Unique integration patterns in an in vitro model of HIV-1 latency. Suha M. Saleh, Dimitrios Vatakis,...
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Transcript of Unique integration patterns in an in vitro model of HIV-1 latency. Suha M. Saleh, Dimitrios Vatakis,...
Unique integration patterns in an in vitro model of HIV-1
latency.
Suha M. Saleh, Dimitrios Vatakis, Andrew Harman, Anthony Cunningham, Paul U. Cameron, and
Sharon R Lewin
Background:
HIV-1 infection cannot be eradicated with highly active antiretroviral therapy (HAART) because of latent infection of long lived resting memory CD4+ T-cells. - Chun et al., Nat. Med., 1995; Chun et al., Nature, 1997; Finzi et al., Science, 1997; Brenchley et al., J Virol., 2004
2009
Latency is maintained in resting T-cells by factors that largely restrict both transcription and translation. - Jordan, et al., EMBO J., 2001; Krishnan and Zeichner., J. Virol., 2004;
Bennasser et al., Immunity., 2005; Coiras et al., Retrovirology , 2007; Hay et al., Cell Host Microbe., 2008; Kauder et al., Plos Pathogens, 2009
Integration of HIV-1 in resting CD4+ T cells from patients on HAART occurs within introns of actively transcribed genes.- Han et al., J Virol. 2004; Shan et al., J Virol 2011
HIV latency and infection of resting T-cells: pre and post activation
Activated CD4+ T-cell
Resting CD4+ T-cell
Pre-activation latency
Post-activation latency
chemokines
In vitro
Unactivated resting cellsResting CD4+ T-cell
Ex vivo tissue blocks
Eckstein et al, Immunity 2001; 15: 671; Kreisberg et al., J Exp Med 2006; 203:865; Saleh et al., Blood 2007; 110:416; Marini et al., J Immunol 2008; 181: 7713-20; Bosque and Planelle, Blood 2009; 113:58; Cameron et al., Proc Natl Acad Sci 2010 epub Sept 18
Infection of resting CD4+ T-cells
Pre-activation latency
Hypothesis:Establishment of latency following direct infection of resting CD4+ T-cells (pre-activation latency) will be associated with a distinct pattern of integration.
Aim 1: To compare the sites of integration following
infection of CCL19 treated, unactivated and fully activated CD4+ T-cells with latently infected cells from patients on cART.
Aim 2: To determine the relationship of integration
sites to transcription factor binding sites and cellular gene expression.
Aims
Sample Unique Integration site
IL2/PHA 432
CCL19 247
Unactivated (media alone)
133
Identification of unique integration sites:
0
50000
100000
150000
200000
250000
p<0.001 p<0.001
p<0.001
Bas
e p
airs
Integration in CCL19 treated cells is further from Transcriptional Start Sites (TSS)
Unact
ivate
d
CCL19
IL2/
PHA
Patie
nts 0 50 100
0
50
100
CCL19
Unactivated
Patients
IL2/PHA
Distance from TSS
% s
ite o
f in
tegr
atio
n
Chromosomal Feature
Unactivated CCL19 IL2/PHA Patients cells Significant
H2AZ ++ +++ ++ + <0.0001
DNAse hypersensitivity sites ++ ++++ ++ + <0.0001
Alu
++ +++ ++ ++ <0.0001
CCL19 treated cells have significantly different integration sites
0
500
1000
1500
2000p<0.001 p<0.001
Bas
e p
air
s
Integration in CCL19 treated cells is closer to Long Interspersed Nuclear Elements
Unactivated CCL19 IL2/PHAPatients
Chromosomal Feature
Unactivated CCL19 IL2/PHA Patients cells Significant
CTCF ++ ++ ++ ++ ns
CPG ++ ++ ++ + ns
Pol II++ ++ ++ + ns
Comparison of HIV integration site distributions
ns: not significant
H4R3me2Intermediate transcriptional activity
Histone methylation sites
H4K20me3transcriptional repression
IL2/PHA PatientsCCL19 UnactivatedPatientsUnactivated CCL19 IL2/PHA
CCL19CCL19
IL2/
PH
A
The majority of the genes near integration sites in all in vitro conditions were involved in cellular housekeeping activities and cell signaling pathways.
Un
acti
vate
CCL19
No differences in expression of genes near integration sites in different in vitro conditions
Gene expression (heat map)
Summary:
HIV-1 integration occurred in transcriptionally active genes in all culture conditions.
Sites of integration of HIV-1 in latently infected CCL19 treated cells was different to other in vitro conditions and patients derived cells.
In CCL19 treated cells, integration was Further from TSS
Closer to
A/T-rich LINE elements
H4K20me3 (heterochromatin marker)
H4K3me2 (involved in priming gene expression).
Conclusions and implications
• Sites of integration of HIV-1 might be determined by activation state of the cell at the time of infection.
• Differing sites of integration may have implications for designing strategies to reverse latency.
Future directions
Integration sites in cells with inducible and non-inducible expression of HIV-1 in CCL19 treated latently infected cells using an EGFP reporter virus.
Analysis of latently infected resting CD4 T-cells from blood and tissue in patients on cART.
Acknowledgements
Department of Medicine, Monash University– Sharon Lewin– Paul Cameron
Department of Medicine, UCLA,California
– Dimitrios Vatakis
Westmead Millenium Research Institute– Tony Cunningham– Andrew Harman