Indonesian Journal of Medical Chemistry and Bioinformatics
Abstract
Introduction: Malaria is a serious tropical disease with Plasmodium falciparum as its most well-known causative parasite for producing higher levels of late stage parasites that leads to sequestration in vital organs which could lead to death. There is a growing trend of antimalarial drugs resistance against Plasmodium falciparum. Molecular assessment using polymerase chain reaction could trace the presence of mutation and also determine single-nucleotide polymorphism (SNP) in Plasmodium falciparum genes. This SNP can determine the particular population’s response to antimalarial drugs. Objectives: This study aims to examine the relationship between SNP in Plasmodium falciparum genes and antimalarial drugs resistance. Methods: Literature searches were carried out through various databases which were then collected and analyzed. Result: We identified various SNPs from eleven known genes in Plasmodium falciparum, each SNPs causes a different mechanism which contributes to antimalarial drug resistance. Mechanisms varying from slower drug clearance to drug transport activity alteration. Conclusion: Results from most studies included in this review suggest that SNPs in Plasmodium falciparum genes participate in the resistance against various antimalarial drugs via several mechanisms and may be necessary for parasite survival when stressed.
Bahasa Abstract
Pendahuluan: Malaria adalah penyakit tropis yang serius dengan Plasmodium falciparum sebagai parasit penyebab yang dikenal memproduksi parasit stadium akhir dalam jumlah tinggi lalu menyebabkan sekuestrasi di organ vital yang dapat menyebabkan kematian. Ada kecenderungan peningkatan resistensi obat antimalaria terhadap Plasmodium falciparum. Uji molekuler menggunakan polymerase chain reaction dapat menunjukkan adanya mutasi dan juga menentukan polimorfisme nukleotida tunggal (SNP) pada gen Plasmodium falciparum SNP ini dapat menentukan respon populasi tertentu terhadap obat antimalaria.
Tujuan: Penelitian ini bertujuan untuk mengetahui hubungan antara SNP pada Plasmodium falciparum resistensi obat antimalaria.
Metode: Penelusuran literatur dilakukan melalui berbagai basis data yang kemudian dikumpulkan dan dianalisis.
Hasil: Kami mengidentifikasi berbagai SNP dari sebelas gen yang diketahui pada Plasmodium falciparum, masing-masing SNP memiliki mekanisme yang berbeda dalam p resistensi obat antimalaria. Mekanisme bervariasi dari pembersihan obat yang lebih lambat hingga perubahan aktivitas transportasi obat.
Kesimpulan: Hasil dari sebagian besar penelitian yang termasuk dalam tinjauan ini menunjukkan bahwa SNP pada Plasmodium falciparum berpartisipasi dalam resistensi terhadap berbagai obat antimalaria melalui beberapa mekanisme dan mungkin juga penting dalam kelangsungan hidup parasit di bawah tekanan.
References
References
- Talapko J, Skrlec I, et al. Malaria: the past and the present. Microorganisms. 2019 Jun;7(6):179.
- WHO. World Malaria Report. Geneva: World Health Organization; 2019.
- WHO. Drug resistance in malaria. Geneva: World Health Organization; 2014.
- Packard RM. The making of a tropical disease: a short history of malaria. Baltimore: Johns Hopkins University Press; 2007.
- Thu AM, Phyo AP, Landier J, Parker DM, Nosten FH. Combating multidrug- resistant Plasmodium falciparum malaria. FEBS J. 2017;284(16):2569-78.
- Ashley EA, Dhorda M, Fairhurst RM, Amaratunga C, Lim P, Suon S, et al. Spread of artemisinin resistance in Plasmodium falciparum malaria. N Engl J Med. 2014;371:411–23.
- Straimer J, Gnadig NF, Witkowski B, Amaratunga C, Duru V, Ramadani AP, et al. Drug resistance. K13-propeller mutations confer artemisinin resistance in Plasmodium falciparum clinical isolates. Science. 2015;347:428–31.
- Heather JM, Chain B. The sequence of sequencers: The history of sequencing DNA. Genomics. 2016 Jan;107(1):1–8.
- Morozova O, Marra MA. Applications of next-generation sequencing technologies in functional genomics. Genomics. 2008 Nov;92(5):255–64.
- Metzker ML. Sequencing technologies — the next generation. Nat Rev Genet. 2010 Jan;11(1):31–46.
- Liu L, Li Y, Li S, Hu N, He Y, Pong R, et al. Comparison of Next-Generation Sequencing Systems. J Biomed Biotechnol. 2012;2012:1–11.
- van Dijk EL, Jaszczyszyn Y, Naquin D, Thermes C. The Third Revolution in Sequencing Technology. Trends Genet. 2018 Sep;34(9):666–81.
- Ishengoma DS, Saidi Q, Sibley CH, Roper C, Alifrangis M. Deployment and utilization of next-generation sequencing of Plasmodium falciparum to guide anti-malarial drug policy decisions in sub-Saharan Africa: opportunities and challenges. Malar J. 2019 Dec;18(1):267.
- Wadapurkar RM, Vyas R. Computational analysis of next generation sequencing data and its applications in clinical oncology. Inform Med Unlocked. 2018;11:75–82.
- Maljkovic Berry I, Melendrez MC, Bishop-Lilly KA, Rutvisuttinunt W, Pollett S, Talundzic E, et al. Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity. J Infect Dis. 2019 Oct 14;jiz286.
- Nussbaum RL, McInnes RR, Willard HF. Thompson & Thompson genetics in medicine. 8th ed. Philadelphia: Elsevier; 2016. Chapter 4, Human genetic diversity: Mutation and polymorphism; p.45-8.
- Deng N, Zhou H, Fan H, Yuan Y. Single nucleotide polymorphisms and cancer susceptibility. Oncotarget. 2017 Dec 15; 8(66): 110635–49.
- Wadapurkar RM, Vyas R. Computational analysis of next generation sequencing data and its applications in clinical oncology. Informatics in Medicine Unlocked. 2018; 11:75-82.
- Santiago I. Quality assessment of NGD data [published lecture notes]. Best practices in the analysis of RNA-seq and ChIP-seq data. Cambridge: University of Cambridge; lecture given 2015 Jul 27-31.
- Rosen KH, Shier DR, Goddard W. Handbook of discrete and combinatorial mathematics. 2nd ed. Boca Raton (FL): CRC Press/Taylor & Francis; 2017 Nov. Chapter 20.1, Sequence Alignment. https://www.ncbi.nlm.nih.gov/books/NBK464187/
- Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, et al. A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform. 2014 Mar; 15(2): 256–78.
- Brevern A, Meyniel J, Fairhead C. Trends in IT innovation to build a next generation bioinformatics solution to manage and analyse biological big data produced by NGS technologies. Biomed Res Int. 2015;2015:904541.
- Poumerol G, Wilder-Smith A. International travel and health. Geneva: World Health Organization; 2012. Chapter 7, Malaria; p.144-66.
- World Health Organization. Malaria [Internet]. Geneva: World Health Organization; 2020 Jan 14 [cited 2020 Oct 17]. Available from: https://www.who.int/news-room/fact-sheets/detail/malaria.
- Centers for Disease Control and Prevention. Malaria [Internet]. Atlanta: U.S. Department of Health & Human Services; 2019 May 22 [cited 2020 Oct 17]. Available from: https://www.cdc.gov/parasites/malaria/index.html.
- Blasco B, Leroy D, Fidock DA. Antimalarial drug resistance: linking Plasmodium falciparum parasite biology to the clinic. Nat Med. 2017 Aug;23(8):917-28.
- Breglio KF, Amato R, Eastman R, Lim P, Sa JM, Guha R. A single nucleotide polymorphism in the Plasmodium falciparum atg18 gene associates with artemisinin resistance and confers enhanced parasite survival under nutrient deprivation. Malar J. 2018;17:391.
- Ocan M, Akena D, Nsobya S, Kamya MR, Senono R, Kinengyere AA, et al. K13-propeller gene polymorphisms in Plasmodium falciparum parasite population in malaria affected countries: a systematic review of prevalence and risk factors. Malar J. 2019 Dec;18(1):60.
- Miotto O, Sekihara M, Tachibana S, Yamuchi M, PEarson R, Amato R, et al. Emergence of artemisinin-resistant Plasmodium falciparum with kelch13 C580Y mutations on the island of New Guinea. 10.1101/621813
- Wang Z, Cabrera M, Yang J, Yuan L, Gupta, Liang X, et al. Genome-wide association analysis identifies genetic loci associated with resistance to multiple antimalarials in Plasmodium falciparum from China-Myanmar border. Sci Rep. 2016; 6:33891
- Schulze J, Kwiatkowski M, Borner J, Schlüter H, Bruchhaus I, Burmester T, et al. The Plasmodium falciparum exportome contains non‐canonical PEXEL/HT proteins. Mol Microbiol. 2015 Jul;97(2):301-14.
- Miotto O, Amato R, Ashley EA, MacInnis B, Almagro-Garcia J, Amaratunga C, et al. Genetic architecture of artemisinin-resistant Plasmodium falciparum. Nat Genet. 2015 Mar;47(3):226–34.
- Briolant S, Bogreau H, Gil M, Bouchiba H, Baret E, Amalvict R, et al. The F423Y Mutation in the pfmdr2 Gene and Mutations N51I, C59R, and S108N in the pfdhfr Gene Are Independently Associated with Pyrimethamine Resistance in Plasmodium falciparum Isolates. Antimicrob Agents Chemother. 2012 May;56(5):2750–2.
- Shafik SH, Cobbold SA, Barkat K, Richards SN, Lancaster NS, Llinás M, et al. The natural function of the malaria parasite’s chloroquine resistance transporter. Nat Commun. 2020 Dec;11(1):3922.
- Afoakwah R, Boampong JN, Egyir-Yawson A, Nwaefuna EK, Verner ON, Asare KK. High prevalence of PfCRT K76T mutation in Plasmodium falciparum isolates in Ghana. Acta Trop. 2014 Aug;136:32–6.
- Johnson DJ, Fidock DA, Mungthin M, Lakshmanan V, Sidhu ABS, Bray PG, et al. Evidence for a Central Role for PfCRT in Conferring Plasmodium falciparum Resistance to Diverse Antimalarial Agents. Mol Cell. 2004 Sep;15(6):867–77.
- Veiga M, Dhingra S, Henrich P, et al. Globally prevalent PfMDR1 mutations modulate Plasmodium falciparum susceptibility to artemisinin-based combination therapies. Nat Commun. 2016 May;7(11553).
- Emilia AE, Victoria UC, Christian MA, et al. Prevalence of Pfmdr 1 N86Y and Y184F Alleles is Associated with Recurrent Parasitemia following Treatment of Uncomplicated Malaria with Artemether-Lumefantrine in Nigerian Patients. JAPS. 2016 Apr;6(4):15-21.
- Jiang T, Chen T, Fu H, et al. High prevalence of Pfdhfr–Pfdhps quadruple mutations associated with sulfadoxine–pyrimethamine resistance in Plasmodium falciparum isolates from Bioko Island, Equatorial Guinea. Malar J. 2019 Mar;18(101).
- Siddiqui FA, Cabrera M, Wang M, Brashear A, Kemirembe K, Wang Z, et al. Plasmodium falciparum falcipain-2a polymorphisms in Southeast Asia and their association with artemisinin resistance. J Infect Dis. 2018 Aug;218(3):434-42.
- Conrad MD, Bigira V, Kapisi J, Muhindo M, Kamya MR, Havlir DV, et al.. Polymorphisms in K13 and falcipain-2 associated with artemisinin resistance are not prevalent in Plasmodium falciparum isolated from Ugandan children. PLoS One. 2014 Aug;9(8):e105690
- Salem MS, Lekweiry KM, Bouchiba H, Pascual A, Pradines B, Boukhary AO, et al.. Characterization of Plasmodium falciparum genes associated with drug resistance in Hodh Elgharbi, a malaria hotspot near Malian–Mauritanian border. Malar J. 2017;16:140.
- Ecker A, Lehane AM, Fidock DA. Molecular markers of Plasmodium resistance to antimalarials. In: Staines HM, Krishna S, editors. Treatment and prevention of malaria: antimalarial drug chemistry, action and use. Berlin: Springer; 2012. p. 249–80.
- Grais RF, Laminou IM, Woi-Messe L, Makarimi R, Bouriema SH, Langendorf C, et al. Molecular markers of resistance to amodiaquine plus sulfadoxine–pyrimethamine in an area with seasonal malaria chemoprevention in south central Niger. Malar J. 2018;17:98.
Recommended Citation
Zahra, Raihanny Andrea; Fanshur, Ananda Maulana; Saraswati, Aurelia Maria Prajna; and Rahmani, Nurul Inayah
(2023)
"Single Nucleotide Polymorphisms in Plasmodium falciparum Genes: Their Roles in Antimalarial Drugs Resistance and Recent Detection Strategies,"
Indonesian Journal of Medical Chemistry and Bioinformatics: Vol. 2:
No.
1, Article 1.
DOI: 10.7454/ijmcb.v2i1.1005
Available at:
https://scholarhub.ui.ac.id/ijmcb/vol2/iss1/1