Volume 27, Number 2—February 2021
Research
Plasma MicroRNA Profiling of Plasmodium falciparum Biomass and Association with Severity of Malaria Disease
, Mercedes Rubio1, Antonio Sitoe, Rosauro Varo, Pau Cisteró, Lola Madrid, Inocencia Cuamba, Alfons Jimenez, Xavier Martiáñez-Vendrell, Diana Barrios, Lorena Pantano, Allison Brimacombe, Mariona Bustamante, Quique Bassat3, and Alfredo Mayor3
Table 1
Quality control and mapped reads in different species of small RNAs from cell-conditioned media of human brain endothelial cells and plasma samples in children with uncomplicated and severe malaria, Mozambique*
| Read type |
Cell condition |
UM, n = 39 | SM, n = 44 | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| niE |
3D7-iE |
ePCR-iE |
|||||||||
| t1, n = 3 | t24, n = 3 | t1, n = 3 | t24, n = 3 | t1, n = 3 | t24, n = 3 | ||||||
| Total reads, millions (SD) | 8.70 (3.55) | 16.71 (14.59) | 10.43 (3.48) | 25.86 (28.14) | 4.78 (2.13) | 6.11 (1.18) | 10.90 (9.69) | 9.26 (6.06) | |||
| Quality filtered, counts (SD) | 46.00 (36.72) | 33.33 (29.67) | 14.67 (23.69) | 125.67 (217.66) | 10.67 (2.31) | 16.33 (25.70) | 557.62 (1,200.76) | 615.75 (1,163.62) | |||
| Complexity filtered, counts (SD) | 910.67 (775.48) | 745.00 (659.60) | 369.33 (567.40) | 3168.67 (5,438.11) | 220.67 (163.57) | 308.00 (526.55) | 535.97 (884.46) | 506.23 (455.16) | |||
| Size filtered, millions (SD) |
0.63 (0.34) |
2.26 (2.99) |
0.68 (0.40) |
2.12 (2.92) |
0.90 (0.48) |
0.49 (0.50) |
1.94 (1.51) |
2.39 (1.82) |
|||
| Good-quality reads† | |||||||||||
| Millions (SD) | 8.07 (3.35) | 14.44 (11.60) | 9.75 (3.10) | 23.74 (25.23) | 3.88 (2.00) | 5.62 (0.84) | 8.96 (8.89) | 6.88 (4.64) | |||
| Percentage (SD) |
92.62 (2.54) |
90.35 (6.98) |
93.93 (2.37) |
94.15 (3.26) |
79.60 (8.86) |
92.62 (6.35) |
77.76 (15.31) |
74.95 (11.08) |
|||
| miRNA | |||||||||||
| Millions (SD) | 0.26 (0.19) | 1.09 (1.57) | 0.27 (0.19) | 0.98 (1.14) | 0.25 (0.07) | 0.15 (0.13) | 2.05 (2.50) | 1.33 (1.42) | |||
| Percentage (SD) |
3.02 (1.73) |
4.97 (4.92) |
2.47 (1.52) |
3.75 (0.54) |
7.41 (3.44) |
2.47 (1.97) |
22.43 (16.01) |
20.21 (13.22) |
|||
| rRNA | |||||||||||
| Millions (SD) | 2.34 (1.82) | 3.12 (2.71) | 1.57 (1.72) | 5.74 (9.19) | 0.72 (0.38) | 0.90 (1.08) | 0.92 (0.97) | 0.81 (0.72) | |||
| Percentage (SD) |
24.72 (16.01) |
20.36 (14.62) |
14.84 (15.37) |
13.41 (15.42) |
19.55 (5.14) |
15.13 (16.99) |
11.11 (7.75) |
11.49 (5.78) |
|||
| tRNA | |||||||||||
| Millions (SD) | 1.72 (0.58) | 3.37 (1.51) | 3.75 (1.80) | 6.35 (3.00) | 0.84 (0.64) | 2.47 (1.47) | 1.13 (1.17) | 1.14 (0.94) | |||
| Percentage (SD) |
27.51 (23.37) |
32.53 (27.16) |
41.04 (20.74) |
43.47 (23.59) |
18.65 (9.43) |
45.24 (26.80) |
13.93 (6.85) |
17.79 (7.70) |
|||
| Unknown | |||||||||||
| Millions (SD) | 3.75 (1.92) | 6.86 (6.80) | 4.16 (1.67) | 10.66 (12.55) | 2.07 (0.97) | 2.11 (0.67) | 4.87 (5.88) | 3.59 (2.62) | |||
| Percentage (SD) |
44.76 (6.35) | 42.14 (11.63) | 41.65 (5.12) | 39.37 (8.36) | 54.40 (3.75) | 37.15 (7.89) | 52.53 (16.01) | 50.51 (13.55) | |||
*Reads were obtained from cell-conditioned media of human brain endothelial cells exposed to cytoadherent P. falciparum–infected and noninfected erythrocytes, and plasma of Mozambique children with SM and UM. Three replicates of the media were collected from each cytoadhesion assay after 1 (t1) and 24 (t24) hours. ePCR-iE, adherent FCR3 expression endothelial receptor of protein C-infected erythrocytes; miRNA, microRNA; niE, noninfected erythrocytes; SM, severe malaria; UM, uncomplicated malaria; 3D7-iE, nonadherent 3D7-infected erythrocytes. †Reads after filtering low quality, low complexity, and short (<18-nt) sequences.
1These authors contributed equally to this article.
2Current affiliation: London School of Hygiene and Tropical Medicine, London, UK.
3These senior authors contributed equally to this article.