Prevalence of resistance mutations related to integrase inhibitor S/GSK1349572 in HIV-1 subtype B raltegravir-naive and -treated patients

ArticleinJournal of Antimicrobial Chemotherapy 66(7):1481-3 · July 2011with81 Reads
Impact Factor: 5.31 · DOI: 10.1093/jac/dkr152 · Source: PubMed
Abstract

To compare the frequency of previously in vitro-selected integrase mutations (T124A, T124A/S153F, S153Y, T124A/S153Y and L101I/T124A/S153Y) conferring resistance to S/GSK1349572 between HIV-1 subtype B integrase inhibitor (INI)-naive and raltegravir-treated patients. Integrase sequences from 650 INI-naive patients and 84 raltegravir-treated patients were analysed. The T124A mutation alone and the combination T124A/L101I were more frequent in raltegravir-failing patients than in INI-naive patients (39.3% versus 24.5%, respectively, P = 0.005 for T124A and 20.2% versus 10.0%, respectively, P = 0.008 for T124A/L101I). The S153Y/F mutations were not detected in any integrase sequence (except for S153F alone, only detected in one INI-naive patient). T124A and T124A/L101I, more frequent in raltegravir-treated patients, could have some effect on raltegravir response and their presence could play a role in the selection of other mutations conferring S/GSK1349572 resistance. The impact of raltegravir-mediated changes such as these on the virological response to S/GSK1349572 should be studied further.

Full-text

Available from: Slim Fourati, Oct 01, 2014
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Journal of Antimicrobial Chemotherapy: under review
Journal of Antimicrobial Chemotherapy
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Prevalence of resistance mutations related to integrase inhibitor S/GSK1349572 in HIV-1 1
subtype B raltegravir-naïve and -treated patients 2
Isabelle Malet
1*
, Marc Wirden
1
, Slim Fourati
1
, Daniele Armenia
2
, Bernard Masquelier
3
, 3
Lavinia Fabeni
2,4
, Sophie Sayon
1
, Christine Katlama
1
, Carlo Federico Perno
2,4
, Vincent 4
Calvez
1
, Anne-Geneviève Marcelin
1
and Francesca Ceccherini-Silberstein
2
5
6
1
Laboratoire de Virologie, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, UPMC Univ Paris 7
06, INSERM U943, Paris, France;
2
Department of Experimental Medicine, University of 8
Rome Tor Vergata, Rome, Italy;
3
Laboratoire de Virologie, CHU de Bordeaux, EA 2968, 9
Université Victor Segalen, Bordeaux, France;
4
National Institute for Infectious Diseases 10
(INMI) L. Spallanzani,
Rome, Italy 11
12
13
*Corresponding author. Mailing address: hôpital Pitié-Salpêtrière, Service de Virologie, 83, 14
bld de l’hôpital, 75013 Paris, France. Phone: 0033 142177401. Fax: 0033 142177411. E-mail: 15
isabelle.malet@psl.aphp.fr 16
17
Short title: S/GSK1349572 mutations in HIV-1 patients 18
19
Keywords: resistance, failure, polymorphism, prevalence 20
Page 1 of 8
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Objectives: To compare the frequency of previously in vitro selected integrase mutations 21
(T124A, T124A/S153F, S153Y, T124A/S153Y and L101I/T124A/S153Y) to S/GSK1349572 22
between HIV-1 subtype B integrase inhibitor (INI)-naïve and raltegravir (RAL)-treated 23
patients. 24
25
Methods: Integrase (IN) sequences from 650 INI-naïve patients and 84 raltegravir-treated 26
patients were analyzed. 27
28
Results: T124A mutation alone and the combination T124A/L101I were more frequent in 29
raltegravir-failing patients than in INI-naïve patients (39.3% versus 24.5%, respectively, with 30
p=0.005 for T124A and 20.2% versus 10%, respectively, with p=0.008 for T124A/L101I) as 31
the S153Y/F mutations have never been detected in any integrase sequence. 32
33
Conclusions: T124A and T124A/L101I, more frequent in raltegravir-treated patients, could 34
have some effect on raltegravir response and their presence could play a role in the selection 35
of other mutations conferring S/GSK1349572 resistance. The impact of such changes 36
mediated by raltegravir should be further studied on the virological response to 37
S/GSK1349572. 38
39
40
41
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Introduction 42
Integrase, the HIV-1 enzyme responsible for the integration of the viral genome into the 43
chromosomes of infected cells, is the target of the recently approved antiretroviral raltegravir 44
(RAL) and currently investigated elvitegravir (EVG). Despite activity against viruses resistant 45
to other antiretrovirals, failures against integrase inhibitors (INIs) therapy were observed, in 46
association with the emergence of resistance due to mutations in the integrase gene.
1
47
S/GSK1349572 is a next generation HIV-1 strand transfer INI with high potency (IC
50
48
measured in presence of human serum = 38 nM).
2
In vitro, serial passage experiments 49
identified five single or combined amino acid substitutions that could confer S/GSK1349572 50
resistance: T124A, T124A/S153F, S153Y, T124A/S153Y and L101I/T124A/S153Y.
2
51
S/GSK1349572, showing low fold changes in activity against site directed molecular clones, 52
including Y143C/H/R, Q148K/R/H and N155H, seems to have limited cross-resistance to 53
raltegravir- and elvitegravir-resistant mutants
3
and may have a higher genetic barrier to 54
resistance than raltegravir.
4
In vivo, preliminary results in 10 HIV-1 infected patients INI 55
naïve and treated by S/GSK1349572 in monotherapy (50 mg once daily) during 10 days 56
reported a HIV-1 plasma viral load decrease of -2.46 log
10
copies/mL.
5
Another recent study 57
evaluated the short-term antiviral activity of S/GSK1349572 (at day 11) in 27 raltegravir-58
experienced patients with raltegravir-resistant viruses. Results showed a HIV-1 plasma viral 59
load decrease of -1.45 log
10
copies/mL in 100% of patients harboring mutations linked to the 60
N155 and Y143 pathways. In contrast, a viral load decrease of -0.72 log
10
copies/mL was 61
observed only in 33% of patients harboring the Q148 pathway associated with L74, E138 or 62
G140 mutations.
6
63
In INI-naïve patients, there is a limited degree of natural polymorphisms in the integrase 64
gene from subtype B HIV-1, since 65% of HIV-1 integrase residues are conserved (< 1% 65
variability). Residues involved in protein stability, multimerization, DNA binding, catalytic 66
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activity, and in the binding with the human cellular cofactor LEDGF/p75 are fully conserved.
7
67
It has also been shown that all primary signature mutations emerging in patients failing 68
raltegravir (Y143C/R, Q148H/K/R, N155H) or elvitegravir (T66I, E92Q, S147G, 69
Q148H/K/R, N155H), as well as secondary mutations (H51Y, T66A/K, E92A/G/Q, F121Y, 70
E138K, G140S/A/C, Y143C/H, K160N, R166S, E170A, S230R, D232N, R263K) were 71
completely absent or highly infrequent (< 0.5%) in INI-naïve patients infected with HIV-1 B 72
subtype.
7
The aims of this study were to explore potential primary genotypic resistance to 73
S/GSK1349572 in INI naïve patients and the ability of this compound to treat patients with 74
raltegravir resistance. Thus, we evaluated the proportion of patients carrying viruses with 75
resistance mutations previously described to S/GSK1349572 in HIV-1 subtype B raltegravir-76
naïve and -treated patients. 77
78
Materials and methods 79
In this report, sequences of the entire integrase gene from 650 INI-naïve patients and 84 80
raltegravir-experienced (all raltegravir-failing) patients, all infected with subtype B HIV-1 81
strains, were analyzed for the presence of previously described in vitro mutations to 82
S/GSK1349572. At the time of the genotypic resistance test, INI-naïve patients (143 HAART 83
(Highly Active Antiretroviral Therapy)-naïve and 507 HAART-experienced) and raltegravir-84
treated patients (all HAART-experienced) received, in their optimized regimen, at least one 85
NRTI (Nucleoside Reverse Transcriptase Inhibitor) with one boosted PI (Protease Inhibitor) 86
or one NNRTI (Non-Nucleoside Reverse Transcriptase Inhibitor) plus, for some of them, 87
enfuvirtide or maraviroc. INI-naïve and raltegravir-treated patients showed a median viral 88
load of 4.2 (3.6 - 4.9) log
10
copies/mL and 3.8 (2.5 - 5.1) log
10
copies/mL, respectively. 89
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RNA was extracted from 500 µL of plasma, and a 1086 base pair fragment encompassing 90
the entire IN gene was amplified, as described previously.
8
The PCR products were purified 91
and sequenced using a cycle sequencing reaction with the Big Dye terminator kit (Applied 92
Biosystems, Foster City, California, USA). The sequences were aligned using SmartGene 93
software (SmartGene GmbH, Zug, Switzerland) and the amino acid sequence of HIV-1 94
integrase (288 amino acids) of clade B consensus was considered as a reference. 95
96
Results 97
The prevalence of in vitro selected mutations by S/GSK1349572 in naïve and raltegravir-98
treated patients is presented in Table 1. Mutations L101I and T124A seem to be polymorphic 99
in INI-naïve patients with frequencies of 45.8% and 24.5%, respectively, the two associated 100
mutations L101I/T124A being present with a frequency of 10%. In raltegravir-treated 101
patients, the genotypic resistance test performed at raltegravir failure, showed that mutations 102
L101I, T124A and L101I/T124A occurred with frequencies of 56%, 39.3% and 20.2%, 103
respectively. Consequently, only mutations T124A and L101I/T124A were more frequent in 104
raltegravir-failing patients than in INI-naïve patients (p = 0.005 and 0.008, respectively). The 105
mutations S153Y/F, and consequently the profiles T124A/S153F, T124A/S153Y and 106
L101I/T124A/S153Y, have never been detected in any sequence from both INI-naïve and 107
raltegravir-failing patients (except for S153F alone, only detected in one INI-naïve patient). 108
109
Discussion 110
In conclusion, some previously in vitro selected mutations by S/GSK1349572 (T124A and 111
L101I/T124A) are polymorphic but significantly more frequent in raltegravir-treated patients 112
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than in raltegravir-naïve patients. This result suggests that these mutations could have some 113
effect on raltegravir response, at least as secondary resistance mutations. The fact that these 114
mutations are increased in raltegravir-failing patients and selected in vitro by S/GSK1349572 115
also suggests that they can participate to raltegravir and S/GSK1349572 cross-resistance. The 116
mutation T124A, alone or associated with L101I, is among the first mutations that appear in 117
culture, under S/GSK1349572 pressure, at day 56,
2
suggesting a role in the resistance to 118
S/GSK1349572. A recent study has shown that baseline viruses with L101I and/or T124A do 119
not seem to have an impact, at day 10, on S/GSK1349572 response in INI-naïve patients.
9
120
However, considering the higher prevalence of T124A and L101I/T124A mutations in 121
raltegravir-treated patients, we could not exclude that their presence in raltegravir-failing 122
patients could favour the selection of other mutations conferring S/GSK1349572 resistance. 123
Thereby, it should be interesting to study the response to S/GSK1349572 treatment in patients 124
failing to raltegravir to evaluate the impact of IN polymorphisms and to study if these 125
polymorphisms can affect the selected resistance mutations in case of failure to 126
S/GSK1349572. 127
Funding 128
The research leading to these results has received funding from Sidaction, the Agence 129
Nationale de Recherche sur le SIDA (ANRS), the Association de Recherche en Virologie et 130
Dermatologie (ARVD) and the European Community’s Seventh framework Program 131
(FP7/2007-2013) under the project ‘Collaborative HIV and Anti-HIV Drug Resistance 132
Network (CHAIN)’. We thank G. Le Mallier and P. Grange for their technical assistance. 133
Transparency declarations 134
None to declare 135
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References 136
137
1. Grinsztejn B, Nguyen BY, Katlama C et al. Protocol 005 Team. Safety and efficacy of the 138
HIV-1 integrase inhibitor raltegravir (MK-0518) in treatment-experienced patients with 139
multidrug-resistant virus: a phase II randomised controlled trial. Lancet 2007; 369: 1261-9. 140
141
2. Sato A, Kobayashi M, Yoshinaga T et al. S/GSK1349572 is a potent next generation HIV 142
integrase inhibitor. In: Abstracts of the fifth IAS Conference on HIV Pathogenesis, Treatment 143
and Prevention, Cape Town, South Africa, 2009. Abstract WEPEA097. 144
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3. Seki T, Kobayashi M, Wakasa-Morimoto C et al. S/GSK1349572 is a potent next 146
generation HIV integrase inhibitor and demonstrates a superior resistance profile 147
substantiated with 60 integrase mutant molecular clones. In: Abstracts of the seventeenth 148
Conference on Retroviruses and Opportunistic Infections, San Francisco, CA, USA, 2010. 149
Abstract 555. 150
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4. Sato A, Seki T, Kobayashi M et al. In vitro passage of drug resistant HIV-1 against a next 152
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2009. Abstract H-932. American Society for Microbiology, Washington, DC, USA. 155
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5. Lalezari J, Sloan L, Dejesus E et al. Potent antiviral activity of S/GSK1349572, a next 157
generation integrase inhibitor (INI), in INI-naïve HIV-1-infected patients. In: Abstracts of the 158
fifth IAS Conference on HIV Pathogenesis, Treatment and Prevention, Cape Town, South 159
Africa, 2009. Abstract TUAB105. 160
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6. Eron J, Durant J, Poizot-Martin I et al. Activity of next generation integrase inhibitor (INI) 162
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Vienne, Austria, 2010. Abstract MOAB0105. 165
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7. Ceccherini-Silberstein F, Malet I, D'Arrigo R et al. Characterization and structural analysis 167
of HIV-1 integrase conservation. AIDS Rev 2009; 11: 17-29. 168
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8. Malet I, Delelis O, Valantin MA et al. Mutations associated with failure of raltegravir 170
treatment affect integrase sensitivity to the inhibitor in vitro. Antimicrob Agents Chemother 171
2008; 52: 1351-8. 172
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9. Vavro C, Underwood M, Madsen H et al. Polymorphisms at position 101 and 124 in the 174
HIV-1 integrase (IN) gene: lack of effects on susceptibility to S/GSK1349572. In: Abstracts 175
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Boston, MA, 2010. Abstract H-935. American Society for Microbiology, Washington, DC, 177
USA. 178
179
180
181
182
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Table 1. Evaluation and comparison of prevalence of L101I, T124A, S153F and S153Y 183
mutations in INI-naïve and RAL-failing patients 184
185
Integrase inhibitor-
naïve patients
(n=650)
Raltegravir failing
patients
(n=84)
Integrase
mutations
n % n %
p value
L101I 298 45.8 47 56.0 0.083
T124A 159 24.5 33 39.3 0.005
a
L101I + T124A 65 10.0 17 20.2 0.008
a
S153Y 0 0 0 0 -
S153F 1 0.2 0 0 -
a
p values shown in bold are valid after multiple comparison tests 186
187
188
189
190
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    • "In contrast, the presence of Q148HKR mutations did lead to further mutations and >100 FC for DTG susceptibility relative to wild type in subtype B viruses [123, 125]. Interestingly, Q148HKR mutations did not affect susceptibility to DTG in HIV-1 subtype C and HIV-2 isolates [125, 134, 135]. An ongoing trial termed SPRING-2 will evaluate the use of once-daily DTG versus twice-daily RAL in treatment-naïve patients. "
    [Show abstract] [Hide abstract] ABSTRACT: This review focuses on the topic of HIV integrase inhibitors that are potent antiretroviral drugs that efficiently decrease viral load in patients. However, emergence of resistance mutations against this new class of drugs represents a threat to their long-term efficacy. Here, we provide new information about the most recent mutations identified and other mutations that confer resistance to several integrase inhibitors, such as new resistance mutations-for example, G118R, R263K, and S153Y-that have been identified through in vitro selection studies with second-generation integrase strand transfer inhibitors (INSTIs). These add to the three main resistance pathways involving mutations at positions Y143, N155, and Q148. Deep sequencing, structural modeling, and biochemical analyses are methods that currently help in the understanding of the mechanisms of resistance conferred by these mutations. Although the new resistance mutations appear to confer only low levels of cross-resistance to second-generation drugs, the Q148 pathway with numerous secondary mutations has the potential to significantly decrease susceptibility to all drugs of the INSTI family of compounds.
    Full-text · Article · Nov 2012 · Current Infectious Disease Reports
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    • "In contrast, the presence of Q148HRK mutations did lead to further mutations and > 100 FC for DTG susceptibility relative to wild-type in subtype B viruses [63,65]. Interestingly, Q148HRK mutations did not affect susceptibility to DTG in HIV-1 subtype C and HIV-2 isolates [65,75,76]. An ongoing trial termed SPRING-2 will evaluate the use of once-daily DTG versus twice-daily RAL in treatment-naïve patients. "
    [Show abstract] [Hide abstract] ABSTRACT: Integration of the viral genome into host cell chromatin is a pivotal and unique step in the replication cycle of retroviruses, including HIV. Inhibiting HIV replication by specifically blocking the viral integrase enzyme that mediates this step is an obvious and attractive therapeutic strategy. After concerted efforts, the first viable integrase inhibitors were developed in the early 2000s, ultimately leading to the clinical licensure of the first integrase strand transfer inhibitor, raltegravir. Similarly structured compounds and derivative second generation integrase strand transfer inhibitors, such as elvitegravir and dolutegravir, are now in various stages of clinical development. Furthermore, other mechanisms aimed at the inhibition of viral integration are being explored in numerous preclinical studies, which include inhibition of 3' processing and chromatin targeting. The development of new clinically useful compounds will be aided by the characterization of the retroviral intasome crystal structure. This review considers the history of the clinical development of HIV integrase inhibitors, the development of antiviral drug resistance and the need for new antiviral compounds.
    Full-text · Article · Apr 2012 · BMC Medicine
    0Comments 42Citations
  • [Show abstract] [Hide abstract] ABSTRACT: Changing antiretroviral regimens and the introduction of new antiretroviral drugs have altered drug resistance patterns in human immunodeficiency virus type 1 (HIV-1). This review summarizes recent information on antiretroviral drug resistance. As tenofovir and abacavir have replaced zidovudine and stavudine in antiretroviral regimens, thymidine analog resistance mutations have become less common in patients failing antiretroviral therapy in developed countries. Similarly, the near universal use of ritonavir-boosted protease inhibitors (PI) in place of unboosted PIs has made the selection of PI resistance mutations uncommon in patients failing a first-line or second-line PI regimen. The challenge of treating patients with multidrug-resistant HIV-1 has largely been addressed by the advent of newer PIs, second-generation non-nucleoside reverse transcriptase inhibitors and drugs in novel classes, including integrase inhibitors and CCR5 antagonists. Resistance to these newer agents can emerge, however, resulting in the appearance of novel drug resistance mutations in the HIV-1 polymerase, integrase and envelope genes. New drugs make possible the effective treatment of multidrug-resistant HIV-1, but the activity of these drugs may be limited by the appearance of novel drug resistance mutations.
    Preview · Article · Dec 2011
    0Comments 24Citations
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