gene pfdhfr

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Olivo Miotto edited this page Sep 17, 2021 · 1 revision

pfdhfr

Locus: PF3D7_0417200 (pfdhfr)

In Plasmodium falciparum, dhfr gene encodes an enzyme, dihidrofolate reductase (DHFR), which is required for tetrahydrofolate synthesis. Pyrimethamine, an antimalarial drug, interferes with the regeneration of tetrahydrofolic acid from dihydrofolate by competitively inhibiting PfDHFR. Parasites with DHFR mutations may resistant to pyrimethamine. PfDHFR S108N mutation is an important predictor for pyrimethamine resistance in Plasmodium falciparum, while S108T mutation has been associated with resistance to chlorcycloguanil drugs.

Table 1 Frequent mutations in PfDHFR

Codon	Wild-type	Mutation
51	N	I
59	C	R
108	S	N,T
164	I	L

Haplotype Distribution

The following table demonstrated the distribution of PfDHFR haplotypes in different geographical subcontinents. This table used the data from Version 6.0 of MalariaGEN Plasmodium falciparum Community Project . The table showed that the occurrence of 51I and 59R single mutations (ICSI, NRSI) and double mutation of 51I/59R (IRSI) are rare. In addition, the 164L mutation is rarely occurred in Africa but it is more common in Southeast Asia.

Table 2 Haplotype distribution of PfDHFR among different geographical locations

Haplotype^a	SAM	EAF	CAF	WAF	SAS	ESEA	WSEA	OCE	TOTAL
NCTI	1	0	0	0	0	2	0	0	3
ICNL	4	1	0	0	0	0	0	0	5
NCNI	43	0	2	6	0	1	1	1	54
NRNL	0	0	0	0	15	3	81	0	99
ICNI	24	39	56	16	1	0	0	0	136
NCSI (wild-type)	21	13	7	315	3	8	0	1	368
NRNI	0	30	3	112	53	95	72	211	576
IRNL	0	3	0	1	29	788	933	0	1754
IRNI	1	780	434	1598	31	835	140	0	3819
TOTAL	94	866	502	2048	132	1732	1227	213	6814

^aRepresents amino acids, left-to-right, at codons 51, 59, 108 and 164, respectively

SAM = South America; EAF = East Africa; CAF = Central Africa; WAF = West Africa;

SAS = South Asia; ESEA = East South-East Asia; WSEA = West South-East Asia; OCE = Oceania

Associations between alleles

To impute the missing codons in PfDHFR, the associations between amino acids at position 51, 59, 108 and 164 were assessed to generate the imputation rules using the data from MalariaGEN Plasmodium falciparum Community Project version 6.0. In addition, studies of the evolutionary process of DHFR mutation have proposed that 164L mutation arose after C59R+S108N and N51I+C59R+S108N mutations [1, 2].

Condons 51 and 108

There is a significant association between PfDHFR codons 51 and 108 in the parasites from all regions (see Table 3). The results suggested the following imputation rules:

51I predicts 108N
S108 predicts N51
108T predicts N51

Table 3 Contingency table of co-occurrence between codons 51 and 108

All regions	N51	51I	Total
108N	746	6283	7029
S108	383	0	383
108T	4	0	4
Total	1133	6283	7416

Fisher's exact test : P < 0.01

Condons 59 and 108

There is a significant association between PfDHFR codons 59 and 108 in the parasites from all regions (see Table 4). The results suggested the following imputation rules:

59R predicts 108N
S108 predicts C59
108T predicts C59

Table 4 Contingency table of co-occurrence between codons 59 and 108

All regions	C59	59R	Total
108N	204	6953	7157
S108	378	0	378
108T	3	0	3
Total	585	6953	7538

Fisher's exact test : P < 0.01

Condons 108 and 164

There is a significant association between PfDHFR codons 108 and 164 in the parasites from all regions (see Table 5). The results suggested the following imputation rules:

164L predicts 108N
S108 predicts I164
108T predicts I164

Table 5 Contingency table of co-occurrence between codons 108 and 164

All regions	I164	164L	Total
108N	5270	1911	7181
S108	391	0	391
108T	4	0	4
Total	5665	1911	7576

Fisher's exact test : P < 0.01

Condons 51 and 59

There is a significant association between PfDHFR codons 108 and 164 (see Table 6) but it is not sufficient to generate a imputation rule for the parasites from all regions. However, the results from Table 7 suggested the following imputation rules for parasites in Southeast Asia (SubContinent: ESEA and WSEA):

C59 predicts N51
51I predicts 59R

Table 6 Contingency table of co-occurrence between codons 51 and 59

All regions	51I	N51	Total
C59	148	455	603
59R	6031	696	6727
Total	6179	1151	7330

Fisher's exact test : P < 0.01

Table 7 Contingency table of co-occurrence between codons 51 and 59 in Southeast Asia

Southeast Asia	51I	N51	Total
C59	0	12	12
59R	2840	261	3101
Total	2840	273	3113

Fisher's exact test : P < 0.01

Condons 59 and 164

There is a significant association between PfDHFR codons 59 and 164 (see Table 8) but it is not sufficient to generate a imputation rule for the parasites from all regions. However, the results from Table 9 suggested the following imputation rules for parasites in Asia (SubContinent: SAS, ESEA and WSEA):

C59 predicts I164
164L predicts 59R

Table 8 Contingency table of co-occurrence between codons 59 and 164

All regions	C59	59R	Total
I164	612	4890	5502
164L	5	1899	1904
Total	617	6789	7406

Fisher's exact test : P < 0.01

Table 9 Contingency table of co-occurrence between codons 59 and 164 in Asia

Asia	C59	59R	Total
I164	16	1288	1304
164L	0	1895	1895
Total	16	3183	3199

Fisher's exact test : P < 0.01

Imputation Rules

Summary of imputation rules generated from association among PfDHFR codons in MalariaGEN Plasmodium falciparum Community Project dataset.

Table 10 Imputation rules for predicting PfDHFR haplotype

Region	Input^a	Output^a	Coding
Any	I - - -	I - N -	if(dhfr_51[N] == “I”){dhfr_108[S] <- “N”}
Any	- R - -	- R N -	if(dhfr_59[C] == “R”){dhfr_108[S] <- “N”}
Any	- - - L	- - N L	if(dhfr_164[I] == “L”){dhfr_108[S] <- “N”}
Any	- - S -	N C S I	if(dhfr_108[S] == "S"){dhfr_51[N] <- “N” & dhfr_59[C] <- “C” & dhfr_164[I] <- “I”}
Any	- - T -	N C T I	if(dhfr_108[S] == "T"){dhfr_51[N] <- “N” & dhfr_59[C] <- “C” & dhfr_164[I] <- “I”}
WSEA, ESEA	- C - -	N C - -	if(dhfr_59[C] == “C”){dhfr_51[N] <- “N”}
WSEA, ESEA	I - - -	I R N -	if(dhfr_51[N] == “I”){dhfr_59[C] <- “R” & dhfr_108[S] <- “N”}
SAS,WSEA, ESEA	- C - -	- C - I	if(dhfr_59[C] == “C”){dhfr_164[I] <- “I”}
SAS,WSEA, ESEA	- - - L	- R N L	if(dhfr_164[I] == “L”){dhfr_59[C] <- “R” & dhfr_108[S] <- “N”}

^aRepresents amino acids, left-to-right, at codons 51, 59, 108 and 164, respectively

Reference

Sirawaraporn W, Sathitkul T, Sirawaraporn R, Yuthavong Y, Santi DV. Antifolate-resistant mutants of Plasmodium falciparum dihydrofolate reductase. Proc Natl Acad Sci U S A. 1997;94(4):1124-9.
Lozovsky ER, Chookajorn T, Brown KM, Imwong M, Shaw PJ, Kamchonwongpaisan S, et al. Stepwise acquisition of pyrimethamine resistance in the malaria parasite. Proc Natl Acad Sci U S A. 2009;106(29):12025-30.

See also

Pyrimethamine