HIV-1 Integrase Variants
Retarget Proviral Integration
and Are Associated with
Disease Progression
July 21st, 2015
IAS meeting Vancouver
© Lisa Demeulemeester
Jonas Demeulemeester, Sofie Vets, Rik Schrijvers,
Paradise Madlala, Thumbi Ndung’u, Zeger Debyser,
Rik Gijsbers
Laboratory for Molecular Virology and Gene Therapy
- KU Leuven, Belgium
Integration site selection
Retroviral integration is not random
nuclear entry route
host-cell cofactors (LEDGF/p75)
viral IN
Integration site selection
Integrase picks the spot
HIV-1
EIAV
Do IN amino acid-tDNA base contacts affect integration site selection?
S119 and R231 of HIV-1 IN Directly Contact tDNA Bases
Homology model of HIV-1 intasome TCC (target capture complex)
Most interactions contact the tDNA phosphodiester backbone
Two sites of direct aa-tDNA base contact in HIV-1 IN
Retroviral sequences show IN119/231 polymorphism
Polymorphism at IN position 119, 122; less variability at 231.
Patient-derived sequences reveal IN119/231 polymorphism
Alternative polymorphism at IN position 119, less variability at 231
- Los Alamos HIV Sequence Database (n=2276)
Patient-derived sequences reveal IN119/231 polymorphism
Alternative polymorphism at IN position 119, less variability at 231
- Los Alamos HIV Sequence Database (n=2276)
What is the effect of these IN polymorphisms on integration?
Variants introduced into multiple-round HIV-1NL4-3
single-round HIV_fLuc reporter virus
No effect on viral infectivity nor replication capacity (MT-4, SupT1, prim. T cells)
Altered tDNA contacts locally retarget viral integration
Infected SupT1 and HeLaP4 cells and sequenced 36,264 viral integration sites
Sequence logo of integration site (intasome footprint)
Altered IN119 tDNA contacts locally retarget viral integration
Altered IN231 tDNA contacts locally retarget viral integration
HIV-1 INS119T-R231G mimics EIAV local integration site preferences
HIV-1 INS119-R231
HIV-1 INS119T-R231G
EIAV INT119-G231
HIV-1 INS119T-R231G mimics EIAV local integration site preferences
HIV-1 INS119T-R231G
HIV-1 IN119G/V and IN231G variants direct integration away from
gene dense regions
HIV-1 INS119G and INR231G are linked to rapid disease progression
Sinikithemba:
chronic HIV-1 subtype C infection cohort
(2003–2008, McCord Hospital, Durban, South Africa)
85 patients with longitudinal follow-up and sequenced IN sequence (Rousseau et al., 2006)
Increase numbers to allow confident generalization
HIV-1 INS119G and INR231G are linked to rapid disease progression
Sinikithemba:
chronic HIV-1 subtype C infection cohort
(2003–2008, McCord Hospital, Durban, South Africa)
85 patients with longitudinal follow-up and sequenced IN sequence (Rousseau et al., 2006)
Increase numbers to allow confident generalization
Conclusions
Integration site targeting role of IN positions 119, 122 and 231 in the virus
Altered local tDNA contacts can shift
the local intasome footprint
the global integration pattern
INS119G and INR231G are linked to disease progression in a chronic HIV-1 infection cohort
Implications
IN119 implicated in immune evasion from HLA-C*05 (Brockman et al. 2012, J Virol)
>> interplay between immune pressure – viral integration site selection
Role of IN119 polymorphisms in IN inhibitor resistance (Ceccherini-Silberstein et al. 2010, J Antimicrob Chemother)
>> interaction antiretroviral therapy – viral integration site selection
Further confirmation of patient disease progression data
>> interaction integration site selection – virulence/viral evolution
Molecular Virology and Gene Therapy
KU Leuven, Belgium
Zeger Debyser
Jonas Demeulemeester, Sofie Vets, Rik Schrijvers
Paulien Van De Velde, Barbara Van Remoortel
HIV Pathogenesis Program, DDMRI
University of KwaZulu-Natal, South Africa
Thumbi Ndung’u, Paradise Madladla, Nonhlanhla Yende
Department of Microbiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
Frederick D. Bushman, Nirav Malani
The participants and clinicians of the Sinikithemba cohort
HIV-1 Integrase Variants
Retarget Proviral Integration
and Are Associated with
Disease Progression
July 21st, 2015
IAS meeting Vancouver
© Lisa Demeulemeester
Jonas Demeulemeester, Sofie Vets, Rik Schrijvers,
Paradise Madlala, Thumbi Ndung’u, Zeger Debyser,
Rik Gijsbers
Laboratory for Molecular Virology and Gene Therapy
- KU Leuven, Belgium