1. Chromosomes and Gene Expression
  2. Immunology and Inflammation
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Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria

  1. Jaclyn E Quin
  2. Ioana Bujila
  3. Mariama Chérif
  4. Guillaume S Sanou
  5. Ying Qu
  6. Manijeh Vafa Homann
  7. Anna Rolicka
  8. Sodiomon B Sirima
  9. Mary A O'Connell
  10. Andreas Lennartsson
  11. Marita Troye-Blomberg
  12. Issa Nebie
  13. Ann-Kristin Östlund Farrants  Is a corresponding author
  1. Stockholm University, Sweden
  2. Centre National de Recherche et de Formation sur le Paludisme, Burkina Faso
  3. Université Polytechnique de Bobo-Dioulasso, Burkina Faso
  4. Karolinska Institute, Sweden
  5. Central European Institute of Technology, Czech Republic
Short Report
Cite this article as: eLife 2017;6:e29156 doi: 10.7554/eLife.29156
4 figures, 1 table and 3 additional files

Figures

Figure 1 with 1 supplement
Characteristics of P.falciparum infection in Mossi and Fulani.

(a) Table describing study population. (b) Rate of infection with P.falciparum (Mossi n = 11/22 and Fulani n = 7/34, *p=0.0388). (c) Plasma levels of IgG antibodies to P.falciparum schizont extract antigens. Uninfected (- P.fal) and Infected (+P.fal). n = 11 Mossi – P.falw, 11 Mossi +P.falx, 27 Fulani – P.faly, 7 Fulani +P.falz (median ±min to max; w vs x n.s. p=0.4385, y vs z *p=0.0189, w vs y *p=0.0141, x vs z n.s. p=0.0693, w and x vs y and z ****p<0.001).

https://doi.org/10.7554/eLife.29156.003
Figure 1—figure supplement 1
Schematic representation of workflow.
https://doi.org/10.7554/eLife.29156.004
Figure 2 with 2 supplements
Differential gene expression in Mossi and Fulani following P.falciparum infection.

(a) Volcano plot of expression of individual genes in CD14+ cells (monocytes) of Fulani –P.fal (n = 7) relative to Mossi –P.fal (n = 4). (b) qRT-PCR analysis of selected DE genes (Up: P2RX7, CPVL, FAM26F. Down: ADAM28, ADGRG3, EPBH1) in validation cohort Mossi –P.fal (n = 4) and Fulani –P.fal (n = 10) (mean ±SD). (c) Table of significantly DE genes in CD14+ cells (monocytes) of Fulani –P.fal (n = 7) relative to Mossi –P.fal (n = 4). (d,e) Volcano plot of expression of individual genes in CD14+ cells (monocytes) of Fulani +P.fal (n = 2) relative to Fulani -P.fal (n = 7) (d), and Mossi +P.fal (n = 3) relative to Mossi -P.fal (n = 4) (e). (f) Table of number of DE genes in CD14+ cells (monocytes) of Mossi +P.fal relative to Mossi –P.fal and Fulani +P.fal relative to Fulani –P.fal. (g,h) Volcano plot of expression of individual genes in CD14- cells (lymphocytes) of Fulani +P.fal (n = 3) relative to Fulani -P.fal (n = 5) (g), and Mossi +P.fal (n = 3) relative to Mossi –P.fal (n = 5) (h).

https://doi.org/10.7554/eLife.29156.005
Figure 2—figure supplement 1
Heat map of Pearson correlation between FPKM (fragments per kilobase of transcript per million mapped reads) values of for all CD14+ (monocytes) samples.

Mossi –P.fal (n = 4), Mossi +P.fal (n = 3), Fulani –P.fal (n = 7), Fulani + P.fal (n = 2).

https://doi.org/10.7554/eLife.29156.006
Figure 2—figure supplement 2
Multidimension scaling for all CD14+ (monocytes) samples.

Mossi –P.fal (n = 4), Mossi +P.fal (n = 3), Fulani –P.fal (n = 7), Fulani + P.fal (n = 2).

https://doi.org/10.7554/eLife.29156.007
Figure 3 with 2 supplements
Characteristics and validation of significantly DE genes in CD14+ cells (monocytes) of Fulani+P.fal relative to Fulani -P.fal.

(a) Classification of the most significantly DE genes in CD14+ cells (monocytes) of Fulani +P.fal relative to Fulani –P.fal (adjusted p-value<0.01, 171 genes). (b,c,d) qRT-PCR analysis of selected DE genes, with individual genes relative to –P.fal individuals (b), and combined genes relative to –P.fal (c) or Mossi (d) individuals (Genes: ALDOA, ARID3A, DUSP8, FES, FURIN, GAA, GAPDH, IRF3, IRF5, NFKBIE, OSM, RFXANK, SQSTM1, STRA13, TOLLIP, TRAF7), in validation cohort of Mossi –P.fal (n = 4), Fulani –P.fal (n = 10), Mossi +P.fal (n = 8) and Fulani + P.fal (n = 5) (mean ±SD) (Also see Figure 3—source data 1). (e,f,g) Cytokine levels in blood plasma of Mossi and Fulani individuals following P.falciparum infection. Uninfected (-P.fal) and Infected (+P.fal). n = 11 Mossi –P.falw, 11 Mossi +P.falx, 25 Fulani –P.faly, 9 Fulani + P.falz(e) Inflammasome cytokines IL-1β (mean ±SD; w vs x n.s. p>0.9999, y vs z ***p=0.0005, w vs y n.s. p=0.9285, x vs z **p=0.0081) and IL-18 (mean ±SD; w vs x n.s. p=0.4813, y vs z *p=0.0106, w vs y n.s. p>0.9999, x vs z n.s p=0.0947). (f) Pro-inflammatory cytokines IFNγ (mean ±SD; w vs x *p=0.0456, y vs z *p=0.0343, w vs y *p=0.0409, x vs z *p=0.0243) and IL-6 (mean ±SD; w vs x n.s. p=0.0862, y vs z n.s. p=0.3023, w vs y n.s. p=0.7166, x vs z *p=0.0359) (g) TGFβ (mean ±SD; w vs x n.s. p=0.5287, y vs z n.s. p=0.5735, w vs y *p=0.0122, x vs z n.s. p=0.2619, w and x vs y and z **p=0.0059) and IL-10 (mean ±SD; w vs x **p=0.032, y vs z n.s. p=0.0659, w vs y n.s. p=0.7154, x vs z n.s. p=0.2014)

https://doi.org/10.7554/eLife.29156.008
Figure 3—source data 1

qRT-PCR analysis of selected DE genes in monocytes of validation cohort of Mossi –P.fal (n = 4), Fulani –P.fal (n = 10), Mossi +P.fal (n = 8) and Fulani +P.fal (n = 5) (mean ±SD).

https://doi.org/10.7554/eLife.29156.011
Figure 3—figure supplement 1
Volcano plot of expression of individual genes in Fulani +P.fal (n = 2) relative to Mossi +P.fal (n = 3) CD14 +PBMCs (monocytes).
https://doi.org/10.7554/eLife.29156.009
Figure 3—figure supplement 2
ELISA of blood plasma in Mossi and Fulani individuals following P.falciparum infection.

Uninfected (-P.fal) and Infected (+P.fal). (n = 11 Mossi –P.falw, 8 Mossi +P.falx, 23 Fulani –P.faly, 9 Fulani +P.falz.) a. IL-1Ra (mean ±SD; w vs x *p=0.0257, y vs z **p=0.0048, w vs y n.s. p=0.5673, x vs z n.s. p=0.4807). b. IL-1RII (mean ±SD; w vs x n.s. p=0.5305, y vs z *p=0.0149, w vs y n.s. p=0.6179, x vs z n.s. p=0.4807). c. IL-18BPa (mean ±SD; w vs x n.s. p=0.3100, y vs z *p=0.0149, w vs y n.s. p=0.2038, x vs z n.s. p=0.2766).

https://doi.org/10.7554/eLife.29156.010
Figure 4 with 1 supplement
Regulation of chromatin in Mossi and Fulani monocytes.

(a) Table of selected DE chromatin regulation factors. (b and c) qRT-PCR analysis of selected DE chromatin regulation genes (Genes: SETD1A, CXXC1, KDM4B, KDM6B, BRG1, RUVBL2, SUV39H1, SIRT7, PHC2, PPP4C) in validation cohort of Mossi -P.fal (n = 4), Fulani -P.fal (n = 10), Mossi +P.fal (n = 8) and Fulani +P.fal (n = 5) relative to –P.fal (b) and Mossi (c) individuals (mean ±SD). (Also see Figure 4—source data 1). (d) Difference in DNA methylation at DE genes (Fulani +P.fal (n = 3) relative to Fulani –P.fal (n = 3)). (e and f) Examples of clusters of DE genes. (e) Change in expression of all significantly DE genes, in selected regions that include cytobands enriched in DE genes (Fulani +P.fal relative to Fulani –P.fal, adjusted p-valued < 0.05). Genes indicated in red are also DE in Fulani +P.fal relative to Mossi +P.fal (FDR < 0.1). * Indicates location of uncharacterised loci associated with resistance to severe P.falciparum malaria. (f) Difference in DNA methylation in selected regions that include cytobands enriched in DE genes (Fulani +P.fal relative to Fulani –P.fal, adjusted p-valued < 0.05), showing individual probes (black) and binned values (300 probes; red).

https://doi.org/10.7554/eLife.29156.012
Figure 4—source data 1

qRT-PCR analysis of selected DE chromatin regulation genes in monocytes of validation cohort of Mossi –P.fal (n = 4), Fulani –P.fal (n = 10), Mossi +P.fal (n = 8) and Fulani +P.fal (n = 5) (mean ±SD).

https://doi.org/10.7554/eLife.29156.014
Figure 4—figure supplement 1
Difference in DNA methylation at between Mossi –P.fal (n = 3), Mossi +P.fal (n = 3), Fulani –P.fal (n = 3), and Fulani +P.fal (n = 3).
https://doi.org/10.7554/eLife.29156.013

Tables

Table 1
Primer sequences used for QRT-PCR analysis
https://doi.org/10.7554/eLife.29156.015
GeneFR
ADGRG3CGAAGGGCCAAGAAACACCTCGTAGTTTAGCCAGTATCTCTGC
ALDOAATGCCCTACCAATATCCAGCAGCTCCCAGTGGACTCATCTG
ARID3AAGCTGCAGCCGCCTGACCACTGTTGGGAGCAGAGGTTGGC
BRG1 (SMARCA4)AGGCAAAATCCAGAAGCTGACGCTTGTCCTTCTTCTGGTC
CATSPER2ATGGCCGCTTACCAACAAGAATGCAAATGCTCAATGAGAGAGAA
CPVLTGGAAGGTGATTGTTTCGCTGGTCTCCCTTAGGTGGCATGGA
CXXC1GCAAACCGGACATCAACTGCGCACTCCCGACAGTACCAC
DACH1GGGGCTTGCATACGGTCTACCGAACTTGTTCCACATTGCACA
DUSP8CGAACTTGTTCCACATTGCACACGAACTTGTTCCACATTGCACA
EPBH1GGCTGCGATGGAAGAAACGCTGGTTGGGCTCGAAGACATT
FAM26FTGTCACCCGATGCCTATCTCTGGCCCTTCGGATTGAAAGTA
FESGGCCGAGCTTCGTCTACTGGTCCTGCATACTCCCTGTCAC
FURINCCTGGTTGCTATGGGTGGTAGAAGTGGTAATAGTCCCCGAAGA
GAACATCCTACTCCATGATTTCCTGCAGCTGGGTGAGTCTCCTCC
GAPDHTGCACCACCAACTGCTTAGCGGCATGGACTGTGGTCATGAG
IRF3IRF3 Set #VHPS-4629 purchased from Realtimeprimers.com
IRF5IRF5 Set #6 purchased from Realtimeprimers.com
KDM4BKDM4B Set #6 purchased from Realtimeprimers.com
KDM6BKDM6B Set #1 purchased from Realtimeprimers.com
NFKBIETCTGGCATTGAGTCTCTGCGAGGAGCCATAGGTGGAATCAG
OSMCACAGACTGGCCGACTTAGAGAGTCCTCGATGTTCAGCCCA
P2R × 7CTCCCATCTCAACTCCCTGATCCTGGTAGAGCAGGAGGAA
PHC2AGGGAACGGAAACTCTGCCTTCGATAACATGCGTCAGGATTTG
PP1AAGACAAGGTCCCAAAGACACCACCCTGACACATAAA
PPP4CAAGGTTCGCTATCCTGATCGCAGCCATAGACCTGCGTGATCT
RFXANKGTGACAACCTCGTCAACAAGCCGAACGGTCTCAATCTCTCCAA
RUVBL2RUVBL2 Set #1 purchased from Realtimeprimers.com
SETD1ASETD1A Set #1 purchased from Realtimeprimers.com
SIRT7GTGGACACTGCTTCAGAAGCACAGTTCTGAGACACCACA
SQSTM1GCACCCCAATGTGATCTGCCGCTACACAAGTCGTAGTCTGG
STRA13CCTCCTGGCCACATTCCTGGATTTATTGATGTTGCTTTGTGAGAA
SUV39H1SUC39H1 Set #2 purchased from Realtimeprimers.com
TOLLIPAGA ATC CCC GCT GGA ATA AGGCG TAG GAC ATG ACG AGG TT
TRAF7TCTGCGCTCCACATTCTCACACCGCGATGTTGTTCACCA

Additional files

Supplementary file 1

(A) Significantly differentially DNA methylated genes in monocytes of Fulani -P.fal relative to Mossi –P.fal. (B) Significantly differentially DNA methylated genes in monocytes of Fulani +P.fal relative to Fulani –P.fal.

https://doi.org/10.7554/eLife.29156.016
Supplementary file 2

(A) List of all significantly DE genes in monocytes for all comparisons (adjusted p-value<0.05, shown in red). Where gene symbol is listed in red, gene is not significantly DE in Fulani +P.fal relative to Fulani –P.fal. (B) List of significantly DE genes in monocytes of Fulani +P.fal relative to Fulani –P.fal (adjusted p-value<0.05). (C) List of significantly DE genes in monocytes of Mossi +P.fal relative to Mossi –P.fal (adjusted p-value<0.05). (D) List of significantly DE genes in monocytes of Fulani +P.fal relative to Mossi +P.fal (adjusted p-value<0.05). (E) List of inflammasome related significantly DE genes in monocytes of Fulani + P.fal relative to Fulani –P.fal (adjusted p-value<0.05). (F) List of transcription factor binding sites enriched at significantly DE genes in monocytes of Fulani +P.fal relative to Fulani –P.fal. (G) qRT-PCR analysis of selected DE genes in Fulani cohort for RNA-sequencing analysis. Fulani –P.fal  (n=7) and Fulani +P.fal  (n=3) (mean ± SD).

https://doi.org/10.7554/eLife.29156.017
Transparent reporting form
https://doi.org/10.7554/eLife.29156.018

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