of Integrase Inhibitors

Transcription

1 Resistance Characteristics of Integrase Inhibitors Dr Charlotte CHARPENTIER Laboratoire de Virologie Hôpital Bichat-Claude Bernard INSERM UMR IAME Université Paris Diderot

2 Plan 1 st generation: Raltegravir (RAL) and Elvitegravir (EVG/c) 2 nd generation: Dolutegravir (DTG) Epidemiology of resistance to integrase inhibitors Ongoing: Bictegravir (BIC) and Cabotegravir (CAB)

3 Plan 1 st generation: Raltegravir (RAL) and Elvitegravir (EVG/c) 2 nd generation: Dolutegravir (DTG) Epidemiology of resistance to integrase inhibitors Ongoing: Bictegravir (BIC) and Cabotegravir (CAB)

4 In vitro selection experiments RAL EVG

5 RAL and EVG mean FC of single mutation SDMs

6 RAL: analysis of resistance in the BENCHMRK trials Phase 3 clinical trials conducted in highly-experienced patients with resistant viruses: RAL + Optimized Background Treatment VL <400 c/ml in 78 % of patients at W16 (vs 42 % in placebo group) Genotypic resistance to RAL in 60 % of patients in VF with available integrase sequence at VF Three major resistance mutations: codons 143, 148 and 155 Emergence of resistance mainly occurred during the first years of the trial, rarely after the third year Cooper et al., NEJM, 2008; Eron et al., Lancet Infect Dis, 2013

7 Combined analysis of resistance at W96 in the TDF and TAF/FTC/EVG/c trials in ARV-naïve patients Patients meeting criteria for resistance analysis E/c/F/TAF (n = 866) E/c/F/TDF (n = 867) 19 (2 %) 16 (2 %) Resistance mutations 10 (1.2 %) 8 (0.9 %) RT mutations 10 (1.2 %) 7 (0.8 %) M184I/V 9 6 K65N/R 2 3 K70R 1 1 Integrase mutations 8 (0.9 %) 5 (0.6 %) T66A/I/V 2 0 E92Q 4 2 Q148R 1 2 N155H/S Resistance development (%) E/C/F/TAF E/C/F/TDF S48 S96 S48 S96 Patients with criteria for resistance analysis Emergence of resistance Distribution of resistance mutations at time of VF FTC FTC TAF TDF EVG EVG Rare selection of resistance and in similar proportions in the TAF and TDF arms Callebaut et al., IHDRW 2016, Abs. 32; CROI 2016, Abs. 496

8 Y143R +T97A Y143C +T97A N155H +E92Q Q148R +G140S Q148H +G140S Y143R +T97A Y143C +T97A N155H +E92Q Q148R +G140S Q148H +G140S Switch from 155 to 148 resistance profile RAL Fold-Change 100 Maximum Fold Change Viral replicative capacity (%) 50 0 Fransen et al., Antimicrob Agents Chemother, 2009 Fransen et al., CROI 2009, Abs. 69

9 Major mutations and secondary mutations Major mutations Q148H/K/R N155H Y143C/H/R Secondary mutations G140A/S, E138K E92Q, L74M, V151I, G163R T97A, E92Q, E157Q Nucleic Acids Research, 2009 Secondary mutations: restoration of viral replicative capacity and of resistance level RAL and EVG Low genetic barrier to resistance High level of cross resistance

10 Plan 1 st generation: Raltegravir (RAL) and Elvitegravir (EVG/c) 2 nd generation: Dolutegravir (DTG) Epidemiology of resistance to integrase inhibitors Ongoing: Bictegravir (BIC) and Cabotegravir (CAB)

11 In vitro selection experiments DTG

12 DTG, RAL and EVG mean FC against RAL & EVG-related single mutation SDMs

13 Resistance Fold-Change to RAL and DTG according to integrase mutations profiles 143 and 155: most favorable resistance profiles for DTG activity 148 (specially 140/148 double mutants): worst resistance profile for DTG activity Underwood et al., IHDRW 2013, Abs. 85

14 VIKING-3 trial: virological response at D8 and W24 according to baseline integrase mutations VIKING-3 is a single-arm, open-label phase III study in which therapy-experienced adults with INI-resistant virus received DTG 50 mg bid while continuing their failing regimen (without raltegravir or elvitegravir) through day 7, after which the regimen was optimized with 1 fully active drug and DTG continued IN mutation Day 8 response Decline in VL (log 10 c/ml) Full response a Week 24 response < 50 c/ml n Median n (%) n n (%) No Q (92 %) (79 %) Q b (71 %) 20 9 (45 %) Q148 + >2 b (45 %) 9 1 (11 %) a Full response: decline in HIV-1 RNA > 1 log 10 c/ml or 50 c/ml at D8 b L74I, E138A/K/T and G140A/C/S Vavro et al., IHVDRW 2013, Abs. 29

15 Change from baseline in plasma HIV-1 RNA at day 8 (log 10 c/ml) VIKING-3 trial: relationship between baseline integrase mutations and D8 virological response Baseline INI resistant mutation category Q148 + > 2 Q N155 Y143 > 2 primary mutations Primary not detected Baseline FC IN IC 95 relative to wild type virus for DTG Vavro et al., IHVDRW 2013, Abs. 29

16 le meilleur de la CROI 2014 Impact of mutations selected by RAL or EVG on DTG activity Assessment of different Q148 mutants on the phenotypic susceptibility to DTG Phenotypic assays using clinical isolates and site-directed mutants Susceptibility of Q148 + E138 mutants and Q148 + G140 to DTG (fold-change) Susceptibility of clinical isolates with Q148H + G140S to DTG (fold-change) n = 127 Median fold-change = 4.3 Range = Q148K mutation associated with other integrase mutations showed a higher of susceptibility to DTG than Q148H/R viruses 1 Mutations 66, 74, 92, 97, 138, 143, 147, 155, and 163 excluded High variability of DTG susceptibility to G140S + Q148H double mutants Huang et al., CROI 2014, Abs. 595

17 DTG in ARV-naïve patients To date, no INI or NRTI resistance mutations detected at VF in the DTG arms of the phase 3 randomized clinical trials: - SPRING: 2 NRTI + DTG vs. RAL - SINGLE: ABC/3TC + DTG vs. EFV - FLAMINGO: 2 NRTI + DTG vs. DRV/r But: - Very few VF, sequences performed on the first plasma samples at VF, only known INI resistance mutations analyzed

18 SAILING trial: resistance analysis through W24 (1) Phase 3 randomized clinical trial, ARV-experienced patients but INI-naïve with VL >400 c/ml (2x) or >1000 c/ml (1x) DTG 50 mg qd, n (%) RAL 400 mg bid, n (%) VF week 24 (VL > 400 c/ml) 14 (4) 34 (9) BL and VF data 9 (64) 27 (80) Any emergent IN substitutions 2 (22) 9 (33) Emergence of IN mutations associated with development of resistance to INI class L68V, L74M, E92Q, T97A, G140A/S, Y143C/H/R, Q148H/R, V151I, N155H, E157Q, G163K 0 9 (33) R263K, R263R/K 2 (22) 0 DTG, RAL and EVG Fold-Change IC 50 Strain IN substitution / FC IC 50 DTG RAL EVG NL432 a R263K HXB2 V260I RVA b R263K V260I/R263K a HeLa-CD4 cells, 3-day assay, B-gal readout, b MT4 cells, 5-day assay, cell tier glow readout Underwood et al., IHDRW 2013, Abs. 21

19 SAILING trial: resistance analysis through W24 (2) Underwood et al., IHDRW 2013, Abs. 21

20 le meilleur de l IAS-EACS 2015 SAILING trial: resistance analysis after W48 Patient 1 VL (log 10 c/ml) Patient 2 VL (log 10 c/ml) Patient 3 VL (log 10 c/ml) Subtype C TDF + DRV/r PSS = 2; GSS = c/ml c/ml c/ml Subtype A ABC + 3TC PSS = 2; GSS = c/ml 407 c/ml Subtype B TDF + FTC PSS = 2; GSS = c/ml 622 c/ml 386 c/ml C 24h DTG (ng/ml): W4 = 1 780, W48 = C 24h DTG: W4 = 1 114, W24 <20, W48 = C 24h DTG (ng/ml): W4 = 360, W24 = 220, W48 = 30 BL W72 BL W108 BL W120 W132 VL (c/ml) IN Mutation WT I60L, T97A, N155H DTG fold change RAL fold change RC (% WT) ND ND VL (c/ml) IN Mutation WT N155H DTG fold change RAL fold change RC (% WT) ND ND VL (c/ml) IN Mutation WT A49G, S230R, R263K A49G, S230R, R263K DTG fold change RAL fold change RC (% WT) 20 % 7 % 12 % Underwood et al., EUHHW 2015, Abs. 6

21 le meilleur de la CROI 2017 First case report of integrase mutation selection at VF of a DTG-based first-line regimen 45 years old man, HIV diagnosis with inaugural pneumocystosis: CD4 = 78/mm 3, VL = c/ml (6.3 log 10 c/ml) Baseline resistance genotype RT: WT; protease: E35D-L63P-A71T-V77I; integrase not performed ARV initiation: TDF/FTC + DTG in the hospital Follow-up of VL and CD4 Add DRV/r RT: M184V IN: G163E Days VL (c/ml) CD4 (/mm 3 ) Integrase ultra-deep sequencing (codons 142 to 165) Time 1 Time 2 Time 3 Wild-type Q148K I151V-G163E Silent mutation I151V G163E I151M Y143L-N144Q-P145S S147N I162M Emergence of M184V mutation in RT Emergence of I151V and G163E mutations in integrase at the second time-point Emergence of Q148K viruses: from % to 20.9 % between T2 and T3 (< 10 days) Fulcher et al., CROI 2017, Abs. 500LB

22 DTG monotherapy in switch: explored and avoided A Dutch multicenter randomized clinical trial: DOMONO trial Pooled analysis of 3 observational cohorts (Barcelona, Montréal, Munich) A monocentric observational cohort in Paris, France DOMONO trial Pooled observational cohorts French observational cohort n Number of VF 8/77 (10 %) 11/122 (9 %) 3/28 (11 %) Number of IN mutations in VF patients IN mutations 3/5 (60 %) 9/11 (82 %) 3/3 (100 %) N155H S230R R263K N155H (n=1) T97A-N155H (n=1) E92Q-N155H (n=1) Q148H-N155H (n=1) E138K-Q148K (n=1) G118R (n=2) G140S-Q148H/R (n=2) N155H L74I-E92Q E138K-G140A-Q148R Wijting et al., CROI 2017, Abs. 451LB Blanco et al., CROI 2017, Abs. 42 Katlama et al., EACS 2015, Abs. PS4/4 High rate of VF and of resistance selection, strategy definitively not recommended

23 Plan 1 st generation: Raltegravir (RAL) and Elvitegravir (EVG/c) 2 nd generation: Dolutegravir (DTG) Epidemiology of resistance to integrase inhibitors Ongoing: Bictegravir (BIC) and Cabotegravir (CAB)

24 Q148H/K/R G140A/C/S N155H Y143C/H/R E138A/K E92Q/V T66A/I/K S147G F121Y R263K le meilleur de la CROI 2014 INI resistance profiles in United States: HIV integrase sequences issued from patients experiencing a VF when receiving a RAL-based treatment INI resistance in 26 % of samples Most prevalent resistance profiles: Q148H/K/R (36 %), N155H (31 %) INI resistance mutations (n) Description of major INI resistance mutations 21 % with other mutations (n = 12) Y143 (n = 57) 20 % with other mutations (n = 27) N155 (n = 135) 35 % with other mutations (n = 54) Q148 (n = 155) 1 % single Q148H/K/R (n = 2) 79 % single Y143C/H/R (n = 45) 80 % single N155H (n = 108) 64 % Q148H/K/R + G140A/C/S (n = 99) Hurt et al., CROI 2013, Abs. 591

25 12.3 % of high level of resistance to DTG in case of major INI resistance mutations selected at time of VF when receiving a RAL-based treatment

26 National multicenter cross-sectional study n = 502 patients experiencing a VF when receiving a RAL-based treatment 71 % subtype B Median VL = 2.9 log 10 c/ml 13.9 % of resistance to DTG 39 % with INI mutation Factors associated with presence of INI resistance mutations at VF: - VL at time of VF - GSS <2

27 le meilleur de VIH 2016 ANRS study: INI resistance prevalence in patients experiencing a VF with an INI (1) INI mutations prevalence at VF (%) National multicenter cross-sectional study n = 439 patients experiencing a VF when receiving an INI-based treatment since October % subtype B Median VL = 3.0 log 10 c/ml INI resistance mutation in 36 % of patients 22 %: 1 INI resistance mutation 8 %: 2 INI resistance mutations 6 %: > 2 INI resistance mutations 23 % of resistance to DTG qd and 3.5 % to DTG bid in patients failing RAL or EVG Marcelin et al., HIV Glasgow 2016, Abs. O332

28 le meilleur de VIH 2016 ANRS study: INI resistance prevalence in patients experiencing a VF with an INI (2) Subgroup analysis of patients in VF of a DTG first-line regimen (n = 41) - Treated in median since 0.4 years (IQR = ) - Median VL at VF: 2.7 log 10 c/ml (IQR = ) - No major INI resistance mutation at VF - Mutations detected at VF: L74M (n = 1) and E157Q (n = 2) INI resistance interpretation (%) DTG bid DTG qd RAL EVG Susceptible, n (%) 39 (95) 39 (95) 39 (95) 39 (95) Possible resistance, n (%) 2* (5) 2* (5) - - Resistance, n (%) 0 0 2* (5) 2* (5) * 2 patients with single E157Q Subtype B (n = 2) Present at baseline in 1 case (ongoing BL sequencing for the second patient) E157Q and L74M are polymorphisms naturally present in some ARV-naïve patients Marcelin et al., HIV Glasgow 2016, Abs. O332

29 E157Q mutation: polymorphic and acquired Prevalence of 5 % in chronically-infected ARV-naïve patients Differential distribution of the E157Q polymorphism among HIV-1 subtypes: Subtype B: 2.3 %, CRF02_AG: 7.5 % Saladini et al., EHDRW 2017, Abs. 72 Selected in vivo in patients failing RAL-based treatment Assoumou et al., IAS 2017, Abs. TUPEC0851 Malet et al., Antimicrob Agents Chemother, 2008 J Antimicrob Chemother, 2009 Case report of a non virological response to a DTG-based regimen Danion et al., J Antimicrob Chemother, 2015

30 E157Q mutation: in vitro analysis Virus from the non response to a DTGbased regimen Phenotypic analysis of 7 clinical isolates - 3 fold increase of the strand-transfer activity - 9 fold factor of resistance compared with WT virus - 1 virus at the limit of the RAL biological cut-off (FC=1.5) - All 7 clinical samples susceptible to DTG Danion et al., J Antimicrob Chemother, 2015 Saladini et al., EHDRW 2017, Abs. 72 Role of the E157Q polymorphism not clearly elucidated

31 INI acquired drug resistance The rate of selection of resistance mutations at time of VF is not so high, between 26 % and 39 % in the US and French studies Do we know everything on INI resistance mechanisms? - Rare resistance profiles? - Genotypic determinants of resistance outside integrase?

32 Newly described and rare resistance RAL pathways Fold Change to RAL and DTG EC50 values were obtained from cell culture assays and IC50 values were obtained from assays using recombinant IN proteins. Each value represents the mean+sd for three independent experiments. These data show that G118R and F121Y represent new RAL resistance pathways that may also be involved in DTG resistance Mutations L74F and V75I: a case report IN: WT VL (c/ml) CD4 (/mm 3 ) RAL TDF/FTC IN: L74F V75I DRV IN: L74V-V75I I60M-V72I RAL EVG DTG CAB L74F V75I L74F-V75I 4.5 8, I60M-L74F-V75I V72I-L74F-V75I I60M-V72I-L74F-V75I Codons that may indirectly affect the Mg 2+ coordination position The I60M mutation restores the viral RC J Antimicrob Chemother, 2015 Hachiya et al., CROI 2017, Abs

33 le meilleur de la CROI 2017 A high level of resistance to DTG associated with mutations outside integrase Objective: in vitro selection experiments but under very high concentrations of DTG ( 500 nm) in order to force the virus to select DTG resistance Results Detection of resistant virus between M2 and M3 of culture Integrase sequencing: no emergent mutation Whole genome sequencing: mutations in 3 PPT region (nef gene) Position 9053 // Reference sequence Mutant virus sequence C // G G G G G G T // G C A G T - 5 AAAAGAAAAG(G9069C)(G9070A)G(G9072T)(G9073del) PPT mutated virus Wild-type virus In vitro analysis High level of resistance to DTG but also RAL and EVG associated with low viral RC (10 %) Able to produce newly infections of MT4 cells Conclusion: mutations selected in vitro by DTG and located outside the integrase gene can confer themselves very high-level of resistance to all known INI DTG (nm) Malet et al., CROI 2017, Abs. 499

34 Transmitted drug resistance to INI National epidemiological survey (ANRS virology network, n = 33 centers, n = 597 patients) Chronically-infected ARV-naïve patients diagnosed between October 2015 and March 2016 % TDR prevalence by drug class % IN mutations : IAS list ** : IAS list + E157Q Two patients with transmission of major INI resistance mutations (Q148) High prevalence of INI transmitted drug resistance mutations Pre-therapeutic integrase resistance testing is recommended in France Assoumou et al., IAS 2017, Abs. TUPEC0851

35 Plan 1 st generation: Raltegravir (RAL) and Elvitegravir (EVG/c) 2 nd generation: Dolutegravir (DTG) Epidemiology of resistance to integrase inhibitors Ongoing: Bictegravir (BIC) and Cabotegravir (CAB) formerly GSK

36 le meilleur de VIH 2016 In vitro activity of bictegravir (BIC) against INI-resistant viruses Q148H/R + G140A/S Susceptible Reduced susceptibility WT Resistance FC < 2,5 2,5 < FC < 10 FC > 10 Susceptible 92Q+157Q 97A +74M 143C +68V 143R +68,74 155H +74M 155H+157Q 148R+138A 155H+163R 148R+138K WT Double mutant Reduced susceptibility Resistance FC < 2,5 2,5 < FC < 10 FC > 10 BIC DTG EVG RAL Susceptible Q148H/R + G140A/C/S + 1 WT +E138K +G163K +E138K 143 +E138K +T97A +E138K +L74M +E138A +T97A +L74M +E138K Resistance FC < 2,5 2,5 < FC < 10 FC > 10 Susceptible Reduced susceptibility WT Reduced susceptibility Single mutant Resistance E92Q E92Q 92 T97A 143 F121Y Y143R Y143R 143 Y143C N155H 143 FC < 2,5 2,5 < FC < 10 FC > 10 White et al., EWHDR 2016, Abs. O-01

37 le meilleur de la CROI 2017 Phase 2 trial comparing BIC versus DTG (+ TAF/FTC) in first-line - Week 48 results VL < 50 c/ml, ITT snapshot VL < 50 c/ml; difference, % (95 % CI) BIC + FTC/TAF (n = 65) W24 DTG + FTC/TAF (n = 33) W48 Favors DTG + FTC/TAF Favors BIC + FTC/TAF W24 2,9-8,5 14, W48 6,4-6 18, Virological success 3 6 Virological failure 0 0 No data Virological success Virological failure 3 No data -12 % 0 12 % No NRTI or INI resistance detected Change in CD4/mm 3 at W48: vs (p = 0.16) Sax et al., CROI 2017, Abs. 41 ; Lancet HIV 2017

38 le meilleur de la CROI 2015 LATTE trial: resistance analysis of a VF in the CAB 10 mg + RPV arm at W48 LATTE trial: RCT assessing the efficacy of a dual-therapy in maintenance with RPV + CAB (10 mg, 30 mg or 60 mg) IM Plasma VL (log 10 c/ml) CAB + TDF/FTC CAB + RPV Weeks Q148R INT E138Q RT Sub-optimal plasma concentrations of CAB and RPV 48 Phenotypic susceptibility to INI of SDM (Fold-change) Mutation CAB DTG RAL EVG Y143C Y143H Y143R Q148H Q148K > Q148R N155H Highest FC to Q148K/R viruses with CAB than with DTG (factor 4), suggesting that CAB might be more impacted by the Q148K/R than DTG Dudas et al., IHDRW 2015, Abs. 13

39 le meilleur de la CROI 2017 Resistance analysis in macaques treated with CAB LA during primary infection (1) Objective: modeling in the macaque the risk of emergence of resistance associated with the initiation of CAB LA during a recent undiagnosed HIV infection Methods 6 Rhésus macaques Infection by intravenous of RT-SHIV virus with SIVmac239 integrase 3 monthly IM injections of CAB LA at the dose of 50 mg/kg RT-SHIV Infection RNA RT-SHIV+ CAB LA injections ELISA+ M1 M2 Radzio et al., CROI 2017, Abs. 84

40 le meilleur de la CROI 2017 Resistance analysis in macaques treated with CAB LA during primary infection (2) Macaque # Resistance analysis by INT sequencing Integrase mutations 1 st day of resistance mutations detection 10D181 E92Q-Q124R-G140R 81 Compartment Blood, rectum, vagina E92G 143 Blood CH54 G118R-A122T 57 Blood, rectum 01D520 None A122T 162 Blood CJ92 I72T-S135A 32 Blood E92Q: SIV (EVG: FC 4; CAB: FC = 2-4); HIV-1 (RAL: FC > 5; DTG: FC > 30) E92G: SIV (not described); HIV-1 (EVG: FC 10) G118R: SIV (DTG: FC = 11; RAL: FC = 3; EVG: FC = 10); HIV-1 (DTG, RAL and EVG: FC = 5-20) Phenotypic tests ongoing Conclusions Frequent selection of resistance Presence of resistant viruses in compartments (rectum, vagina) risk of resistance transmission Radzio et al., CROI 2017, Abs. 84

41 To summarize: 1 st generation: Raltegravir (RAL) and Elvitegravir (EVG/c) - Low genetic barrier to resistance - Cross resistance Selection of mutations in 40 % of VF 2 nd generation: Dolutegravir (DTG) - Higher genetic barrier to resistance than RAL/EVG but not a PI (cf monotherapy strategy) - bid dosing is required after a VF under INI first generation - Q148+G140 double mutants, most prevalent mutants at VF, showed an increased phenotypic FC to DTG

42 Virology Pr Diane Descamps Dr Charlotte Charpentier Dr Florence Damond Dr Nadhira Houhou-Fidouh Dr Houria Ichou Dr Lucile Larrouy Dr Vincent Mackiewicz Dr Marine Perrier Dr Benoit Visseaux Dr Quentin Le Hingrat Mélanie Bertine Gilles Collin Alice Mariaggi Sarah Peerbaccus Alexandre Storto Infectious Diseases Pr Yazdan Yazdanpanah Pr Elisabeth Bouvet Pr Sophie Matheron Pr Patrick Yéni Dr Véronique Joly Dr Roland Landman Dr Sylvie Lariven Dr Xavier Lescure Dr Christophe Rioux Dr Paul Loubet Clinical Pharmacology Dr Gilles Peytavin Dr Minh Lê Clinical trials Dr Bao-Chau Phung Dr Adriana Pinto Dr Ornella Cabras Cindy Godard Djamila Rahli Françoise Louni Malikhone Chansombat Zelie Julia