immunotherapy: novel immunomodulatory targets

Paul D Rennert, Founder & Principal SugarCone Biotech LLC

Exploring evolution of diverse immune checkpoint pathways

ImVacs, August 11-12, 2014

www.sugarconebiotech.com

How can we discover novel immune checkpoints?

•  Focus on specific gene familes that we know contribute to immune checkpoint modulation

•  Query these target collections using an evolutionary

perspective, to derive specific new therapeutic hypotheses

•  Why? Ad hoc sampling of such families, especially the large ones, is time-consuming and expensive

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This is what we usually see ... and it’s useful

Drew M Pardoll, 2012. Nat Rev Cancer

•  e.g. we know that CTLA4, an Ig-superfamily member, is a critical immune checkpoint target

•  We’ve found out through the very hard

work of many labs that PD-1 is another critical immune checkpoint target

•  But, can we use this level of information to guide our investigation of other Ig-superfamily members?

Using clustering to inform hypotheses •  The prior figure is an example of functional clustering and can only inform us

about members whose function has been elucidated

•  Highly refined distance methods are of interest, and by design use distance cutoff algorithms to unlink related families

Yap et al. 2013 JMB 4

Butyrophilins Siglecs

B7s PD-Ls

TIMs


What is this showing us? •  Relatedness is a term of convenience/relativity

•  We “look” for relatedness to CD28 and B7s when we identify novel proteins !  PD-1 is cited as CD28/CTLA4 relative: PD-1 binds PD-L1 and 2 and

B7-1; the receptor has inhibitory activity !  In strict distance analyses, PD-1 is a singleton, with distant homology

to CD8 and the antigen receptor Ig domains !  ICOS can be aligned with CD28 and CTLA4 using pairwise

comparison methods

•  ICOS-L, B7-H3 and B7-H4 align more closely with butyrophilins than B7s

•  VISTA is a weak PD-L1 homologue, structurally unique

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Where do B7-1 & 2 and CD28 lead us?

ICOS! CTLA4! CD28!

PD-1!

VISTA!

????!

?"

?"

B7-H3 !

B7-H4 ! ICOS-L !

?"

????!

?"

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We have a big butyrophilin/B7 family B7-H3 !

B7-H4 ! ICOS-L !

We have a small CD28 receptor family

ICOS! CTLA4! CD28!

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Interesting New Directions

•  Focus on new targets ! VISTA, B7-H3, B7-H4

•  Novel families !  Butyrophilins are likely underexploited targets

•  Different cell types !  NK cells, NKT cells, γ/δ T cells

•  An insight: ! There is no a priori reason to anticipate high homology

when looking for the receptors/ligands of orphan proteins (e.g. IgSF BTLA binds TNFRSF HVEM)

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B7-H3 and B7-H4 B7-H3 •  Biology poorly understood; low expression in normal tissues •  Macrogenics (MGNX) and Servier are co-developing MGA271, a

humanized, Fc-optimized mAb that is in a Phase 1 trial, recruiting refractory prostate cancer and melanoma patients based on abundant expression of the target on these tumors

B7-H4 •  Biology poorly understood, marks diverse normal and cancer cell types •  Well-established biomarker of tumor progression •  B7-H4 is expressed on infiltrating myeloid cells, vasculature, and tumor

cells in melanoma, NSCLC, prostate, ovarian, pancreatic, breast, renal and other cancers

•  Amplimmune (now owned by the Medimmune division of Astra Zeneca; AZN) had listed B7-H4 in its’ portfolio

•  Five Prime Therapeutics (FPRX) also has promoted this target

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VISTA •  Normally expressed on hematopoietic cells including myeloid

cells and T cells •  In multiple cancer models VISTA is found at particularly high

levels on tumor-infiltrating myeloid cells

•  Appears to be a negative regulator of T cell responses, may suppress myeloid cell responses in the tumor microenvironment

•  Anti-VISTA antibody treatment blunts tumor development even in the presence of high PD-1 expression

•  Antibodies to VISTA are being developed by a private company, ImmuNext, in collaboration with Johnson&Johnson (JNJ)

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New “B7s”

•  you can always force a phylogeny by limiting the input sequences, as shown here

•  utility: can highlight relationships of suspected novel family members

•  B7H6, tumor-specific in human?, binds NKp30, function poorly understood, an outlier

•  B7H7/HHLA2 – likely related to butyrophilins

PD-L2

PD-L1 B7-H7 B7-H4

B7-H3

ICOS-L

B7-1

B7-2

VISTA

B7-H6

Flajnick et al. 2012. immunogenetics

The “true” Butyrophilins

•  The failure to identify clear ligand/receptor interactions has limited drug development

•  A reasonable prediction is that further study of the butyrophilin family will yield novel targets

Arnett & Viney. 2014. Nat Rev Immunol.

Underexploited Ig-families •  Precedence here may come from the distinct but instructive LIR/KIR and NKG2

families of NK cell surface proteins

•  Despite a huge complexity of family members and confusing biology, useful targets are emerging, notably from Innate Pharma (IPH)

•  Bristol-Myers Squibb (BMY) is sponsoring trials of lirilumab in combination with ipilimumab (anti-CTLA4) and nivolumab (anti-PD-1) in patients with solid tumors. These trials will start to read out over the next 2 years.

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Lets try this again: TIM family proteins •  TIM-1 identified as a critical T cell control protein (2001)

•  Member of a small subfamily of receptors featuring IgV domains atop mucin domains and short stalks !  Human proteins are TIM-1, TIM-3, TIM-4

•  We knew as early as 2002 that these were Siglec homologues !  TIM-1 cell binding was cation-sensitive suggesting a carbohydrate

component but a screen by he Consortium for Functional Glycomics failed

!  Based on publications we chased semaphorins, CD300b, others

!  Galectin-1,8 identified as binding proteins, unclear specificity?

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TIM family proteins: nearest neighbors •  Extensive homology modeling places TIM-1 between

Siglecs and Butyrophilins

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Rubenstein et al. 2013 Structure.

TIM-1 relationship to Siglecs

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•  TIM-1 IgV domain resembles a Siglec with a modified sialic acid binding motif

•  Minimal energy modeling suggest carbohydrate docks as in a typical Siglec

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17 *: Miyanishi et al. Nature 450: 435; Kobayashi et al. Immunity 27: 927; Santiago et al. Immunity 27: 941; Ichimura et al. 2008. J. Clin. Immunol. 118: 1657.

•  TIM-1, TIM-4 and TIM-3 bind PS

•  PS binding site: a cation buried in a charged cavity

•  The sialic-acid binding residues lie atop the PS-binding site.

The real key to unlocking TIM-family function was phosphotydylserine (PS)


•  A reasonable hypothesis is that TIM-3 antagonism is efficacious in preclinical tumor models because it prevents T-cells from receiving inhibitory signals delivered by PS expressed by tumor cells and tumor associated macrophages (MDSC) !  Whether the putative TIM-3 ligand Galectin-9 also plays a role is

unclear

•  Novartis (NVS)/CoStim, Bristol-Myers Squibb (BMS), Tesaro (TSRO)/Anaptsys all have active programs targeting TIM-3, with many others coming along ... why?

PS, tumors and TIM-3

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TIM-3 preclinical data are compelling

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Not so TIM-1: our evolving view of TIM-1 expression

•  Focal, bright expression on mucosal endothelium

•  Expressed on kidney epithelium (lumenal), and highly expressed in the injured kidney

•  Highly (drastically) upregulated not only on kidney and ovarian carcinoma but also non-cancerous kidney and liver cells after chemo/radiation

•  It’s reasonable to predict that the anti-TIM-1-ADC being developed by Celldex’ (CLDX) will have a difficult time finding a safe therapeutic window in the context of standard of care

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Other programs targeting cell death pathways

•  Cell surface expression of PS is triggered by apoptosis; the appearance of sufficient PS on the cell surface triggers phagocytosis

•  However, PS expression is quite widespread even on

normal cells

•  SIRPα/CD47 is an explicitly anti-phagocytic signaling mechanism

•  However, CD47 is widely expressed, and is abundantly

expressed on platelets

•  Both targets seem problematic, however... 21


Other programs targeting apoptotic signaling

These independent lines of evidence support the hypothesis that TIM-3 is acting in the context of PS-binding

•  Peregrine Pharmaceutical’s (PPHM) anti-PS antibody bavituximab has advanced to Phase 3 with fast-track desination in r/r solid tumors including NSCLC (+ platinum-based chemo)

•  In Phase 2, the ORR was only 17%, those responding had a median increase in OS of just over 4 months. It is predictable that this program will seek rational combination therapy trials.

•  Celgene (CELG) handed privately held Inhibrx LLC a 50MM USD upfront with potential royalties running to 500MM for an anti-CD47 antibody specifically designed not to activate platelets

•  Additional CD47 and SIRPα programs are under development

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•  uh-oh... One more example...

•  shown are two proteins that been investigated in the context of immune oncology:

•  TIGIT

•  CD200

•  The fact that these cluster in the complex Nectin family is a little worrisome: these family members homo and hetero-dimerize fairly promiscuously, and this may complicate analysis and use of biologics targeting these proteins

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•  CD200 was being targeted by an antibody ALXN6000/samalizumab (Alexion, ALXN) although there are no recent clinical updates - the company abandoned oncology for rare diseases

•  TIGIT is a relatively new IgSF protein, with clear cell inhibitory function. There is defined binding to PVR and Nectin-2, potentially leading the way to influencing both T cells and NK cells through inhibition of this pathway

•  However, proteins in the nectin family may have diverse binding partners, complicating development, e.g. the TIGIT ligands may also bind DNAM

Targeting “Nectins”?

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Finally ... such analyses go only so far

LAG3 BTLA

FLT3

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other applications ...

•  this type of analysis can be productively applied to the TNF and TNFR superfamilies ... which are much smaller

•  allowing us to look for interesting and distinct pathways ...

•  recent work has highlighted TNFRSF25 as a critical node in the immune response to tumors as you will hear more about from Taylor Schreiber

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Acknowledgements

Slides will be available on SLIDESHARE

Link through the sugarconebiotech.com blog

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•  TIM-1 program: BiogenIdec •  TIM-1 oncology: CoStim •  TIM-1 homology and binding specificity: Alexey Lugovskoy (Merrimack), Yen-

Ming Hsu (AbBio), Veronique Bailly (BIIB), Patricia McCoon (AZN), Gabriela Constantin (U Verona, IT)

•  TIM-1 virology: !  Ebola, Marburg: Wendy Maury (U Iowa), Rob Davies (Tx Biomed) !  HIV: Shan-Lu Liu (U Missouri)

immunotherapy: novel immunomodulatory targets

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