Genomics & Informatics

Korea Genome Organization (한국유전체학회)
권호 표지
DOI QR코드

DOI QR Code

Analysis of gene expression profiles to study malaria vaccine dose efficacy and immune response modulation

  • Received : 2022.07.29
  • Accepted : 2022.09.04
  • Published : 2022.09.30
Download PDF
⟨ Previous Next ⟩

Abstract

Malaria is a life-threatening disease, and Africa is still one of the most affected endemic regions despite years of policy to limit infection and transmission rates. Further, studies into the variable efficacy of the vaccine are needed to provide a better understanding of protective immunity. Thus, the current study is designed to delineate the effect of each dose of vaccine on the transcriptional profiles of subjects to determine its efficacy and understand the molecular mechanisms underlying the protection this vaccine provides. Here, we used gene expression profiles of pre and post-vaccination patients after various doses of RTS,S based on samples collected from the Gene Expression Omnibus datasets. Subsequently, differential gene expression analysis using edgeR revealed the significantly (false discovery rate < 0.005) 158 downregulated and 61 upregulated genes between control vs. controlled human malaria infection samples. Further, enrichment analysis of significant genes delineated the involvement of CCL8, CXCL10, CXCL11, XCR1, CSF3, IFNB1, IFNE, IL12B, IL22, IL6, IL27, etc., genes which found to be upregulated after earlier doses but downregulated after the 3rd dose in cytokine-chemokine pathways. Notably, we identified 13 cytokine genes whose expression significantly varied during three doses. Eventually, these findings give insight into the dual role of cytokine responses in malaria pathogenesis. The variations in their expression patterns after various doses of vaccination are linked to the protection as it decreases the severe inflammatory effects in malaria patients. This study will be helpful in designing a better vaccine against malaria and understanding the functions of cytokine response as well.

Keywords

Acknowledgement

We thankfully acknowledge Pine Biotech for helping us with their efforts on this project. The groundwork of this project was completed during the Omics Logic Internship Program. The processing and visualization pipelines were generated with the T-BioInfo Server.

References

  1. Marsh K, Forster D, Waruiru C, Mwangi I, Winstanley M, Marsh V, et al. Indicators of life-threatening malaria in African children. N Engl J Med 1995;332:1399-1404. https://doi.org/10.1056/NEJM199505253322102
  2. World Health Oragnization. WHO International Travel and Health publication 2014, chapter 7: Malaria. Geneva: World Health Oragniazation, 2014.
  3. World Health Oragnization. World malaria report 2019. Geneva: World Health Oragniazation, 2019.
  4. Wassmer SC, Taylor TE, Rathod PK, Mishra SK, Mohanty S, Arevalo-Herrera M, et al. Investigating the pathogenesis of severe malaria: a multidisciplinary and cross-geographical approach. Am J Trop Med Hyg 2015;93:42-56. https://doi.org/10.4269/ajtmh.14-0841
  5. Kwiatkowski D, Hill AV, Sambou I, Twumasi P, Castracane J, Manogue KR, et al. TNF concentration in fatal cerebral, non-fatal cerebral, and uncomplicated Plasmodium falciparum malaria. Lancet 1990;336:1201-1204. https://doi.org/10.1016/0140-6736(90)92827-5
  6. Duffy PE, Patrick Gorres J. Malaria vaccines since 2000: progress, priorities, products. NPJ Vaccines 2020;5:48. https://doi.org/10.1038/s41541-020-0196-3
  7. Millet P. Current status and prospects of malaria vaccines. J Travel Med 1995;2:96-98. https://doi.org/10.1111/j.1708-8305.1995.tb00634.x
  8. Kester KE, Cummings JF, Ofori-Anyinam O, Ockenhouse CF, Krzych U, Moris P, et al. Randomized, double-blind, phase 2a trial of falciparum malaria vaccines RTS,S/AS01B and RTS,S/ AS02A in malaria-naive adults: safety, efficacy, and immunologic associates of protection. J Infect Dis 2009;200:337-346. https://doi.org/10.1086/600120
  9. Ockenhouse CF, Regules J, Tosh D, Cowden J, Kathcart A, Cummings J, et al. Ad35.CS.01-RTS,S/AS01 heterologous prime boost vaccine efficacy against sporozoite challenge in healthy malaria-naive adults. PLoS One 2015;10:e0131571. https://doi.org/10.1371/journal.pone.0131571
  10. Rampling T, Ewer KJ, Bowyer G, Bliss CM, Edwards NJ, Wright D, et al. Safety and high level efficacy of the combination malaria vaccine regimen of RTS,S/AS01B with chimpanzee adenovirus 63 and modified vaccinia ankara vectored vaccines expressing ME-TRAP. J Infect Dis 2016;214:772-781. https://doi.org/10.1093/infdis/jiw244
  11. Arora N, L CA, Pannu AK. Towards eradication of malaria: is the WHO's RTS,S/AS01 vaccination effective enough? Risk Manag Healthc Policy 2021;14:1033-1039. https://doi.org/10.2147/RMHP.S219294
  12. Mahmoudi S, Keshavarz H. Efficacy of phase 3 trial of RTS, S/ AS01 malaria vaccine: the need for an alternative development plan. Hum Vaccin Immunother 2017;13:2098-2101. https://doi.org/10.1080/21645515.2017.1295906
  13. Regules JA, Cicatelli SB, Bennett JW, Paolino KM, Twomey PS, Moon JE, et al. Fractional third and fourth dose of RTS,S/AS01 malaria candidate vaccine: a phase 2a controlled human malaria parasite infection and immunogenicity study. J Infect Dis 2016;214:762-771. https://doi.org/10.1093/infdis/jiw237
  14. Moncunill G, Scholzen A, Mpina M, Nhabomba A, Hounkpatin AB, Osaba L, et al. Antigen-stimulated PBMC transcriptional protective signatures for malaria immunization. Sci Transl Med 2020;12:e. aay8924. https://doi.org/10.1126/scitranslmed.aay8924
  15. Zagury D, Burny A, Gallo RC. Toward a new generation of vaccines: the anti-cytokine therapeutic vaccines. Proc Natl Acad Sci U S A 2001;98:8024-8029. https://doi.org/10.1073/pnas.141224798
  16. Kazmin D, Nakaya HI, Lee EK, Johnson MJ, van der Most R, van den Berg RA, et al. Systems analysis of protective immune responses to RTS,S malaria vaccination in humans. Proc Natl Acad Sci U S A 2017;114:2425-2430. https://doi.org/10.1073/pnas.1621489114
  17. Du Y, Thompson EG, Muller J, Valvo J, Braun J, Shankar S, et al. The ratiometric transcript signature MX2/GPR183 is consistently associated with RTS,S-mediated protection against controlled human malaria infection. Front Immunol 2020;11:669. https://doi.org/10.3389/fimmu.2020.00669
  18. Yeung KY, Ruzzo WL. Principal component analysis for clustering gene expression data. Bioinformatics 2001;17:763-774. https://doi.org/10.1093/bioinformatics/17.9.763
  19. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010;26:139-140. https://doi.org/10.1093/bioinformatics/btp616
  20. Li W. Volcano plots in analyzing differential expressions with mRNA microarrays. J Bioinform Comput Biol 2012;10:1231003. https://doi.org/10.1142/S0219720012310038
  21. Tinsley HE, Brown SD. Handbook of Applied Multivariate Statistics and Mathematical Modeling. San Diego: Academic Press, 2000. pp. xxi-xxiii.
  22. Huang DW, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, et al. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res 2007;35:W169-W175. https://doi.org/10.1093/nar/gkm415
  23. Huang R, Grishagin I, Wang Y, Zhao T, Greene J, Obenauer JC, et al. The NCATS BioPlanet: an integrated platform for exploring the universe of cellular signaling pathways for toxicology, systems biology, and chemical genomics. Front Pharmacol 2019;10:445. https://doi.org/10.3389/fphar.2019.00445
  24. Kanehisa M, Sato Y, Furumichi M, Morishima K, Tanabe M. New approach for understanding genome variations in KEGG. Nucleic Acids Res 2019;47:D590-D595. https://doi.org/10.1093/nar/gky962
  25. Clem AS. Fundamentals of vaccine immunology. J Glob Infect Dis 2011;3:73-78. https://doi.org/10.4103/0974-777X.77299
  26. Broadbent KM, Park D, Wolf AR, Van Tyne D, Sims JS, Ribacke U, et al. A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs. Genome Biol 2011;12:R56. https://doi.org/10.1186/gb-2011-12-6-r56
  27. Amit-Avraham I, Pozner G, Eshar S, Fastman Y, Kolevzon N, Yavin E, et al. Antisense long noncoding RNAs regulate var gene activation in the malaria parasite Plasmodium falciparum. Proc Natl Acad Sci U S A 2015;112:E982-E991.
  28. Sherman BT, Lane HC, Lempicki RA. Identifying biological themes within lists of genes with EASE. Genome Biol 2003;4:R70. https://doi.org/10.1186/gb-2003-4-10-r70
  29. Huang DW, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, et al. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol 2007;8:R183. https://doi.org/10.1186/gb-2007-8-9-r183
  30. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009;4:44-57. https://doi.org/10.1038/nprot.2008.211
  31. Ioannidis LJ, Nie CQ, Hansen DS. The role of chemokines in severe malaria: more than meets the eye. Parasitology 2014;141:602-613. https://doi.org/10.1017/S0031182013001984
  32. Clark IA, Rockett KA. The cytokine theory of human cerebral malaria. Parasitol Today 1994;10:410-412. https://doi.org/10.1016/0169-4758(94)90237-2
  33. Prakash D, Fesel C, Jain R, Cazenave PA, Mishra GC, Pied S. Clusters of cytokines determine malaria severity in Plasmodium falciparum-infected patients from endemic areas of Central India. J Infect Dis 2006;194:198-207. https://doi.org/10.1086/504720
  34. Clark IA, Budd AC, Alleva LM, Cowden WB. Human malarial disease: a consequence of inflammatory cytokine release. Malar J 2006;5:85. https://doi.org/10.1186/1475-2875-5-85
  35. Olson TS, Ley K. Chemokines and chemokine receptors in leukocyte trafficking. Am J Physiol Regul Integr Comp Physiol 2002;283:R7-R28. https://doi.org/10.1152/ajpregu.00738.2001
  36. Biankin AV, Kench JG, Colvin EK, Segara D, Scarlett CJ, Nguyen NQ, et al. Expression of S100A2 calcium-binding protein predicts response to pancreatectomy for pancreatic cancer. Gastroenterology 2009;137:558-568. https://doi.org/10.1053/j.gastro.2009.04.009
  37. Boeckel GR, Ehrlich BE. NCS-1 is a regulator of calcium signaling in health and disease. Biochim Biophys Acta Mol Cell Res 2018;1865:1660-1667. https://doi.org/10.1016/j.bbamcr.2018.05.005
  38. Morino H, Matsuda Y, Muguruma K, Miyamoto R, Ohsawa R, Ohtake T, et al. A mutation in the low voltage-gated calcium channel CACNA1G alters the physiological properties of the channel, causing spinocerebellar ataxia. Mol Brain 2015;8:89. https://doi.org/10.1186/s13041-015-0180-4
  39. Saraswati S, Adolfsen B, Littleton JT. Characterization of the role of the Synaptotagmin family as calcium sensors in facilitation and asynchronous neurotransmitter release. Proc Natl Acad Sci U S A 2007;104:14122-14127. https://doi.org/10.1073/pnas.0706711104
  40. Lang B, Newbold CI, Williams G, Peshu N, Marsh K, Newton CR. Antibodies to voltage-gated calcium channels in children with falciparum malaria. J Infect Dis 2005;191:117-121. https://doi.org/10.1086/426512
  41. Lyke KE, Burges R, Cissoko Y, Sangare L, Dao M, Diarra I, et al. Serum levels of the proinflammatory cytokines interleukin-1 beta (IL-1beta), IL-6, IL-8, IL-10, tumor necrosis factor alpha, and IL-12(p70) in Malian children with severe Plasmodium falciparum malaria and matched uncomplicated malaria or healthy controls. Infect Immun 2004;72:5630-5637. https://doi.org/10.1128/IAI.72.10.5630-5637.2004
  42. Naka I, Patarapotikul J, Tokunaga K, Hananantachai H, Tsuchiya N, Ohashi J. A replication study of the association between the IL12B promoter allele CTCTAA and susceptibility to cerebral malaria in Thai population. Malar J 2009;8:290. https://doi.org/10.1186/1475-2875-8-290
  43. Kern P, Hemmer CJ, Van Damme J, Gruss HJ, Dietrich M. Elevated tumor necrosis factor alpha and interleukin-6 serum levels as markers for complicated Plasmodium falciparum malaria. Am J Med 1989;87:139-143. https://doi.org/10.1016/S0002-9343(89)80688-6
  44. Mshana RN, Boulandi J, Mshana NM, Mayombo J, Mendome G. Cytokines in the pathogenesis of malaria: levels of IL-I beta, IL-4, IL-6, TNF-alpha and IFN-gamma in plasma of healthy individuals and malaria patients in a holoendemic area. J Clin Lab Immunol 1991;34:131-139.
  45. Wenisch C, Linnau KF, Looaresuwan S, Rumpold H. Plasma levels of the interleukin-6 cytokine family in persons with severe Plasmodium falciparum malaria. J Infect Dis 1999;179:747-750. https://doi.org/10.1086/314630
  46. Boldt ABW, van Tong H, Grobusch MP, Kalmbach Y, Dzeing Ella A, Kombila M, et al. The blood transcriptome of childhood malaria. EBioMedicine 2019;40:614-625. https://doi.org/10.1016/j.ebiom.2018.12.055
  47. Cockburn IA, Seder RA. Malaria prevention: from immunological concepts to effective vaccines and protective antibodies. Nat Immunol 2018;19:1199-1211. https://doi.org/10.1038/s41590-018-0228-6
  48. Kumar A, Thota V, Dee L, Olson J, Uretz E, Parrillo JE. Tumor necrosis factor alpha and interleukin 1beta are responsible for in vitro myocardial cell depression induced by human septic shock serum. J Exp Med 1996;183:949-958. https://doi.org/10.1084/jem.183.3.949
  49. Odeh M. Tumor necrosis factor-alpha as a myocardial depressant substance. Int J Cardiol 1993;42:231-238. https://doi.org/10.1016/0167-5273(93)90053-J
  50. Pathan N, Hemingway CA, Alizadeh AA, Stephens AC, Boldrick JC, Oragui EE, et al. Role of interleukin 6 in myocardial dysfunction of meningococcal septic shock. Lancet 2004;363:203-209. https://doi.org/10.1016/S0140-6736(03)15326-3
  51. Idda ML, Lodde V, Galleri G, Martindale JL, Munk R, Abdelmohsen K, et al. NF90 regulation of immune factor expression in response to malaria antigens. Cell Cycle 2019;18:708-722. https://doi.org/10.1080/15384101.2019.1580496
  52. Che JN, Nmorsi OP, Nkot BP, Isaac C, Okonkwo BC. Chemokines responses to Plasmodium falciparum malaria and co-infections among rural Cameroonians. Parasitol Int 2015;64:139-144. https://doi.org/10.1016/j.parint.2014.11.003
  53. Kwiatkowski DP. How malaria has affected the human genome and what human genetics can teach us about malaria. Am J Hum Genet 2005;77:171-192. https://doi.org/10.1086/432519
  54. Nordor AV, Bellet D, Siwo GH. Cancer-malaria: hidden connections. Open Biol 2018;8:180127. https://doi.org/10.1098/rsob.180127
  55. Kaushansky A, Ye AS, Austin LS, Mikolajczak SA, Vaughan AM, Camargo N, et al. Suppression of host p53 is critical for Plasmodium liver-stage infection. Cell Rep 2013;3:630-637. https://doi.org/10.1016/j.celrep.2013.02.010
  56. McNamara HA, Idris AH, Sutton HJ, Vistein R, Flynn BJ, Cai Y, et al. Antibody feedback limits the expansion of B cell responses to malaria vaccination but drives diversification of the humoral response. Cell Host Microbe 2020;28:572-585. https://doi.org/10.1016/j.chom.2020.07.001
  57. Torgbor C, Awuah P, Deitsch K, Kalantari P, Duca KA, Thorley-Lawson DA. A multifactorial role for P. falciparum malaria in endemic Burkitt's lymphoma pathogenesis. PLoS Pathog 2014; 10:e1004170. https://doi.org/10.1371/journal.ppat.1004170
  58. Brochet M, Billker O. Calcium signalling in malaria parasites. Mol Microbiol 2016;100:397-408. https://doi.org/10.1111/mmi.13324
  59. Soni R, Sharma D, Rai P, Sharma B, Bhatt TK. Signaling strategies of malaria parasite for its survival, proliferation, and infection during erythrocytic stage. Front Immunol 2017;8:349.
  60. Almeida ME, Vasconcelos MG, Tarrago AM, Mariuba LA. Circumsporozoite surface protein-based malaria vaccines: a review. Rev Inst Med Trop Sao Paulo 2021;63:e11. https://doi.org/10.1590/s1678-9946202163011
  61. Gordon DM, McGovern TW, Krzych U, Cohen JC, Schneider I, LaChance R, et al. Safety, immunogenicity, and efficacy of a recombinantly produced Plasmodium falciparum circumsporozoite protein-hepatitis B surface antigen subunit vaccine. J Infect Dis 1995;171:1576-1585. https://doi.org/10.1093/infdis/171.6.1576
  62. Bojang KA, Milligan PJ, Pinder M, Vigneron L, Alloueche A, Kester KE, et al. Efficacy of RTS,S/AS02 malaria vaccine against Plasmodium falciparum infection in semi-immune adult men in The Gambia: a randomised trial. Lancet 2001;358:1927-1934. https://doi.org/10.1016/S0140-6736(01)06957-4
  63. Hunt NH, Grau GE. Cytokines: accelerators and brakes in the pathogenesis of cerebral malaria. Trends Immunol 2003;24:491-499. https://doi.org/10.1016/S1471-4906(03)00229-1
  64. Franklin BS, Parroche P, Ataide MA, Lauw F, Ropert C, de Oliveira RB, et al. Malaria primes the innate immune response due to interferon-gamma induced enhancement of toll-like receptor expression and function. Proc Natl Acad Sci U S A 2009;106:5789-5794. https://doi.org/10.1073/pnas.0809742106
  65. Scharte M, Fink MP. Red blood cell physiology in critical illness. Crit Care Med 2003;31(12 Suppl):S651-S657. https://doi.org/10.1097/01.CCM.0000098036.90796.ED
  66. English M, Muambi B, Mithwani S, Marsh K. Lactic acidosis and oxygen debt in African children with severe anaemia. QJM 1997;90:563-569. https://doi.org/10.1093/qjmed/90.9.563
  67. Kumar R, Ng S, Engwerda C. The role of IL-10 in malaria: a double edged sword. Front Immunol 2019;10:229. https://doi.org/10.3389/fimmu.2019.00229
  68. Kany S, Vollrath JT, Relja B. Cytokines in inflammatory disease. Int J Mol Sci 2019;20:6008. https://doi.org/10.3390/ijms20236008