Expression profiling of chromatin-modifying enzymes and global DNA methylation in CD4+ T cells from patients with chronic HIV infection at different HIV control and progression states
Bogoi et al. Clinical Epigenetics
Expression profiling of chromatin- modifying enzymes and global DNA methylation in CD4+ T cells from patients with chronic HIV infection at different HIV control and progression states
Roberta Nicoleta Bogoi 1 2
Alicia de Pablo 1 2
Eulalia Valencia 0
Luz Martín-Carbonero 0
Victoria Moreno 0
Helem Haydee Vilchez-Rueda 6
Victor Asensi 5
Rosa Rodriguez 2 4
Victor Toledano 2 3
Berta Rodés 1 2 7
0 Infectious Diseases Department, Hospital Universitario La Paz - Carlos III , Madrid , Spain
1 HIV and Infectious Diseases group, IdiPAZ , Madrid , Spain
2 Foundation for Biomedical Research of Hospital Universitario La Paz , Madrid , Spain
3 Innate Immunity group, IdiPAZ , Madrid , Spain
4 Diagnosis and Treatment of Allergic Diseases group, IdiPAZ , Madrid , Spain
5 Infectious Unit-HIV, Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo , Oviedo , Spain
6 Infectious Diseases Department, Internal Medicine, Hospital Universitari Son Espases, IDIPSA , Palma de Mallorca , Spain
7 FIB-Hospital Universitario La Paz- IdiPAZ , Edificio IdiPAZ, Paseo de la Castellana, 261, 28046 Madrid , Spain
Background: Integration of human immunodeficiency virus type 1 (HIV-1) into the host genome causes global disruption of the chromatin environment. The abundance level of various chromatin-modifying enzymes produces these alterations and affects both the provirus and cellular gene expression. Here, we investigated potential changes in enzyme expression and global DNA methylation in chronically infected individuals with HIV-1 and compared these changes with non-HIV infected individuals. We also evaluated the effect of viral replication and degree of disease progression over these changes. Results: Individuals with HIV-1 had a significant surge in the expression of DNA and histone methyltransferases (DNMT3A and DNMT3B, SETDB1, SUV39H1) compared with non-infected individuals, with the exception of PRMT6, which was downregulated. Some histone deacetylases (HDAC2 and HDAC3) were also upregulated in patients with HIV. Among individuals with HIV-1 with various degrees of progression and HIV control, the group of treated patients with undetectable viremia showed greater differences with the other two groups (untreated HIV-1 controllers and non-controllers). These latter two groups exhibited a similar behavior between them. Of interest, the overexpression of genes that associate with viral protein Tat (such as SETDB1 along with DNMT3A and HDAC1, and SIRT-1) was more prevalent in treated patients. We also observed elevated levels of global DNA methylation in individuals with HIV-1 in an inverse correlation with the CD4/CD8 ratio. Conclusions: The current study shows an increase in chromatin-modifying enzymes and remodelers and in global DNA methylation in patients with chronic HIV-1 infection, modulated by various levels of viral control and progression.
HIV; Progression; Epigenetics; Methyltransferases; HDAC; Chromatin-modifying enzymes; DNA methylation
Chromatin is a highly dynamic structure that, during
human immunodeficiency virus (HIV) infection, is altered by
the viral integration into the host genome and the host
immune response that follows. This virus-host interaction
creates an epigenetic environment with a two-way effect.
On the one hand, the virus can be modified by
chromatinrelated events either to increase its replication efficiency
or to become transcriptionally inert [
]. On the other
hand, T lymphocyte gene expression is modulated to
create a cellular environment that favors the establishment of
infection, promotes viral replication, and facilitates viral
persistence. These chromatin changes are directed by a
wide battery of chromatin-modifying enzymes and
Many phases of the HIV cycle—integration, maintenance
of the provirus, and transcriptional activation or
silencing—are directly influenced by local chromatin reorganization
and abundance of related enzymes. In newly infected cells,
the virus is led by chromatin-interacting proteins to targeted
DNA sites, especially CpG islands and promoters [
Upon integration, the balance between several
chromatinmodifying factors creates a more or less permissive
environment for viral transcription . The proviral long terminal
repeat (LTR) promoter is complexed with two nucleosomes
(nuc-0 and nuc-1) that can modify their conformation
through binding of multimolecular complexes of histone
acetyltransferases (HATs), histone deacetyltransferases
(HDACs), and other enzymes. The deposition of nuc-1 is
key to the regulation of HIV gene expression. For example,
HDAC1, HDAC2, and HDAC3 are main factors that
mediate the deacetylation of nuc-1 and compact chromatin [
Other proteins that interact with nuc-1 and modulate
HIV1 replication through chromatin reorganization are histone
methyltransferases (HMTs) such as SUV39H1 [
methyltransferases (DNMTs) such as DNMT1 [
methyl-CpG binding domain protein 2 (MBD2) [
proteins are highly involved in this complex interplay of
chromatin rearrangements. Among them, the viral protein
Tat is crucial for maintaining the equilibrium of various
chromatin-modifying factors for the benefit of viral
persistence. Following its synthesis, Tat favors the recruitment of
various HATs toward a more permissive chromatin state
and active viral replication [
]. Tat itself can be acetylated
by some HATs (CBP/p300 and GCN5) to facilitate its
interaction with critical cellular proteins and activate viral RNA
transcription; without this modification, viral expression
would be minimal [
]. At the end of the viral transcription
process, Tat is deacetylated by Sirtuin 1 (SIRT1, a class III
HDAC) to allow for its recycling [
]. At the same time,
however, Tat appears to be a potent inhibitor of SIRT1 in
]. This second effect of Tat over SIRT1 results in T
cell hyperactivation. Although a paradox, this process
suggests a complex interaction of Tat with host epigenetic
mechanisms, with various effects dependent on Tat
concentration and possibly disease stage.
Methyltransferases such as SET domain bifurcated 1
(SETDB1) and protein arginine methyltransferase 6
(PRMT6) also associate with Tat, creating additional levels
of viral transcriptional regulation. SETDB1 methylates Tat
at lysine 50 and 51 residues, which might initiate
transcriptional repression machinery through chromatin remodeling
], whereas methylation of Tat at lysine 52 and 53 residues
by PRMT6 decreases Tat binding to TAR and results in a
reduction of HIV transcription [
]. PRMT6 has been
suggested to be an HIV restriction factor used by the host.
Methyltransferases are also responsible for modifications of
DNA methylation. In this regard, the expression of DNA
methyltransferases appears to be altered by HIV infection.
DNMT1 expression has been reported to increase with
HIV-1 infection in vitro and to correlate with gene
]. Likewise, methyltransferases can also
modify proviral DNA. In vitro studies have shown that
hypermethylation of the viral LTR promoter silences the
virus and helps establish a viral reservoir [
]. However, this
effect has been difficult to determine in vivo, because
hypomethylated viral genomes appear to predominate in primary
blood cells from patients with HIV [
]; thus, further
exploration is required to quantify its contribution to latency
On the other hand, chromatin reorganization drives the
plasticity of immune cell populations in response to stimuli.
Differentiation of T cell subsets toward helper or regulatory
lineages is regulated by DNA methylation events, histones,
and other chromatin-modifying enzymes [
]. Key genes
such as IFNg, FOXP3, IL17, IL-2, and PD-1, among many
others, are modified by several epigenetic mechanisms. In
this regard, HIV-1 infection causes important epigenetic
changes in the T cell population that result in abnormal
expression of proinflammatory cytokines and other
immunerelated genes. This expression eventually leads to a
persistent deregulation of the immune system that is linked to
AIDS progression. DNA methylation changes caused by
HIV infection have been reported in many of these genes
(IFNg, IL-1, PD-1), and these changes are responsible for
the broad dysfunction of these cells [
Despite recognition of the participation of epigenetic
mechanisms in HIV-1 infection, there is a paucity of
data on the effects of HIV replication levels and the
duration of disease on the epigenetic profiles of CD4+ T
cells in infected patients. A few in vitro studies
mimicking the acute infection in primary PBMCs and CD4+ T
cells have observed changes in expression of
chromatinmodifying enzymes [
]; however, there are no data
on patients with long-term chronic infection.
In this context, the present study aimed to evaluate
the expression profiles of chromatin-modifying enzymes
in vivo in patients with chronic HIV-1. We also assessed
how these factors behaved in various stages of disease by
analyzing patients with various phenotypes of viral
control and degrees of disease progression.
A total of 129 individuals were included in the study.
Samples from 43 individuals who were HIV-seropositive with
various degrees of disease progression and viral control
were kindly provided by the HIV BioBank integrated in the
Spanish AIDS Research Network [
]; the other 51
individuals who were HIV-seropositive were recruited at Hospital
Carlos III in Madrid. Thirty-five HIV-seronegative
individuals were also enrolled for the study. Group assignment
within the HIV-seropositive individuals was based on their
degree of viral control and disease progression. The
resulting groups for the final analysis were as follows: 26 chronic
progressors treated with cART who presented with
undetectable plasmatic viral load for more than a year
(hereafter, “cART recipients”); 32 untreated chronic viremic
patients with plasma viral loads above 10,000 copies/mL
(hereafter, “noncontrollers”); and 36 patients who controlled
viremia without treatment (hereafter, “HIV controllers”).
Within this latter group, 14 were long-term nonprogressors
(LTNPs: untreated patients, with more than 10 years of
infection and stable CD4+ T cell count above 500 cells/μL
and low levels of viremia) and 22 were elite controllers (EC:
untreated patients with undetectable viral load). The
patients’ characteristics are described in detail in Table 1.
All participating individuals provided their informed
written consent, and the protocols were approved by the
institutional ethics committees. The clinical and
epidemiological data provided for patients from the HIV
BioBank were included in the adult cohort of the Spanish
AIDS Research Network (CoRIS), launched in 2004 [
Sample processing and nucleic acid extraction
Peripheral blood mononuclear cells were obtained from
each patient. Subsequently, CD4+ T cells were isolated
using the Dynabeads CD4 positive Isolation Kit from Life
Technologies, following the manufacturer’s instructions.
The purity of the cell fraction was > 98%, as determined by
flow cytometry (BD FACSCalibur). Finally, the extraction of
RNA and DNA from the CD4+ cells was performed using
the AllPrep DNA/RNA/Protein MiniKit (Qiagen). The
obtained RNA and DNA were quantified by
spectrophotometry using a NanoDrop, purity was also assessed by
spectrophotometry, and quality of nucleic acids was
analyzed by electrophoresis. The RNA and DNA were
conserved at − 80 °C until their further use.
Quantification of mRNA by real-time PCR
Isolated mRNAs were reverse transcribed with the
AMVRT Access RT-PCR System, (Promega Biotech), using
random primers (Biotools B&M Labs, Madrid, Spain) under
the following conditions: 95 °C for 5 min before adding the
AMV-RT enzyme, followed by incubation at 25 °C for
10 min, 40 °C for 30 min, 48 °C for 30 min, and a final
inactivation step of 80 °C for 2 min. Five separate reverse
transcription reactions were performed for each patients’
mRNAs, and the resulting cDNAs were pooled for qPCR
analysis. The obtained cDNA was amplified by quantitative
polymerase chain reaction using TaqMan® technology from
Life Technologies. The relative quantification of the genes
of interest was performed using TaqMan Array Gene
Signature 96-well custom plates, structured as follows: 6 sets of
one manufacturing control (18 s), 2 endogenous controls
(GAPDH, B2M), and 12 gene expression assays (SETDB1,
DNMT3a, DNMT3b, HDAC1, HDAC2, HDAC3, HDAC6,
MBD2, HAT1, SUV39H1, PRMT6, SIRT1). One set was
occupied in all assays by the same reference sample, which
(n = 26)
HIV-controller (without cART)
(n = 36)
cART combination antiretroviral therapy, NA not applicable, NS not significant
aData are median (interquartile range, IQR)
bData denote results of comparisons between HIV-positive vs. HIV-negative
(n = 35)
allow us to normalize intra- and inter-assays. The DNMT1
gene expression was analyzed using the TaqMan Gene
Expression assay by Life Technologies in an individual format
using the same endogenous controls. All the samples were
run in duplicate. The assays were performed using an ABI
7500 System, following the manufacturer’s instructions.
Relative levels of gene expression were calculated using the
ΔΔCt method as previously described [
Protein extraction and Western blot analysis
Cells pellets were lysed on ice using the following
extraction buffer: 50 mM Tris HCl pH = 7,5; 150 nM NaCl;
0,5%SDS; 30 mM PPi; NaF 0,5 M; and 100 μM Na3VO4
20 mM. A protease inhibitors cocktail (Calbiochem) was
added before extraction. Cell lysates were separated by
10% SDS-PAGE gel (Mini-PROTEAN TGX gels) and
transferred to nitrocellulose membrane (Amersham
Protran 0,2 μm, GE Healthcare Life Science).Western blotting
was performed using primary antibodies anti DNMT1
(monoclonal antibody DNMT1 clone 60B1220.1,
Epigentek, Inc) and DNMT3a (anti-Dnmt3a ab4897, Abcam)
and anti ACTB (Actin C-11 sc1615, Santa Cruz
Bitotechnology, Inc.) at dilutions 1:1000, 1:1000, and 1:750,
respectively. Secondary antibodies conjugated with HRP
were used at a dilution of 1:2000, and the reaction was
revealed using Amersham ECL Prime Western Blotting
Detection Reagent by GE Healthcare Life Sciences, according
to the manufacturer’s instructions.
Due to sample limitation, only 27 individuals could be
analyzed: 8 HIV-seronegative and 19 HIV-seropositive
individuals (3 non-controllers, 10 cART recipients, and
Global DNA methylation analysis
The amount of CpG 5′-methylcytosines in DNA was
measured in 100 ng of genomic DNA with the
MethylFlash Methylated DNA Quantification kit (Epigentek),
following the manufacturer’s instructions. Positive and
negative DNA methylation controls were included in the
kit. A standard curve was prepared in duplicate with the
positive control provided. All DNA samples were
measured in duplicate.
To compare gene expression among the study groups,
nonparametric Mann-Whitney U and Kruskal-Wallis
tests were used when appropriate. For the correlation
analyses, we performed the Spearman rank correlation
test. Student’s t test was used to assess between-group
differences in DNA methylation. The association
between the categorical variables was evaluated using the
Chi-squared test. A p value cutoff of 0.05 was used for
significance. The statistical analysis was performed using
SPSS software 15.0 (SPSS Inc., Chicago, Illinois, USA).
First, we compared the expression of genes involved in
chromatin modification and other epigenetic mechanisms
on the CD4+ T cells of patients with HIV versus non-HIV
infected individuals. Results showed relevant differences
between both groups in almost all the analyzed genes
(Fig. 1). In detail, among the analyzed histone
methyltransferases (HMTs: SETDB1, SUV39H1, and PRMT6)
shown in Fig. 1a, the expression of histone-lysine
Nmethyltransferase SETDB1 was approximately four times
higher in patients with HIV (median = 2.01 vs. 0.52, p
< .001). The expression of PRMT6, however, was
downregulated (three times lower) in individuals who were
HIV-positive (median = 0.44 vs. 1.38, p = .005). As for the
class I, II, and III histone deacetylases (HDAC1, HDAC2,
HDAC3, HDAC6, and SIRT1), all showed differences in
expression except HDAC1 (Fig. 1b). The highest
difference was observed for HDAC2, with over sixfold
upregulation in patients with HIV-1 (median = 1.02 vs. 0.15, p
< .001). The three genes encoding for DNA
methyltransferases (DNMT1, DNMT3A, and DNMT3B) were also
upregulated in HIV-infected individuals (Fig. 1c, d), with
the highest difference observed in DNMT3B (over sixfold
higher, median = 2.15 vs. 0.41, p < 0.001) (Fig. 1d). The
methyl-CpG binding protein MBD2 was also found to be
twofold higher in patients with HIV-1 (median = 1.28 vs.
0.64, p < 0.001) (Fig. 1c). Finally, histone acetyltransferase
1 (HAT1) also showed upregulation in patients with
HIV1 (Fig. 1e). In a multivariate linear regression analysis,
none of these results was significantly confounded by age
or gender. Only HIV infection independently associated
with changes in gene expression.
We then compared gene expression within the various
groups of individuals with HIV-1, classified according to
their progression status, treatment, and viral control.
The group of combination antiretroviral therapy (cART)
recipients showed an overall surge in expression
compared with the noncontrollers’ group. We note the
elevated expression seen in DNMT3A and DNMTB in
cART recipients who control viral replication. All the
genes with significant differences between these two
groups are shown in detail in Table 2. On the other
hand, the HIV controllers behaved highly similar to
noncontrollers with no differences in median values for any
analyzed gene, except for the expression of DNA
methyltransferases, which were slightly increased, although
not reaching significance due to wide dispersion of
values. Finally, we analyzed associations between genes
and observed a positive correlation of expression among
SETDB1, HDAC1, and DNMT3A (Fig. 2a). It is in the
group of cART recipients that these three genes showed
the greatest differences (Fig. 2b). The cART recipients
also showed the highest frequency of increased
expression in these three genes simultaneously (Table 3).
Western blot analysis showed slightly increased levels of
DNMT3a and DNMT1 expression in HIV-positive
individuals compared to non-HIV infected, but due to small
sample size, differences were not significant. The median
values [IQR] for DNMT3a in HIV+ vs. HIV− were as
follows: 0.215 [0.162–0.263] vs. 0.178 [0.111–0.214] p value
= 0.119 (Fig. 3b) and for DNMT1 1.390 [0.640–1.620] vs.
0.860 [0.35–1.52], p value = 0.260 (Fig. 3c).
The analysis of global 5′-methylcytosine in the genomic
DNA of CD4+ T cells showed a higher percentage of
methylation in the individuals with HIV-1 compared with
non-HIV infected individuals (Fig. 4a). Irrespective of HIV
status, the global DNA methylation was lower in older
individuals (Spearman correlation coefficient rho = − 0.238, p =
0.015) and no effect of gender was observed. Within the
HIV-1 infected patients, the noncontroller and
HIVcontroller groups showed a negative correlation between
DNA methylation and CD4+/CD8+ T cell ratio (Fig. 4b),
whereas this increase in global DNA methylation showed a
positive correlation with the expression levels of DNMT1
in the group of HIV controllers (Fig. 4c).
Several studies performed in vitro have analyzed how
HIV-1 influences cellular epigenetic mechanisms [
Viral infection alters the expression of cellular genes that
modify chromatin structure and affect the process of
infection. In addition, the viral genome itself is modified by
some of these mechanisms, which regulate its level of
Here, we investigated in vivo how the expression of genes
that regulate the chromatin environment is modulated in
Due to missing values, only patients with expression values for SEDTB1,
DNMT3A, and HDAC1 were included in this analysis (n = 117). P value indicates
differences between the cART recipients compared to the other subgroups
CD4+ T cells depending on the viral control and the degree
of progression of patients with HIV.
Overall, the individuals with HIV-1 in our study showed
upregulation in all analyzed chromatin-modifying genes
compared with the non-HIV infected individuals, with
the exception of the PRMT6 gene, which showed
downregulation. PRMT6 is able to methylate host proteins
such as histone 3, as well as the Tat, Rev, and
nucleocapsid viral proteins. This interaction with viral proteins
restricts HIV-1 replication [
]. For example, PRMT6 is
able to bind HIV-1 Rev, decrease its stability, and
attenuate the Rev-Rev response element-dependent export of
viral transcripts to cytoplasm, thus negatively affecting
HIV replication [
]. Likewise, Tat methylation by
PRMT6 decreases viral transcription [
]. Thus, the virus
might modulate PRMT6 expression to fine-tune its cycle
for its own benefit. An in vitro study mimicking acute
HIV-1 infection found PRMT6 to be downregulated
immediately after infection, and its expression further
decreased over time [
]. Also, knockdown experiments of
PRMT6 showed an increase in viral production and faster
]. The lower PRMT6 expression found in
our patients with HIV-1 is in accordance with these
observations in vitro and might favor viral replication.
Otherwise, the expression of PRMT6 has been found to
increase in young cells but to decline in replicative and
stressed-induced senescence cells [
], suggesting a
regulatory role in cell proliferation and senescence. The low
PRMT6 expression in patients with HIV might also
signify CD4+ T cell exhaustion due to a permanent state of
activation, even under antiretroviral treatment. In this
regard, the HIV-controllers’ group behaved similarly to
noncontrollers, whereas the cART recipients exhibited a
slightly higher expression of PRMT6 compared with the
other two groups, but still lower than the expression
observed in non-HIV infected individuals; this result might
indicate residual levels of cell activation despite the
success of therapy.
Among the upregulated genes, we can highlight the
SETDB1 gene, which not only showed higher expression in
individuals with HIV-1, but which also had a positive
correlation with DNMT3A and HDAC1 expression. The
SETDB1 protein is a histone H3 methyltranferase that, in
the context of HIV-1 infection, interacts with and also
methylates Tat [
], and its knockdown in vitro produces
an increase in viral transactivation. At the same time,
SETDB1 has been shown to associate with DNMT3A to
promote gene silencing and also with HDAC1, promoting
closed conformation of chromatin [
]. It has been
proposed that methylation of Tat by SETDB1 facilitates viral
silencing by recruiting several gene silencing proteins to
remodel chromatin. In our study, we observed that the
cART recipients showed higher upregulation of SETDB1,
and in most of these patients, this increase in expression
was combined with the upregulation of the DNMT3A and
HDAC1 genes. This effect was not observed in the other
two groups of study patients. Moreover, the group of
HIVcontrollers behaved similarly to the noncontrollers group.
This observation might suggest the recruitment of
repression machinery toward the HIV-LTR promoter during
antiretroviral treatment, ultimately increasing viral silencing
and favoring the establishment of a latent reservoir. It
would be interesting to quantify the latent viruses in the
cART recipients and compare them with the group of HIV
controllers. In addition, the poor performance observed in
HIV-controllers regarding SETDB1-DNMT3A-HDAC1,
despite viral control, and their closer phenotype to
noncontrollers advocates for the beneficial effect of therapy and its
extended use for all patients with HIV-1.
SIRT1 is another gene that associates with Tat and that
showed differences between the cART recipients and the
other two groups of patients with HIV-1. At later phases
of infection, Tat inhibition of SIRT1 appears to be
critical for inducing cell transformation and apoptosis [
The cART recipients, due to the effective therapy, might
have lower concentrations of Tat, which in combination
with higher expression of SIRT1, could preserve cells
and attenuate the effect of Tat in disease progression.
We also analyzed the impact of HIV-1 infection on global
DNA methylation. All three groups of patients who were
HIV-1 positive had more methylated DNA than the
nonHIV infected individuals. An increase in DNA methylation
had been observed in vitro within a few hours of HIV-1
] and in vivo [
]. Likewise, acute HIV infection
alters DNA methyltransferase mRNA expression and DNA
methyltransferase activity, resulting in an increase in
genomic methylation in primary cells [
]; Tat itself has been
found to induce overexpression of all three DNMTs [
Several studies have linked this increase in methylation to
the upregulation and induction in promoter activity of
]. In our patients, there is an increase in
DNMT3A/3B expression, which are the DNA
methyltransferases responsible for de novo DNA methylation. However,
the observed gains in global DNA methylation show a better
correlation with the expression of DNMT1, especially within
the HIV-controller’s group, which concurs with the early
studies mentioned above and with a previous study
published by our group , in which we observed an increase
in methylation in the LTR region in controllers over time.
DNMT1 is usually referred to as the maintenance DNA
methyltransferase, but it also exhibits significant de novo
]. In a recent study, Trejbalová and colleagues
postulated that transitory activation of T cells contributes to the
accumulation of DNA methylation in the viral promoter
and that DNMT1 was the enzyme responsible for this [
In our HIV-1 controllers, the increase in LTR methylation
over time, the correlation of global DNA methylation, and
DNMT1 expression would support this hypothesis.
Global DNA methylation also alters cellular function.
The changes observed in the methylome of the CD4+ T
cells in infected patients also suggest that HIV-1 mediates
transcriptional repression affecting cell reorganization. In a
recent study, the changes in methylation and increases in
methylome variation observed in CD4+ and CD8+ T cells
occur in aging T cells and affect the expression levels of
genes associated with T cell-mediated immune response,
resulting in impaired T cell function [
]. The global DNA
methylation observed in our patients with HIV-1 as well as
its negative correlation with the CD4+/CD8+ T cell ratio
might resemble what is found in an aging immune system.
We would like to acknowledge some limitations in our
study. First, the number of analyzed patients in HIV
subgroups is small, and it would be of great interest to
replicate these findings in more individuals and other HIV
populations. Second, global DNA methylation has been
measured using an ELISA-based method which serves to
identify large differences in DNA methylation. In our
study differences between HIV and non-HIV infected
individuals were significant; however, other more sensitive
methods should be used to detect smaller differences
within the HIV subgroups. Finally, due to sample
limitation, it was not possible to measure the level of each
protein by Western blot to correlate them with mRNA
expression in all studied subjects.
Our study shows alterations in epigenetic mechanisms
due to HIV-1 infection in patients with various degrees
of progression and viral control. There is an increase in
chromatin-modifying enzymes and remodelers, as well
as an increase in global DNA methylation. The group of
treated patients with controlled viremia differs
substantially from the other two groups, which show a similar
behavior between them. The fact that patients who have
controlled viral replication without treatment show
profiles similar to noncontrollers and quite different from
cART recipients supports the benefit of therapy.
We thank Juliette Siegfried at ServingMed.com for the manuscript revision. We
want to particularly acknowledge the patients in the study for their participation
and the HIV BioBank integrated in the Spanish AIDS Research Network and
collaborating centers for the generous gift of clinical samples used in this study.
The following clinical centers contributed to the HIV BioBank and CoRIS:
Hospital General Universitario de Alicante (Alicante): Joaquín Portilla, Esperanza
Merino, Sergio Reus, Vicente Boix, Livia Giner, Carmen Gadea, Irene Portilla,
Maria Pampliega, Marcos Díez, Juan Carlos Rodríguez, Jose Sánchez-Payá.
Hospital Universitario de Canarias (Santa Cruz de Tenerife): Juan Luis Gómez,
Jehovana Hernández, María Remedios Alemán, María del Mar Alonso, María
Inmaculada Hernández, Felicitas Díaz-Flores, Dácil García, Ricardo Pelazas.
Hospital Universitario Central de Asturias (Oviedo): Victor Asensi, Eulalia Valle,
José Antonio Cartón.
Hospital Doce de Octubre (Madrid): Rafael Rubio, Federico Pulido, Otilia Bisbal,
Mariano Matarranz, Maria Lagarde, Rafael Rubio-Martín, Asunción Hernando,
Laura Bermejo y Lourdes Dominguez.
Hospital Universitario Donostia (San Sebastián): José Antonio Iribarren, Julio
Arrizabalaga, María José Aramburu, Xabier Camino, Francisco
RodríguezArrondo, Miguel Ángel von Wichmann, Lidia Pascual Tomé, Miguel Ángel
Goenaga, Mª Jesús Bustinduy, Harkaitz Azkune Galparsoro. Maialen Ibarguren,
Mirian Aguado, Maitane Umerez.
Hospital General Universitario de Elche (Elche): Félix Gutiérrez, Mar Masiá,
Cristina López, Sergio Padilla, Andrés Navarro, Fernando Montolio, Catalina
Robledano, Joan Gregori Colomé, Araceli Adsuar, Rafael Pascual, Federico
Carlos, Maravillas Martinez, Jara Llenas García, Marta Fernández, Elena García.
Hospital General Universitario Gregorio Marañón (Madrid): Juan Berenguer, Juan
Carlos López Bernaldo de Quirós, Pilar Miralles, Isabel Gutiérrez, Margarita
Ramírez, Belén Padilla, Paloma Gijón, Ana Carrero, Teresa Aldamiz-Echevarría,
Francisco Tejerina, Francisco Jose Parras, Pascual Balsalobre, Cristina Diez.
Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili
(Tarragona): Francesc Vidal, Joaquín Peraire, Consuelo Viladés, Sergio Veloso,
Montserrat Vargas, Miguel López-Dupla, Montserrat Olona, Alba Aguilar, Joan
Josep Sirvent, Verónica Alba, Olga Calavia .
Hospital Universitario La Fe (Valencia): Marta Montero, José Lacruz, Marino
Blanes, Eva Calabuig, Sandra Cuellar, José López, Miguel Salavert.
Hospital Universitario La Paz/IdiPaz (Madrid): Juan González, Ignacio
Bernardino de la Serna, José Ramón Arribas, María Luisa Montes, Jose Mª
Peña, Blanca Arribas, Juan Miguel Castro, Fco Javier Zamora, Ignacio Pérez,
Miriam Estébanez, Silvia García, Marta Díaz, Natalia Stella Alcáriz, Jesús
Mingorance, Dolores Montero, Alicia González, Maria Isabel de José.
Hospital de la Princesa (Madrid): Ignacio de los Santos, Jesús Sanz, Ana Salas,
Cristina Sarriá, Ana Gómez Berrocal, Lucio Garcia-Fraile.
Hospital San Pedro-CIBIR (Logroño): José Antonio Oteo, José Ramón Blanco,
Valvanera Ibarra, Luis Metola, Mercedes Sanz, Laura Pérez-Martínez.
Complejo Hospitalario de Navarra (Pamplona): María Rivero, Marina Itziar Casado,
Jorge Alberto Díaz, Javier Uriz, Jesús Repáraz, Carmen Irigoyen, María Jesús Arraiza.
Hospital Ramón y Cajal (Madrid): Santiago Moreno, José Luis Casado,
Fernando Dronda, Ana Moreno, María Jesús Pérez Elías, Dolores López,
Carolina Gutiérrez, Nadia Madrid, Angel Lamas, Paloma Martí, Alberto de
Diaz, Sergio Serrrano, Lucas Donat.
Hospital Reina Sofía (Murcia): Alfredo Cano, Enrique Bernal, Ángeles Muñoz.
Hospital San Cecilio (Granada): Federico García, José Hernández, Alejandro
Peña, Leopoldo Muñoz, Jorge Parra, Marta Alvarez, Natalia Chueca, Vicente
Guillot, David Vinuesa, Jose Angel Fernández.
Centro Sanitario Sandoval (Madrid): Jorge Del Romero, Carmen Rodríguez,
Teresa Puerta, Juan Carlos Carrió, Mar Vera, Juan Ballesteros.
Hospital Universitario Santiago de Compostela (Santiago de Compostela):
Antonio Antela, Elena Losada.
Hospital Son Espases (Palma de Mallorca): Melchor Riera, Maria Peñaranda,
Maria Leyes, Mª Angels Ribas, Antoni A Campins, Carmen Vidal, Leire Gil,
Francisco Fanjul, Carmen Marinescu.
Hospital Virgen de la Victoria (Málaga): Jesús Santos, Manuel Márquez, Isabel
Viciana, Rosario Palacios, Isabel Pérez, Carmen Maria González.
Hospital Universitario Virgen del Rocío (Sevilla): Pompeyo Viciana, Manuel Leal,
Luis Fernando López-Cortés, Nuria Espinosa.
This work was supported by grants from the Instituto de Salud Carlos III,
Subdirección General y Fomento de la Investigación, the Spanish Ministry of
Economy and Competitiveness and the European Regional Development Fund
(PI12/00850). Alicia de Pablo was supported by Grant CA12/00333, Rosa Rodriguez
by Grant CPII13/00022 and PI12/00581, Victor Toledano by Grant PTA2013-8265-I,
and Berta Rodés by Grant CES11/021. The HIV BioBank, integrated in the Spanish
AIDS Research Netwrok, is supported by Instituto de Salud Carlos III, Spanish
Ministry of Health (Grant RD06/0006/0035), European Regional Development Fund,
and Fundación para la Investigación y Prevención en Sida (FIPSE).
Availability of data and materials
All data generated or analyzed during this study are included in this
RB performed the research, analyzed the data, and wrote the paper. AP
performed the gene expression analysis. EV, LMC, VM, HHVR, and VA
provided the clinical data. RR and VT provided the control samples and data.
BR was the principal investigator, performed the research, analyzed the data,
and wrote the paper. Participation of authors HHVR and VA was on behalf of
the CoRIS and HIV Biobank integrated into the Spanish Research Network. All
authors read and approved the final manuscript.
Ethics approval and consent to participate
All participating individuals provided their informed written consent, and the
protocols were approved by the Hospital Universitario La Paz and Spanish
AIDS Research Network ethics committees.
Consent for publication
The authors declare that they have no competing interests.
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