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Clinical and Vaccine Immunology, October 2007, p. 1334-1341, Vol. 14, No. 10
1071-412X/07/$08.00+0 doi:10.1128/CVI.00181-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
Differential B-Cell Responses Are Induced by Mycobacterium tuberculosis PE Antigens Rv1169c, Rv0978c, and Rv1818c
Yeddula Narayana,1
Beenu Joshi,2
V. M. Katoch,2
Kanhu Charan Mishra,1 and
Kithiganahalli N. Balaji1*
Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012,1
National Jalma Institute of Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282-001, India2
Received 26 April 2007/
Returned for modification 29 May 2007/
Accepted 27 July 2007

ABSTRACT
The multigene PE and PPE family represents about 10% of the
genome of
Mycobacterium tuberculosis. Here, we report that three
members of the PE family, namely, Rv1169c, Rv0978c, and Rv1818c,
elicit a strong, but differential, B-cell humoral response among
different clinical categories of tuberculosis patients. The
study population (
n = 211) was comprised of different clinical
groups of both adult and child patients: group 1 (
n = 94) patients
with pulmonary infection, group 2 (
n = 30) patients with relapsed
infection, group 3 (
n = 31) patients with extrapulmonary infections,
and clinically healthy donors (
n = 56). Among the PE proteins
studied, group 1 adult patient sera reacted to Rv1818c and Rv0978c,
while Rv1169c elicited immunoreactivity in group 3 children.
However, all three PE antigens studied as well as the 19-kDa
antigen did not demonstrate humoral reactivity with sera from
group 2 patients with relapsed infection. The current study
shows that while responsiveness to all three PE antigens is
a good marker for
M. tuberculosis infection, a strong response
to Rv0978c or to Rv1818c by group 1 adult patients with pulmonary
infection or largely restricted reactivity to Rv1169c antigen
in child patients with extrapulmonary infections offers the
possibility of differential utility in the serodiagnosis of
tuberculosis.

INTRODUCTION
Mycobacterium tuberculosis, the causative agent of pulmonary
tuberculosis (TB), infects one-third of the world's population
(
22). Despite the multiplicity of antimicrobial responses mounted
by its host,
M. tuberculosis shows a remarkable ability to survive
either by evoking survival strategies or by interfering with
critical macrophage functions that are required to successfully
respond to infection (
12,
21,
30). One such immune evasion or
survival strategy may be to express different sets of proteins
during various clinical stages of the disease in infected macrophages
of granulomas, which provides survival advantages amid robust
host immune responses. A group of genes carried by
M. tuberculosis that are expressed upon infection of macrophages belongs to
the PE family (
1,
4,
9). This family is comprised of about 100
genes, scattered throughout the genome, with highly homologous
sequences corresponding to a signature Pro-Glu (PE) amino acid
sequence near the amino terminus (
1,
4,
9). In many proteins,
the PE domain is often linked to a unique domain of various
lengths that is rich in alanine and glycine amino acids, termed
the PGRS domain (PE_PGRS subfamily). It is generally believed
that the PGRS domain of PE family genes could be a source of
antigenic variability (
5,
10,
13,
26,
29). The uniqueness of
the PE genes is further illustrated by the fact that these genes
are restricted to mycobacteria (
4). However, despite their abundance
in mycobacteria, very little is known regarding the expression
or the functions of PE family genes. Recent studies have provided
some insights into functional roles of selected PE family proteins.
It has been shown that
Mycobacterium marinum expresses a homologue
of the
M. tuberculosis PE (PE_PGRS) Rv1651c gene in infected
granulomas (
27). Mutation studies have shown that Rv1818c, a
PE (PE_PGRS) gene product, may play a role during growth in
liquid medium as well as in the infection of macrophages (
5).
In addition, aerosol infection of mice with virulent
M. tuberculosis strains generates a humoral response to the Rv1818c protein
(
10). The involvement of PE family genes in the virulence of
the pathogen has also been reported, and many members of PE
family proteins, including Rv1818c, are reported be localized
on the surface of
M. tuberculosis bacilli (
3,
11,
27). Additionally,
it has been suggested that the PE_PGRS subfamily of PE genes
is enriched in genes with a high probability of being essential
for
M. tuberculosis (
19). Although those studies strongly support
a role for the PE family proteins in the biology, and possibly
pathogenesis, of
M. tuberculosis, an understanding of the function
of PE proteins will require extensive investigations.
In the current study, Rv1169c, Rv0978c, and Rv1818c were selected based on the following observations. These PE family proteins display a differential antigenic profile and are associated with pathological conditions, as evident from DNA microarray expression data (17, 26, 28, 31, 32). Furthermore, Rv0978c and Rv1169c were upregulated in TB bacilli upon infection of macrophages (28, 31). As mentioned above, a mutation in Rv1818c affects the growth of bacilli as well as the infection of macrophages (5). Recently published studies suggested that the ectopic expression of Rv1818c in a nonpathogenic Mycobacterium smegmatis strain results in specific properties more typical of virulent mycobacteria, including increased survival in macrophages and host tissues (13). In addition, Rv1818c and Rv1169c have been detected in M. tuberculosis bacilli isolated from the granulomas of lungs of human pulmonary TB patients (26). Rv0978c was demonstrated to be a member of a group of genes called in vivo-expressed genomic island genes, which were shown to be upregulated in M. tuberculosis bacilli during infection of mice (31). Rv0978c was also shown to be upregulated, at least eightfold, in human brain microvascular endothelial cell-associated M. tuberculosis, suggesting a role for endothelial cell invasion and intracellular survival (17). Furthermore, Rv0978c and Rv1169c are expressed upon infection by pathogenic species such as M. tuberculosis and Mycobacterium bovis only and not by environmental mycobacteria like M. smegmatis or Mycobacterium avium. Similarly, Rv1818c is constitutively expressed (5) by strains of M. tuberculosis and M. bovis but not by environmental mycobacteria like M. smegmatis or M. avium. In the current investigation, we report that the above-mentioned antigens of the PE family elicited differential humoral antibody reactivities in a panel of human sera obtained from different clinical categories of TB patients as measured by enzyme-linked immunosorbent assay (ELISA).

MATERIALS AND METHODS
Patients and control subjects.
The study population (
n = 211) was comprised of TB-infected
patients reporting to the National Jalma Institute of Leprosy
and Other Mycobacterial Diseases in Agra, India. The patient
population was categorized into different clinical groups as
follows. Group 1 (
n = 94) patients were diagnosed with pulmonary
TB for the first time and had no history of chemotherapeutic
intervention. Group 1 had 69 adults and 25 children. Group 2
(
n = 30) patients had relapsed infection, and all recruited
patients were adults. Group 3 (
n = 31) patients with extrapulmonary
TB infections consisted of 9 adults and 22 children. The patients
were categorized according to guidelines of the National TB
Control Program, Central TB Division, Government of India. Pulmonary
TB in patients in groups 1 and 2 was confirmed by the presence
of acid-fast bacilli in at least two initial sputum smear examinations
and growth of bacilli in BACTEC cultures. Patients with active
TB infection were also examined for radiological abnormalities
by chest X-ray. In the case of group 2 patients with relapsed
infection, all patients were adults and were diagnosed with
pulmonary TB. After diagnosis, these patients had a full course
of antitubercular chemotherapeutic treatment but had a recurrence
of the infection and disease symptoms after therapy. On the
other hand, group 1 patients were patients with active pulmonary
TB at the onset of disease who were attending the Outpatient
Department at the National Jalma Institute of Leprosy and Other
Mycobacterial Diseases, Agra, India, and had not received any
antitubercular chemotherapeutic intervention previously. Members
from group 3 had primarily abdominal TB infection and tubercular
meningitis. The diagnosis of extrapulmonary TB was carried out
by histological examination as well as with culture positivity
of the bacillus in specimens obtained from extrapulmonary sites.
The age ranges of adults and children were 18 to 60 years and
2 to 15 years, respectively. In the case of pulmonary TB patients
as well as patients belonging to other categories, samples were
obtained from active untreated patients (both adults and children)
at the time of diagnosis. Samples were taken prior to commencement
of chemotherapy. Relapsed patients were those patients who had
a recurrence of symptoms after taking a full course of antitubercular
treatment. Sera were separated from blood and kept at –20°C
until use. The samples were obtained from all donors upon entry
into the study, and samples from human immunodeficiency virus-positive
subjects were excluded from the study. The healthy donors (
n = 56) included in the study were recruited after radiological
and clinical examination to exclude individuals with active
TB. Additionally, healthy donors included in the study were
age and gender matched to the different clinical groups. The
included subjects had given written consent, and the current
study was carried out after approval from the institutional
bioethics committee.
Cloning, expression, and in silico analysis of Rv0978c, Rv1169c, and Rv1818c.
The selected PE genes were PCR amplified from genomic DNA using gene-specific primers: 5'-GCGGATCCATGTCGTTTGTCAACGTGGC-3' (forward) and 5'-CGCTCGAGAGCTGATTACCGACACCGTGT-3' (reverse) for Rv0978c, 5'-TGTCTTTTGTCACCACACGG-3' (forward) and 5'-GGTGGAGGTGCCCGCGCGGTT-3' (reverse) for Rv1169c, and 5'-CCGGAATTCATGTCATTTGTGGTCACG-3' (forward) and 5'-CGCGGATCCCGGTAACCCGTTCATCCC-3' (reverse) for Rv1818c. The amplified PE gene PCR product was ligated into the pGEMT-Easy vector (Promega Inc.), and the recombinant clones carrying the appropriate PE gene insert were confirmed by DNA sequencing. The PE gene inserts were subcloned into cloned pRSET series vectors for protein expression and purification. Escherichia coli BL21 cells carrying recombinant plasmids were induced with IPTG (isopropyl-ß-D-thiogalactopyranoside), and His-tagged recombinant proteins were purified with Ni-nitrilotriacetic acid columns (QIAGEN). In addition, recombinant E. coli clones expressing Rv1818c and 19-kDa antigens were kind gifts from M. J. Brennan, FDA, and Neil Reiner, University of British Columbia, Canada, respectively.
In silico analyses of Rv0978c, Rv1169c, and Rv1818c were carried out according to a method described previously by Jameson and Wolf (18). The program generates values for surface accessibility parameters and combines these values with those obtained for regional backbone flexibility and predicted secondary structure. Furthermore, the program offers a reliable prediction of potential antigenic determinants.
Serological characterization of Rv0978c, Rv1169c, and Rv1818c.
ELISAs were carried out with 96-well microtiter plates (Nunc) using the above-mentioned recombinant PE proteins. The plates were incubated with recombinant PE proteins (1.25 µg/ml) overnight at 4°C, followed by three washes with phosphate-buffered saline (PBS)-Tween 20 (0.05%) buffer. After being blocked with 3% bovine serum albumin in PBS, wells were incubated with human sera (1:400 dilution in blocking buffer) for 1 h at 37°C, followed by washing with PBS-Tween 20 buffer. The above-mentioned serum dilution was selected after careful titration experiments with different dilutions of the patient sera were carried out. The plates were further incubated with anti-human immunoglobulin (Ig)-horseradish peroxidase, followed by development with o-phenylenediamine tetrahydrochloride. The absorbance values were measured at 492 nm by using an ELISA reader (Molecular Devices).
Statistical analysis.
Student's t test was used for analysis of statistical significance (P value). The data for serological reactivities of different categories of patients were compared with data for healthy controls. Graphpad Quickcalcs (online t test calculator [http://www.graphpad.com/quickcalcs/ttest1.cfm]) was used for this purpose. Only P values that were less than 0.05 were considered to be significant. Comparisons of immunoreactivities within clinical groups were carried out using Bonferroni's multiple-comparison test (Graphpad Prism).

RESULTS
Expression and purification of Rv0978c, Rv1169c, and Rv1818c.
The recombinant PE proteins Rv0978c, Rv1169c, and Rv1818c were
cloned, expressed, and purified as described in Materials and
Methods (Fig.
1). In silico analysis of PE Rv0978c (331 amino
acids [aa]), Rv1169c (100 aa), and Rv1818c (498 aa) was performed
according to a method described previously by Jameson and Wolf
(
18), which predicts the topological features of a protein directly
from its primary amino acid sequence. The output of this algorithm,
the antigenic index, is used to create a linear surface contour
profile of the protein. Since most of the antigenic sites are
located within surface-exposed regions of a protein, the program
offers a reliable means of predicting potential antigenic determinants.
The antigenic index is calculated by summing several weighted
measures of secondary structure. The hypothetical PE open reading
frames Rv0978c, Rv1169c, and Rv1818c have a high antigenic profile
score, as obtained by in silico analysis, revealing the regions
with a high antigenic index for potential antigenic determinants
(Fig.
1A to C). Among all the proteins belonging to the PE family
analyzed, the selected PE proteins Rv1169c, Rv0978c, and Rv1818c
exhibited very high antigenic indices for potential antigenic
determinants as mentioned in the legend of Fig.
1A to C. Furthermore,
only 8 PE proteins out of 37 PE proteins and 23 PE_PGRS proteins
out of 62 proteins exhibited similarly high antigenic indices.
However, according to recent reports in the literature (
26,
32), Rv1169c, Rv0978c, and Rv1818c are among nine PE family
proteins that were shown to be expressed in
M. tuberculosis bacilli upon infection of macrophages. As shown in Fig.
1, experiments
utilizing the peptides with boxed protein sequences for assessing
reactivity with humoral and cell-mediated immune responses of
TB patients are under way.
Rv0978c, Rv1169c, and Rv1818c elicit differential B-cell responses during infection with TB.
Humoral immune responses of group 1 patients (those reporting
pulmonary TB disease symptoms for the first time) to the recombinant
proteins Rv0978c, Rv1169c, and Rv1818c and the 19-kDa antigen
were evaluated along with healthy controls as shown in Fig.
2A to D. In the case of group 1 adult pulmonary TB patients,
only Rv0978c and Rv1818c showed statistically significant IgG
and IgM immunoreactivities, while Rv1169c or the 19-kDa antigen
did not react to the humoral response in either the IgG or IgM
subtype. However, in the case of children in group 1, only Rv0978c,
but not Rv1818c, Rv1169c, or the 19-kDa antigen, elicited IgG
antibody reactivity (Fig.
3). In contrast, all three PE proteins
studied as well as the 19-kDa antigen did not demonstrate statistically
significant reactivity to IgG and IgM antibodies (Fig.
4 and
data not shown, respectively) in sera from adult patients with
relapsed infection in group 2. The sera derived from group 2
children were not available for our studies.
In the case of group 3 patients who reported extrapulmonary
infections, only children and not adults elicited significant
IgG immunoreactivity (Fig.
5 and data not shown). Among the
PE antigens studied, only Rv0978c and Rv1169c showed strong
reactivity to IgG, but not to IgM, in sera from group 3 children
over healthy controls (Fig.
5 and Table
1). However, the lack
of reactivity to Rv1818c suggests the possibility of stage-specific
expression of Rv1818c in group 1 patients reporting pulmonary
TB infection. Similarly, the specific reactivity of Rv1169c
with sera from patients with extrapulmonary TB infection indicates
the likelihood of the stage-specific expression of some of the
above-mentioned PE antigens.
The specificity and sensitivity of IgG and IgM antibody reactivity
to Rv0978c, Rv1169c, and Rv1818c were calculated in order to
address the serodiagnostic efficacy of these antigens. The specificities
for Rv1818c and Rv0978c immunoreactivity in the case of adult
patients belonging to group 1 or group 3 were 93% and 94%, respectively,
for IgG and 98% and 96%, respectively, for IgM. However, Rv1169c
did not elicit immunoreactivity in the case of group 1 or group
3 adult patients. The specificity for Rv1169c and Rv0978c immunoreactivity
in the case of child patients belonging to group 3 was 84% for
IgG, and the immunoreactivity of IgM antibodies to Rv1169c or
Rv0978c was not statistically significant. In addition, Rv1818c
did not elicit IgG or IgM reactivity in the case of group 3
children. The sensitivity was generally over 85% for the above-mentioned
cases where specificity was over 80%.
To compare the serological sensitivities (both IgG and IgM) to Rv0978c, Rv1169c, and Rv1818c, the data presented in Fig. 2 to 5 were recalculated as percentages of individuals showing ELISA absorbance values above the means plus 2 standard errors of the means for healthy controls (Table 1). Among all patients, Rv0978c and Rv1818c elicited strong IgM antibody responses in a very high percentage of adult group 1 individuals (78% for Rv0978c and 90% for Rv1818c), while Rv1169c elicited IgG responses (56%) more frequently than it elicited IgM responses (41%) in group 3 children with extrapulmonary infection. In addition, when the immunoreactivities to two selected PE_PGRS antigens were compared within the clinical groups of patients, Rv1818c elicited specific reactivity in sera from group 1 adult pulmonary TB patients (Fig. 6A and B), while Rv0978c elicited immunoreactivity in sera from adult and child patients with pulmonary TB infection belonging to group 1 as well as in sera from children with extrapulmonary infection in group 3. However, Rv1169c elicited specific reactivity in sera from group 3 patients only (data not shown). The data presented in Fig. 6 represent the immunoreactivities of the IgG class of the humoral response.
These results indicate that while Rv0978c is recognized by sera
from pulmonary TB patients belonging to group 1 or by sera from
child patients belonging to group 3, Rv1818c and Rv1169c elicit
specific reactivity with adult group 1 patients and group 3
patients, respectively. More importantly, the immunoreactivity
elicited in patient sera demonstrated differential reactivities
of the humoral antibodies to Rv1818c versus Rv0978c (Fig.
6 and
7). The data presented in Fig.
6 and
7 represent the immunoreactivities
of the IgG class of the humoral response. The ratios of responses
to Rv1818c and Rv0978c are quite different in adult and child
pulmonary TB patients belonging to group 1. The ratio of responses
to Rv1818c and Rv0978c in the case of adult pulmonary TB patients
was anywhere between two- and ninefold, while the ratio was
much less than onefold in the case of child pulmonary TB patients.
The possible reasons for such a discrepancy in the ratio of
reactivity are described above, as Rv1818c clearly demonstrated
significant immunoreactivity only with adult, not with the majority
of child, group 1 patients. Overall, this differential reactivity
to Rv1818c and to Rv0978c clearly suggests the degree of difference
in recognition by patient sera even though they share similar
glycine-rich C-terminal regions.

DISCUSSION
M. tuberculosis is the etiologic agent of TB and a major cause
of morbidity and mortality worldwide, with one-third of the
world's population estimated to be infected with this microorganism
(
22). After acquiring
M. tuberculosis by inhaling aerosolized
bacteria, the majority of healthy individuals develop a cellular
immune response and arrest the growth and spread of the microorganism,
without it progressing to clinical TB. This protective cellular
immune response to
M. tuberculosis is initiated in the lung
and consists primarily of alveolar macrophages and activated
T cells. However,
M. tuberculosis survives for prolonged periods
of time in the phagosomes of infected macrophages in a hypoxic
environment within the host (
21) in an asymptomatic latent state
and can reactivate years later if the host's immune system wanes.
In this context,
M. tuberculosis was reported to upregulate
the expression of many genes that might be important for its
survival amid a hostile host response. One such set of genes
is the PE family of genes (
9-
12,
14). As mentioned above, some
members of the PE family are implicated in the replication and
survival of bacilli in granulomas as well as being the source
of antigenic variations upon infection. However, the exact nature
of the role played by PE genes in providing survival benefits
to macrophages harboring
M. tuberculosis from surrounding T
cells in granulomas or during pathogenesis associated with infection
remains unclear.
The principal objective of the current study is to compare the selected PE proteins Rv1169c, Rv0978c, and Rv1818c to a well-characterized antigen, the 19-kDa antigen, in terms of the humoral immunoreactivities that they elicit in the sera of TB patients as well as healthy individuals. The 19-kDa antigen is a culture filtrate protein known to elicit strong humoral as well as cell-mediated host immune responses (6, 15, 16, 20). Furthermore, the 19-kDa antigen was suggested to exhibit several immunomodulatory functions such as the inhibition of major histocompatibility complex class II expression and antigen processing and the inhibition of gamma interferon-induced immune genes, etc. (23-25).
In the current investigation, Rv0978c, Rv1169c, and Rv1818c elicited statistically significant yet differential immunoreactivities among three selected categories of TB patients. Importantly, not-so-significant or poorer reactivities were observed against the three PE proteins in the sera of all healthy individuals tested. Furthermore, the immunoreactivity data presented in Fig. 2 to 6 suggest that Rv1818c or Rv1169c may be expressed during a specific stage of the disease. In contrast, Rv0978c seems to be immunoreactive with sera derived from either group 1 (pulmonary infection) or group 3 (extrapulmonary) patients. In order to understand the molecular mechanisms that underlie the humoral response elicited by PE antigens, we would like to assess patient T-cell reactivity with specific HLA class I and class II binding peptides derived from the above-described PE family antigens, as the antibody response in many cases is often regulated by initial T-cell responses during infection. However, we agree with the fact that assessments of T-cell reactivity may not necessarily be a logical step in the further establishment of the selected PE antigens as serodiagnostic tools.
The presence of antibodies to Rv0978c, Rv1169c, and Rv1818c in sera of TB patients clearly suggests that these PE proteins are expressed in vivo during active infection with M. tuberculosis and that the above-described PE molecules are immunogenic. It has been observed that some of the PE_PGRS proteins are antigenic, where antibodies raised against five PE_PGRS proteins by DNA vaccination reacted with the respective proteins expressed in epithelial cells or in reticulocyte extracts (3, 5). Some of the antibodies showed cross-reactivity with more than one PE_PGRS protein, suggesting the presence of common epitopes. However, the dot blot technique used in the above-mentioned study is not a very reliable method to ascertain either the size or the nature of the cross-reactivity of antibodies raised against any given PE_PGRS protein. In our studies, we have found that rabbit polyclonal antibodies generated against Rv0978c do not cross-react with recombinant Rv1818c (data not shown). In addition, Rv0978c contains novel tandem repeats, called AB repeats, in the C terminus, which are absent in most of the PE (or PE_PGRS subfamily) genes, including Rv1818c (2).
Other studies have demonstrated that sera from TB patients showed immunoreactivity to many of the PPE family proteins, in addition to PE family proteins (7, 8). Many studies in the literature clearly emphasized the observation of a lack of a sufficient immune response in TB patients against many well-characterized serodiagnostic antigens of TB bacilli. The above-mentioned condition is more severe in newer cases of pulmonary TB infection where the host immune system is not sufficiently primed to elicit a strong humoral response against most antigens of M. tuberculosis. Overall, our observations suggest the possible serodiagnostic potential of Rv1818c, Rv1169c, and Rv0978c during different stages of infection.

ACKNOWLEDGMENTS
We are grateful to Kiran Katoch and D. S. Chauhan for the generous
gift of TB patient sera. We are thankful to M. J. Brennan, FDA,
and to Neil Reiner, University of British Columbia, Canada,
for the kind gifts of recombinant expression clones for Rv1818c
and 19-kDa antigens. We thank Dipankar Nandi for critical comments
and Nagasuma Chandra, Rashmi Chaturvedi, and V. L. Suhas for
their help during the preparation of the manuscript.
The current study was funded by the Sir Dorabji Tata Center for Research in Tropical Diseases to K.N.B. and V.M.K. as well as funds from the Council for Scientific and Industrial Research, Department of Biotechnology, and Department of Science and Technology, Government of India, to K.N.B. Y.N. and K.C.M. are supported by a fellowship from the Council for Scientific and Industrial Research and the University Grants Commission, Government of India, respectively.

FOOTNOTES
* Corresponding author. Mailing address: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India. Phone: 91-80-22933223. Fax: 91-80-23602697. E-mail:
balaji{at}mcbl.iisc.ernet.in 
Published ahead of print on 8 August 2007. 

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Clinical and Vaccine Immunology, October 2007, p. 1334-1341, Vol. 14, No. 10
1071-412X/07/$08.00+0 doi:10.1128/CVI.00181-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
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