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Pandit K, Surolia N, Bhattacharjee S, Karmodiya K. The many paths to artemisinin resistance in Plasmodium falciparum. Trends Parasitol 2023; 39:1060-1073. [PMID: 37833166 DOI: 10.1016/j.pt.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
Emerging resistance against artemisinin (ART) poses a major challenge in controlling malaria. Parasites with mutations in PfKelch13, the major marker for ART resistance, are known to reduce hemoglobin endocytosis, induce unfolded protein response (UPR), elevate phosphatidylinositol-3-phosphate (PI3P) levels, and stimulate autophagy. Nonetheless, PfKelch13-independent resistance is also reported, indicating extensive complementation by reconfiguration in the parasite metabolome and transcriptome. These findings implicate that there may not be a single 'universal identifier' of ART resistance. This review sheds light on the molecular, transcriptional, and metabolic pathways associated with ART resistance, while also highlighting the interplay between cellular heterogeneity, environmental stress, and ART sensitivity.
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Affiliation(s)
- Kushankur Pandit
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Namita Surolia
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Souvik Bhattacharjee
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research, Pune, India.
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Sandoval-Bances J, Saavedra-Samillán M, Huyhua-Gutiérrez S, Rojas LM, Tejada-Muñoz S, Tapia-Limonchi R, Chenet SM. Molecular characterization of the Plasmodium falciparum k13 gene helix domain in samples from native communities of Condorcanqui, Amazonas, Perú. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2023; 43:352-359. [PMID: 37871569 PMCID: PMC10624420 DOI: 10.7705/biomedica.6849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/27/2023] [Indexed: 10/25/2023]
Abstract
Introduction. Resistance of Plasmodium falciparum to different antimalarial drugs is an obstacle to disease elimination. The artemisinin-resistant genotype of P. falciparum can be assessed by examining polymorphisms in the helix domain of the Pfk13 gene. The World Health Organization recommends these mutations as molecular markers to detect artemisinin-resistant in countries where P. falciparum malaria is endemic. Objective. To identify artemisinin resistance-related mutations present in the helix domain of the P. falciparum k13 gene. Materials and methods. We collected a total of 51 samples through passive case detection, positive for Plasmodium by microscopy, from six communities in the district of Río Santiago in Condorcanqui, Amazonas. Molecular species confirmation was performed by real-time PCR and Pfk13 helix domain was amplified and sequenced by capillary electrophoresis. The obtained sequences were compared with the wild type 3D7 reference strain. Results. A total of 51 positive samples were confirmed for P. falciparum from the communities of Ayambis, Chapiza, Palometa, Muchinguis, Alianza Progreso and Caterpiza. DNA sequences alignment showed the absence of resistance-associated mutations in the k13 gene of the collected samples. Discussion. The obtained results are consistent with similar studies conducted in other South American countries, including Perú, so these data provide a baseline for artemisinin-resistance molecular surveillance in the Amazon region and reinforce the efficacy of artemisinin-based combination therapy in this area.
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Affiliation(s)
- Julio Sandoval-Bances
- nstituto de Enfermedades Tropicales, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Triunfo, Chachapoyas, Perú.
| | - Milagros Saavedra-Samillán
- nstituto de Enfermedades Tropicales, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Triunfo, Chachapoyas, Perú.
| | - Sonia Huyhua-Gutiérrez
- Instituto de Enfermedades Tropicales, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Triunfo, Chachapoyas, Perú; Facultad de Ciencias de la Salud, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Triunfo, Chachapoyas, Perú.
| | - Luis M Rojas
- Dirección Regional de Salud de Amazonas, Chachapoyas, Perú.
| | - Sonia Tejada-Muñoz
- Instituto de Enfermedades Tropicales, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Triunfo, Chachapoyas, Perú 2 Facultad de Ciencias de la Salud, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Triunfo, Chachapoyas, Perú.
| | - Rafael Tapia-Limonchi
- Instituto de Enfermedades Tropicales, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Triunfo, Chachapoyas, Perú; Instituto de Investigaciones en Ciencias Biomédicas, Universidad Ricardo Palma, Lima, Perú.
| | - Stella M Chenet
- Instituto de Enfermedades Tropicales, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Triunfo, Chachapoyas, Perú; Instituto de Investigaciones en Ciencias Biomédicas, Universidad Ricardo Palma, Lima, Perú.
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Simmons C, Gibbons J, Wang C, Pires CV, Zhang M, Siddiqui F, Oberstaller J, Casandra D, Seyfang A, Cui L, Otto TD, Adams JH. A novel Modulator of Ring Stage Translation (MRST) gene alters artemisinin sensitivity in Plasmodium falciparum. mSphere 2023; 8:e0015223. [PMID: 37219373 PMCID: PMC10449512 DOI: 10.1128/msphere.00152-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
The implementation of artemisinin (ART) combination therapies (ACTs) has greatly decreased deaths caused by Plasmodium falciparum malaria, but increasing ACT resistance in Southeast Asia and Africa could reverse this progress. Parasite population genetic studies have identified numerous genes, single-nucleotide polymorphisms (SNPs), and transcriptional signatures associated with altered artemisinin activity with SNPs in the Kelch13 (K13) gene being the most well-characterized artemisinin resistance marker. However, there is an increasing evidence that resistance to artemisinin in P. falciparum is not related only to K13 SNPs, prompting the need to characterize other novel genes that can alter ART responses in P. falciparum. In our previous analyses of P. falciparum piggyBac mutants, several genes of unknown function exhibited increased sensitivity to artemisinin that was similar to a mutant of K13. Further analysis of these genes and their gene co-expression networks indicated that the ART sensitivity cluster was functionally linked to DNA replication and repair, stress responses, and maintenance of homeostatic nuclear activity. In this study, we have characterized PF3D7_1136600, another member of the ART sensitivity cluster. Previously annotated as a conserved Plasmodium gene of unknown function, we now provide putative annotation of this gene as a Modulator of Ring Stage Translation (MRST). Our findings reveal that the mutagenesis of MRST affects gene expression of multiple translation-associated pathways during the early ring stage of asexual development via putative ribosome assembly and maturation activity, suggesting an essential role of MRST in protein biosynthesis and another novel mechanism of altering the parasite's ART drug response.IMPORTANCEPlasmodium falciparum malaria killed more than 600,000 people in 2021, though ACTs have been critical in reducing malaria mortality as a first-line treatment for infection. However, ACT resistance in Southeast Asia and emerging resistance in Africa are detrimental to this progress. Mutations to Kelch13 (K13) have been identified to confer increased artemisinin tolerance in field isolates, however, genes other than K13 are implicated in altering how the parasite responds to artemisinin prompts additional analysis. Therefore, in this study we have characterized a P. falciparum mutant clone with altered sensitivity to artemisinin and identified a novel gene (PF3D7_1136600) that is associated with alterations to parasite translational metabolism during critical timepoints for artemisinin drug response. Many genes of the P. falciparum genome remain unannotated, posing a challenge for drug-gene characterizations in the parasite. Therefore, through this study, we have putatively annotated PF3D7_1136600 as a novel MRST gene and have identified a potential link between MRST and parasite stress response mechanisms.
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Affiliation(s)
- Caroline Simmons
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Justin Gibbons
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Camilla Valente Pires
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Min Zhang
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Faiza Siddiqui
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Jenna Oberstaller
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Debora Casandra
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Andreas Seyfang
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Liwang Cui
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Thomas D. Otto
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - John H. Adams
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
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Azmi WA, Rizki AFM, Djuardi Y, Artika IM, Siregar JE. Molecular insights into artemisinin resistance in Plasmodium falciparum: An updated review. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023:105460. [PMID: 37269964 DOI: 10.1016/j.meegid.2023.105460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/05/2023]
Abstract
Malaria still poses a major burden on human health around the world, especially in endemic areas. Plasmodium resistance to several antimalarial drugs has been one of the major hindrances in control of malaria. Thus, the World Health Organization recommended artemisinin-based combination therapy (ACT) as a front-line treatment for malaria. The emergence of parasites resistant to artemisinin, along with resistant to ACT partner drugs, has led to ACT treatment failure. The artemisinin resistance is mostly related to the mutations in the propeller domain of the kelch13 (k13) gene that encodes protein Kelch13 (K13). The K13 protein has an important role in parasite reaction to oxidative stress. The most widely spread mutation in K13, with the highest degree of resistance, is a C580Y mutation. Other mutations, which are already identified as markers of artemisinin resistance, are R539T, I543T, and Y493H. The objective of this review is to provide current molecular insights into artemisinin resistance in Plasmodium falciparum. The trending use of artemisinin beyond its antimalarial effect is described. Immediate challenges and future research directions are discussed. Better understanding of the molecular mechanisms underlying artemisinin resistance will accelerate implementation of scientific findings to solve problems with malarial infection.
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Affiliation(s)
- Wihda Aisarul Azmi
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, Bogor 16911, Indonesia; Master's Programme in Biomedical Sciences, Faculty of Medicine Universitas Indonesia, Jakarta 10430, Indonesia
| | - Andita Fitri Mutiara Rizki
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, Bogor 16911, Indonesia; Master's Programme in Biomedical Sciences, Faculty of Medicine Universitas Indonesia, Jakarta 10430, Indonesia
| | - Yenny Djuardi
- Department of Parasitology, Faculty of Medicine Universitas Indonesia, Jakarta 10430, Indonesia
| | - I Made Artika
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, Bogor 16911, Indonesia; Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Bogor 16680, Indonesia
| | - Josephine Elizabeth Siregar
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, Bogor 16911, Indonesia.
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Choubey D, Deshmukh B, Rao AG, Kanyal A, Hati AK, Roy S, Karmodiya K. Genomic analysis of Indian isolates of Plasmodium falciparum: Implications for drug resistance and virulence factors. Int J Parasitol Drugs Drug Resist 2023; 22:52-60. [PMID: 37269630 PMCID: PMC10248731 DOI: 10.1016/j.ijpddr.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/04/2023] [Accepted: 05/18/2023] [Indexed: 06/05/2023]
Abstract
The emergence of drug resistance to frontline treatments such as Artemisinin-based combination therapy (ACT) is a major obstacle to the control and eradication of malaria. This problem is compounded by the inherent genetic variability of the parasites, as many established markers of resistance do not accurately predict the drug-resistant status. There have been reports of declining effectiveness of ACT in the West Bengal and Northeast regions of India, which have traditionally been areas of drug resistance emergence in the country. Monitoring the genetic makeup of a population can help to identify the potential for drug resistance markers associated with it and evaluate the effectiveness of interventions aimed at reducing the spread of malaria. In this study, we performed whole genome sequencing of 53 isolates of Plasmodium falciparum from West Bengal and compared their genetic makeup to isolates from Southeast Asia (SEA) and Africa. We found that the Indian isolates had a distinct genetic makeup compared to those from SEA and Africa, and were more similar to African isolates, with a high prevalence of mutations associated with antigenic variation genes. The Indian isolates also showed a high prevalence of markers of chloroquine resistance (mutations in Pfcrt) and multidrug resistance (mutations in Pfmdr1), but no known mutations associated with artemisinin resistance in the PfKelch13 gene. Interestingly, we observed a novel L152V mutation in PfKelch13 gene and other novel mutations in genes involved in ubiquitination and vesicular transport that have been reported to support artemisinin resistance in the early stages of ACT resistance in the absence of PfKelch13 polymorphisms. Thus, our study highlights the importance of region-specific genomic surveillance for artemisinin resistance and the need for continued monitoring of resistance to artemisinin and its partner drugs.
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Affiliation(s)
- Deepak Choubey
- Department of Technology, Savitribai Phule Pune University, Pune, India
| | - Bhagyashree Deshmukh
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| | - Anjani Gopal Rao
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| | - Abhishek Kanyal
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| | - Amiya Kumar Hati
- Department of Medical Entomology, Calcutta School of Tropical Medicine, Kolkata, West Bengal, India
| | - Somenath Roy
- Department of Human Physiology, Vidyasagar University, Paschim Medinipur, West Bengal, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India.
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Brown AC, Warthan MD, Aryal A, Liu S, Guler JL. Nutrient Limitation Mimics Artemisinin Tolerance in Malaria. mBio 2023:e0070523. [PMID: 37097173 DOI: 10.1128/mbio.00705-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Mounting evidence demonstrates that nutritional environment can alter pathogen drug sensitivity. While the rich media used for in vitro culture contains supraphysiological nutrient concentrations, pathogens encounter a relatively restrictive environment in vivo. We assessed the effect of nutrient limitation on the protozoan parasite that causes malaria and demonstrated that short-term growth under physiologically relevant mild nutrient stress (or "metabolic priming") triggers increased tolerance of a potent antimalarial drug. We observed beneficial effects using both short-term survival assays and longer-term proliferation studies, where metabolic priming increases parasite survival to a level previously defined as resistant (>1% survival). We performed these assessments by either decreasing single nutrients that have distinct roles in metabolism or using a media formulation that simulates the human plasma environment. We determined that priming-induced tolerance was restricted to parasites that had newly invaded the host red blood cell, but the effect was not dependent on genetic background. The molecular mechanisms of this intrinsic effect mimic aspects of genetic tolerance, including translational repression and protein export. This finding suggests that regardless of the impact on survival rates, environmental stress could stimulate changes that ultimately directly contribute to drug tolerance. Because metabolic stress is likely to occur more frequently in vivo compared to the stable in vitro environment, priming-induced drug tolerance has ramifications for how in vitro results translate to in vivo studies. Improving our understanding of how pathogens adjust their metabolism to impact survival of current and future drugs is an important avenue of research to slow the evolution of resistance. IMPORTANCE There is a dire need for effective treatments against microbial pathogens. Yet, the continuing emergence of drug resistance necessitates a deeper knowledge of how pathogens respond to treatments. We have long appreciated the contribution of genetic evolution to drug resistance, but transient metabolic changes that arise in response to environmental factors are less recognized. Here, we demonstrate that short-term growth of malaria parasites in a nutrient-limiting environment triggers cellular changes that lead to better survival of drug treatment. We found that these strategies are similar to those employed by drug-tolerant parasites, which suggests that starvation "primes" parasites to survive and potentially evolve resistance. Since the environment of the human host is relatively nutrient restrictive compared to growth conditions in standard laboratory culture, this discovery highlights the important connections among nutrient levels, protective cellular pathways, and resistance evolution.
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Affiliation(s)
- Audrey C Brown
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Michelle D Warthan
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Anush Aryal
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Shiwei Liu
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Jennifer L Guler
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
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