The Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family plays a central role in antigenic variation and cytoadhesion of P. falciparum infected erythrocytes. PfEMP1 proteins/var genes are classified into three main subfamilies (UpsA, UpsB, and UpsC) that are hypothesized to have different roles in binding and disease. To investigate whether these subfamilies have diverged in binding specificity and test if binding could be predicted by adhesion domain classification, we generated a panel of 19 parasite lines that primarily expressed a single dominant var transcript and assayed binding against 12 known host receptors. By limited dilution cloning, only UpsB and UpsC var genes were isolated, indicating that UpsA var gene expression is rare under in vitro culture conditions. Consequently, three UpsA variants were obtained by rosette purification and selection with specific monoclonal antibodies to create a more representative panel. Binding assays showed that CD36 was the most common adhesion partner of the parasite panel, followed by ICAM-1 and TSP-1, and that CD36 and ICAM-1 binding variants were highly predicted by adhesion domain sequence classification. Binding to other host receptors, including CSA, VCAM-1, HABP1, CD31/PECAM, E-selectin, Endoglin, CHO receptor "X", and Fractalkine, was rare or absent. Our findings identify a category of larger PfEMP1 proteins that are under dual selection for ICAM-1 and CD36 binding. They also support that the UpsA group, in contrast to UpsB and UpsC var genes, has diverged from binding to the major microvasculature receptor CD36 and likely uses other mechanisms to sequester in the microvasculature. These results demonstrate that CD36 and ICAM-1 have left strong signatures of selection on the PfEMP1 family that can be detected by adhesion domain sequence classification and have implications for how this family of proteins is specializing to exploit hosts with varying levels of anti-malaria immunity.
The Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family plays a central role in antigenic variation and cytoadhesion of P. falciparum infected erythrocytes. PfEMP1 proteins/var genes are classified into three main subfamilies (UpsA, UpsB, and UpsC) that are hypothesized to have different roles in binding and disease. To investigate whether these subfamilies have diverged in binding specificity and test if binding could be predicted by adhesion domain classification, we generated a panel of 19 parasite lines that primarily expressed a single dominant var transcript and assayed binding against 12 known host receptors. By limited dilution cloning, only UpsB and UpsC var genes were isolated, indicating that UpsA var gene expression is rare under in vitro culture conditions. Consequently, three UpsA variants were obtained by rosette purification and selection with specific monoclonal antibodies to create a more representative panel. Binding assays showed that CD36 was the most common adhesion partner of the parasite panel, followed by ICAM-1 and TSP-1, and that CD36 and ICAM-1 binding variants were highly predicted by adhesion domain sequence classification. Binding to other host receptors, including CSA, VCAM-1, HABP1, CD31/PECAM, E-selectin, Endoglin, CHO receptor "X", and Fractalkine, was rare or absent. Our findings identify a category of larger PfEMP1 proteins that are under dual selection for ICAM-1 and CD36 binding. They also support that the UpsA group, in contrast to UpsB and UpsC var genes, has diverged from binding to the major microvasculature receptor CD36 and likely uses other mechanisms to sequester in the microvasculature. These results demonstrate that CD36 and ICAM-1 have left strong signatures of selection on the PfEMP1 family that can be detected by adhesion domain sequence classification and have implications for how this family of proteins is specializing to exploit hosts with varying levels of anti-malaria immunity.
Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is a
clonally variant adhesion protein that mediates binding of infected erythrocytes
(IE) to blood microvasculature and other host cells [1]. Adherence of IEs to
microvascular endothelium is a major virulence factor and, in conjunction with the
related phenomenon of rosetting with uninfected erythrocytes, prevents parasitized
erythrocyte circulation to the spleen where parasites may be destroyed [2]. Each parasite
strain encodes ∼60 PfEMP1 proteins, or var genes, which are
expressed in a mutually exclusive fashion [3], [4]. Switches in
var gene expression enable infected erythrocytes to evade host
immunity and may modify disease manifestations by changing parasite binding tropism
[5]–[7].Efforts to unravel the role of PfEMP1 proteins in disease are complicated by the vast
diversity of var genes. Each parasite has a diverse repertoire of
genes, and there is limited overlap of repertoires between parasite genomes [8]–[10]. However, genes can be classified into three main
subfamilies denoted Groups A, B, and C [11], plus three unusual
strain-transcendent variants (var1csa, var2csa,
and type 3 var) [12]–[15]. The var gene subfamilies possess
distinctive upstream flanking regions termed UpsA, UpsB, and UpsC and are found in
characteristic locations in the subtelomeric or central regions of chromosomes [4], [9], [11], [12]. It has been
hypothesized that var gene organization may contribute to a gene
recombination hierarchy that influences gene function and evolution [1].A number of studies have sought to correlate specific parasite adhesion traits with
disease outcome [16]–[19]. To date, at least 12 host receptors have been reported
to mediate P. falciparum IE binding [20]. CD36 binding is the most common
adhesion trait in the parasite population, followed by intercellular adhesion
molecule 1 (ICAM-1) [17], [19]. These two receptors can synergize under flow conditions
to mediate infected erythrocyte binding to microvasculature endothelium [21]–[23]. Most other binding
properties appear to be rarer or have not been studied in more than one or a few
parasite isolates. ICAM-1 binding has been associated with cerebral malaria in some
studies [17],
[24], but not
in others [19],
[25]. In
addition, infected erythrocyte rosetting, or binding of parasitized red blood cells
to uninfected red blood cells, has been associated with disease severity in African
children [26]–[28]. The clearest disease association is placental malaria,
in which parasites express the unusually strain-transcendent VAR2CSA PfEMP1 protein
and adhere to chondroitin sulfate A (CSA) in the placenta [14], [29]. VAR2CSA is a leading candidate
for a pregnancy malaria vaccine and a paradigm for syndrome-specific anti-disease
vaccine efforts.Although the molecular basis for other adhesion-based complications of P.
falciparum is less established than for pregnancy malaria, several
observations suggest the antigenic diversity of severe malaria isolates may also be
limited. For instance, immunity to severe malaria appears to be acquired after
relatively few infections [30], [31]. In addition, isolates from severe malaria cases appear
to express a relatively restricted variant antigen surface repertoire [32]–[34]. Furthermore,
seroepidemiological and var transcriptional profiling studies
suggest that UpsA variants are more commonly expressed in young African children
with limited immunity and in severe malaria infections [35]–[39]. Therefore it is possible the
UpsA group has become specialized to exploit individuals with limited anti-malaria
immunity, and it is important to understand what may account for this expression
profile.To gain insight into PfEMP1 binding properties, sequence classification has been
performed [40]. The
extracellular binding region of PfEMP1 proteins is comprised of 2–7
receptor-like domains called Duffy Binding-Like (DBL) and Cysteine Rich Interdomain
Region (CIDR) [41], [42]. DBL and CIDR domains are classified into different major
types (α to ε) and sub-types by sequence criteria [10], [40]. PfEMP1 proteins can be further
subdivided by protein architecture into small proteins with a four-domain
extracellular binding region (DBL-CIDR-DBL-CIDR) and large proteins with a more
complex domain composition [43]. By comparison to other groups, nearly all of the UpsA
proteins are in the large protein category [9], [10]. The best characterized binding
interactions are between CIDR::CD36 and DBLβ::ICAM-1 [44]–[46]. In a repertoire-wide binding
comparison with CIDR recombinant proteins, the majority of proteins encoded CD36
binding function, except for the UpsA group, which had different CIDR sequence types
than the UpsB and UpsC groups [11], [12], [46]. UpsA proteins may also be under less selection to bind
ICAM-1, as 7 of 23 DBLβ domains from the IT4 parasite strain bound ICAM-1, but
none of the 9 DBLβ domains tested from the UpsA group were ICAM-1 binders [44]. However, using
a different binding analysis in a BioPlex system, only a single DBLβ recombinant
protein from the 3D7 parasite strain bound ICAM-1, and it was from an UpsA protein
[45]. UpsA
proteins have also been reported to bind ICAM-1 (PFD1235w) and PECAM-1 (PF11_0008)
[47].
Taken together, sequence and binding analysis suggest the UpsA group forms a
preferential gene recombination group that is under less selection to bind the
primary microvasculature receptor CD36. Furthermore, it is possible UpsA genes may
have evolved specialized binding properties that contribute to their preferential
expression in the malaria non-immune.While sequence and binding analysis of isolated domains have provided significant
insights into PfEMP1 function, few binding predictions have been confirmed for
native proteins at the IE surface, and it is not yet established whether binding
differences truly exist between var gene subfamilies. Furthermore,
it is possible that recombinant protein binding properties may be modified by
adjacent domains [48] or may not extrapolate to the native PfEMP1 molecule
[49]. Thus,
there remain significant uncertainties in our ability to predict IE binding, and
there is still limited understanding of how host selection is shaping the PfEMP1
variant antigen repertoire for parasite survival and transmission. For this study,
we generated a large panel of cloned parasite lines from the cytoadhesive IT4/FCR3
parasite strain and selected three highly enriched UpsA parasite lines with specific
monoclonal antibodies. This panel was employed to both investigate the major host
selection binding pressures operating on the protein family and to evaluate binding
predictions based on sequence information and isolated domain binding assays.
Results
Generation of a panel of cloned parasite lines from a cytoadhesive parasite
line
To create a panel of parasites for phenotypic analysis, parasites were cloned
from a long-term, continuous culture of the IT4/25/5 clone A4 (Figure 1) [6]. The
IT4/25/5 (IT4) parasite genotype is unusual because the parasite maintained its
cytoadhesion capabilities after in vitro adaptation [50], [51], making it
a primary model for this virulence determinant. A set of 54 var
genes has been reported from the IT4 parasite genotype [9], [10]. The A4 cloned parasite line
expresses a var gene (A4var/IT4var14) that has
an unusually high switch frequency (∼1–2% per generation) [6], [52],
resulting in PfEMP1 heterogeneity at the population level in the long term
culture. After 70 parasite divisions in continuous culture, the long-term A4
culture had completely switched away from the A4var gene
(IT4var14) and expressed a mixture of different
var genes at low levels with IT4var26,
IT4var31, and IT4var37 predominating
(Figure 2). Both
IT4var31 (previously referred to as
C18var) and IT4var37 (previously referred to
as AFBR6) were also found to be common switch events in two
previous studies of var gene switching within the A4 parasite
lineage [7],
[52],
suggesting that these particular genes may have high “on” rates in
unselected cultures.
Figure 1
Derivation of parasite lines for phenotypic analysis.
A panel of 19 P. falciparum parasite lines (clear boxes)
was generated from parental laboratory lines (black boxes) using limited
dilution cloning or various selection techniques. All parasite lines
express a unique predominant var transcript by qRT-PCR
or monoclonal antibody reactivity except for two lines (a) that both
express IT4var31.
Figure 2
Analysis of var gene transcription in the long-term
A4 parasite clone culture.
A4 parasites were grown under continuous culture in the absence of
selection for more than 70 parasite divisions, and RNA was harvested.
The profile of var gene expression was measured by
qRT-PCR, using specific primers to the IT4var genes.
After 70 cycles, the parasite culture had nearly completely switched
away from IT4var14/A4var and predominantly expressed
three var transcripts (IT4var26,
IT4var31, and IT4var37), plus many
genes at lower levels. Gene expression was normalized to the
housekeeping control gene adenylosuccinate lyase (asl).
The A4 primer set is arranged along the x-axis by Ups
category: UpsA (red), UpsB (blue), UpsC, (yellow), and UpsE (gray)
groups, as well as three genes for which the Ups type has not been
determined (white).
Derivation of parasite lines for phenotypic analysis.
A panel of 19 P. falciparum parasite lines (clear boxes)
was generated from parental laboratory lines (black boxes) using limited
dilution cloning or various selection techniques. All parasite lines
express a unique predominant var transcript by qRT-PCR
or monoclonal antibody reactivity except for two lines (a) that both
express IT4var31.
Analysis of var gene transcription in the long-term
A4 parasite clone culture.
A4 parasites were grown under continuous culture in the absence of
selection for more than 70 parasite divisions, and RNA was harvested.
The profile of var gene expression was measured by
qRT-PCR, using specific primers to the IT4var genes.
After 70 cycles, the parasite culture had nearly completely switched
away from IT4var14/A4var and predominantly expressed
three var transcripts (IT4var26,
IT4var31, and IT4var37), plus many
genes at lower levels. Gene expression was normalized to the
housekeeping control gene adenylosuccinate lyase (asl).
The A4 primer set is arranged along the x-axis by Ups
category: UpsA (red), UpsB (blue), UpsC, (yellow), and UpsE (gray)
groups, as well as three genes for which the Ups type has not been
determined (white).Initially, 17 subclones were isolated from the long-term A4 parasite culture by
limited dilution cloning (Figure
1). From var transcription profiling, 6 of the
subclones transcribed IT4var31 as either the primary or
secondary var transcript, 8 transcribed dominant
var gene transcripts distinct from each other, and a
dominant var transcript (present at greater than 50% of
the total var transcripts) could not be identified in 3 of the
subclones by qRT-PCR analysis (Table 1, and data not shown). Ten subclones that primarily expressed
single dominant var transcripts, including two that expressed
IT4var31, were selected for phenotypic analysis (Figure 3).
Table 1
Phenotypic and var transcriptional profile of
parasite panel.
qRT-PCR initial typingc
qRT-PCR: bindingd
Parasite
Gelatina
kahrpb
major transcript
% transcripts
major transcript
% transcripts
R29
-
+
nd
nd
nd
nd
Pf13
-
+
nd
nd
nd
nd
VarO
-
+
nd
nd
nd
nd
CS2
+
+
nd
nd
var4
99%
A4ultra
+
+
nd
nd
var14; var24
25%;6%
P6D12
+
+
var39; var67
60%; 36%
var39; var67
74%;21%
P6A1
+
+
var11
92%
var11
81%
P4H12
+
+
var44
100%
var44
100%
P2E11
+
+
var33
90%
var33
96%
ItG-ICAM-1
+
+
nd
nd
var16
60%
P6G2
+
+
var29;var31
57%;42%
var31
97%
P5B6
+
+
var31
100%
var31
89%
P5C2
+
+
var43/var66;var31
71%;19%
var43/66
78%
3G8
+
+
var1
99%
var1
98%
P6A8
+
+
var24;var37
79%;16%
var24;var37
66%;32%
4E12
+
+
var37
94%
var37
95%
P5F12
+
+
var21;var59
70%;30%
var21;var59
73%;27%
P3G5
+
+
var10;var32
52%;48%
var10;var32
80%;19%
2G2
-
-
var20
88%
var20
96%
The ability of infected erythrocytes to float in 0.7% gelatin
was used as a surrogate for knob positivity.
Indicates whether the knob-associated histidine rich protein gene
could be amplified from cDNA.
Profiling of var transcription was performed after
initial parasite expansion following limited dilution cloning.
Transcripts representing greater than 5% of the total
var messages are listed.
Profiling of var transcription was repeated at the
time of infected erythrocyte binding assays as above. nd - not
done.
Figure 3
Analysis of var gene transcription in parasite lines
at the time of infected erythrocyte binding assays.
RNA was harvested from ring stage parasites in the same cycle that
infected erythrocyte binding assays were performed, and
var expression profiling was performed by qRT-PCR.
Most parasite lines expressed a single dominant var
gene transcript, and some parasite lines had a secondary
var transcript. Other var genes
were expressed at negligible levels. Gene expression was normalized to
the housekeeping control gene adenylosuccinate lyase
(asl). The scale of the Y-axis is the same for all
parasite lines. The A4 primer set is arranged along the
x-axis by Ups category; UpsA (red), UpsB (blue),
UpsC, (yellow), and UpsE (gray) groups, as well as three genes for which
the Ups type has not been determined (white). The name of each parasite
line is indicated at the right of its respective transcription
profile.
Analysis of var gene transcription in parasite lines
at the time of infected erythrocyte binding assays.
RNA was harvested from ring stage parasites in the same cycle that
infected erythrocyte binding assays were performed, and
var expression profiling was performed by qRT-PCR.
Most parasite lines expressed a single dominant var
gene transcript, and some parasite lines had a secondary
var transcript. Other var genes
were expressed at negligible levels. Gene expression was normalized to
the housekeeping control gene adenylosuccinate lyase
(asl). The scale of the Y-axis is the same for all
parasite lines. The A4 primer set is arranged along the
x-axis by Ups category; UpsA (red), UpsB (blue),
UpsC, (yellow), and UpsE (gray) groups, as well as three genes for which
the Ups type has not been determined (white). The name of each parasite
line is indicated at the right of its respective transcription
profile.The ability of infected erythrocytes to float in 0.7% gelatin
was used as a surrogate for knob positivity.Indicates whether the knob-associated histidine rich protein gene
could be amplified from cDNA.Profiling of var transcription was performed after
initial parasite expansion following limited dilution cloning.
Transcripts representing greater than 5% of the total
var messages are listed.Profiling of var transcription was repeated at the
time of infected erythrocyte binding assays as above. nd - not
done.Of interest, there was negligible UpsA transcription in the long-term A4 culture
(Figure 2), and none of
the isolated subclones expressed an UpsA var gene (Figure 3). To attempt to
enrich for UpsA variants, the long-term A4 culture was panned on CD36 receptor
protein and non-adherent parasites were selected. Although the
var transcriptional profile was modified after CD36
negative selection, this approach did not enrich for UpsA variants. Instead, the
frequent switch variant IT4var31 was the resulting major
transcript (data not shown). This again indicates that UpsA genes are rare
switch events in long-term A4 cultures.To create a more representative panel for phenotypic analysis, six previously
isolated parasite lines from the IT4/FCR3 strain and three UpsA parasite lines
from different parasite strains (IT4/FCR3, Palo Alto 89F5, and 3D7) (Figure 1) were included in the
binding studies. The three UpsA parasite lines (R29, VarO, and Pf13) were
isolated by rosette enrichment and selected for high purity using specific
monoclonal antibodies to the respective PfEMP1 proteins [53]. Altogether, 19
parasite lines were examined representing all three major var
gene groups. Three of the parasites in the panel expressed an UpsA protein as
the dominant var transcript, ten expressed an UpsB
var gene, three expressed an UpsC var, one
expressed the unique UpsE linked transcript (IT4var4,
var2CSA), and for one parasite, the Ups category of the
dominant var transcript has yet to be determined (Figure 4). The remaining
parasite in the panel, 2G2, is knobless and was employed as a negative binding
control (Table 1) [54]. Most
parasites in the panel expressed distinct dominant var
transcripts, except two subclones (P6G2 and P5B6) expressed
IT4var31, and two others (P6A8 and 4E12) expressed
IT4var37/AFBR6 as either the dominant or secondary
var transcript (Figure 3 and Table 1).
Figure 4
Schematic representation of var transcription in the
parasite panel and summary binding to CD36 and ICAM-1 receptor
proteins.
Parasite name, predominant var transcript(s) by qRT-PCR,
Ups categorization, and predicted protein architecture are shown for
parasite lines included in the panel, with the exception of the negative
binding control line (2G2). Predicted binding of native PfEMP1 to CD36
and ICAM-1 receptor proteins based on previous analysis of CIDR::CD36
[46] and DBLβ::ICAM-1 interactions [44] are
shown, along with observed binding to these receptor proteins in both
cell and recombinant protein platforms. Low, moderate, and high binding
levels are indicated in gray-scale: clear = <15
IE per 100 CHO cells, <80 IE per mm2; light
gray = 16–50 IE per 100 CHO cells,
81–500 IE per mm2; dark
gray = 51–100 IE per 100 CHO cells,
501–1000 IE per mm2;
black = >101 IE per 100 CHO cells, >1000 IE
per mm2. Ukn means the Ups type or binding behavior is
unknown.
Schematic representation of var transcription in the
parasite panel and summary binding to CD36 and ICAM-1 receptor
proteins.
Parasite name, predominant var transcript(s) by qRT-PCR,
Ups categorization, and predicted protein architecture are shown for
parasite lines included in the panel, with the exception of the negative
binding control line (2G2). Predicted binding of native PfEMP1 to CD36
and ICAM-1 receptor proteins based on previous analysis of CIDR::CD36
[46] and DBLβ::ICAM-1 interactions [44] are
shown, along with observed binding to these receptor proteins in both
cell and recombinant protein platforms. Low, moderate, and high binding
levels are indicated in gray-scale: clear = <15
IE per 100 CHO cells, <80 IE per mm2; light
gray = 16–50 IE per 100 CHO cells,
81–500 IE per mm2; dark
gray = 51–100 IE per 100 CHO cells,
501–1000 IE per mm2;
black = >101 IE per 100 CHO cells, >1000 IE
per mm2. Ukn means the Ups type or binding behavior is
unknown.To confirm the presence of knobs on the IE surface, which are known to be
important in PfEMP1 anchoring and infected erythrocyte binding [41], [54], [55], parasites
were tested for transcription of the knob associated histidine rich protein
(kahrp
+) by RT-PCR and floated by gelatin
sedimentation (gelatin+). All parasites in the panel were
positive in both assays, except for the negative control 2G2 parasite line,
which lacks kahrp and therefore sedimented in gelatin. In
addition, the three rosette-forming UpsA parasites all transcribed
kahrp but sedimented in gelatin because they were
originally isolated on the basis of their property to sediment in Ficoll (Table 1). To confirm the
identity of var gene transcription at the time of binding
assays, RNA was harvested within the same growth cycle that binding assays were
performed. For these assays, thawed parasite stabilates were grown for 4 to 5
cycles to generate sufficient parasite material, and parasites were generally
analyzed a total of 18–20 cycles from initial parasite cloning. In
general, the dominant var transcript did not change between the
initial qRT-PCR characterization performed after limited dilution cloning and
the second round of -typing done at the binding assay (Table 1). In only one parasite line, P6G2,
the previous dominant transcript was replaced by the secondary
var transcript that was present before freezing (Table 1). At the time of the
binding analysis, the average fold transcription of dominant
var transcripts relative to the asl
housekeeping gene was 14.2 (range 2.8–28.1). Furthermore, most parasite
lines were significantly enriched for a single predominant var
transcript (Figure 3), and
only 8 parasite lines contained a secondary var transcript at
greater than 5% of the total var transcripts (Table 1). In most cases, the
secondary transcript was present at much lower levels than the dominant
var transcript. Thus, var gene
transcription was stable over the short-term culture period used to perform
these assays. For the three UpsA variants, PfEMP1 expression was established by
flow cytometry with specific monoclonal antibodies to be 79% or higher
using conservative gating criteria (Figure S1). Furthermore, all three lines
formed rosettes in O-type RBCs: R29 (rosetting
rate = 37%, 89% mAb reactivity R29), VarO
(rosetting rate = 73%, 79% mAb reactivity
VarO), Pf13 (rosetting rate = 52%, 94% mAb
reactivity Pf13_0003). Therefore, all of the parasites in the panel were highly
homogenous for one or two var transcripts, and UpsA parasite
lines were highly pure for a single expressed PfEMP1 variant.
CD36 binding of infected erythrocytes is highly predicted by the type of CIDR
domain in PfEMP1 proteins
To investigate whether infected erythrocyte binding to CD36 could be predicted
from sequence information and binding studies of isolated CIDR domains [46], the
complete panel of parasite lines was analyzed for binding to both CHO745-CD36
and immobilized CD36 recombinant protein. Because rosettes of uninfected red
blood cells can interfere with binding or make bound IEs more susceptible to
disruption during washing stages, the rosettes of the three UpsA variants were
first disrupted using heparin sulfate prior to binding analysis. Previous work
has shown that sulfated glycoconjugates can enhance binding to CD36 on cell
surfaces [56]. Therefore, as a control for the three rosetting
parasite lines, all of the parasites in the panel were treated with heparin
sulfate and tested for binding to immobilized CD36 recombinant protein. Heparin
sulfate treatment greatly diminished rosette formation in the three UpsA
parasite lines (<10%) (Figure S2), but had minimal effect on
infected erythrocyte binding to immobilized CD36 recombinant protein. Overall,
parasites had comparable binding levels in the presence or absence of heparin
sulfate (Figure
S2). In addition, two non-rosetting, CD36 binding parasite lines
(A4ultra and ItG-ICAM-1) were tested for binding to CHO745-CD36 cells in the
presence or absence of heparin sulfate. Similar to what has been reported
previously [56], sulfated glycoconjugates increased IE binding to
CHO745-CD36 (Figure S3). Because heparin sulfate may slightly enhance IE adhesion
to CHO-CD36 and did not modify IE adhesion to immobilized CD36, the binding
assay was then repeated for all of the non-UpsA parasites in the absence of
sulfated glycoconjugates. In contrast, binding of the three UpsA lines to
CHO-CD36 and immobilized CD36 was repeated in the presence of sulfated
glyconjugates to prevent infected erythrocyte rosetting interfering with the
binding results.Overall, there was a significant correlation between CHO745-CD36 and spotted CD36
protein formats (Figure 5,
Spearman's Rho = 0.75, p<0.001). Although the level
of CD36 binding varied between parasite lines, most of the parasites bound CD36,
with the exception of UpsA/E groups (Figure 6). The three UpsA parasites were at
the lower spectrum of CD36 binding in both cell and recombinant protein binding
assays, and were basically indistinguishable from the negative control, knobless
parasite line, and the UpsE parasite line that does not bind CD36 (Figure 6). Furthermore, CD36
binding was highly predicted by the type of CIDR1 domain in the PfEMP1 head
structure (Figure 4).
Indeed, only two parasites in the panel that were predicted to bind CD36 did not
bind to CHO-CD36 cells. However, both exceptions (P4H12 and P3G5) bound at a low
level to 50 µg/mL rCD36, but not to 5 µg/mL rCD36 (Figure 5), and therefore may
be lower affinity CD36 binders. In group-wide comparisons, UpsB and UpsC had a
higher mean CD36 binding level than UpsA. This difference was significantly
different in the immobilized CD36 binding assay and between the UpsC and UpsA
groups in the CHO-CD36 assay, and just missed significance between the UpsB and
UpsA groups in the CHO-CD36 assay (Figure 6). Taken together, infected erythrocyte binding was highly
predictable based on the type of CIDR domain (Figure 4), and the UpsA group appears to be
under less selection to bind CD36.
Figure 5
Infected erythrocyte binding to CD36 and ICAM-1.
Parasites in the panel were assessed for binding to transfected CHO745
cell lines or recombinant proteins. (A) Infected
erythrocyte binding to CHO745 cell transfectants expressing human CD36
receptor. (B) Infected erythrocyte binding to recombinant
CD36-Fc protein immobilized on polypropylene substrate at 50 µg/mL
and 5 µg/mL concentrations. (C) Infected erythrocyte
binding to CHO cell transfectants expressing human ICAM-1 receptor.
(D) Infected erythrocyte binding to recombinant
ICAM-1-Fc protein immobilized on polypropylene substrate at 100
µg/mL and 50 µg/mL. The two parasite lines that express
IT4var31 as the predominant var
gene are indicated by boxes with horizontal bars. An arbitrary threshold
for positive binding (grey dashed line) was calculated as the mean level
of infected erythrocyte binding plus two standard deviations either to
untransfected CHO745 cells or to spots containing 2% bovine serum
albumin, respectively. Error bars represent the range of binding between
two replicate experiments.
Figure 6
Infected erythrocyte binding to CD36 and ICAM-1.
Dot plots show averaged results of replicate infected erythrocyte binding
experiments for individual cloned parasites lines contained in the panel
(Figure 5) and
grouped either by (A, B) Ups classification of major
var transcript or (C, D) presence of DBLβ
adhesion domain in the major var transcript. Mean
infected erythrocyte binding was compared between groups using
non-paired, 1-tailed t-tests. P-values are indicated according to the
95% confidence interval. An arbitrary threshold for positive
binding (grey dashed line) was calculated as the mean level of infected
erythrocyte binding plus two standard deviations either to untransfected
CHO745 cells or to spots containing 2% bovine serum albumin,
respectively. (A) Infected erythrocyte binding to
CHO745-CD36. (B) Infected erythrocyte binding to
recombinant CD36-Fc fusion protein immobilized in 10 µL spots at
50 µg/mL onto polystyrene substrate. (C) Infected
erythrocyte binding to CHO745-ICAM-1. (D) Infected
erythrocyte binding to recombinant ICAM-1-Fc fusion protein immobilized
in 10 µL spots at 100 µg/mL onto polystyrene substrate.
Infected erythrocyte binding to CD36 and ICAM-1.
Parasites in the panel were assessed for binding to transfected CHO745
cell lines or recombinant proteins. (A) Infected
erythrocyte binding to CHO745 cell transfectants expressing humanCD36
receptor. (B) Infected erythrocyte binding to recombinant
CD36-Fc protein immobilized on polypropylene substrate at 50 µg/mL
and 5 µg/mL concentrations. (C) Infected erythrocyte
binding to CHO cell transfectants expressing humanICAM-1 receptor.
(D) Infected erythrocyte binding to recombinant
ICAM-1-Fc protein immobilized on polypropylene substrate at 100
µg/mL and 50 µg/mL. The two parasite lines that express
IT4var31 as the predominant var
gene are indicated by boxes with horizontal bars. An arbitrary threshold
for positive binding (grey dashed line) was calculated as the mean level
of infected erythrocyte binding plus two standard deviations either to
untransfected CHO745 cells or to spots containing 2% bovine serum
albumin, respectively. Error bars represent the range of binding between
two replicate experiments.Dot plots show averaged results of replicate infected erythrocyte binding
experiments for individual cloned parasites lines contained in the panel
(Figure 5) and
grouped either by (A, B) Ups classification of major
var transcript or (C, D) presence of DBLβ
adhesion domain in the major var transcript. Mean
infected erythrocyte binding was compared between groups using
non-paired, 1-tailed t-tests. P-values are indicated according to the
95% confidence interval. An arbitrary threshold for positive
binding (grey dashed line) was calculated as the mean level of infected
erythrocyte binding plus two standard deviations either to untransfected
CHO745 cells or to spots containing 2% bovineserum albumin,
respectively. (A) Infected erythrocyte binding to
CHO745-CD36. (B) Infected erythrocyte binding to
recombinant CD36-Fc fusion protein immobilized in 10 µL spots at
50 µg/mL onto polystyrene substrate. (C) Infected
erythrocyte binding to CHO745-ICAM-1. (D) Infected
erythrocyte binding to recombinant ICAM-1-Fc fusion protein immobilized
in 10 µL spots at 100 µg/mL onto polystyrene substrate.
ICAM-1 binding was strongly associated with larger, DBLβ containing
PfEMP1 proteins
To test whether ICAM-1 binding was associated with larger PfEMP1 proteins
containing DBLβ domains [44], the parasite panel was analyzed for binding to
CHO745-ICAM-1 and recombinant ICAM-1 protein. Again, to prevent rosettes from
interfering with the binding analysis, the three UpsA parasite lines were
treated with sulfated glycoconjugates prior to binding analysis, and as a
control, two non-rosetting, ICAM-1 binding parasite lines (A4ultra and
ItG-ICAM-1) were tested for ICAM-1 binding in the presence or absence of
sulfated glycoconjugates. Sulfated glyconjugates reduced binding of A4ultra in
the CHO745-ICAM-1 assay and binding of both parasite lines to spotted ICAM-1
recombinant protein (Figure S3), similar to what has been reported
before [56]. Because of the potential for sulfated glyconjugates to
interfere with ICAM-1 binding in the cell and recombinant protein assays, the
three UpsA parasite lines were not considered in the ICAM-1 binding
analysis.In the cell binding assay, two parasite lines bound at a high level (>2
IEs/CHO745-ICAM-1), three bound at moderate level (0.5–2
IEs/CHO745-ICAM-1), and the remaining parasite lines bound at a low level or did
not bind ICAM-1 (Figure 5).
While there was good consistency between the cell and recombinant protein assays
for the two high level ICAM-1 binders, there was more discordance for weaker
ICAM-1 binders (Figure 5).
Only three parasite lines bound ICAM-1 in both platforms (3G8, ItG-ICAM-1, and
A4ultra), and two parasite lines that bound at a moderate level to CHO745-ICAM-1
did not bind to immobilized ICAM-1 protein (Figure 5). Notably, both parasite lines
express the IT4var31 transcript, which has been suggested to be
a weaker ICAM-1 binding variant that is trypsin-resistant [57], [58]. To confirm whether binding
was trypsin-resistant, P5B6-infected erythrocytes expressing
IT4var31 were treated with 1 mg/mL trypsin prior to ICAM-1
binding analysis. Trypsin treatment reduced CD36 binding and increased binding
to recombinant ICAM-1 (Figure S4), and therefore may have cleaved or
truncated the PfEMP1 head structure. The increase in ICAM-1 binding could be
blocked by anti-ICAM-1 antibody (mAb 15.2) and not by anti-CD36 isotype control
antibody (FA6-152) (Figure S4). In contrast, identical trypsin
treatment of 3G8 (IT4var1) and ItG-ICAM-1 parasite lines
(IT4var16) abolished binding to both CD36 and ICAM-1 (data
not shown). Thus, as predicted from binding of the isolated DBLβ domain
[58],
IT4var31 was associated with ICAM-1 binding, but the cell binding assay was more
sensitive than immobilized protein in detecting this interaction. Two of the
parasite lines also bound at a low level to immobilized ICAM-1 recombinant
protein but did not bind CHO745-ICAM-1. Thus, there may be differences in the
sensitivity of the two platforms to detect lower affinity ICAM-1 interactions,
or some of the low level binding interactions may not have been specific.Overall, ICAM-1 binding was strongly associated with larger PfEMP1 proteins that
contained a DBLβ domain. Seven of the ten parasites lines that expressed a
dominant var transcript containing a DBLβ domain bound to
ICAM-1 in either the cell or recombinant protein platform (Figure 4), and parasite lines without a
DBLβ either bound extremely weakly or did not bind ICAM-1 (Figure 6). This difference was
significant in the immobilized ICAM-1 assays (1-tailed t-test,
p = 0.020) and just missed significance in the
CHO745-ICAM-1 assay (1-tailed t-test, p = 0.103). Recently,
there has been a reclassification of DBL and CIDR domains into additional
subtypes based on a comparison of 7 parasite genomes in which DBLβ domains
were subclassified into 13 sub-types [10]. Of interest, all three
parasites that bound in both the CHO-ICAM-1 and immobilized ICAM-1 assays
expressed a DBLβ5 domain (Figure 4). To investigate if DBLβ5 could be a marker for ICAM-1
binding, we reanalyzed the recombinant DBLβ-ICAM-1 binding data [44]. In the IT4
parasite genotype, 7 of 23 DBLβ domains bound ICAM-1. Of the 7 ICAM-1
binders, 6 were DBLβ5 sequences, and there were no DBLβ5 domains that
did not bind ICAM-1 (Figure
7). Significantly, an ICAM-1 binding parasite from India
(JDP8-ICAM-1, AY028643) [59] also uses a DBLβ5 domain to bind ICAM-1 (Figure 7). The fact that
ICAM-1 binding was 100% predictable in the IT4 parasite genotype, and
that a different parasite isolate from India also uses DBLβ5 for binding,
strongly supports this domain as a marker for ICAM-1 binding. There are also two
DBLβ3 sequences that bound ICAM-1, one from the IT4 parasite genotype and
one from the 3D7 parasite genotype [45], but several other
DBLβ3 sequences did not bind ICAM-1 as recombinant proteins (Figure 7). Taken together,
ICAM-1 binding was strongly associated with the DBLβ domain, and the
DBLβ5 marks a category of larger PfEMP1 variants that encode this adhesion
property.
Figure 7
Phylogentic comparison of DBLβ domains that bind or do not bind
ICAM-1.
A tree of DBLβ sequences was constructed using new domain boundaries
[10]
and was used to reanalyze the DBLβ-ICAM-1 interaction. Bootstrap
values over 70% are indicated with open circles. Recombinant
DBLβ proteins from the IT4 parasite genotype that were previously
shown to bind ICAM-1 are indicated with red lines, non-binding sequences
have blue lines, and untested sequences are indicated with black lines
[46]. Two ICAM-1 binding sequences from the 3D7
and JD8 parasite isolates are also included [45], [59]. Ups A–C grouping is indicated next to
the gene name, as well as the DBL subclassification according to Rask et
al [10].
Phylogentic comparison of DBLβ domains that bind or do not bind
ICAM-1.
A tree of DBLβ sequences was constructed using new domain boundaries
[10]
and was used to reanalyze the DBLβ-ICAM-1 interaction. Bootstrap
values over 70% are indicated with open circles. Recombinant
DBLβ proteins from the IT4 parasite genotype that were previously
shown to bind ICAM-1 are indicated with red lines, non-binding sequences
have blue lines, and untested sequences are indicated with black lines
[46]. Two ICAM-1 binding sequences from the 3D7
and JD8 parasite isolates are also included [45], [59]. Ups A–C grouping is indicated next to
the gene name, as well as the DBL subclassification according to Rask et
al [10].
Infected erythrocyte binding to additional receptors was rare
Infected erythrocytes have been reported to bind a number of host receptors [20], but for the
most part binding has only been tested on one or a few parasite lines. Using
transfected cells or recombinant proteins, the 19 parasite lines were assayed
against 8 additional receptors: Endothelial Leukocyte Adhesion Molecule 1
(E-selectin), Vascular Cell Adhesion Molecule 1 (VCAM-1), CHO receptor
“X”, Hyaluronan Binding Protein 1 (HABP1), Platelet Endothelial Cell
Adhesion Molecule-1 (CD31/PECAM-1), Thrombospondin-1 (TSP-1), CSA, and
Fractalkine. Whereas a few parasite lines bound at a low level to TSP-1 and
CHO-ELAM-1, there was negligible binding to most receptors tested (Figure 8). Two of the UpsA
parasites (Pf13 and VarO) bound at a low level to HABP1, CD31, and CSA. However,
binding of UpsA parasites was performed in the presence of sulfated
glycoconjugates to disrupt rosettes, and they also had higher background binding
to bovineserum albumin (BSA) employed as a blocking agent for binding assays
(Figure 8, and data not
shown). As expected, the strongest CSA-binder in the panel was the CS2 parasite
line in both the CHO-K1 cell and CSA spot formats (Figure 8). CS2 expresses the VAR2CSA PfEMP1
protein that has been shown to be the primary PfEMP1 variant associated with CSA
binding [60],
[61]. Most
of the other receptors tested did not support strong adhesion of infected
erythrocytes in these binding assays and it is questionable whether all of the
observed weak interactions are physiologically relevant.
Figure 8
Infected erythrocyte binding to other candidate cytoadhesion
receptors.
Parasites in the panel were assessed for binding to transfected CHO745
cell lines or recombinant proteins. (A) Infected
erythrocyte binding to CHO cells expressing chondroitin sulfate A
(CHO-K1), E-selectin (CHO745-ELAM-1), or vascular leukocyte adhesion
molecule 1 (CHO745-VCAM-1). (B) Infected erythrocyte
binding to immobilized chondroitin sulfate A (CSA) and the recombinant
proteins TSP-1, HABP1, CD31, endoglin, and fractalkine. All proteins and
CSA were immobilized on polystyrene substrate at 50 µg/mL.
Infected erythrocyte binding to transfected cell lines were corrected by
subtracting background binding to untransfected CHO-745 cells. Binding
to recombinant proteins was corrected by substracting binding to bovine
serum albumin, which was employed as the blocking agent in all assays.
An arbitrary threshold for positive binding (grey dashed line) was
calculated as the mean level of infected erythrocyte binding plus two
standard deviations either to untransfected CHO745 cells or to spots
containing 2% bovine serum albumin, respectively. Error bars
represent the range of binding between two replicate experiments.
Infected erythrocyte binding to other candidate cytoadhesion
receptors.
Parasites in the panel were assessed for binding to transfected CHO745
cell lines or recombinant proteins. (A) Infected
erythrocyte binding to CHO cells expressing chondroitin sulfate A
(CHO-K1), E-selectin (CHO745-ELAM-1), or vascular leukocyte adhesion
molecule 1 (CHO745-VCAM-1). (B) Infected erythrocyte
binding to immobilized chondroitin sulfate A (CSA) and the recombinant
proteins TSP-1, HABP1, CD31, endoglin, and fractalkine. All proteins and
CSA were immobilized on polystyrene substrate at 50 µg/mL.
Infected erythrocyte binding to transfected cell lines were corrected by
subtracting background binding to untransfected CHO-745 cells. Binding
to recombinant proteins was corrected by substracting binding to bovineserum albumin, which was employed as the blocking agent in all assays.
An arbitrary threshold for positive binding (grey dashed line) was
calculated as the mean level of infected erythrocyte binding plus two
standard deviations either to untransfected CHO745 cells or to spots
containing 2% bovineserum albumin, respectively. Error bars
represent the range of binding between two replicate experiments.
Discussion
PfEMP1 proteins/var genes are classified into three main subfamilies
(UpsA, UpsB, and UpsC) that have different host expression profiles [35]–[37], [39]. Both binding
strength and specificity of IEs are likely to influence disease severity during an
infection; therefore, it is important to understand whether PfEMP1 subfamilies have
evolved specialized properties for distinct host/biological niches. Studies of
malaria during pregnancy have demonstrated how a specific PfEMP1 variant can
precipitate severe disease in otherwise immune women by altering IE tropism for the
placenta [14],
[29], [62]. Although
VAR2CSA appears to be unique in its ability to confer high-affinity binding to CSA
in the placenta [60], [61], [63], it offers a paradigm for the role of specific PfEMP1s in
disease. UpsA classified PfEMP1 proteins are frequently observed in young children
with limited anti-malaria immunity or experiencing severe malaria [35]–[39]. Unlike
VAR2CSA, the adherence characteristics of UpsA proteins are poorly understood and
limited largely to predictions of binding based on studies of isolated adhesion
domains [44]–[46]. To investigate a correlation of PfEMP1 binding
specificities with disease outcome, the binding characteristics of at least a
representative sample of the three main subgroups (UpsA, UpsB and UpsC) have to be
known. In this study, we employed a panel of different PfEMP1 types to test binding
predictions based upon studies of single PfEMP1 domains.While UpsA variants appear to be commonly expressed in early childhood infections and
non-immune individuals [35]–[39], very little is known about what may account for this
preferential expression in the malaria naïve. Investigation is hampered because
most P. falciparum infections contain a mixture of PfEMP1 variants
and even minor parasite subsets may obscure binding analysis. In addition, gene
silencing of UpsA variants has been observed upon in vitro
adaptation [64].
In long term in vitro adapted parasite cultures grown without
selection for specific var gene expression, UpsA variants were
expressed at a low level, and an UpsB (IT4var31/C18var) and an UpsC
(IT4var37/AFBR6) var gene
appeared to be the most common switch events. Both were also found to be frequently
activated in previous clonal analyses in this strain background [7], [52] and thus may
have a higher “on” rate under in vitro culture
conditions. One study found that var genes in central chromosome
regions had lower switch rates than those in telomeric regions [65], but inherent differences were
not consistently observed in a different parasite line [52]. The chromosome positions of
IT4var31 (UpsB) and IT4var37 (UpsC) have not
been mapped and therefore we cannot comment on whether this observation held true in
our study or not. However, our findings indicate that promoter type is not the main
determinant of var gene “on” rate as far as UpsB and
UpsC type var genes are concerned. In the case of UpsA variants,
the promoter type did seem to determine var gene expression rate by
significantly reducing it. To overcome these problems, we used specific monoclonal
antibodies to generate three distinct UpsA parasite lines of high purity for the
parasite panel.In epidemiological studies, CD36 and ICAM-1 binding are the most common adhesion
traits in the parasite population [17], [19], but their distribution among different members of the
PfEMP1 family is only partially understood [44]–[46], [58], [66]. In the parasite panel, CD36
was by far the most common binding partner, followed by ICAM-1 and TSP-1.
CD36-binding was nearly 100% predictable and was always associated with a
CIDRα type domain in the protein head structure, while the three UpsA variants
had different sequence types (CIDRγ and CIDRδ) and did not bind CD36 or only
bound at a low level. Thus, in the absence of a CIDRα domain, other potential
CD36 ligands [67], [68] were unable to compensate for infected erythrocyte
binding. Moreover, the level of CD36 binding differed between isogenic parasites
expressing different PfEMP1 variants, suggesting that PfEMP1 sequence variability or
surface expression levels have an important role in influencing the overall binding
affinity of infected erythrocytes.The UpsA group contains three different types of CIDR1 sequences (α1, γ, or
δ) [10], [12], [40], [46]. Although the
three UpsA parasites in the panel were all selected for rosetting,
“rosetting” and “non-CD36 binding” can exist as independent
phenotypes. For instance, the non-CD36 binding CIDR domains identified in this study
may potentially be found in non-rosetting group A genes, and there is evidence that
CD36 is able to act as a host receptor for rosetting in the Malayan Camp parasite
strain and some field isolates [69]. This parasite panel did not contain any representation
of the CIDRα1 subtype, which is found in approximately half of UpsA proteins
[10]. However,
it has previously been shown that recombinant CIDRα1 subtype domains do not bind
CD36 [46], and
CD36 selection led to loss of expression of an UpsA gene in a mixed parasite culture
that expressed a CIDRα1 subtype [70]. Taken together, the
results suggest the UpsA group is not under strong selection for CD36 binding, and
it will be interesting to determine if the UpsA protein head structure is selected
for specific binding properties that support microvasculature sequestration by a
mechanism different from CD36 binding. Part of this selection may be for infected
erythrocyte rosetting [71], [72], but the UpsA group may encode other adhesion properties
[47].After CD36, ICAM-1 is one of the most common adhesion properties, and the two
receptors synergize to mediate infected erythrocyte binding under flow [22], [23]. ICAM-1 is
upregulated on brain endothelium during malaria infections and has been proposed to
be a potential cerebral sequestration receptor [24]. ICAM-1 binding has previously
been mapped to the DBLβ domain [44], [45], [58], [59], [73]. Our study confirms this association as the DBLβ5
domain was 100% associated with ICAM-1 binding in both parasite lines and
recombinant proteins. It also shows that not all DBLβ domains bind to ICAM-1. In
future work using patient samples it may be interesting to investigate how well
transcription of var genes containing a DBLβ5 domain can
predict ICAM-1 binding. Overall, this study identifies a category of large UpsB and
UpsC PfEMP1 containing CIDRα and DBLβ5 subtype domains that were 100%
associated with CD36 and ICAM-1 binding. In a comparison of var
gene repertoires from 7 parasite strains, the CIDRα and DBLβ5 domains were
always found together in tandem arrangement (27 of 399 full or partial length
var genes), and the DBLβ5 domain was never associated with
a predicted “non-CD36 binding” CIDR domain. This suggests the
association has not evolved by chance and that the CIDRα-DBLβ5 domain
combination may be under dual selection for binding to CD36 and ICAM-1. Both
receptors are co-displayed on many of the same cell types (endothelial, monocyte,
and dendritic cells) and may provide the parasite opportunities to manipulate host
cells [74], [75], thus
contributing to their strong selection in the PfEMP1 repertoire. There were also a
few DBLβ3 domains that bound to ICAM-1, but these were found in association with
both CD36 binding and non-CD36 binding CIDR domains. Thus, CD36 and ICAM-1 have left
strong signatures of selection detectable by PfEMP1 adhesion domain sequence
classification, despite the extensive sequence diversity in the family.Other PfEMP1 adhesion properties examined appear to be much rarer or may only play an
additive role in overall binding affinity. Nearly all PfEMP1 proteins have four or
more extracellular domains. In addition to undefined binding properties, other
PfEMP1 domains may also function as “spacers” to position the PfEMP1
head structure and adjacent DBLβ away from the IE surface in order to engage
CD36 and ICAM-1 [76]. A potential caveat is that binding was performed under
static adhesion conditions, and individual host recombinant proteins were employed
in the protein binding assays. However, all host receptors examined were originally
defined under similar static adhesion conditions. Furthermore, static adhesion
assays are capable of detecting host receptor interactions that support both rolling
(ICAM-1, TSP-1) and stationary (CD36) cytoadhesion of infected erythrocytes under
flow conditions [21]. Cooperative binding is likely necessary to mediate firm
adhesion under flow [21]–[23], but from this analysis CD36 binding is under greatest
selection and contributes the greatest binding avidity in different PfEMP1
proteins.These results reveal a fundamental difference in CD36 binding between Ups groups that
has important implications for how parasites establish infections in individuals of
varying levels of immunity. UpsA proteins are more commonly expressed in children
with low immunity [35], [36], [39]. Later, as malaria immunity develops, it may be
significant that the proportion of non-UpsA types and CD36 binding variants
increases. It is interesting to speculate that non-CD36-binding parasites may
experience a selective advantage over their CD36-binding counterparts in patients
with limited exposure to malaria. CD36-binding parasites are thought to manipulate
both host innate and adaptive immune responses by interacting with monocytes and
dendritic cells [74], [75], [77], [78]. In the malaria naïve, these interactions may be
less important, or UpsA variants may possess other advantages or means of host
manipulation. While UpsA variants have not been clearly associated with disease in
all studies [79], they are more abundant in patients with severe malaria [80], [81] and have been
associated with cerebral malaria infections in children in Mali [38]. A greater
proportion of UpsA variants in early infections could potentially contribute to why
CD36 binding levels are very low in children with severe malaria anemia [17], [19], or these
variants could alter the pattern of sequestration to microvascular beds, such as
brain endothelium, where CD36 binding levels are extremely low [24]. Therefore, it will be
important to learn more about this group of proteins.In conclusion, the PfEMP1 protein family has diversified under dual selection to
evade host immunity and mediate infected erythrocyte binding. The development of a
parasite panel enriched for distinct PfEMP1 expression from the major Ups groups has
facilitated the testing of binding predictions, and may have potential applications
for investigating immune acquisition to the family of proteins. This comparative
analysis demonstrates the predictability of P. falciparum-IE
binding to the two major cytoadhesion receptors CD36 and ICAM-1 and provides new
insight into how natural selection may be shaping the PfEMP1 binding repertoire to
exploit distinct host niches of varying anti-malaria immunity.
Materials and Methods
Ethics statement
Human blood was used for P. falciparum culture in this study.
Donor blood was obtained from healthy volunteers under a minimal risk,
standardized, Institute protocol (protocol number HS013) that was approved by
the Western Institutional Review Board. Written informed consent was obtained
from all blood donor study participants.
P. falciparum culture conditions
The three UpsA variants were isolated by gelatin sedimentation followed by
positive selection with specific monoclonal antibodies against the respective
NTS-DBLα domain. The VarO parasite clone was generated from the Palo Alto
strain as described by rosette enrichment and selection with monoclonal antibody
D15–50 [82]. The R29 parasite (IT4 parasite strain) has been
described previously [6], [7], [83]. Highly enriched parasite cultures expressing the R29
PfEMP1 protein and Pf13 (3D7 strain) were isolated by similar methodologies to
the VarO parasite line using rosette enrichment and specific monoclonal
antibodies against the R29-DBLα domain (3B13C5) or the Pf13_0003-DBLα
domain (J3.21) [53]. The ItG-ICAM-1 parasite line was derived by ICAM-1
selection [18], CS2 by CSA selection [84], and the 3G8, 4E12, and 2G2
parasite lines by limited dilution cloning [52]. The remaining parasite
lines were derived from IT4/25/5 clone A4 [6] by limited dilution
cloning. Infected erythrocytes were cultured under standard conditions using
human O red blood cells (RBCs) in RPMI-1640 medium (Invitrogen) supplemented
with 10% pooled human A+ serum and an atmosphere of
5% CO2, 5% O2, and 95% N2
at 37°C. Synchronization of parasite growth was achieved by treatment with
5% sorbitol in PBS. Gelatin sedimentation assays were performed in
RPMI-1640 medium containing 0.7% porcine gelatin (Sigma) for 45 minutes
at 37°C. Enrichment of infected erythrocytes (IE) in the gelatin supernatant
was determined by counting >300 methanol-fixed, Giemsa-stained RBCs under
1000X magnification. Rosette formation was visualized after infected red blood
cell nuclei were stained by ethidium bromide. The rosetting rate was calculated
by determining the percentage of rosette-forming infected cells in the mature
parasite population.
Chinese hamster ovary cell culture conditions
CHO-K1, CHO745, and CHO745 transfectants expressing CD36, ICAM-1, E-selectin, or
VCAM-1 were cultured in F-12 Kaighn's medium supplemented with 10%
fetal calf serum and 0.5 mg/mL geneticin (Gibco). The CHO745 transfectants were
described in Buffet et al. [85]. Recombinant protein surface expression was monitored
by flow cytometry on a monthly basis using receptor-specific monoclonal
antibodies (R&D Systems), and cells were replaced if the percentage of
transfected cells or mean fluorescence intensity diminished by greater than
20%.
Limited dilution cloning of parasite lines
An A4 parasite clonal line [6] was grown continuously under standard conditions for
more than 70 growth cycles in the absence of overt selection. IEs were
periodically enriched for knob expression by floatation in 0.7% porcine
gelatin (Sigma) dissolved in RPMI-1640 (Invitrogen) at 37°C. Prior to
limited dilution cloning, RNA was collected and a profile of
var transcription was determined by quantitative real-time
polymerase chain reaction (qRT-PCR) using a primer set designed to amplify
unique sequence tags within the repertoire of IT4 var genes
[86].
Individual infected erythrocytes were obtained on two separate occasions by
limited dilution cloning after more than 78 and 84 cycles of continuous parasite
growth, respectively, at a seeding rate of 0.5 infected erythrocytes per well.
Initial frozen stabilates were collected after approximately 14–15 cycles
of growth and parasite lines were typed for var gene expression
by qRT-PCR.
Determination of var transcription by qRT-PCR
The determination of var gene transcription profiles was
performed using primers and PCR conditions as previously described [86]. In brief,
RNA was extracted in Trizol LS (Invitrogen) from ring stage parasites at
∼6–12 hours post-invasion and purified on RNeasy Micro columns with
on-column DNaseI treatment (QIAGEN) according to manufacturer's protocols.
cDNA was synthesized from 4 µg total RNA using Multi-Scribe reverse
transcriptase (Applied Biosystems) and one half of this material was used for
each real-time reaction against the complete set of primers. Real-time reactions
were performed on an ABI Prism 7500 thermocycler at optimized final primer
concentrations of 0.05 µM-0.5 µM using Power-SYBR Green Master Mix
in 20 µL reaction volumes under the following PCR conditions: 50°C for
1 min, 95°C for 10 min, then 40 cycles of dissociation, annealing, and
extension at 95°C for 15 sec, 52°C for 15 sec, and 60°C for 45 sec,
respectively. Relative transcription was determined by normalization to the
adenylosuccinate lyase (ASL, PFB0295w) control housekeeping gene. After
optimizing primer efficiencies, residual primer bias was corrected by
calculating the average difference in CT values between each
optimized IT4 var primer pair and ASL using genomic DNA as
template to provide a final normalized correction.
Infected erythrocyte binding assays
Parasite RNA was collected and binding assays performed within the same growth
cycle to accurately assess var transcription at the time of the
binding assay. For binding assays, individual CHO cell lines were grown to
subconfluent levels on 60-mm tissue culture-treated dishes (BD Falcon) and
recombinant proteins were immobilized by overnight incubation onto 60-mm
polystyrene dishes (Corning). The following proteins were analyzed: CD36-Fc
(R&D Systems), ICAM-1-Fc (R&D Systems), HABP1/gC1qR-6x HIS (R&D
Systems), Fractalkine-6x-HIS (R&D Systems), CD31/PECAM-1 (R&D Systems),
TSP-1-10x HIS (R&D Systems), and CSA (Sigma). All proteins and CSA were
applied at 50 µg/mL except for CD36 and ICAM-1, which were additionally
applied at 5 µg/mL and 100 µg/mL. On the day of the assay, dishes
containing CHO cells were washed twice with pre-warmed cell binding medium
(BMcell: RPMI-1640 medium containing 0.1% bovine serum
albumin, pH 7.2) and protein spots were blocked with 2% bovine serum
albumin for 45 min at 37°C, then washed twice with pre-warmed protein
binding medium (BMprotein: RPMI-1640 medium containing 0.1%
bovineserum albumin, pH 6.8). Infected erythrocytes (3-8% parasitemia)
were washed and resuspended to 1% hematocrit in either BMcell
or BMprotein then overlayed onto CHO cells or spotted onto
immobilized proteins, respectively, and incubated for 1 hr at 37°C. Prior to
binding assays, rosettes in the three UpsA parasite lines were disrupted in
binding medium containing 100 Units/mL heparin sulfate (Sigma). The same
conditions were used when testing the effect of heparin sulfate on all of the
parasites in the panel. In additional assays to test the effect of sulfated
glycoconjugates on IE binding, either 10 µg/mL dextran sulfate (MW
>500,000; Sigma) or 100 Units/mL heparin sulfate were included during binding
assays. Non-binding erythrocytes were removed by gently flooding each dish with
warm binding medium, rocking the dish back and forth several times to resuspend
non-binding erythrocytes, then pouring off and replacing the medium. The initial
washing procedure was performed on CHO745 cells and 2% BSA spots and was
repeated until non-binding erythrocytes were sufficiently removed by observation
under 400X magnification. The remaining cells and spots then received the same
number of washes. For quantification, dishes were fixed in 1%
glutaraldehyde for 20 min at room temperature, then stained with 1X Giemsa for
15 minutes. Binding was quantified by determining the number of IE adhering to
at least 300 cells under 1000X magnification or the number of IE per
mm2 in 4 random fields under 400X magnification. All binding
assays were repeated in duplicate.
Flow cytometry analysis
Trophozoite stage infected RBCs were incubated for one hour at room temperature
with specific monoclonal mouse antibodies against R29var NTS-DBLα (mAb
3B13C5, 1∶500) Pf13_0003 NTS-DBLα (mAb J3.21, 1∶20), or VarO
NTS-DBLα (mAb D15-50, 1∶20). Antibody labeling was detected with goat
anti-mouse IgG-R-Phycoerythrin (Sigma) (1∶20) for 30 minutes. Infected
erythrocyte nuclei were detected with SYTO 61 DNA dye (Invitrogen)
(1∶1000) added with the secondary antibody. Stained cells were washed in
PBS and analyzed on an LSRII FACS machine (BD Biosciences). Analysis was
performed using FlowJo 8 (Tree Star, Inc).Flow cytometric analysis of infected erythrocytes expressing UpsA PfEMP1
proteins. Infected erythrocytes were labeled with specific monoclonal
antibodies made against the NTS-DBLα domain in R29var, Pf13_0003, or
VarO PfEMP1 proteins. FACS histograms of gated infected erythrocytes labeled
with monoclonal antibodies (blue lines) or without (red lines). The
rosetting rate (RR), or the ability of infected erythrocytes to bind
non-infected RBCs at the time of antibody labeling, is indicated in
parentheses as the percentage of IE forming rosettes with uninfected red
blood cells.(TIF)Click here for additional data file.Binding to immobilized CD36 in the presence of heparin sulfate.
(A) Infected erythrocyte binding to triplicate spots of
immobilized CD36 protein (50 µg/mL) was compared with or without
addition of heparin sulfate (100 U/mL) to the binding medium.
(B) Rosetting rate for three UpsA parasite variants with
and without heparin sulfate (100 U/mL) was determined by live staining of
parasite cultures with ethidium bromide (10 µg/mL) followed by
fluorescent microscopy. The rosetting rate was calculated as the percentage
of fluorescent infected erythrocytes bound to 2 or more non-fluorescent
uninfected erythrocytes. (C) Comparison of median infected
erythrocyte binding to triplicate spots of immobilized CD36 protein (50
µg/mL) with or without addition of heparin sulfate.(TIF)Click here for additional data file.CD36 and ICAM-1 binding in the presence of sulfated glycoconjugates. Infected
erythrocyte binding was determined for two parasite lines
(ItG-ICAM/ITvar16 and A4ultra/ITvar14)
without or in the presence of either 100 U/mL heparin sulfate or 10
µg/mL dextran sulfate. (A) Infected erythrocyte binding
to CHO745 cells and CHO745 cell transfectants expressing either humanCD36
or ICAM-1 receptor protein. (B) Infected erythrocyte binding to
recombinant CD36-Fc or ICAM-1-Fc fusion proteins at 50 µg/mL and to
2% bovineserum albumin employed as a blocking agent. All proteins
were immobilized in 10 µL spots onto polystyrene substrate prior to IE
binding analysis.(TIF)Click here for additional data file.Trypsin-resistant infected erythrocyte binding to recombinant ICAM-1 protein.
The IT4var31-expressing parasite line P5B6 was either
pretreated with 1 mg/mL trypsin or untreated and then tested for binding to
immobilized ICAM-1 protein at 50 µg/mL (A) or to
immobilized CD36 protein at 50 µg/mL (B). P5B6-infected
erythrocytes displayed trypsin-resistant binding to ICAM-1. Binding could be
blocked with a monoclonal antibody to ICAM-1 (mAb 15.2), but not an isotype
control antibody.(TIF)Click here for additional data file.
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