Combinatorial CRISPR/Cas9 approaches targeting different steps in the HIV life cycle can prevent the selection of resistance

Transcription

1 Combinatorial CRISPR/Cas9 approaches targeting different steps in the HIV life cycle can prevent the selection of resistance Monique Nijhuis, University Medical Center Utrecht, the Netherlands IAS 2016 Towards an HIV Cure Symposium Durban, South Africa

2 Current cart strategies Current cart is designed to efficiently control HIV replication The current arsenal of antiretroviral compounds can neither suppress viral production nor target the viral reservoir Alternative strategies, such as gene editing, are required to permanently disrupt the HIV genome in the cellular reservoir Gene editing tool: RNA-guided CRISPR/Cas9 nuclease

3 grna-guided CRISPR/Cas9 nuclease Repair by the error-prone non-homologous end joining (NHEJ) machinery.

4 Current CRISPR/Cas9 HIV genome editing strategies grnas targeting different regions of the HIV genome have been developed. -inactivate and delete HIV DNA from latently infected cells 1,2,3,4,5 -inhibit short-term HIV replication 2,4 Objective: whether and how HIV might escape from CRISPR/Cas9 targeting single or multiple steps in the viral life cycle. 1 Ebina et al, Sci Rep, 2013; 2Hu et al, PNAS, 2014; 3 Zhu et al, Retrovirology, 2015; 4 Liao et al, Nat Commun, 2015; 5 Kaminski et al, Sci Rep, 2016.

5 grna targeting different HIV genomic regions

6 The effect of single grnas on -Generated T-cells stably expressing single grnas and Cas9 -Infect with HIV and measure protection against infection (day 4) MA3, PR2, IN2 and IN5 provide 97-99% protection against infection RT2 provide 84% protection against infection

7 The effect of single grnas on -Generated T-cells stably expressing single grnas and Cas9 -Long-term infection with HIV reporter virus (luciferase) (n=4) Viral breakthrough/escape variants? -Amplified and deep-sequenced the CRISPR/Cas9 target regions of the viral RNA from the culture supernatants

8 The effect of single grnas on Mutant (indels) Wild type RT2 escape variants Mutant (nucleotide changes) Wild type MA3, PR2, IN5 escape variants

9 The effect of single grnas on -MA3, PR2 and IN5 are very potent inhibitors -Viral escape is very rapid, compare to antiretroviral compounds -Two very recent studies have suggested that NHEJ repair machine may facilitate HIV escape 1,2 -Investigated the nucleotide substitution patterns observed in HIV escape variants

10 The effect of single grnas on Nucleotide substitution patterns in HIV escape variants HIV target gene PR RT IN MA Totaal Samples (n) target sequence ATTAGT AAGGAA GTGCTA GATCGA A-->T A-->C A-->G T-->A 0 0* T-->C 13 0* T-->G 1 0* C-->A 0* 0* C-->T 0* 0* C-->G 0* 0* G-->A G-->T G-->C The cellular error-prone non-homologous end joining (NHEJ) machinery Accelerating viral escape HIV-RT and APOBEC3G * Nucleotide is not present in target site -These observations have questioned the feasibility of the CRISPR/Cas9 based gene-editing approach 1,2 1 Callaway, Nature News, 2016; 2 Liang et al, Retrovirology, 2016.

11 CPE score The effect of two grnas on -Generated T-cells stably expressing two grnas and Cas9 -Long-term infection with HIV reporter virus (luciferase) (n=4) RT2+MA3 RT2+PR2 RT2+IN5 MA3+PR2 MA3-IN5 PR2+IN HIV infection (days)

12 The effect of two grnas on -Generated T-cells stably expressing two grnas and Cas9 -Long-term infection with HIV reporter virus (luciferase) (n=4) -Amplified and deep-sequenced the CRISPR/Cas9 target regions of the viral RNA from the culture supernatants

13 The effect of two grnas on Mutant (indels- nucleotide changes) Wild type RT2 escape variants Mutant (nucleotide changes) Wild type MA3, PR2, IN5 escape variants

14 Concluding remarks -grnas differ in potency to inhibit HIV replication -rapid viral escape is observed to all single grnas -error-prone NHEJ repair mechanism is accelerating viral escape -a combination of two potent grnas can successfully prevent viral replication and escape Gene-editing may provide a future alternative for control of HIV-infection.

15 Acknowledgment Robert Jan Lebbink Emmanuel Wiertz