DEVELOPMENT AND REVERSAL

Transcription

1 DEVELOPMENT AND REVERSAL OF T CELL EXHAUSTION E. John Wherry Institute for Immunology University of Pennsylvania IAS 2016 Towards an HIV Cure Symposium Durban, South Africa

2 T cell exhaustion Highly functional Rapid & robust secondary response Long-term Ag-independent maintenance Lose effector functions Poorly protective Actively inhibited PD-1 etc Ag-dependent maintenance & constant proliferation Long-term stalemate Exhaustion is common in mice as well as humans

3 HIV PATHOGENESIS AND T CELL EXHAUSTION Tetrame r IFNg ~15% functional Paul A. Goepfert et al. J. Virol. 2000;74: PD-1 Cheryl Day et al. Nature. 2006;443:

4 T CELL EXHAUSTION AND DYSFUNCTION IN HIV VIREMIC: Loss of function Negative regulation by inhibitory receptors Poor proliferation Transcription factor alterations Deletion in some cases NON-VIREMIC (I.E. ART TREATED): Poor durability / memory maintence Permanent defects in reactivation/differentiation?

5 A simple model to study T cell exhaustion Lymphocytic Choriomeningitis Virus (LCMV) LCMV Armstrong LCMV Cl-13 Acute Infection Chronic Infection Differ by 2 AA altering in vivo distribution, replication rate and spread. (Ahmed et al, JEM 1984: Ahmed, et al J Virol 1988; Ahmed et al J Virol 1991; Matloubian et al JEM 1990; Matloubian et al J Virol 1993; Mueller et al Science 2007; Mueller et al PNAS 2007)

6 Uncontrolled Chronic Viral Infection Day p.i.

7 Transcriptional Program of T EX Acute Chronic Naive Day 6 Day 8 Day 15 Day 30 Day 6 Day 8 Day 15 Day 30 Sorted on DbGP33 tetramer+ CD8 T cells from LCMV Armstrong or clone 13 infection TCR and cytokine signaling Chemotaxis, Migration, etc Metabolism Transcription factors PD-1 & other Inhibitory receptors Wherry, Immunity, 2007 Doering, Immunity, 2012

8 Common Program of T Cell Exhaustion Enrichment of Exhausted signature HIV Progressor HIV Controller Testing whether the gene expression signature from LCMV-specific CD8 T cells is enriched in the gene expression signatures of sorted HIV-specific CD8 T cells from progressors or controllers using Gene Set Enrichment Analysis In collaboration w/ Nick Haining, and Bruce Walker

9 Reversing Exhaustion PD Trautman, et al Nat. Med : Petrovas, et al JEM : Velu, et al Nature :

10 CANCER IMMUNOTHERAPY

11 In melanoma patients anti-pd-1 reinvigorates T EX Ki67+ Ki67- RESPONDING CELLS T EX PD-1+Eomes Hi CTLA-4+, Lag3, 2B4, CD39 GzmB OVERALL SURVIVAL Alex Huang, Submitted

12 RELEVANCE OF REINVIGORATING T EX TO HIV CURE Correcting or avoiding exhaustion in late stage HIV Reversing persisting imprint of previous exhaustion relevance for cure strategies in treated subjects Avoid exhaustion in vaccine approaches Understand the mechanism of T cell exhaustion related to pathogenesis (i.e. duration of infection, viral load, inflammation, immunoregulatory pathways) Need to understand molecular mechanisms

13 Stability of T EX differentiation state: Can T EX be redifferentiated T Mem 2) Trans-Differentiation T N T EF 1) De-Differentiation 3)? T EX

14 Transcriptional changes following PD-1 blockade? Kristen Pauken, Submitted

15 Sustained benefit after PD-1 blockade? High persisting antigen +1 day +20 wks +1 day +20 wks Kristen Pauken, Submitted

16 Sustained expression of PD-1 after chronic infection T EX TRANSFERRED INTO IMMUNE MICE Pauken, et al submitted Angelosanto, et al J. Virol : Utzschneider, et al Nat. Immunol : DNA Demeythylation at the Pdcd1 locus in T EX NAIVE EFFECTOR MEMORY EXHAUSTED Youngblood, et al Immunity :

17 What is the epigenetic landscape of T EX? Nature Rev. Genet., Shlyueva et al.

18 ATAC-seq for T EX Day T EX VS T N T EFF T MEM LCMV Arm or clone 13 ATAC-Seq Makoto Kurachi, Omar Khan, Caroline Bartman and Tony Barnitz

19 Altered epigenetic landscape in T EX Kristen Pauken, Submitted ~18,000 enhancers changed compared to T naive > 8,000 enhancer changes unique to T EX

20 Epigenetic landscape of T EX is dramatically different from T EF and T MEM What happens upon PD-1 pathway blockade?

21 Reversing Exhaustion Changes in the enhancer landscape? Kristen Pauken and Morgan Sammons

22 Enhancer landscape changes CO-CLUSTER OF VARIANCE FOR ENHANCERS AND CELL TYPES PRINCIPLE COMPONENT ANALYSIS Only ~650 enhancers changed Kristen Pauken and Morgan Sammons

23 Are there important features of the epigenetic changes? Kristen Pauken and Morgan Sammons

24 Additional transcriptional network changes ENHANCER CHANGES CHANGES IN TF EXPRESSION TF BINDING GENE EXPRESSION TRANSCRIPTIONAL NETWORK NFKB IRF1 IRF2 BZIP NFAT NR4A1 EGR2 Kristen Pauken and Sasi Manne

25 Does PD-1 blockade allow T EX to re-access effector-like epigenetic landscapes?

26 Additional transcriptional network changes GENES WITH ENHANCERS CONTAINING TF BINDING SITE TEFF TEX TF NFkb1 Irf2 Nr4a1 Runx2 prdm1 Irf1 Runx1 Tbet BATF EOMES Egr2 Runx3 NFATC1 bzip nfat-ap1 IRF4 Kristen Pauken and Sasi Manne % more in overlap than TEX -20 Overlap T EX only % of genes changed with anti-pd-l1

27 Differentiation of T EX following PD-1 blockade T MEM T EX Reinvigorated T EX Epigenetic Reprogramming X Re wired Transcriptional Network

28 EPIGENETIC PROGRAMMING OF T EX : IMPLICATIONS FOR HIV T EX are a distinct T cell lineage with a unique epigenetic landscape Re-invigoration of T EX does not re-program Early intervention preserves more fate flexibility Lessons and Opportunities for HIV: Early ART may prevent epigenetic permanence of dysfunction Cure strategies may want to include strategies to re-program T EX Vaccine monitoring could include phenotypic, transcriptional and/or epigenetic signatures of T EX to avoid

29 Acknowledgements Wherry Lab Sharon Adamski Sasi Manne Mohammed Ali Laura McLane Mohamed Abdel Hakeem Shin Ngiow John Attanasio Robert Orlowski Bertram Bengsch Kunal Patel Zeyu Chen Kristen Pauken Josephine Giles Ryan Staupe Sarah Henrickson Erietta Stelekati Ramin Herati Vesko Tomov Alex Huang Laura Vella Jonathan Johnnidis Jennifer Wu Andy Johnson Omar Khan *Caroline Bartman Makoto Kurachi *Tony Barnitz UPenn Tara Gangadhar Lynn Schuchter Bob Vonderheide Andy Minn Suzanne McGettigan Ravi Amaravadi Giorgos Karakousis George Xu Federico Valdivieso Wei Xu Shannon Harmon Morgan Sammons Shelley Berger Dana Farber Nick Haining Jernej Godec Deb Sen Funding

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31 DISCLAIMER POPULATION DYNAMICS Less exhausted More exhausted

32 IMMUNE DYSFUNCTION IN HIV AND CANCER CANCER T cell exhaustion Immunoregulatory pathways PD-1 etc HIV Chronic inflammation

33 Differentiation of T EX following PD-1 blockade T Mem X 2) Trans-Differentiation T N T EF X 1) De-Differentiation 3)? T EX