation Capture experiment (Hi-C), we demonstrate that deletion of PfAP2-MRP results in significant reduction of both intra-chromosomal and inter-chromosomal interactions in heterochromatin clusters. We conclude that PfAP2-MRP is a vital upstream transcriptional regulator controlling essential processes in two distinct developmental stages during the IDC that include parasite growth, chromatin structure and var gene expression.
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Affiliation(s)
- Amit Kumar Subudhi
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Judith L Green
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Rohit Satyam
- Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi, Delhi 110025, India
| | - Todd Lenz
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Rahul P Salunke
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Muhammad Shuaib
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ioannis Isaioglou
- Cell Migration and Signaling Laboratory, Bioscience Program, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Mohit Gupta
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Luke Esau
- KAUST Core Labs, KAUST, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Tobias Mourier
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Raushan Nugmanova
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Sara Mfarrej
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Rupali Sivapurkar
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Zenaida Stead
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Fathia Ben Rached
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Yogesh Otswal
- Laboratory of Chromatin Biochemistry, Bioscience Program, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Rachid Sougrat
- KAUST Core Labs, KAUST, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ashraf Dada
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Kingdom of Saudi Arabia
| | - Abdullah Fuaad Kadamany
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Kingdom of Saudi Arabia
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Bioscience Program, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Jasmeen Merzaban
- Cell Migration and Signaling Laboratory, Bioscience Program, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ellen Knuepfer
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - David J P Ferguson
- Nuffield Department of Clinical Laboratory Science, University of Oxford, John Radcliffe Hospital, Oxford OX1 2JD, United Kingdom
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Anthony A Holder
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Arnab Pain
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- International Institute for Zoonosis Control; Hokkaido University, Sapporo, Japan
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12
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Singh P, Lonardi S, Liang Q, Vydyam P, Khabirova E, Fang T, Gihaz S, Thekkiniath J, Munshi M, Abel S, Ciampossin L, Batugedara G, Gupta M, Lu XM, Lenz T, Chakravarty S, Cornillot E, Hu Y, Ma W, Gonzalez LM, Sánchez S, Estrada K, Sánchez-Flores A, Montero E, Harb OS, Le Roch KG, Mamoun CB. Babesia duncani multi-omics identifies virulence factors and drug targets. Nat Microbiol 2023; 8:845-859. [PMID: 37055610 PMCID: PMC10159843 DOI: 10.1038/s41564-023-01360-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 03/14/2023] [Indexed: 04/15/2023]
Abstract
Babesiosis is a malaria-like disease in humans and animals that is caused by Babesia species, which are tick-transmitted apicomplexan pathogens. Babesia duncani causes severe to lethal infection in humans, but despite the risk that this parasite poses as an emerging pathogen, little is known about its biology, metabolic requirements or pathogenesis. Unlike other apicomplexan parasites that infect red blood cells, B. duncani can be continuously cultured in vitro in human erythrocytes and can infect mice resulting in fulminant babesiosis and death. We report comprehensive, detailed molecular, genomic, transcriptomic and epigenetic analyses to gain insights into the biology of B. duncani. We completed the assembly, 3D structure and annotation of its nuclear genome, and analysed its transcriptomic and epigenetics profiles during its asexual life cycle stages in human erythrocytes. We used RNA-seq data to produce an atlas of parasite metabolism during its intraerythrocytic life cycle. Characterization of the B. duncani genome, epigenome and transcriptome identified classes of candidate virulence factors, antigens for diagnosis of active infection and several attractive drug targets. Furthermore, metabolic reconstitutions from genome annotation and in vitro efficacy studies identified antifolates, pyrimethamine and WR-99210 as potent inhibitors of B. duncani to establish a pipeline of small molecules that could be developed as effective therapies for the treatment of human babesiosis.
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Affiliation(s)
- Pallavi Singh
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA.
| | - Qihua Liang
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Pratap Vydyam
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | | | - Tiffany Fang
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Shalev Gihaz
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Jose Thekkiniath
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Muhammad Munshi
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Loic Ciampossin
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Gayani Batugedara
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Mohit Gupta
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Xueqing Maggie Lu
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Todd Lenz
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Sakshar Chakravarty
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Emmanuel Cornillot
- Institut de Biologie Computationnelle (IBC), and Institut de Recherche en Cancérologie de Montpellier (IRCM - INSERM U1194), Institut régional du Cancer Montpellier (ICM) and Université de Montpellier, Montpellier, France
| | - Yangyang Hu
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Wenxiu Ma
- Department of Statistics, University of California, Riverside, CA, USA
| | - Luis Miguel Gonzalez
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Sergio Sánchez
- Reference and Research Laboratory on Food and Waterborne Bacterial Infections, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Karel Estrada
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Alejandro Sánchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Estrella Montero
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Omar S Harb
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA.
| | - Choukri Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA.
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13
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Zeeshan M, Rea E, Abel S, Vukušić K, Markus R, Brady D, Eze A, Rashpa R, Balestra AC, Bottrill AR, Brochet M, Guttery DS, Tolić IM, Holder AA, Le Roch KG, Tromer EC, Tewari R. Plasmodium ARK2-EB1 axis drives the unconventional spindle dynamics, scaffold formation and chromosome segregation of sexual transmission stages. Res Sq 2023:rs.3.rs-2539372. [PMID: 36798191 PMCID: PMC9934748 DOI: 10.21203/rs.3.rs-2539372/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Mechanisms of cell division are remarkably diverse, suggesting the underlying molecular networks among eukaryotes differ extensively. The Aurora family of kinases orchestrates the process of chromosome segregation and cytokinesis during cell division through precise spatiotemporal regulation of their catalytic activities by distinct scaffolds. Plasmodium spp., the causative agents of malaria, are unicellular eukaryotes that have three divergent aurora-related kinases (ARKs) and lack most canonical scaffolds/activators. The parasite uses unconventional modes of chromosome segregation during endomitosis and meiosis in sexual transmission stages within mosquito host. This includes a rapid threefold genome replication from 1N to 8N with successive cycles of closed mitosis, spindle formation and chromosome segregation within eight minutes (termed male gametogony). Kinome studies had previously suggested likely essential functions for all three Plasmodium ARKs during asexual mitotic cycles; however, little is known about their location, function, or their scaffolding molecules during unconventional sexual proliferative stages. Using a combination of super-resolution microscopy, mass spectrometry, omics and live-cell fluorescence imaging, we set out to investigate the contribution of the atypical Aurora paralog ARK2 to proliferative sexual stages using rodent malaria model Plasmodium berghei. We find that ARK2 primarily localises to the spindle apparatus associated with kinetochores during both mitosis and meiosis. Interactomics and co-localisation studies reveal a unique ARK2 scaffold at the spindle including the microtubule plus end-binding protein EB1 and lacking some other conserved molecules. Gene function studies indicate complementary functions of ARK2 and EB1 in driving endomitotic divisions and thereby parasite transmission. Our discovery of a novel Aurora spindle scaffold underlines the emerging flexibility of molecular networks to rewire and drive unconventional mechanisms of chromosome segregation in the malaria parasite Plasmodium.
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Affiliation(s)
- Mohammad Zeeshan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Edward Rea
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave., Riverside, USA
| | - Kruno Vukušić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Robert Markus
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Declan Brady
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Antonius Eze
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Ravish Rashpa
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Andrew R. Bottrill
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, UK
| | - Mathieu Brochet
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - David S. Guttery
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, UK
| | - Iva M. Tolić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Anthony A. Holder
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, UK
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave., Riverside, USA
| | - Eelco C. Tromer
- Faculty of Science and Engineering, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Cell Biochemistry, Groningen, The Netherlands
| | - Rita Tewari
- School of Life Sciences, University of Nottingham, Nottingham, UK
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14
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Poghosyan AH, Abel S, Koetz J. Simulation of AOT reverse micelles with polyethylenimine in hexane. Colloid Polym Sci 2023. [DOI: 10.1007/s00396-023-05059-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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15
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Zeeshan M, Rea E, Abel S, Vukušić K, Markus R, Brady D, Eze A, Raspa R, Balestra A, Bottrill AR, Brochet M, Guttery DS, Tolić IM, Holder AA, Roch KGL, Tromer EC, Tewari R. Plasmodium ARK2-EB1 axis drives the unconventional spindle dynamics, scaffold formation and chromosome segregation of sexual transmission stages. bioRxiv 2023:2023.01.29.526106. [PMID: 36778504 PMCID: PMC9915484 DOI: 10.1101/2023.01.29.526106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Mechanisms of cell division are remarkably diverse, suggesting the underlying molecular networks among eukaryotes differ extensively. The Aurora family of kinases orchestrates the process of chromosome segregation and cytokinesis during cell division through precise spatiotemporal regulation of their catalytic activities by distinct scaffolds. Plasmodium spp., the causative agents of malaria, are unicellular eukaryotes that have three divergent aurora-related kinases (ARKs) and lack most canonical scaffolds/activators. The parasite uses unconventional modes of chromosome segregation during endomitosis and meiosis in sexual transmission stages within mosquito host. This includes a rapid threefold genome replication from 1N to 8N with successive cycles of closed mitosis, spindle formation and chromosome segregation within eight minutes (termed male gametogony). Kinome studies had previously suggested likely essential functions for all three Plasmodium ARKs during asexual mitotic cycles; however, little is known about their location, function, or their scaffolding molecules during unconventional sexual proliferative stages. Using a combination of super-resolution microscopy, mass spectrometry, and live-cell fluorescence imaging, we set out to investigate the role of the atypical Aurora paralog ARK2 to proliferative sexual stages using rodent malaria model Plasmodium berghei . We find that ARK2 primarily localises to the spindle apparatus in the vicinity of kinetochores during both mitosis and meiosis. Interactomics and co-localisation studies reveal a unique ARK2 scaffold at the spindle including the microtubule plus end-binding protein EB1, lacking conserved Aurora scaffold proteins. Gene function studies indicate complementary functions of ARK2 and EB1 in driving endomitotic divisions and thereby parasite transmission. Our discovery of a novel Aurora kinase spindle scaffold underlines the emerging flexibility of molecular networks to rewire and drive unconventional mechanisms of chromosome segregation in the malaria parasite Plasmodium .
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McArthur G, Abel S, Volpin G, Barber DM. Strategies for the Enantioselective Synthesis of 2‐Isoxazolines and 2‐Isoxazolin‐5‐ones Bearing Fully Substituted Stereocenters**. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Gillian McArthur
- Research and Development, Weed Control Chemistry, Bayer AG, Crop Science Division Industriepark Höchst 65926 Frankfurt am Main Germany
| | - Steven Abel
- Research and Development, Weed Control Chemistry, Bayer AG, Crop Science Division Industriepark Höchst 65926 Frankfurt am Main Germany
| | - Giulio Volpin
- Research and Development, Small Molecules Technologies, Process Research, Bayer AG, Crop Science Division Industriepark Höchst 65926 Frankfurt am Main Germany
| | - David M. Barber
- Research and Development, Weed Control Chemistry, Bayer AG, Crop Science Division Industriepark Höchst 65926 Frankfurt am Main Germany
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Abel S, Shamsesfandabadi P, Renz P, Monga D, Wegner R. Utilization of Advanced Radiation Techniques in Neuroendocrine Carcinoma of the Pancreas. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.1089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Zeeshan M, Rashpa R, Ferguson DJP, Abel S, Chahine Z, Brady D, Vaughan S, Moores CA, Le Roch KG, Brochet M, Holder AA, Tewari R. Genome-wide functional analysis reveals key roles for kinesins in the mammalian and mosquito stages of the malaria parasite life cycle. PLoS Biol 2022; 20:e3001704. [PMID: 35900985 PMCID: PMC9333250 DOI: 10.1371/journal.pbio.3001704] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/10/2022] [Indexed: 11/18/2022] Open
Abstract
Kinesins are microtubule (MT)-based motors important in cell division, motility, polarity, and intracellular transport in many eukaryotes. However, they are poorly studied in the divergent eukaryotic pathogens Plasmodium spp., the causative agents of malaria, which manifest atypical aspects of cell division and plasticity of morphology throughout the life cycle in both mammalian and mosquito hosts. Here, we describe a genome-wide screen of Plasmodium kinesins, revealing diverse subcellular locations and functions in spindle assembly, axoneme formation, and cell morphology. Surprisingly, only kinesin-13 is essential for growth in the mammalian host while the other 8 kinesins are required during the proliferative and invasive stages of parasite transmission through the mosquito vector. In-depth analyses of kinesin-13 and kinesin-20 revealed functions in MT dynamics during apical cell polarity formation, spindle assembly, and axoneme biogenesis. These findings help us to understand the importance of MT motors and may be exploited to discover new therapeutic interventions against malaria.
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Affiliation(s)
- Mohammad Zeeshan
- University of Nottingham, School of Life Sciences, Nottingham, United Kingdom
| | - Ravish Rashpa
- University of Geneva, Faculty of Medicine, Geneva, Switzerland
| | - David J P Ferguson
- Oxford Brookes University, Department of Biological and Medical Sciences, Oxford, United Kingdom
- University of Oxford, John Radcliffe Hospital, Nuffield Department of Clinical Laboratory Science, Oxford, United Kingdom
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Declan Brady
- University of Nottingham, School of Life Sciences, Nottingham, United Kingdom
| | - Sue Vaughan
- Oxford Brookes University, Department of Biological and Medical Sciences, Oxford, United Kingdom
| | - Carolyn A Moores
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London, United Kingdom
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Mathieu Brochet
- University of Geneva, Faculty of Medicine, Geneva, Switzerland
| | - Anthony A Holder
- The Francis Crick Institute, Malaria Parasitology Laboratory, London, United Kingdom
| | - Rita Tewari
- University of Nottingham, School of Life Sciences, Nottingham, United Kingdom
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Hollin T, Abel S, Falla A, Pasaje CFA, Bhatia A, Hur M, Kirkwood JS, Saraf A, Prudhomme J, De Souza A, Florens L, Niles JC, Le Roch KG. Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum. Nat Commun 2022; 13:1275. [PMID: 35277503 PMCID: PMC8917122 DOI: 10.1038/s41467-022-28981-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/14/2022] [Indexed: 12/31/2022] Open
Abstract
The RAP (RNA-binding domain abundant in Apicomplexans) protein family has been identified in various organisms. Despite expansion of this protein family in apicomplexan parasites, their main biological functions remain unknown. In this study, we use inducible knockdown studies in the human malaria parasite, Plasmodium falciparum, to show that two RAP proteins, PF3D7_0105200 (PfRAP01) and PF3D7_1470600 (PfRAP21), are essential for parasite survival and localize to the mitochondrion. Using transcriptomics, metabolomics, and proteomics profiling experiments, we further demonstrate that these RAP proteins are involved in mitochondrial RNA metabolism. Using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (eCLIP-seq), we validate that PfRAP01 and PfRAP21 are true RNA-binding proteins and interact specifically with mitochondrial rRNAs. Finally, mitochondrial enrichment experiments followed by deep sequencing of small RNAs demonstrate that PfRAP21 controls mitochondrial rRNA expression. Collectively, our results establish the role of these RAP proteins in mitoribosome activity and contribute to further understanding this protein family in malaria parasites.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Alejandra Falla
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Anil Bhatia
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Manhoi Hur
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Jay S Kirkwood
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Amancio De Souza
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA.
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Johnson P, Chan JK, Vavasour IM, Abel S, Lee LE, Yong H, Laule C, Li DKB, Tam R, Traboulsee A, Carruthers RL, Kolind SH. Quantitative MRI findings indicate diffuse white matter damage in Susac Syndrome. Mult Scler J Exp Transl Clin 2022; 8:20552173221078834. [PMID: 35186315 PMCID: PMC8851927 DOI: 10.1177/20552173221078834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/21/2022] [Indexed: 11/15/2022] Open
Abstract
Background Susac Syndrome (SuS) is an autoimmune endotheliopathy impacting the brain, retina and cochlea that can clinically mimic multiple sclerosis (MS). Objective To evaluate non-lesional white matter demyelination changes in SuS compared to MS and healthy controls (HC) using quantitative MRI. Methods 3T MRI including myelin water imaging and diffusion basis spectrum imaging were acquired for 7 SuS, 10 MS and 10 HC participants. Non-lesional white matter was analyzed in the corpus callosum (CC) and normal appearing white matter (NAWM). Groups were compared using ANCOVA with Tukey correction. Results SuS CC myelin water fraction (mean 0.092) was lower than MS(0.11, p = 0.01) and HC(0.11, p = 0.04). Another myelin marker, radial diffusivity, was increased in SuS CC(0.27μm2/ms) compared to HC(0.21μm2/ms, p = 0.008) and MS(0.23μm2/ms, p = 0.05). Fractional anisotropy was lower in SuS CC(0.82) than HC(0.86, p = 0.04). Fiber fraction (reflecting axons) did not differ from HC or MS. In NAWM, radial diffusivity and apparent diffusion coefficient were significantly increased in SuS compared to HC(p < 0.001 for both measures) and MS(p = 0.003, p < 0.001 respectively). Conclusions Our results provided evidence of myelin damage in SuS, particularly in the CC, and more extensive microstructural injury in NAWM, supporting the hypothesis that there are widespread microstructural changes in SuS syndrome including diffuse demyelination.
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Affiliation(s)
| | - JK Chan
- Department of Medicine (Neurology), University of British Columbia, Canada
| | - IM Vavasour
- Department of Radiology, University of British Columbia, Canada
- International Collaboration on Repair Discoveries (ICORD)
| | | | | | - H Yong
- Department of Medicine (Neurology), University of British Columbia, Canada
| | - C Laule
- Department of Radiology, University of British Columbia, Canada
- International Collaboration on Repair Discoveries (ICORD)
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
- Department of Physics and Astronomy, University of British Columbia, Canada
| | - DKB Li
- Department of Medicine (Neurology), University of British Columbia, Canada
- Department of Radiology, University of British Columbia, Canada
| | - R Tam
- Department of Radiology, University of British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Canada
| | | | - RL Carruthers
- Department of Medicine (Neurology), University of British Columbia, Canada
| | - SH Kolind
- Department of Medicine (Neurology), University of British Columbia, Canada
- Department of Radiology, University of British Columbia, Canada
- International Collaboration on Repair Discoveries (ICORD)
- Department of Physics and Astronomy, University of British Columbia, Canada
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21
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Campelo Morillo RA, Tong X, Xie W, Abel S, Orchard LM, Daher W, Patel DJ, Llinás M, Le Roch KG, Kafsack BFC. Publisher Correction: The transcriptional regulator HDP1 controls expansion of the inner membrane complex during early sexual differentiation of malaria parasites. Nat Microbiol 2022; 7:464. [PMID: 35136229 DOI: 10.1038/s41564-022-01082-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Xinran Tong
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Wei Xie
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Lindsey M Orchard
- Department of Biochemistry and Molecular Biology, and Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, USA
| | - Wassim Daher
- Dynamique des Interactions Membranaires Normales et Pathologiques, UMR5235 CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, and Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, USA.,Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Björn F C Kafsack
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA.
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22
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Abel S, Colonias A, Beriwal S, Weksler B, Finley G, Long S, Wegner R. Comparing Clinicopathologic Factors and Survival in Stage III Adenocarcinoma and Squamous Cell Carcinoma of the Lung Following Definitive Chemoradiotherapy. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2021.10.183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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23
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Abel S, Renz P, Colonias A, Raj M, Wegner R. PD-0847 Dose escalation in locally advanced NSCLC: comparing outcomes in adenocarcinoma and squamous cell carcinoma. Radiother Oncol 2021. [DOI: 10.1016/s0167-8140(21)07126-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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24
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Chauhan G, Norred E, Simpson M, Abel S. Crowding-Induced Spatial Organization of Gene Expression in Cell-Sized Vesicles. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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25
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Cotte L, Hocqueloux L, Lefebvre M, Pradat P, Bani-Sadr F, Huleux T, Poizot-Martin I, Pugliese P, Rey D, Cabié A, Chirouze C, Drobacheff-Thiébaut C, Foltzer A, Bouiller K, Hustache-Mathieu L, Lepiller Q, Bozon F, Babre O, Brunel AS, Muret P, Chevalier E, Jacomet C, Laurichesse H, Lesens O, Vidal M, Mrozek N, Aumeran C, Baud O, Corbin V, Goncalvez E, Mirand A, brebion A, Henquell C, Lamaury I, Fabre I, Curlier E, Ouissa R, Herrmann-Storck C, Tressieres B, Receveur MC, Boulard F, Daniel C, Clavel C, Roger PM, Markowicz S, Chellum Rungen N, Merrien D, Perré P, Guimard T, Bollangier O, Leautez S, Morrier M, Laine L, Boucher D, Point P, Cotte L, Ader F, Becker A, Boibieux A, Brochier C, Brunel-Dalmas F, Cannesson O, Chiarello P, Chidiac C, Degroodt S, Ferry T, Godinot M, Livrozet JM, Makhloufi D, Miailhes P, Perpoint T, Perry M, Pouderoux C, Roux S, Triffault-Fillit C, Valour F, Charre C, Icard V, Tardy JC, Trabaud MA, Ravaux I, Ménard A, Belkhir AY, Colson P, Dhiver C, Madrid A, Martin-Degioanni M, Meddeb L, Mokhtari M, Motte A, Raoux A, Toméi C, Tissot-Dupont H, Poizot-Martin I, Brégigeon S, Zaegel-Faucher O, Obry-Roguet V, Laroche H, Orticoni M, Soavi MJ, Ressiot E, Ducassou MJ, Jaquet I, Galie S, Colson H, Ritleng AS, Ivanova A, Debreux C, Lions C, Rojas-Rojas T, Cabié A, Abel S, Bavay J, Bigeard B, Cabras O, Cuzin L, Dupin de Majoubert R, Fagour L, Guitteaud K, Marquise A, Najioullah F, Pierre-François S, Pasquier J, Richard P, Rome K, Turmel JM, Varache C, Atoui N, Bistoquet M, Delaporte E, Le Moing V, Makinson A, Meftah N, Merle de Boever C, Montes B, Montoya Ferrer A, Tuaillon E, Reynes J, Lefèvre B, Jeanmaire E, Hénard S, Frentiu E, Charmillon A, Legoff A, Tissot N, André M, Boyer L, Bouillon MP, Delestan M, Goehringer F, Bevilacqua S, Rabaud C, May T, Raffi F, Allavena C, Aubry O, Billaud E, Biron C, Bonnet B, Bouchez S, Boutoille D, Brunet-Cartier C, Deschanvres C, Gaborit BJ, Grégoire A, Grégoire M, Grossi O, Guéry R, Jovelin T, Lefebvre M, Le Turnier P, Lecomte R, Morineau P, Reliquet V, Sécher S, Cavellec M, Paredes E, Soria A, Ferré V, André-Garnier E, Rodallec A, Pugliese P, Breaud S, Ceppi C, Chirio D, Cua E, Dellamonica P, Demonchy E, De Monte A, Durant J, Etienne C, Ferrando S, Garraffo R, Michelangeli C, Mondain V, Naqvi A, Oran N, Perbost I, Carles M, Klotz C, Maka A, Pradier C, Prouvost-Keller B, Risso K, Rio V, Rosenthal E, Touitou I, Wehrlen-Pugliese S, Zouzou G, Hocqueloux L, Prazuck T, Gubavu C, Sève A, Giaché S, Rzepecki V, Colin M, Boulard C, Thomas G, Cheret A, Goujard C, Quertainmont Y, Teicher E, Lerolle N, Jaureguiberry S, Colarino R, Deradji O, Castro A, Barrail-Tran A, Yazdanpanah Y, Landman R, Joly V, Ghosn J, Rioux C, Lariven S, Gervais A, Lescure FX, Matheron S, Louni F, Julia Z, Le GAC S, Charpentier C, Descamps D, Peytavin G, Duvivier C, Aguilar C, Alby-Laurent F, Amazzough K, Benabdelmoumen G, Bossi P, Cessot G, Charlier C, Consigny PH, Jidar K, Lafont E, Lanternier F, Leporrier J, Lortholary O, Louisin C, Lourenco J, Parize P, Pilmis B, Rouzaud C, Touam F, Valantin MA, Tubiana R, Agher R, Seang S, Schneider L, PaLich R, Blanc C, Katlama C, Bani-Sadr F, Berger JL, N’Guyen Y, Lambert D, Kmiec I, Hentzien M, Brunet A, Romaru J, Marty H, Brodard V, Arvieux C, Tattevin P, Revest M, Souala F, Baldeyrou M, Patrat-Delon S, Chapplain JM, Benezit F, Dupont M, Poinot M, Maillard A, Pronier C, Lemaitre F, Morlat C, Poisson-Vannier M, Jovelin T, Sinteff JP, Gagneux-Brunon A, Botelho-Nevers E, Frésard A, Ronat V, Lucht F, Rey D, Fischer P, Partisani M, Cheneau C, Priester M, Mélounou C, Bernard-Henry C, de Mautort E, Fafi-Kremer S, Delobel P, Alvarez M, Biezunski N, Debard A, Delpierre C, Gaube G, Lansalot P, Lelièvre L, Marcel M, Martin-Blondel G, Piffaut M, Porte L, Saune K, Robineau O, Ajana F, Aïssi E, Alcaraz I, Alidjinou E, Baclet V, Bocket L, Boucher A, Digumber M, Huleux T, Lafon-Desmurs B, Meybeck A, Pradier M, Tetart M, Thill P, Viget N, Valette M. Microelimination or Not? The Changing Epidemiology of Human Immunodeficiency Virus-Hepatitis C Virus Coinfection in France 2012–2018. Clin Infect Dis 2021; 73:e3266-e3274. [DOI: 10.1093/cid/ciaa1940] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/01/2021] [Indexed: 01/15/2023] Open
Abstract
Abstract
Background
The arrival of highly effective, well-tolerated, direct-acting antiviral agents (DAA) led to a dramatic decrease in hepatitis C virus (HCV) prevalence. Human immunodeficiency virus (HIV)-HCV–coinfected patients are deemed a priority population for HCV elimination, while a rise in recently acquired HCV infections in men who have sex with men (MSM) has been described. We describe the variations in HIV-HCV epidemiology in the French Dat’AIDS cohort.
Methods
This was a retrospective analysis of a prospective cohort of persons living with HIV (PLWH) from 2012 to 2018. We determined HCV prevalence, HCV incidence, proportion of viremic patients, treatment uptake, and mortality rate in the full cohort and by HIV risk factors.
Results
From 2012 to 2018, 50 861 PLWH with a known HCV status were followed up. During the period, HCV prevalence decreased from 15.4% to 13.5%. HCV prevalence among new HIV cases increased from 1.9% to 3.5% in MSM but remained stable in other groups. Recently acquired HCV incidence increased from 0.36/100 person-years to 1.25/100 person-years in MSM. The proportion of viremic patients decreased from 67.0% to 8.9%. MSM became the first group of viremic patients in 2018 (37.9%). Recently acquired hepatitis represented 59.2% of viremic MSM in 2018. DAA treatment uptake increased from 11.4% to 61.5%. More treatments were initiated in MSM in 2018 (41.2%) than in intravenous drug users (35.6%). In MSM, treatment at the acute phase represented 30.0% of treatments in 2018.
Conclusions
A major shift in HCV epidemiology was observed in PLWH in France from 2012 to 2018, leading to a unique situation in which the major group of HCV transmission in 2018 was MSM.
Clinical Trials Registration. NCT02898987.
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Affiliation(s)
- Laurent Cotte
- Department of Infectious Diseases, Croix-Rousse Hospital, Hospices Civils de Lyon, Lyon, Institut National de la Santé et de la Recherche Médicale (INSERM) U1052, Lyon, France
| | - Laurent Hocqueloux
- Department of Infectious Diseases, Centre Hospitalier Régional d’Orléans – La Source, Orléans, France
| | - Maeva Lefebvre
- Department of Infectious Diseases, Centre Hospitalier Universitaire Hôtel-Dieu, Nantes; Centre d’Investigation Clinique (CIC) 1413, INSERM, Nantes, France
| | - Pierre Pradat
- Center for Clinical Research, Croix-Rousse Hospital, Hospices Civils de Lyon, Lyon, France
| | - Firouze Bani-Sadr
- Department of Internal Medicine, Clinical Immunology and Infectious Diseases, Robert Debré Hospital, University Hospital, Reims, France
| | - Thomas Huleux
- Department of Infectious Diseases and Travel Diseases, Centre Hospitalier Gustave-Dron, Tourcoing, France
| | - Isabelle Poizot-Martin
- Immuno-Hematology Clinic, Assistance Publique–Hôpitaux de Marseille, Hôpital Sainte-Marguerite, Marseille, Aix-MarseilleUniversity–Inserm–Institut de Recherche pour le Développement (IRD), Sciences Economiques & Sociales de la Santé & Traitement de l’Information Médicale, Marseille, France
| | - Pascal Pugliese
- Department of Infectious Diseases, Centre Hospitalier Universitaire de Nice, Hôpital l’Archet, Nice, France
| | - David Rey
- HIV Infection Care Centre, Hôpitaux Universitaires, Strasbourg
| | - André Cabié
- Department of Infectious Diseases, Centre Hospitalier Universitaire de Martinique, Fort de France, Université des Antilles EA4537, Fort de France, INSERM CIC1424, Fort-de-France, France
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Abstract
Over the last decades, identification of RNA-proteins complexes and their binding sites was challenging. Recently, techniques based on crosslinking, immunoprecipitation, and high-throughput sequencing have been developed. An optimized method, called eCLIP-seq, enables to identify precisely the targeted RNAs as well as the transcriptome-wide binding sites at nucleotide resolution. Here we describe the eCLIP-seq protocol in asexual stages of the human malaria parasite, Plasmodium falciparum. This method could facilitate the characterization of RNA-binding proteins in this organism for which few data are currently available.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA.
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27
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Abel S, Karlovits S, Yu A, Renz P, Xu L, Wegner R. Patterns Of Care In The Non-Operative Management Of Elderly Patients With NSCLC Brain Metastases. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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28
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Bregigeon S, Obry-Roguet V, Delpierre C, Cotte L, Duvivier C, Pugliese P, Abel S, Huleux T, Poizot-Martin I. Impact de la zone géographique de résidence dans la prévalence du surpoids et de l’obésité au sein de la cohorte Dat’AIDS. Med Mal Infect 2020. [DOI: 10.1016/j.medmal.2020.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Zeeshan M, Pandey R, Ferguson DJP, Tromer EC, Markus R, Abel S, Brady D, Daniel E, Limenitakis R, Bottrill AR, Le Roch KG, Holder AA, Waller RF, Guttery DS, Tewari R. Real-time dynamics of Plasmodium NDC80 reveals unusual modes of chromosome segregation during parasite proliferation. J Cell Sci 2020; 134:jcs245753. [PMID: 32501284 PMCID: PMC7340582 DOI: 10.1242/jcs.245753] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/29/2020] [Indexed: 12/24/2022] Open
Abstract
Eukaryotic cell proliferation requires chromosome replication and precise segregation to ensure daughter cells have identical genomic copies. Species of the genus Plasmodium, the causative agents of malaria, display remarkable aspects of nuclear division throughout their life cycle to meet some peculiar and unique challenges to DNA replication and chromosome segregation. The parasite undergoes atypical endomitosis and endoreduplication with an intact nuclear membrane and intranuclear mitotic spindle. To understand these diverse modes of Plasmodium cell division, we have studied the behaviour and composition of the outer kinetochore NDC80 complex, a key part of the mitotic apparatus that attaches the centromere of chromosomes to microtubules of the mitotic spindle. Using NDC80-GFP live-cell imaging in Plasmodium berghei, we observe dynamic spatiotemporal changes during proliferation, including highly unusual kinetochore arrangements during sexual stages. We identify a very divergent candidate for the SPC24 subunit of the NDC80 complex, previously thought to be missing in Plasmodium, which completes a canonical, albeit unusual, NDC80 complex structure. Altogether, our studies reveal the kinetochore to be an ideal tool to investigate the non-canonical modes of chromosome segregation and cell division in Plasmodium.
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Affiliation(s)
- Mohammad Zeeshan
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Rajan Pandey
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - David J P Ferguson
- Nuffield Department of Clinical Laboratory Science, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
- Department of Biological and Medical Sciences, Faculty of Health and Life Science, Oxford Brookes University, Gipsy Lane, Oxford OX3 0BP, UK
| | - Eelco C Tromer
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Robert Markus
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Declan Brady
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Emilie Daniel
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | | | - Andrew R Bottrill
- School of Life Sciences, Gibbelt Hill Campus, University of Warwick, Coventry CV4 7AL, UK
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Anthony A Holder
- Malaria Parasitology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - David S Guttery
- Leicester Cancer Research Centre, University of Leicester, Leicester LE2 7LX, UK
| | - Rita Tewari
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
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30
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Abel S, Le Roch KG. The role of epigenetics and chromatin structure in transcriptional regulation in malaria parasites. Brief Funct Genomics 2020; 18:302-313. [PMID: 31220857 DOI: 10.1093/bfgp/elz005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/25/2019] [Accepted: 03/14/2019] [Indexed: 12/28/2022] Open
Abstract
Due to the unique selective pressures and extreme changes faced by the human malaria parasite Plasmodium falciparum throughout its life cycle, the parasite has evolved distinct features to alter its gene expression patterns. Along with classical gene regulation by transcription factors (TFs), of which only one family, the AP2 TFs, has been described in the parasite genome, a large body of evidence points toward chromatin structure and epigenetic factors mediating the changes in gene expression associated with parasite life cycle stages. These attributes may be critically important for immune evasion, host cell invasion and development of the parasite in its two hosts, the human and the Anopheles vector. Thus, the factors involved in the maintenance and regulation of chromatin and epigenetic features represent potential targets for antimalarial drugs. In this review, we discuss the mechanisms in P. falciparum that regulate chromatin structure, nucleosome landscape, the 3-dimensional structure of the genome and additional distinctive features created by parasite-specific genes and gene families. We review conserved traits of chromatin in eukaryotes in order to highlight what is unique in the parasite.
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Affiliation(s)
- Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
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31
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Horne Z, Abel S, Wegner R, Colonias A. Patterns of care and outcomes of early-stage sarcomatoid squamous cell carcinomas of the larynx. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2019.11.218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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32
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Pandey R, Abel S, Boucher M, Wall RJ, Zeeshan M, Rea E, Freville A, Lu XM, Brady D, Daniel E, Stanway RR, Wheatley S, Batugedara G, Hollin T, Bottrill AR, Gupta D, Holder AA, Le Roch KG, Tewari R. Plasmodium Condensin Core Subunits SMC2/SMC4 Mediate Atypical Mitosis and Are Essential for Parasite Proliferation and Transmission. Cell Rep 2020; 30:1883-1897.e6. [PMID: 32049018 PMCID: PMC7016506 DOI: 10.1016/j.celrep.2020.01.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 11/12/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Condensin is a multi-subunit protein complex regulating chromosome condensation and segregation during cell division. In Plasmodium spp., the causative agent of malaria, cell division is atypical and the role of condensin is unclear. Here we examine the role of SMC2 and SMC4, the core subunits of condensin, during endomitosis in schizogony and endoreduplication in male gametogenesis. During early schizogony, SMC2/SMC4 localize to a distinct focus, identified as the centromeres by NDC80 fluorescence and chromatin immunoprecipitation sequencing (ChIP-seq) analyses, but do not form condensin I or II complexes. In mature schizonts and during male gametogenesis, there is a diffuse SMC2/SMC4 distribution on chromosomes and in the nucleus, and both condensin I and condensin II complexes form at these stages. Knockdown of smc2 and smc4 gene expression reveals essential roles in parasite proliferation and transmission. The condensin core subunits (SMC2/SMC4) form different complexes and may have distinct functions at various stages of the parasite life cycle.
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Affiliation(s)
- Rajan Pandey
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave., Riverside, CA 92521, USA
| | - Matthew Boucher
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Richard J Wall
- Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Mohammad Zeeshan
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Edward Rea
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Aline Freville
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Xueqing Maggie Lu
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave., Riverside, CA 92521, USA
| | - Declan Brady
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Emilie Daniel
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Rebecca R Stanway
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
| | - Sally Wheatley
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Gayani Batugedara
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave., Riverside, CA 92521, USA
| | - Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave., Riverside, CA 92521, USA
| | - Andrew R Bottrill
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, UK
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Anthony A Holder
- Malaria Parasitology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave., Riverside, CA 92521, USA.
| | - Rita Tewari
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
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33
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Batugedara G, Lu XM, Saraf A, Sardiu ME, Cort A, Abel S, Prudhomme J, Washburn MP, Florens L, Bunnik EM, Le Roch KG. The chromatin bound proteome of the human malaria parasite. Microb Genom 2020; 6:e000327. [PMID: 32017676 PMCID: PMC7067212 DOI: 10.1099/mgen.0.000327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/20/2019] [Indexed: 12/15/2022] Open
Abstract
Proteins interacting with DNA are fundamental for mediating processes such as gene expression, DNA replication and maintenance of genome integrity. Accumulating evidence suggests that the chromatin of apicomplexan parasites, such as Plasmodium falciparum, is highly organized, and this structure provides an epigenetic mechanism for transcriptional regulation. To investigate how parasite chromatin structure is being regulated, we undertook comparative genomics analysis using 12 distinct eukaryotic genomes. We identified conserved and parasite-specific chromatin-associated domains (CADs) and proteins (CAPs). We then used the chromatin enrichment for proteomics (ChEP) approach to experimentally capture CAPs in P. falciparum. A topological scoring analysis of the proteomics dataset revealed stage-specific enrichments of CADs and CAPs. Finally, we characterized, two candidate CAPs: a conserved homologue of the structural maintenance of chromosome 3 protein and a homologue of the crowded-like nuclei protein, a plant-like protein functionally analogous to animal nuclear lamina proteins. Collectively, our results provide a comprehensive overview of CAPs in apicomplexans, and contribute to our understanding of the complex molecular components regulating chromatin structure and genome architecture in these deadly parasites.
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Affiliation(s)
- Gayani Batugedara
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Xueqing M. Lu
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Mihaela E. Sardiu
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Anthony Cort
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Michael P. Washburn
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Evelien M. Bunnik
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
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Zeeshan M, Shilliday F, Liu T, Abel S, Mourier T, Ferguson DJP, Rea E, Stanway RR, Roques M, Williams D, Daniel E, Brady D, Roberts AJ, Holder AA, Pain A, Le Roch KG, Moores CA, Tewari R. Plasmodium kinesin-8X associates with mitotic spindles and is essential for oocyst development during parasite proliferation and transmission. PLoS Pathog 2019; 15:e1008048. [PMID: 31600347 PMCID: PMC6786531 DOI: 10.1371/journal.ppat.1008048] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 08/26/2019] [Indexed: 12/17/2022] Open
Abstract
Kinesin-8 proteins are microtubule motors that are often involved in regulation of mitotic spindle length and chromosome alignment. They move towards the plus ends of spindle microtubules and regulate the dynamics of these ends due, at least in some species, to their microtubule depolymerization activity. Plasmodium spp. exhibit an atypical endomitotic cell division in which chromosome condensation and spindle dynamics in the different proliferative stages are not well understood. Genome-wide shared orthology analysis of Plasmodium spp. revealed the presence of two kinesin-8 motor proteins, kinesin-8X and kinesin-8B. Here we studied the biochemical properties of kinesin-8X and its role in parasite proliferation. In vitro, kinesin-8X has motility and depolymerization activities like other kinesin-8 motors. To understand the role of Plasmodium kinesin-8X in cell division, we used fluorescence-tagging and live cell imaging to define its location, and gene targeting to analyse its function, during all proliferative stages of the rodent malaria parasite P. berghei life cycle. The results revealed a spatio-temporal involvement of kinesin-8X in spindle dynamics and an association with both mitotic and meiotic spindles and the putative microtubule organising centre (MTOC). Deletion of the kinesin-8X gene revealed a defect in oocyst development, confirmed by ultrastructural studies, suggesting that this protein is required for oocyst development and sporogony. Transcriptome analysis of Δkinesin-8X gametocytes revealed modulated expression of genes involved mainly in microtubule-based processes, chromosome organisation and the regulation of gene expression, supporting a role for kinesin-8X in cell division. Kinesin-8X is thus required for parasite proliferation within the mosquito and for transmission to the vertebrate host.
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Affiliation(s)
- Mohammad Zeeshan
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Fiona Shilliday
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London, United Kingdom
| | - Tianyang Liu
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London, United Kingdom
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Tobias Mourier
- Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - David J. P. Ferguson
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Department of Biological and Medical Sciences, Faculty of Health and Life Science, Oxford Brookes University, Gipsy Lane, Oxford, United Kingdom
| | - Edward Rea
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | | | - Magali Roques
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Desiree Williams
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Emilie Daniel
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Declan Brady
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Anthony J. Roberts
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London, United Kingdom
| | - Anthony A. Holder
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Arnab Pain
- Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah, Kingdom of Saudi Arabia
- Research Center for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-ku, Sapporo, Japan
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Carolyn A. Moores
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London, United Kingdom
| | - Rita Tewari
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, United Kingdom
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35
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Wegner R, Verma V, Abel S, Hasan S, Weksler B, Colonias A. P1.12-20 Surgical Resection Versus Stereotactic Body Radiation Therapy for T1-2 N0 Typical Bronchopulmonary Carcinoid Tumors. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.1133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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36
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Abel S, Schiffman S, Monga D, Finley G, Williams H, Thakkar S, Kirichenko A, Wegner R. Neoadjuvant Stereotactic Body Radiotherapy in Addition to Chemotherapy and Its Effect on Outcome in Resected Pancreatic Cancer. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.2000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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37
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Zeeshan M, Ferguson DJ, Abel S, Burrrell A, Rea E, Brady D, Daniel E, Delves M, Vaughan S, Holder AA, Le Roch KG, Moores CA, Tewari R. Kinesin-8B controls basal body function and flagellum formation and is key to malaria transmission. Life Sci Alliance 2019; 2:e201900488. [PMID: 31409625 PMCID: PMC6696982 DOI: 10.26508/lsa.201900488] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 12/29/2022] Open
Abstract
Eukaryotic flagella are conserved microtubule-based organelles that drive cell motility. Plasmodium, the causative agent of malaria, has a single flagellate stage: the male gamete in the mosquito. Three rounds of endomitotic division in male gametocyte together with an unusual mode of flagellum assembly rapidly produce eight motile gametes. These processes are tightly coordinated, but their regulation is poorly understood. To understand this important developmental stage, we studied the function and location of the microtubule-based motor kinesin-8B, using gene-targeting, electron microscopy, and live cell imaging. Deletion of the kinesin-8B gene showed no effect on mitosis but disrupted 9+2 axoneme assembly and flagellum formation during male gamete development and also completely ablated parasite transmission. Live cell imaging showed that kinesin-8B-GFP did not co-localise with kinetochores in the nucleus but instead revealed a dynamic, cytoplasmic localisation with the basal bodies and the assembling axoneme during flagellum formation. We, thus, uncovered an unexpected role for kinesin-8B in parasite flagellum formation that is vital for the parasite life cycle.
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Affiliation(s)
- Mohammad Zeeshan
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - David Jp Ferguson
- Department of Biological and Medical Sciences, Faculty of Health and Life Science, Oxford Brookes University, Oxford, UK
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Alana Burrrell
- Department of Biological and Medical Sciences, Faculty of Health and Life Science, Oxford Brookes University, Oxford, UK
| | - Edward Rea
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Declan Brady
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Emilie Daniel
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Michael Delves
- London School of Hygiene and Tropical Medicine, Keppel, London, UK
| | - Sue Vaughan
- Department of Biological and Medical Sciences, Faculty of Health and Life Science, Oxford Brookes University, Oxford, UK
| | - Anthony A Holder
- Malaria Parasitology Laboratory, Francis Crick Institute, London, UK
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Carolyn A Moores
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London, UK
| | - Rita Tewari
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
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Abel S, Muller C, Sasanti B. Effect of alternating total mixed ration and pasture feeding on the fatty acid content and health indices of Jersey and Fleckvieh x Jersey milk. S AFR J ANIM SCI 2019. [DOI: 10.4314/sajas.v49i3.4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Abel S, Whitehead LC, Coppell KJ. Making dietary changes following a diagnosis of prediabetes: a qualitative exploration of barriers and facilitators. Diabet Med 2018; 35:1693-1699. [PMID: 30092618 DOI: 10.1111/dme.13796] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/06/2018] [Indexed: 11/30/2022]
Abstract
AIM To explore the experiences of people recently diagnosed with prediabetes and overweight or obese in making dietary changes following a six-month primary care nurse-delivered dietary intervention pilot. METHODS Semi-structured interviews were conducted with 20 participants, purposefully selected to ensure a mix of ethnicity, gender and glycaemic outcome. Thematic analysis of interview data was undertaken. RESULTS Participants described feeling shocked when they received the diagnosis of prediabetes. Three core themes, each containing subthemes, emerged: (i) supportive factors - determination not to develop diabetes, clear information and manageable strategies, and supportive relationships; (ii) barriers - lack of family support, financial constraints, social expectations around food, and chronic health issues; and (iii) overcoming challenges - growing and sharing food, using frozen vegetables and planning. Challenges related to cultural expectations around providing and partaking of food were more evident for indigenous Māori participants. CONCLUSIONS A diagnosis of prediabetes provides a window of opportunity for healthcare professionals to work with those diagnosed and their families to make healthful dietary changes. Dietary guidance is likely to be most effective when individuals' life circumstances are taken into account. Clear information and supportive relationships to facilitate lifestyle change are extremely important. (Clinical Trials Registry No; ANZCTR ACTRN1261500080656).
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Affiliation(s)
- S Abel
- Kaupapa Consulting Ltd, Napier, New Zealand
| | - L C Whitehead
- School of Nursing and Midwifery, Edith Cowan University, Joondalup, Australia
| | - K J Coppell
- Department of Medicine, University of Otago, Dunedin, New Zealand
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Burger HM, Abel S, Gelderblom WCA. Modulation of key lipid raft constituents in primary rat hepatocytes by fumonisin B 1 - Implications for cancer promotion in the liver. Food Chem Toxicol 2018; 115:34-41. [PMID: 29510220 DOI: 10.1016/j.fct.2018.03.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 02/07/2018] [Accepted: 03/02/2018] [Indexed: 01/15/2023]
Abstract
Fumonisin B1 (FB1), a group 2B natural occurring carcinogenic mycotoxin, modulated lipid and fatty acid (FA) constituents of lipid rafts isolated from primary hepatocytes following exposure to a cytotoxic concentration of FB1 (250 μM). The major effects observed in rafts, included a significant (p < 0.05) increase in raft cholesterol (CHOL) and glycerophospholipid such as phosphatidylethanolamine (PE), whereas sphingomyelin (SM) decreased (p < 0.05). Changes in lipid constituents resulted in the disruption of important membrane fluidity parameters represented as a decreased (p < 0.05) in the phosphatidylcholine (PC)/PE and PC/(PE+SM) ratios and an increase (p < 0.05) in the CHOL/PL (PL=PC+PE) ratio, suggesting the preservation of lipid raft rigidity and integrity. Observed FA changes in the raft PE fraction included a significant (p < 0.05) increase in C18:2ω-6, C20:3ω-6, C20:4ω-6, C22:4ω-6, C22:5ω-3 and C22:6ω-3, with an increase in total ω-6 and ω-3 polyunsaturated fatty acids (PUFAs). Modulation of the FA content in PE, specifically the C20:4ω-6 PC/PE ratio and PUFA levels, together with changes in CHOL and SM are key determinants regulating the integrity and function of lipid rafts. In primary hepatocytes these changes are associated with the inhibition of cell proliferation and induction of apoptosis. A lipogenic mechanism is proposed whereby FB1 modulates lipid rafts and differentially target cell survival indices of normal and preneoplastic hepatocytes during cancer promotion in the liver.
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Affiliation(s)
- H-M Burger
- Institute of Biomedical and Microbial Biotechnology, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa.
| | - S Abel
- Institute of Biomedical and Microbial Biotechnology, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa.
| | - W C A Gelderblom
- Institute of Biomedical and Microbial Biotechnology, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa; Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa.
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Renz P, Hasan S, Abel S, Uemura T, Machado L, Thai N, Kirichenko A. Multimodality Local Therapy Improves Survival Without Hastening Liver Failure in Patients With Locally Advanced Hepatocellular Carcinoma. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.1035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Hasan S, Abel S, Renz P, Kudithipudi V, Uemura T, Machado L, Thai N, Kirichenko A. The Albumin-Bilirubin Model in Hepatocellular Carcinoma May Better Predict Progression of Cirrhosis in Traditionally Low Risk Patients Following Definitive Stereotactic Body Radiation Therapy. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Pradat P, Pugliese P, Poizot-Martin I, Valantin MA, Cuzin L, Reynes J, Billaud E, Huleux T, Bani-Sadr F, Rey D, Frésard A, Jacomet C, Duvivier C, Cheret A, Hustache-Mathieu L, Hoen B, Cabié A, Cotte L, Chidiac C, Ferry T, Ader F, Biron F, Boibieux A, Miailhes P, Perpoint T, Schlienger I, Lippmann J, Braun E, Koffi J, Longuet C, Guéripel V, Augustin-Normand C, Brochier C, Degroodt S, Pugliese P, Ceppi C, Cua E, Cottalorda J, Courjon J, Dellamonica P, Demonchy E, De Monte A, Durant J, Etienne C, Ferrando S, Fuzibet J, Garraffo R, Joulie A, Risso K, Mondain V, Naqvi A, Oran N, Perbost I, Pillet S, Prouvost-Keller B, Wehrlen-Pugliese S, Rosenthal E, Sausse S, Rio V, Roger P, Brégigeon S, Faucher O, Obry-Roguet V, Orticoni M, Soavi M, Geneau de Lamarlière P, Laroche H, Ressiot E, Carta M, Ducassou M, Jacquet I, Gallie S, Galinier A, Ritleng A, Ivanova A, Blanco-Betancourt C, Lions C, Debreux C, Obry-Roguet V, Poizot-Martin I, Agher R, Katlama C, Valantin M, Duvivier C, Lortholary O, Lanternier F, Charlier C, Rouzaud C, Aguilar C, Henry B, Lebeaux D, Cessot G, Gergely A, Consigny P, Touam F, Louisin C, Alvarez M, Biezunski N, Cuzin L, Debard A, Delobel P, Delpierre C, Fourcade C, Marchou B, Martin-Blondel G, Porte M, Mularczyk M, Garipuy D, Saune K, Lepain I, Marcel M, Puntis E, Atoui N, Casanova M, Faucherre V, Jacquet J, Le Moing V, Makinson A, Merle De Boever C, Montoya-Ferrer A, Psomas C, Reynes J, Raffi F, Allavena C, Billaud E, Biron C, Bonnet B, Bouchez S, Boutoille D, Brunet C, Jovelin T, Hall N, Bernaud C, Morineau P, Reliquet V, Aubry O, Point P, Besnier M, Larmet L, Hüe H, Pineau S, André-Garnier E, Rodallec A, Choisy P, Vandame S, Huleux T, Ajana F, Alcaraz I, Baclet V, Huleux T, Melliez H, Viget N, Valette M, Aissi E, Allienne C, Meybeck A, Riff B, Bani-Sadr F, Rouger C, Berger J, N'Guyen Y, Lambert D, Kmiec I, Hentzien M, Lebrun D, Migault C, Rey D, Batard M, Bernard-Henry C, Cheneau C, de Mautort E, Fischer P, Partisani M, Priester M, Lucht F, Frésard A, Botelho-Nevers E, Gagneux-Brunon A, Cazorla C, Guglielminotti C, Daoud F, Lutz M, Jacomet C, Laurichesse H, Lesens O, Vidal M, Mrozek N, Corbin V, Aumeran C, Baud O, Casanova S, Coban D, Hustache-Mathieu L, Thiebaut-Drobacheff M, Foltzer A, Gendrin V, Bozon F, Chirouze C, Abel S, Cabié A, Césaire R, Santos GD, Fagour L, Najioullah F, Ouka M, Pierre-François S, Pircher M, Rozé B, Hoen B, Ouissa R, Lamaury I. Direct-acting antiviral treatment against hepatitis C virus infection in HIV-Infected patients - "En route for eradication"? J Infect 2017; 75:234-241. [PMID: 28579302 DOI: 10.1016/j.jinf.2017.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/17/2017] [Accepted: 05/11/2017] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Direct-Acting Antivirals (DAAs) opened a new era in HCV treatment. We report the impact of HCV treatment in French HIV-HCV coinfected patients. METHODS All HIV-HCV patients from the Dat'AIDS cohort followed between 2012 and 2015 were included. HCV status was defined yearly as naive, spontaneous cure, sustained virological response (SVR12), failure or reinfection. RESULTS Among 32,945 HIV-infected patients, 15.2% were positive for anti-HCV antibodies. From 2012 to 2015, HCV incidence rate increased from 0.35%PY to 0.69%PY in MSM, while median incidence was 0.08%PY in other patients. Median reinfection rate was 2.56%PY in MSM and 0.22%PY in other patients. HCV treatment initiation rate rose from 8.2% in 2012 to 29.6% (48.0% in pre-treated patients vs 22.6% in naïve patients). SVR12 rate increased from 68.7% to 95.2%. By the end of 2015, 62.7% of the patients were cured either spontaneously or following SVR. CONCLUSIONS HCV treatment dramatically increased in HIV-HCV patients in France from 2012 to 2015 resulting in HCV cure in nearly two-thirds of the patients in this cohort. Combined with a declining HCV prevalence, the prevalence of active HCV infection among HIV patients will drastically decrease in the forthcoming years.
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Affiliation(s)
- Pierre Pradat
- Center for Clinical Research, Department of Hepatology, Croix-Rousse Hospital, Hospices Civils de Lyon, Lyon, France.
| | - Pascal Pugliese
- Department of Infectious Diseases, Centre Hospitalier Universitaire de Nice, Hôpital l'Archet, Nice, France
| | - Isabelle Poizot-Martin
- Immuno-hematology Clinic, Assistance Publique - Hôpitaux de Marseille, Hôpital Sainte-Marguerite, Marseille, France; Aix-Marseille University, Inserm U912 (SESSTIM), Marseille, France
| | - Marc-Antoine Valantin
- Department of Infectious Diseases, Assistance Publique - Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris, France; Sorbonne Universités, UPMC Université Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
| | - Lise Cuzin
- CHU Toulouse, COREVIH, Toulouse, France; Université de Toulouse III, Toulouse, France; INSERM, UMR, 1027, Toulouse, France
| | - Jacques Reynes
- Department of Infectious Diseases, UMI 233 INSERM U1175, CHU de Montpellier, Montpellier, France
| | - Eric Billaud
- Department of Infectious Diseases, Hotel Dieu Hospital, Nantes, France
| | - Thomas Huleux
- Department of Infectious Diseases and Travel Diseases, Centre Hospitalier Gustave-Dron, Tourcoing, France
| | - Firouze Bani-Sadr
- Department of Internal Medicine, Infectious Diseases and Clinical Immunology, Hôpital Robert Debré, CHU, Reims, France; Université de Reims Champagne-Ardenne, Faculté de médecine, EA-4684/SFR CAP-SANTE, Reims, France
| | - David Rey
- HIV Infection Care Centre, Hôpitaux Universitaires, Strasbourg, France
| | - Anne Frésard
- Department of Infectious Diseases, CHU, Saint-Etienne, France
| | - Christine Jacomet
- Department of Infectious Diseases, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Claudine Duvivier
- Department of Infectious Diseases, Centre d'Infectiologie Necker-Pasteur, IHU Imagine, Assistance Publique - Hôpitaux de Paris, Hôpital Necker-Enfants Malades, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, EA7327, Paris, France
| | - Antoine Cheret
- Department of Internal Medicine, CHU, Bicètre, France; Université Paris Descartes, Sorbonne Paris Cité, EA7327, Paris, France
| | | | - Bruno Hoen
- Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles, and Service de Maladies Infectieuses et Tropicales, Dermatologie et Médecine Interne, and Inserm CIC 1424, Centre Hospitalier Universitaire de Pointe-à-Pitre, Pointe-à-Pitre, France
| | - André Cabié
- Department of Infectious Diseases, CHU de Martinique, Fort-de-France, France; Université des Antilles EA4537 and INSERM CIC1424, Fort-de-France, France
| | - Laurent Cotte
- Department of Infectious Diseases, Croix-Rousse Hospital, Hospices Civils de Lyon, Lyon, France; INSERM U1052, Lyon, France.
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Waring JF, Davis JW, Dumas E, Cohen D, Idler K, Abel S, Georgantas R, Podsadecki T, Dutta S. Epigenetic analysis of the IFNλ3 gene identifies a novel marker for response to therapy in HCV-infected subjects. J Viral Hepat 2017; 24:397-403. [PMID: 27925355 DOI: 10.1111/jvh.12661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/22/2016] [Indexed: 12/31/2022]
Abstract
Chronic hepatitis C virus (HCV) infection is characterized by high interindividual variability in response to pegylated interferon and ribavirin. A genetic polymorphism on chromosome 19 (rs12979860) upstream of interferon-λ3 (IFNλ3) is associated with a twofold change in sustained virologic response rate after 48 weeks of treatment with pegylated interferon/ribavirin in HCV genotype 1 (GT1) treatment-naïve patients. We conducted epigenetic analysis on the IFNλ3 promoter to investigate whether DNA methylation is associated with response to HCV therapy. DNA samples from HCV GT1-infected subjects receiving an interferon-free paritaprevir-containing combination regimen (N=540) and from HCV-uninfected, healthy controls (N=124) were analysed for IFNλ3 methylation levels. Methylation was strongly associated with rs12979860 allele status whether adjusting for HCV status (r=65.0%, 95% CI: [60.2%, 69.5%]), or not (r=64.4%), both with P<2.2×10-16 . In HCV GT1-infected subjects, C/C genotypes had significantly lower methylation levels relative to C/T or T/T genotypes (P<1×10-14 ), with each T allele resulting in a nine-unit increase in mean methylation level. Methylation levels did not correlate with response in subjects treated for 12 or 24 weeks. However, non-C/C subjects with higher methylation levels were more likely to relapse when treatment duration was 8 weeks. This analysis suggests that methylation status of the IFNλ3 promoter region may be a useful parameter that identifies patients more likely to relapse following HCV therapy; however, continuing therapy for a sufficient duration can overcome this difference. These findings may provide mechanistic insight into the role of IFNλ3 genetic variants in HCV treatment response.
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Affiliation(s)
| | | | - E Dumas
- AbbVie Inc., North Chicago, IL, USA
| | - D Cohen
- AbbVie Inc., North Chicago, IL, USA
| | - K Idler
- AbbVie Inc., North Chicago, IL, USA
| | - S Abel
- AbbVie Inc., North Chicago, IL, USA
| | | | | | - S Dutta
- AbbVie Inc., North Chicago, IL, USA
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Putot A, Rozé B, Pierre-François S, Pircher M, Vilain R, Miossec C, Desbois N, Hochedez P, Abel S, Cabié A. IST-06 - Réémergence de la syphilis chez les personnes infectées par le VIH en Martinique en 2015. Med Mal Infect 2016. [DOI: 10.1016/s0399-077x(16)30437-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Thioune M, Bertolotti A, Césaire R, Carme B, Nacher M, Calmont I, Jean-Marie J, Abel S, Cabié A. COL 7-01 - Prévalence et facteurs de risques associés de la forme chronique du Chikungunya ; une étude de cohorte. Med Mal Infect 2016. [DOI: 10.1016/s0399-077x(16)30286-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Riedel S, Abel S, Burger HM, van der Westhuizen L, Swanevelder S, Gelderblom WCA. Differential modulation of the lipid metabolism as a model for cellular resistance to fumonisin B1-induced cytotoxic effects in vitro. Prostaglandins Leukot Essent Fatty Acids 2016; 109:39-51. [PMID: 27269712 DOI: 10.1016/j.plefa.2016.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/21/2016] [Accepted: 04/21/2016] [Indexed: 12/30/2022]
Abstract
Differential sensitivity of primary hepatocytes and Chang cells to the cancer promoter fumonisin B1 (FB1)-induced cytotoxic effects were investigated in relation to changes in membrane lipid distribution. In contrast to primary hepatocytes, Chang cells were resistant to FB1-induced cytotoxic effects. This was associated with a high cholesterol (Chol) and sphingomyelin (SM) and low phosphatidylcholine (PC) content, resulting in a significant (P<0.05) decrease in phosphatidylethanolamine (PE)/PC ratio, increased Chol/total phosphoglyceride (TPG) ratios and low total polyunsaturated fatty acids (PUFA) content in PC and PE, suggesting a more rigid membrane structure. High levels of C18:1 and reduced polyunsaturated fatty acid (PUFA) levels are likely to provide selective resistance to FB1-induced oxidative stress. FB1-associated lipid changes included decreases in SM and Chol, increases in sphinganine (Sa) and PE with the increases in key saturated, monounsaturated, and PUFAs in PE as key role players in the differential responses to FB1-induced cell growth responses in cells.
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Affiliation(s)
- S Riedel
- Biomedical Research and Innovation Platform, South African Medical Research Council, PO Box 19070, Tygerberg 7505, South Africa.
| | - S Abel
- Mycotoxicology and Chemoprevention Research Group, Institute of Biomedical and Microbial Biotechnology, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa.
| | - H-M Burger
- Mycotoxicology and Chemoprevention Research Group, Institute of Biomedical and Microbial Biotechnology, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa.
| | - L van der Westhuizen
- Oxidative Stress Research Centre, Institute of Biomedical and Microbial Biotechnology, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa.
| | - S Swanevelder
- Biostatistics Unit, South African Medical Research Council, PO Box 19070, Tygerberg, South Africa.
| | - W C A Gelderblom
- Mycotoxicology and Chemoprevention Research Group, Institute of Biomedical and Microbial Biotechnology, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa; Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa.
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Affiliation(s)
- J. Dittmann
- Albert-Ludwigs-Universität, Germanistische Linguistik, Freiburg i. Br
| | - S. Abel
- University of Manchester, School of Psychological Sciences, Manchester, United Kingdom of Great Britain and Northern Ireland
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Waring JF, Dumas EO, Abel S, Coakley E, Cohen DE, Davis JW, Podsadecki T, Dutta S. Serum miR-122 may serve as a biomarker for response to direct acting antivirals: effect of paritaprevir/R with dasabuvir or ombitasvir on miR-122 in HCV-infected subjects. J Viral Hepat 2016; 23:96-104. [PMID: 26436610 DOI: 10.1111/jvh.12470] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/27/2015] [Indexed: 12/14/2022]
Abstract
Circulating microRNAs (miRNA) have been intensely investigated as biomarkers in disease and therapy. Several studies have identified miR-122 as an important regulator of HCV replication. The effect of new therapies that directly target the HCV replication life cycle on circulating microRNA levels has not been elucidated. We performed expression profiling of circulating miRNA in serum in subjects treated with HCV direct-acting antiviral agents (DAAs). Serum miRNA levels were evaluated from two studies in HCV GT1-infected treatment-naïve subjects and prior nonresponders to pegylated interferon (pegIFN) and ribavirin (RBV) who received paritaprevir/ritonavir + dasabuvir + RBV for 12 weeks, and in treatment-naïve genotype (GT)1-3-infected subjects who received paritaprevir/ritonavir + ombitasvir ± RBV for 12 weeks. Over 100 different miRNA species were detected in serum. Of these, levels of miR-122 showed the most consistent change in response to treatment across all HCV genotypes. In all subjects, miR-122 showed an average four-fold reduction between baseline and week 2, and remained below baseline through post-treatment week 12 in subjects who achieved sustained virological response. In contrast, in subjects who did not achieve SVR, miR-122 levels began to return to baseline levels after the second week of treatment. The change in miR-122 levels was similar across genotypes, and was comparable with or without RBV. This is the first report comparing expression levels of circulating miRNA in HCV GT1-3 subjects treated with IFN-free combinations of DAAs. The results suggest that serum levels of miR-122 are reduced following treatment in subjects who achieve SVR, and correlate with HCV RNA levels across genotypes.
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Affiliation(s)
- J F Waring
- Department of Pharmacogenetics and Pharmacogenomics, Clinical Pharmacology, AbbVie, North Chicago, IL, USA
| | - E O Dumas
- Department of Clinical Virology, AbbVie, North Chicago, IL, USA
| | - S Abel
- Department of Pharmacogenetics and Pharmacogenomics, Clinical Pharmacology, AbbVie, North Chicago, IL, USA
| | - E Coakley
- Department of Clinical Virology, AbbVie, North Chicago, IL, USA
| | - D E Cohen
- Department of Clinical Virology, AbbVie, North Chicago, IL, USA
| | - J Wade Davis
- Department of Pharmacogenetics and Pharmacogenomics, Clinical Pharmacology, AbbVie, North Chicago, IL, USA
| | - T Podsadecki
- Department of Clinical Virology, AbbVie, North Chicago, IL, USA
| | - S Dutta
- Department of Pharmacogenetics and Pharmacogenomics, Clinical Pharmacology, AbbVie, North Chicago, IL, USA
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