Exome-wide association study reveals largely distinct gene sets underlying specific resistance to dengue virus types 1 and 3 in Aedes aegypti
Autoři:
Laura B. Dickson aff001; Sarah H. Merkling aff001; Mathieu Gautier aff002; Amine Ghozlane aff003; Davy Jiolle aff001; Christophe Paupy aff004; Diego Ayala aff004; Isabelle Moltini-Conclois aff001; Albin Fontaine aff001; Louis Lambrechts aff001
Působiště autorů:
Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
aff001; CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
aff002; Hub de Bioinformatique et Biostatistique–Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
aff003; MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
aff004; Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
aff005
Vyšlo v časopise:
Exome-wide association study reveals largely distinct gene sets underlying specific resistance to dengue virus types 1 and 3 in Aedes aegypti. PLoS Genet 16(5): e32767. doi:10.1371/journal.pgen.1008794
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1008794
Souhrn
Although specific interactions between host and pathogen genotypes have been well documented in invertebrates, the identification of host genes involved in discriminating pathogen genotypes remains a challenge. In the mosquito Aedes aegypti, the main dengue virus (DENV) vector worldwide, statistical associations between host genetic markers and DENV types or strains were previously detected, but the host genes underlying this genetic specificity have not been identified. In particular, it is unknown whether DENV type- or strain-specific resistance relies on allelic variants of the same genes or on distinct gene sets. Here, we investigated the genetic architecture of DENV resistance in a population of Ae. aegypti from Bakoumba, Gabon, which displays a stronger resistance phenotype to DENV type 1 (DENV-1) than to DENV type 3 (DENV-3) infection. Following experimental exposure to either DENV-1 or DENV-3, we sequenced the exomes of large phenotypic pools of mosquitoes that are either resistant or susceptible to each DENV type. Using variation in single-nucleotide polymorphism (SNP) frequencies among the pools, we computed empirical p values based on average gene scores adjusted for the differences in SNP counts, to identify genes associated with infection in a DENV type-specific manner. Among the top 5% most significant genes, 263 genes were significantly associated with resistance to both DENV-1 and DENV-3, 287 genes were only associated with DENV-1 resistance and 290 were only associated with DENV-3 resistance. The shared significant genes were enriched in genes with ATP binding activity and sulfur compound transmembrane transporter activity, whereas the genes uniquely associated with DENV-3 resistance were enriched in genes with zinc ion binding activity. Together, these results indicate that specific resistance to different DENV types relies on largely non-overlapping sets of genes in this Ae. aegypti population and pave the way for further mechanistic studies.
Klíčová slova:
Aedes aegypti – Dengue virus – Gabon – Gene pool – Host-pathogen interactions – Mosquitoes – Population genetics – Invertebrate genetics
Zdroje
1. Lambrechts L. Dissecting the genetic architecture of host-pathogen specificity. PLoS Pathog. 2010;6(8):e1001019. doi: 10.1371/journal.ppat.1001019 20700450.
2. Carius HJ, Little TJ, Ebert D. Genetic variation in a host-parasite association: potential for coevolution and frequency-dependent selection. Evolution. 2001;55(6):1136–45. doi: 10.1111/j.0014-3820.2001.tb00633.x 11475049.
3. Schmid-Hempel P. On the evolutionary ecology of host-parasite interactions: addressing the question with regard to bumblebees and their parasites. Naturwissenschaften. 2001;88(4):147–58. Epub 2001/08/02. doi: 10.1007/s001140100222 11480702.
4. Schulenburg H, Ewbank JJ. Diversity and specificity in the interaction between Caenorhabditis elegans and the pathogen Serratia marcescens. BMC Evol Biol. 2004;4(1):49. doi: 10.1186/1471-2148-4-49 15555070.
5. Harris C, Lambrechts L, Rousset F, Abate L, Nsango SE, Fontenille D, et al. Polymorphisms in Anopheles gambiae Immune Genes Associated with Natural Resistance to Plasmodium falciparum. PLoS Pathog. 2010;6(9). doi: 10.1371/journal.ppat.1001112 20862317.
6. Lambrechts L, Halbert J, Durand P, Gouagna LC, Koella JC. Host genotype by parasite genotype interactions underlying the resistance of anopheline mosquitoes to Plasmodium falciparum. Malar J. 2005;4(1):3. doi: 10.1186/1475-2875-4-3 15644136.
7. de Roode JC, Altizer S. Host-parasite genetic interactions and virulence-transmission relationships in natural populations of Monarch butterflies. Evolution. 2009;64(2):502–14. doi: 10.1111/j.1558-5646.2009.00845.x 19796153.
8. Luijckx P, Ben-Ami F, Mouton L, Du Pasquier L, Ebert D. Cloning of the unculturable parasite Pasteuria ramosa and its Daphnia host reveals extreme genotype-genotype interactions. Ecol Lett. 2011;14(2):125–31. doi: 10.1111/j.1461-0248.2010.01561.x 21091597.
9. Little TJ, Hultmark D, Read AF. Invertebrate immunity and the limits of mechanistic immunology. Nat Immunol. 2005;6(7):651–4. doi: 10.1038/ni1219 15970937.
10. Schulenburg H, Boehnisch C, Michiels NK. How do invertebrates generate a highly specific innate immune response? Mol Immunol. 2007;44(13):3338–44. Epub 2007/03/30. doi: 10.1016/j.molimm.2007.02.019 17391764.
11. Dong Y, Taylor HE, Dimopoulos G. AgDscam, a hypervariable immunoglobulin domain-containing receptor of the Anopheles gambiae innate immune system. PLoS Biol. 2006;4(7):e229. Epub 2006/06/16. doi: 10.1371/journal.pbio.0040229 16774454.
12. Watson F, Püttmann-Holgado R, Thomas F, Lamar D, Hughes M, Kondo M, et al. Extensive diversity of Ig-superfamily proteins in the immune system of insects. Science. 2005;309(5742):1874–8. doi: 10.1126/science.1116887 16109846
13. Koch H, Schmid-Hempel P. Gut microbiota instead of host genotype drive the specificity in the interaction of a natural host-parasite system. Ecol Lett. 2012;15(10):1095–103. Epub 2012/07/07. doi: 10.1111/j.1461-0248.2012.01831.x 22765311.
14. Barribeau SM, Sadd BM, du Plessis L, Schmid-Hempel P. Gene expression differences underlying genotype-by-genotype specificity in a host-parasite system. Proc Natl Acad Sci U S A. 2014;111(9):3496–501. Epub 2014/02/20. doi: 10.1073/pnas.1318628111 24550506.
15. Fansiri T, Fontaine A, Diancourt L, Caro V, Thaisomboonsuk B, Richardson JH, et al. Genetic Mapping of Specific Interactions between Aedes aegypti Mosquitoes and Dengue Viruses. PLoS Genet. 2013;9(8):e1003621. Epub 2013/08/13. doi: 10.1371/journal.pgen.1003621 23935524.
16. Lambrechts L, Quillery E, Noel V, Richardson JH, Jarman RG, Scott TW, et al. Specificity of resistance to dengue virus isolates is associated with genotypes of the mosquito antiviral gene Dicer-2. Proc Biol Sci. 2013;280(1751):20122437. Epub 2012/11/30. doi: 10.1098/rspb.2012.2437 23193131.
17. Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, et al. Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature. 2018;563(7732):501–7. Epub 2018/11/16. doi: 10.1038/s41586-018-0692-z 30429615.
18. Hauton C, Smith VJ. Adaptive immunity in invertebrates: a straw house without a mechanistic foundation. Bioessays. 2007;29(11):1138–46. Epub 2007/10/16. doi: 10.1002/bies.20650 17935208.
19. Little TJ, Colegrave N, Sadd BM, Schmid-Hempel P. Studying immunity at the whole organism level. Bioessays. 2008;30(4):404–5; Epub 2008/03/19. doi: 10.1002/bies.20738 18348252.
20. Schmid-Hempel P. Natural insect host-parasite systems show immune priming and specificity: puzzles to be solved. Bioessays. 2005;27(10):1026–34. doi: 10.1002/bies.20282 16163710.
21. Lambrechts L. Quantitative genetics of Aedes aegypti vector competence for dengue viruses: towards a new paradigm? Trends Parasitol. 2011;27(3):111–4. doi: 10.1016/j.pt.2010.12.001 21215699.
22. Lambrechts L, Chevillon C, Albright RG, Thaisomboonsuk B, Richardson JH, Jarman RG, et al. Genetic specificity and potential for local adaptation between dengue viruses and mosquito vectors. BMC Evol Biol. 2009;9:160. doi: 10.1186/1471-2148-9-160 19589156.
23. Katzelnick LC, Fonville JM, Gromowski GD, Bustos Arriaga J, Green A, James SL, et al. Dengue viruses cluster antigenically but not as discrete serotypes. Science. 2015;349(6254):1338–43. Epub 2015/09/19. doi: 10.1126/science.aac5017 26383952.
24. Gloria-Soria A, Ayala D, Bheecarry A, Calderon-Arguedas O, Chadee DD, Chiappero M, et al. Global genetic diversity of Aedes aegypti. Mol Ecol. 2016;25(21):5377–95. doi: 10.1111/mec.13866 27671732.
25. Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, et al. The global distribution and burden of dengue. Nature. 2013;496(7446):504–7. Epub 2013/04/09. doi: 10.1038/nature12060 23563266.
26. Shaw WR, Catteruccia F. Vector biology meets disease control: using basic research to fight vector-borne diseases. Nat Microbiol. 2019;4(1):20–34. Epub 2018/08/29. doi: 10.1038/s41564-018-0214-7 30150735.
27. Kean J, Rainey SM, McFarlane M, Donald CL, Schnettler E, Kohl A, et al. Fighting Arbovirus Transmission: Natural and Engineered Control of Vector Competence in Aedes Mosquitoes. Insects. 2015;6(1):236–78. Epub 2015/10/16. doi: 10.3390/insects6010236 26463078.
28. Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, et al. Genome sequence of Aedes aegypti, a major arbovirus vector. Science. 2007;316(5832):1718–23. doi: 10.1126/science.1138878 17510324.
29. Schlotterer C, Tobler R, Kofler R, Nolte V. Sequencing pools of individuals—mining genome-wide polymorphism data without big funding. Nat Rev Genet. 2014;15(11):749–63. Epub 2014/09/24. doi: 10.1038/nrg3803 25246196.
30. Sham P, Bader JS, Craig I, O'Donovan M, Owen M. DNA Pooling: a tool for large-scale association studies. Nat Rev Genet. 2002;3(11):862–71. Epub 2002/11/05. doi: 10.1038/nrg930 12415316.
31. Gautier M. Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates. Genetics. 2015;201(4):1555–79. Epub 2015/10/21. doi: 10.1534/genetics.115.181453 26482796.
32. Olazcuaga L, Loiseau A, Parrinello H, Paris M, Fraimout A, Guedot C, et al. A whole-genome scan for association with invasion success in the fruit fly Drosophila suzukii using contrasts of allele frequencies corrected for population structure. Mol Biol Evol. msaa098. In press. Epub 2020/04/17. https://doi.org/10.1093/molbev/msaa098
33. Warr A, Robert C, Hume D, Archibald A, Deeb N, Watson M. Exome Sequencing: Current and Future Perspectives. G3. 2015;5(8):1543–50. Epub 2015/07/04. doi: 10.1534/g3.115.018564 26139844.
34. Crawford JE, Alves JM, Palmer WJ, Day JP, Sylla M, Ramasamy R, et al. Population genomics reveals that an anthropophilic population of Aedes aegypti mosquitoes in West Africa recently gave rise to American and Asian populations of this major disease vector. BMC Biol. 2017;15(1):16. doi: 10.1186/s12915-017-0351-0 28241828.
35. Dickson LB, Campbell CL, Juneja P, Jiggins FM, Sylla M, Black WC. Exon-Enriched Libraries Reveal Large Genic Differences Between Aedes aegypti from Senegal, West Africa, and Populations Outside Africa. G3. 2017;7(2):571–82. doi: 10.1534/g3.116.036053 28007834.
36. Juneja P, Ariani CV, Ho YS, Akorli J, Palmer WJ, Pain A, et al. Exome and Transcriptome Sequencing of Aedes aegypti Identifies a Locus That Confers Resistance to Brugia malayi and Alters the Immune Response. PLoS Pathog. 2015;11(3):e1004765. Epub 2015/03/31. doi: 10.1371/journal.ppat.1004765 25815506.
37. Black WC, Bennett KE, Gorrochotegui-Escalante N, Barillas-Mury CV, Fernandez-Salas I, de Lourdes Munoz M, et al. Flavivirus susceptibility in Aedes aegypti. Arch Med Res. 2002;33(4):379–88. doi: 10.1016/s0188-4409(02)00373-9 12234528.
38. Agrawal A, Lively CM. Infection genetics: gene-for-gene versus matching-alleles models and all points in between. Evol Ecol Res. 2002;4:79–90.
39. Kubinak JL, Ruff JS, Hyzer CW, Slev PR, Potts WK. Experimental viral evolution to specific host MHC genotypes reveals fitness and virulence trade-offs in alternative MHC types. Proc Natl Acad Sci U S A. 2012;109(9):3422–7. Epub 2012/02/11. doi: 10.1073/pnas.1112633109 22323587.
40. Bento G, Routtu J, Fields PD, Bourgeois Y, Du Pasquier L, Ebert D. The genetic basis of resistance and matching-allele interactions of a host-parasite system: The Daphnia magna-Pasteuria ramosa model. PLoS Genet. 2017;13(2):e1006596. Epub 2017/02/22. doi: 10.1371/journal.pgen.1006596 28222092.
41. Luijckx P, Fienberg H, Duneau D, Ebert D. A matching-allele model explains host resistance to parasites. Curr Biol. 2013;23(12):1085–8. Epub 2013/05/28. doi: 10.1016/j.cub.2013.04.064 23707426.
42. Bartha I, Carlson JM, Brumme CJ, McLaren PJ, Brumme ZL, John M, et al. A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control. eLife. 2013;2:e01123. Epub 2013/10/31. doi: 10.7554/eLife.01123 24171102.
43. Wang M, Roux F, Bartoli C, Huard-Chauveau C, Meyer C, Lee H, et al. Two-way mixed-effects methods for joint association analysis using both host and pathogen genomes. Proc Natl Acad Sci U S A. 2018;115(24):E5440–E9. Epub 2018/06/01. doi: 10.1073/pnas.1710980115 29848634.
44. Mitri C, Jacques JC, Thiery I, Riehle MM, Xu J, Bischoff E, et al. Fine pathogen discrimination within the APL1 gene family protects Anopheles gambiae against human and rodent malaria species. PLoS Pathog. 2009;5(9):e1000576. Epub 2009/09/15. doi: 10.1371/journal.ppat.1000576 19750215.
45. Molina-Cruz A, DeJong RJ, Ortega C, Haile A, Abban E, Rodrigues J, et al. Some strains of Plasmodium falciparum, a human malaria parasite, evade the complement-like system of Anopheles gambiae mosquitoes. Proc Natl Acad Sci U S A. 2012;109(28):E1957–62. Epub 2012/05/25. doi: 10.1073/pnas.1121183109 22623529.
46. White BJ, Lawniczak MK, Cheng C, Coulibaly MB, Wilson MD, Sagnon N, et al. Adaptive divergence between incipient species of Anopheles gambiae increases resistance to Plasmodium. Proc Natl Acad Sci U S A. 2010;108(1):244–9. doi: 10.1073/pnas.1013648108 21173248.
47. Bosio CF, Fulton RE, Salasek ML, Beaty BJ, Black WC. Quantitative trait loci that control vector competence for dengue-2 virus in the mosquito Aedes aegypti. Genetics. 2000;156(2):687–98. 11014816.
48. Gomez-Machorro C, Bennett KE, del Lourdes Munoz M, Black WC. Quantitative trait loci affecting dengue midgut infection barriers in an advanced intercross line of Aedes aegypti. Insect Mol Biol. 2004;13(6):637–48. doi: 10.1111/j.0962-1075.2004.00522.x 15606812.
49. Wilfert L, Schmid-Hempel P. The genetic architecture of susceptibility to parasites. BMC Evol Biol. 2008;8:187. doi: 10.1186/1471-2148-8-187 18590517.
50. Hall AB, Basu S, Jiang X, Qi Y, Timoshevskiy VA, Biedler JK, et al. A male-determining factor in the mosquito Aedes aegypti. Science. 2015;348(6240):1268–70. Epub 2015/05/23. doi: 10.1126/science.aaa2850 25999371.
51. Fontaine A, Filipovic I, Fansiri T, Hoffmann AA, Cheng C, Kirkpatrick M, et al. Extensive Genetic Differentiation between Homomorphic Sex Chromosomes in the Mosquito Vector, Aedes aegypti. Genome biology and evolution. 2017;9(9):2322–35. doi: 10.1093/gbe/evx171 28945882.
52. Merkling SH, Raquin V, Dabo S, Henrion-Lacritick A, Blanc H, Moltini-Conclois I, et al. Tudor-SN Promotes Early Replication of Dengue Virus in the Aedes aegypti Midgut. iScience. 2020;23(2):100870. Epub 2020/02/15. doi: 10.1016/j.isci.2020.100870 32059176.
53. Raquin V, Merkling SH, Gausson V, Moltini-Conclois I, Frangeul L, Varet H, et al. Individual co-variation between viral RNA load and gene expression reveals novel host factors during early dengue virus infection of the Aedes aegypti midgut. PLoS Negl Trop Dis. 2017;11(12):e0006152. Epub 2017/12/21. doi: 10.1371/journal.pntd.0006152 29261661.
54. Kistler KE, Vosshall LB, Matthews BJ. Genome engineering with CRISPR-Cas9 in the mosquito Aedes aegypti. Cell Rep. 2015;11(1):51–60. Epub 2015/03/31. doi: 10.1016/j.celrep.2015.03.009 25818303.
55. Lazarczyk M, Favre M. Role of Zn2+ ions in host-virus interactions. J Virol. 2008;82(23):11486–94. Epub 2008/09/13. doi: 10.1128/JVI.01314-08 18787005.
56. Cogni R, Cao C, Day JP, Bridson C, Jiggins FM. The genetic architecture of resistance to virus infection in Drosophila. Mol Ecol. 2016;25(20):5228–41. Epub 2016/07/28. doi: 10.1111/mec.13769 27460507.
57. Carpenter JA, Hadfield JD, Bangham J, Jiggins FM. Specific interactions between host and parasite genotypes do not act as a constraint on the evolution of antiviral resistance in Drosophila. Evolution. 2012;66(4):1114–25. Epub 2012/04/11. doi: 10.1111/j.1558-5646.2011.01501.x 22486692.
58. Abe H, Ushijima Y, Loembe MM, Bikangui R, Nguema-Ondo G, Mpingabo PI, et al. Re-emergence of dengue virus serotype 3 infections in Gabon in 2016–2017, and evidence for the risk of repeated dengue virus infections. Int J Infect Dis. 2020;91:129–36. Epub 2019/12/11. doi: 10.1016/j.ijid.2019.12.002 31821892.
59. Caron M, Grard G, Paupy C, Mombo IM, Bikie Bi Nso B, Kassa Kassa FR, et al. First evidence of simultaneous circulation of three different dengue virus serotypes in Africa. PLoS ONE. 2013;8(10):e78030. Epub 2013/11/10. doi: 10.1371/journal.pone.0078030 24205075.
60. Fansiri T, Pongsiri A, Klungthong C, Ponlawat A, Thaisomboonsuk B, Jarman RG, et al. No evidence for local adaptation of dengue viruses to mosquito vector populations in Thailand. Evol Appl. 2016;9(4):608–18. Epub 2016/04/22. doi: 10.1111/eva.12360 27099625.
61. Fontaine A, Jiolle D, Moltini-Conclois I, Lequime S, Lambrechts L. Excretion of dengue virus RNA by Aedes aegypti allows non-destructive monitoring of viral dissemination in individual mosquitoes. Sci Rep. 2016;6:24885. Epub 2016/04/28. doi: 10.1038/srep24885 27117953.
62. Payne AF, Binduga-Gajewska I, Kauffman EB, Kramer LD. Quantitation of flaviviruses by fluorescent focus assay. J Virol Methods. 2006;134(1–2):183–9. doi: 10.1016/j.jviromet.2006.01.003 16510196.
63. Black WC, DuTeau NM. RAPD-PCR and SSCP analysis for insect population genetic studies. In: Crampton JM, Beard CB, Louis C, editors. The Molecular Biology of Insect Disease Vectors: A Methods Manual. Dordrecht: Springer Netherlands; 1997. p. 361–73.
64. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20. doi: 10.1093/bioinformatics/btu170 24695404.
65. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM2013. arXiv:1303.3997 [q-bio.GN].
66. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–60. Epub 2009/05/20. doi: 10.1093/bioinformatics/btp324 19451168.
67. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. doi: 10.1093/bioinformatics/btp352 19505943.
68. Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, et al. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009;25(17):2283–5. Epub 2009/06/23. doi: 10.1093/bioinformatics/btp373 19542151.
69. Nicholson G, Smith AV, Jonsson F, Gustafsson O, Stefansson K, Donnelly P. Assessing population differentiation and isolation from single-nucleotide polymorphism data. Journal of the Royal Statistical Society B. 2002;64:695–715.
70. Gautier M, Hocking TD, Foulley JL. A Bayesian outlier criterion to detect SNPs under selection in large data sets. PLoS One. 2010;5(8):e11913. Epub 2010/08/07. doi: 10.1371/journal.pone.0011913 20689851.
71. Sherman BT, Huang da W, Tan Q, Guo Y, Bour S, Liu D, et al. DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC bioinformatics. 2007;8:426. Epub 2007/11/06. doi: 10.1186/1471-2105-8-426 17980028.
72. Supek F, Bosnjak M, Skunca N, Smuc T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One. 2011;6(7):e21800. Epub 2011/07/27. doi: 10.1371/journal.pone.0021800 21789182.
Článek vyšel v časopise
PLOS Genetics
2020 Číslo 5
- Případ Bulovka: Jak postupují jiné nemocnice, aby podobným tragédiím zabránily?
- Jak často se u masových střelců vyskytují duševní choroby?
- FDA varuje před selfmonitoringem cukru pomocí chytrých hodinek. Jak je to v Česku?
- Není statin jako statin aneb praktický přehled rozdílů jednotlivých molekul
- Metamizol jako analgetikum první volby: kdy, pro koho, jak a proč?
Nejčtenější v tomto čísle
- The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2)
- Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus
- Congenital hearing impairment associated with peripheral cochlear nerve dysmyelination in glycosylation-deficient muscular dystrophy
- A new neuropeptide insect parathyroid hormone iPTH in the red flour beetle Tribolium castaneum