Category Archives: Roche

Some Adjacencies in Immuno-oncology

Some thoughts to fill the space between AACR and ASCO (and the attendant frenzied biopharma/biotech IO deals).

Classical immune responses are composed of both innate and adaptive arms that coordinate to drive productive immunity, immunological expansion, persistence and resolution, and in some cases, immunological memory. The differences depend on the “quality” of the immune response, in the sense that the immunity is influenced by different cell types, cytokines, growth factors and other mediators, all of which utilize diverse intracellular signaling cascades to (usually) coordinate and control the immune response. Examples of dysregulated immune responses include autoimmunity, chronic inflammation, and ineffective immunity. The latter underlies the failure of the immune system to identify and destroy tumor cells.

Let’s look at an immune response as seen by an immunologist, in this case to a viral infection:

 immune viral

Of note are the wide variety of cell types involved, a requirement for MHC class I and II responses, the presence of antibodies, the potential role of the complement cascade, direct lysis by NK cells, and the potentially complex roles played by macrophages and other myeloid cells.

In the immune checkpoint field we have seen the impact of very specific signals on the ability of the T cell immune response to remain productive. Thus, the protein CTLA4 serves to blunt de novo responses to (in this case) tumor antigens, while the protein PD-1 serves to halt ongoing immune responses by restricting B cell expansion in the secondary lymphoid organs (spleen, lymph nodes and Peyer’s Patches) and by restricting T cell activity at the site of the immune response, thus, in the tumor itself. Approved and late stage drugs in the immune checkpoint space are those that target the CTLA4 and PD-1 pathways, as has been reviewed ad nauseum. Since CTLA4 and PD-1 block T cell-mediated immune responses at different stages it is not surprising that they have additive or synergistic activity when both are targeted. Immune checkpoint combinations have been extensively reviewed as well.

We’ll not review those subjects again today.

If we step back from those approved drugs and look at other pathways, it is helpful to look for hints that we can reset a productive immune response by reengaging the innate and adaptive immune systems, perhaps by targeting the diverse cell types and/or pathways alluded to above.

One source of productive intelligence comes from the immune checkpoint field itself, and its’ never-ending quest to uncover new pathways that control immune responses. Indeed, entire companies are built on the promise of yet to be appreciated signals that modify immunity: Compugen may be the best known of these. It is fair to say however that we remain unclear how best to use the portfolio of checkpoint modulators we already have in hand, so perhaps we can look for hints there to start.

New targets to sift through include the activating TNF receptor (TNFR) family proteins, notably 4-1BB, OX40, and GITR; also CD40, CD27, TNFRSF25, HVEM and others. As discussed in earlier posts this is a tricky field, and antibodies to these receptors have to be made just so, otherwise they will have the capacity to signal aberrantly either because the bind to the wrong epitope, or they mediate inappropriate Fc-receptor engagement (more on FcRs later). At Biogen we showed many years ago that “fiddling” with the properties of anti-TNFR antibodies can profoundly alter their activity, and using simplistic screens of “agonist” activity often led to drug development disaster. Other groups (Immunex, Amgen, Zymogenetics, etc) made very similar findings. Careful work is now being done in the labs of companies who have taken the time to learn such lessons, including Amgen and Roche/Genentech, but also BioNovion in Amsterdam (the step-child of Organon, the company the originally created pembrolizumab), Enumeral in Cambridge US, Pelican Therapeutics, and perhaps Celldex and GITR Inc (I’ve not studied their signaling data). Of note, GITR Inc has been quietly advancing it’s agonist anti-GITR antibody in Phase 1, having recently completed their 8th dose cohort without any signs of toxicity. Of course this won’t mean much unless they see efficacy, but that will come in the expansion cohort and in Phase 2 trials. GITR is a popular target, with a new program out of Wayne Marasco’s lab at the Dana Farber Cancer Institute licensed to Coronado and Tg Therapeutics. There are many more programs remaining in stealth for now.

More worrisome are some of the legacy antibodies that made it into the clinic at pharma companies, as the mechanisms of action of some of these agonist antibodies are perhaps less well understood. But lets for the sake of argument assume that a correctly made anti-TNFR agonist antibody panel is at hand, where would we start, and why? One obvious issue we confront is that the functions of many of these receptors overlap, while the kinetics of their expression may differ. So I’d start by creating a product profile, and work backward from there.

An ideal TNFR target would complement the immune checkpoint inhibitors, an anti-CTLA4 antibody or a PD-1 pathway antagonist, and also broaden the immune response, because, as stated above, the immune system has multiple arms and systems, and we want the most productive response to the tumor that we can generate. While cogent arguments can be made for all of the targets mentioned, at the moment 4-1BB stands as a clear frontrunner for our attention.

4-1BB is an activating receptor for not only T cells but also NK cells, and in this regard the target provides us with an opportunity to recruit NK cells to the immune response. Of note, it has been demonstrated by Ron Levy and Holbrook Khort at Stanford that engagement of activating Fc receptors on NK cells upregulates 4-1BB expression on those cells. This gives us a hint of how to productively combine antibody therapy with anti-4-1BB agonism. Stanford is already conducting such trials. Furthermore we can look to the adjacent field of CAR T therapeutics and find that CAR T constructs containing 4-1BB signaling motifs (that will engage the relevant signaling pathway) confer upon those CAR T cells persistence, longevity and T cell memory – that jewel in the crown of anti-tumor immunity that can promise a cure. 4-1BB-containing CAR T constructs developed at the University of Pennsylvania by Carl June and colleagues are the backbone of the Novartis CAR T platform. It is a stretch to claim that the artificial CAR T construct will predict similar activity for an appropriately engineered anti-4-1BB agonist antibody, but it is suggestive enough to give us some hope that we may see the innate immune system (via NK cells) and an adaptive memory immune response (via activated T cells) both engaged in controlling a tumor. Pfizer and Bristol Myers Squibb have the most advanced anti-4-1BB agonist antibody programs; we’ll see if these are indeed best-in-class therapeutics as other programs advance.

Agonism of OX40, GITR, CD27, TNFRSF25 and HVEM will also activate T cells, and some careful work has been done by Taylor Schreiber at Pelican to rank order the impact of these receptors of CD8+ T cell memory (the kind we want to attack tumors). In these studies TNFRSF25 clearly is critical to support CD8 T cell recall responses, and may provide yet another means of inducing immune memory in the tumor setting. Similar claims have been made for OX40 and CD27. Jedd Wolchok and colleagues recently reviewed the field for Clinical Cancer Research if you wish to read further.

Looking again beyond T cells another very intriguing candidate TNFR is CD40. This activating receptor is expressed on B cells, dendritic cells, macrophages and other cell types involved in immune responses – it’s ligand (CD40L) is normally expressed on activated T cells. Roche/Genentech and Pfizer have clinical stage agonist anti-CD40 programs in their immuno-oncology portfolios. Agonist anti-CD40 antibodies would be expected to activated macrophages and dendritic cells, thus increasing the expression of MHC molecules, costimulatory proteins (e.g. B7-1 and B7-2) and adhesion proteins like VCAM-1 and ICAM-1 that facilitate cell:cell interactions and promote robust immune responses.

I mentioned above that interaction of antibodies with Fc receptors modulates immune cell activity. In the case of anti-CD40 antibodies, Pfizer and Roche have made IgG2 isotype antibodies, meaning they will have only weak interaction with FcRs and will not activate the complement cascade. Thus all of the activity of the antibody should be mediated by it’s binding to CD40. Two other agonist anti-CD40 antibodies in development are weaker agonists, although it is unclear why this is so; much remains to be learned regarding the ideal epitope(s) to target and the best possible FcR engagement on human cells. Robert Vonderheide and Martin Glennie tackled this subject in a nice review in Clinical Cancer Research in 2013 and Ross Stewart from Medimmune did likewise for the Journal of ImmunoTherapy of Cancer, so I won’t go on about it here except to say that it has been hypothesized that crosslinking via FcgRIIb mediates agonist activity (in the mouse). Vonderheide has also shown that anti-CD40 antibodies can synergize with chemotherapy, likely due to the stimulation of macrophages and dendritic cells in the presence of tumor antigens. Synergy with anti-CTLA4 has been demonstrated in preclinical models.

One of the more interesting CD40 agonist antibodies recently developed comes from Alligator Biosciences of Lund, Sweden. This antibody, ADC-1013, is beautifully characterized in their published work and various posters, including selection for picomolar affinity and activity at the low pH characteristic of the tumor microenvironment (see work by Thomas Tötterman, Peter Ellmark and colleagues). In conversation the Alligator scientists have stated that the antibody signals canonically, i.e. through the expected NF-kB signaling cascade. That would be a physiologic signal and a good sign indeed that the antibody was selected appropriately. Not surprisingly, this company is in discussion with biopharma/biotech companies about partnering the program.

Given the impact of various antibody/FcR engagement on the activity of antibodies, it is worth a quick mention that Roghanian et al have just published a paper in Cancer Cell showing that antibodies designed to block the inhibitory FcR, FcgRIIB, enhance the activity of depleting antibodies such as rituximab. Thus we again highlight the importance of this sometimes overlooked feature of antibody activity. Here is their graphical abstract:

 graphical abstract

The idea is that engagement of the inhibitory FcR reduces the effectiveness of the (in this case) depleting antibody.

Ok, moving on.

Not all signaling has to be canonical to be effective, and in the case of CD40 we see this when we again turn to CAR T cells. Just to be clear, T cells do not normally express CD40, and so it is somewhat unusual to see a CAR T construct containing CD3 (that’s normal) but also CD40. We might guess that there is a novel patent strategy at work here by Bellicum, the company that is developing the CAR construct. The stated goal of having a CD40 intracellular domain is precisely to recruit NF-kB, as we just discussed for 4-1BB. Furthermore, the Bellicum CAR T construct contains a signaling domain from MYD88, and signaling molecule downstream of innate immune receptors such as the TLRs that signal via IRAK1 and IRAK4 to trigger downstream signaling via NF-kB and other pathways.

Here is Bellicum’s cartoon:

 cidecar

If we look through Bellicum’s presentations (see their website) we see that they claim increased T cell proliferation, cytokine secretion, persistence, and the development of long-term memory T cells. That’s a long detour around 4-1BB but appears very effective.

The impact of innate immune signaling via typical TLR-triggered cascades brings us to the world of pattern-recognition receptors, and an area of research explored extensively by use of TLR agonists in tumor therapy. Perhaps the most notable recent entrant in this field is the protein STING. This pathway of innate immune response led to adaptive T cell responses in a manner dependent on type I interferons, which are innate immune system cytokines. STING signals through IRF3 and TBK1, not MYD88, so it is a parallel innate response pathway. Much of the work has come out of a multi-lab effort at the University of Chicago and has stimulated great interest in a therapeutic that might be induce T cell priming and also engage innate immunity. STING agonists have been identified by the University of Chicago, Aduro Biotech, Tekmira and others; the Aduro program is already partnered with Novartis. They published very interesting data on a STING agonist formulated as a vaccine in Science Translational Medicine on April 15th (2 weeks ago). Let’s remember however that we spent several decades waiting for TLR agonists to become useful, so integration of these novel pathways may take a bit of time.

This emerging mass of data suggest that the best combinations will not necessarily be those that combine T cell immune checkpoints (anti-CTLA4 + anti-PD-1 + anti-XYZ) but rather those that combine modulators of distinct arms of the immune system. Recent moves by biopharma to secure various mediators of innate immunity (see Innate Pharma’s recent deals) and mediators of the immunosuppressive tumor microenvironment (see the IDO deals and the interest in Halozyme’s enzymatic approach) suggest that biopharma and biotech strategists are thinking along the same lines.

The twisted tale of neoantigens and anti-tumor immune responses

Two papers out this week add to a pile of data addressing the role of neoantigens in tumor therapy. While these papers address tumor neoantigen “load” in the context of immune checkpoint therapy the results have implications for TIL therapeutics, TCR therapeutics and onco-vaccine development.

A really dramatic paper from diverse groups at the University of Pennsylvania and their collaborators, just published in Nature (link-1), explores the complex interplay of radiation therapy and anti-CTLA4 antibody therapy (ipilimumab, from BMS) in patients with stage IV metastatic melanoma (relapsed or previously untreated). In this Phase 1/2 clinical trial (NCT01497808) patients with multiple melanoma metastases received various doses of radiation therapy delivered to a single metastasis, termed the “index lesion”. They then received 4 doses of ipilimumab (3 mg/kg, i.v., once every 3 weeks) and non-irradiated lesions were evaluated within 2 months of the last dose.

Although the sample size reported is small (n=22) some interesting lessons emerged from the study. The response rate was low, and the progression free survival (PFS: 3.8 months) and overall survival (OS: 10.7 months) data bear this out. It appears that just shy of 40% of patients were still alive at ~30 months (see Figure 1c in the paper). It is too early to tell if there will be a “long-tail” effect going forward. In the original ipilimumab study a very small percentage of patients lived for a very long time, “pulling” the PFS and OS curves to the right. Regardless, most patients in this study did not respond and the questions posed in this paper are directed to the mechanisms of resistance.

The mouse B16-F10 melanoma model was used to model resistance. Mice with tumors were locally irradiated then treated with an anti-mouse-CTLA4 antibody, to mimic the clinical trial. Only 17% of the treated mice responded. Two predictors of response/non-response were elucidated: 1) the ratio of effector T cells (Teff) to regulatory T cells (Treg) and 2) a gene signature in the tumor cells that is dominated by the expression of PD-L1 and IFNgamma regulated genes. In short, if the melanoma cells are expressing PD-L1 and the tumor infiltrating lymphocyte (TIL) population is dominated by Tregs (which are PD-1+), then the radiation + anti-CTLA4 therapy failed.

To further subset TIL into active Teff versus non-responsive “exhausted” Teff, the authors used an expression profile of PD-1+/Eomes+ to identify exhausted Teff and PD-1+/Eomes+/Ki67+/GzmB+ for active Teff. Importantly, exhausted Teff could be reanimated upon treatment with PD-1 pathway antagonists: anti-PD-1 antibody or anti-PD-L1 antibody. This reanimation led to an improved CD8+ Teff/Treg ratio and led to tumor control in the majority of the mice (up to 80%) when the treatment consisted of irradiation plus anti-CTLA4 plus anti-PD-L1. Of note, radiation plus anti-PD-L1 did not achieve this effect; the triple therapy was required (see Figure 2d).

The striking conclusion is that upregulation of PD-L1 on tumor cells can subvert the effect of anti-CTLA4 antibody therapy, and this therefore qualifies as a mechanism of resistance.

What about the role of irradiation? In both the patients and the mouse model irradiation was local, not systemic. Further, this local irradiation was required to achieve complete responses in the mouse model. What is going on here? Irradiation was linked to a modest increase in TIL infiltration of melanoma tumors in the mouse model, but sequencing of the T cell receptors (TCR) revealed that there was an increase in the diversity of TCRs, meaning that more antigens were being recognized and responded to by TIL after irradiation. In this context then, anti-CTLA4 reduced the Treg population, anti-PD-L1 allowed CD8+ TIL expansion, and irradiation set the antigenic landscape for response.

Returning to the patients armed with this information from the mouse study, the authors find that low PD-L1 expression on the melanoma cells correlates with productive response to irradiation plus ipilimumab therapy, while PD-L1 high expressing tumors were associated with persistent T cell exhaustion. In addition, monitoring the state of the CD8+ T cell population (PD-1+/Eomes+ versus PD-1+/Eomes+/Ki67+/GzmB+) suggested that these phenotypes might be useful as peripheral blood biomarkers. The patient numbers are very small for this analysis however, which awaits further validation.

The conclusion: irradiation combined with ipilimumab plus anti-PD-L1 antibody therapy should be a productive therapeutic combination in PD-L1+ stage IV melanoma. Similar strategies may be beneficial in other solid tumor types. This is interesting news for companies developing anti-PD-L1 antibodies, including BMS-936559 (also from BMS), MPDL3280A (Roche/Genentech), MEDI4736 (AZN) and MSB0010718C (Merck Serono).

A second paper (link) bring our focus back to PD-1, in the context of non-small cell lung cancer (NSCLC). Using the anti-PD-1 antibody pembrolizumab (from Merck) a group from the Memorial Sloan-Kettering Cancer Center sought to determine correlates of response of NSCLC patients to anti-PD-1 therapy. Their findings again hone in on neoantigen load, as the best predictors of response were the non-synonymous mutational burden of tumors, including neoantigen burden and mutations in DNA repair pathways. What all this means is that mutations that change the amino acid sequence (thus, are non-synonymous) can produce neoantigens that can be recognized by CD8+ T cells; mutations in the DNA repair pathways increase the rate that such mutations go uncorrected by a cell.

The authors sequenced the exomes (expressed exons – these encode proteins) from tumors versus normal tissue, as a measure of non-synonymous mutational burden that could produce neoantigens. Patients were subsetted based on response: those with durable clinical benefit (DCB) and those with no durable benefit (NDB). High mutational burden was correlated with clinical efficacy: DCB patients averaged 302 such mutations, while NDB patients averaged 148; ORR, PFS and OS also tracked with mutational burden. In a validation cohorts the number of non-synonymous mutations was 244 (DCB) versus 125 (NDB).

Examination of the pattern of exome mutations across both cohorts was studied in an attempt to discern a pattern of response to pembrolizumab treatment. The mutational landscape was first refined using an algorithm that predicts neoepitopes that can be expressed in the context of each patients specific class I HLA repertoire – these are the molecules that bring antigens to cell surfaces and present them to T cells for recognition (I’m simplifying this process but that is the gist of it). The algorithm identified more potential neoepitopes in the DCB patient tumors than in the NDB cohort, more impressively, a dominant T cell epitope was identified in an individual patient using a high-throughput HLA multimer screen. At the start of therapy this T cell clone represented 0.005% of peripheral blood T cells, after therapy the population had risen 8-fold, to 0.04% of peripheral blood T cells. Note that most of this clone of T cell would be found in the tumor, not in circulation, so that 8-fold increase is impressive. The T cells were defined as activated CD8+ Teff cells by expression markers: CD45RA-/CCR7-/LAG3-. As in the first paper we discussed, it is useful that these markers of systemic response to immunotherapy treatment are being developed.

There is an interesting biology at work here. It is often noted that high mutational burden is associated with better outcome, for example to chemotherapy in ovarian cancer, and irrespective of therapy across different tumor types (link-2). This suggests that tumor neoepitopes are stimulating an ongoing immune response that is stifled by active immunosuppression, yet is still beneficial. Once unleashed by immune checkpoint blockade, the immune system can rapidly expand it’s efforts.

We recently reviewed the importance of neoantigens in anti-tumor therapy (link-3) although the focus then was on cellular therapeutics rather than on immune checkpoint modifiers such as anti-CTLA4 and anti-PD-1 or PD-L1 antibodies. We can mow add that our ability to track neoantigens and the immune response to neoantigens is opening new avenues for investigating immuno-oncology therapeutics and their efficacy.

The widget TIGIT

Genentech continues to work on TIGIT, so what the heck is this target? Lets have a look, but first, some context.

T cell constraint is a fundamental attribute of tumor-induced immunosuppression. CTLA4 and PD-1 are central regulators of this process, and antibody blockade of these pathways can restore anti-tumor responses. The state of T cell constraint (non-responsiveness) has been termed anergy in reference to CD4+ T cells and exhaustion in reference to CD8+ T cells. Exhausted CD8+ T cells have a recognizable T cell phenotype characterized by the expression of diverse inhibitory pathways and proteins, including PD-1, TIM-3, LAG-3 and TIGIT. Whether such a phenotype is absolutely selective for exhausted CD8s is a matter of debate, but is a good starting point for a discussion of the need for so many regulatory pathways.

Dual gene-deficient (knock-out) mice and the administration of blocking antibody combinations have shown that the inhibitory receptors can function synergistically to reject tumors in mouse models. The hypothesis that individual co-inhibitory receptors contribute distinct functions to collectively limit T cell responses has recently been tested in human cancer clinical trials, yielding the impressive result that co-blockade of CTLA4 and PD-1 has synergistic and beneficial anti-tumor activity. Such benefit comes with a toxicity cost, as pathological autoimmunity is revealed when the “brakes” come off the immune system.

Why does the T cell arm of immune system require so many different control pathways? This is a reasonable question, which can be answered somewhat glibly with the observation that uncontrolled immunity leads to autoimmune disease and/or chronic inflammation. Still, though, why are multiple breaks required? The working hypothesis is that one pathway (CTLA4) regulates T cell activation by CD28 that normally occurs in the spleen, lymph nodes, Peyer’s patches and other “secondary lymphoid organs” (the thymus, bone marrow and fetal liver are the major primary lymphoid organs). A second pathway (PD-1) is generally thought to regulate “peripheral” T cell activation at the sites of pathogen encounter – in this sense “peripheral” means outside of the lymphoid organs themselves, that is, in the tissues and circulation, or, in the case of cancer immunology, within the tumor. So, simplistically, there is one control pathway (CTLA4) in the house and another (PD-1) in the yard. The recent paper (link 1) describing the release of T cell recognition of tumor antigens upon CTLA4 blockade in melanoma suggests either cross-talk between the compartment (i.e. tumor beds have lymphatic or circulatory drainage to secondary lymphoid organs) or that the role of CTLA4 is more complex than we think.

What about the other control pathways? LAG-3 is a competitive regulator of CD4/MHCII antigen recognition activity and was shown to confer Treg function when transfected into naive CD4+ T cells. The expression of LAG-3 on CD8+ T cells (which are critical for anti-tumor activity) suggests a role in the interaction of CD4+ and CD8+ T cells. LAG-3 is also expressed on tumor cells and may mask tumors from immune recognition. LAG3/PD-1 doubly gene-deficient mice can reject poorly immunogenic tumors that wild-type mice cannot reject. However, the doubly deficient knockout mice also develop pathological and aggressive autoimmunity. These results show that these proteins have distinct roles in regulating immune responses.

TIM-3 has several immune regulatory activities, one of which is to suppress T cell recognition of phosphatidylserine, a molecule expressed on dead and dying cells but also on tumor cells. As with LAG-3 the combination of anti-PD-1 and anti-TIM-3 antibodies had enhanced anti-tumor efficacy in mouse tumor models when compared to either antibody alone.

And now we have TIGIT, an Ig superfamily protein and a member of the PVR/nectin family that includes CD226 (DNAM-1), CD96, CD112 (PVRL2), and CD155 (PVR), among others. The biology of this family of proteins is complex and a little intimidating. Genentech has been prosecuting this pathway for several years, and their new paper (link 2) has perhaps shed additional light on the biology and utility of this target.

One mechanism by which TIGIT modulated immune responses is via the interaction of TIGIT on T cells with CD155 expressed on immature or resting dendritic cells, which blocks maturation signals normally delivered by CD226, that is, TIGIT is a competitive inhibitor of the interaction of CD226 with CD155. The authors note that this system resembles the co-stimulatory/co-inhibitory receptor pair of CD28 and CTLA-4, where CTLA4 is a competitive inhibitor of the interaction of CD28 with B7-1/CD80 and B7-2/CD86. The expression pattern of the receptors is also similar: both TIGIT and CTLA-4 are induced upon cell activation, while the expression of CD226 and CD28 is constitutive.

As alluded to above, and noted explicitly by the Genentech team, the molecular and functional relationships between TIGIT and it’s various ligands/co-receptors are poorly characterized. Furthermore, TIGIT’s role in regulating CD8+ T cell responses and the mechanisms underlying such regulation are not known. Of note, antibodies to TIGIT or PD-L1 alone enhanced CD8+ T cell effector function in tumor-draining lymph nodes, but blockade of both receptors was required to allow activation of CD8+ T cells within the tumor microenvironment, as measured by IFNy production. The authors conclude that TIGIT is a critical and regulator of CD8+ T cell anti-tumor activity. The mechanism of action evoked to explain the role of TIGIT in the tumor setting was addressed using FRET and other analyses. The authors show that TIGIT interacts directly with CD226 to prevent homodimerization, a component of the interaction of CD226 with CD155.

There are a few things to consider here. The animal models were run with very high amounts of anti-TIGIT and anti-PD-L1 antibodies on board (10 mg/kg anti-PD-L1 and 25 mg/kg anti-TIGIT) given 3 times a week. That’s nearly a gram of antibody approximately every 2.5 days. While the anti-PD-L1 antibody used has a mutated Fc domain that cannot mediate direct cell killing by ADCC, the anti-TIGIT antibody used is a wild-type IgG2a isotype antibody and almost certainly mediates direct killing of TIGIT+ cells. While the in vitro FRET assays are suggestive of the proposed mechanism of action, what is actually occurring in vivo is less clear. TIGIT expression on NK cells is also worthy of further exploration.

So I have a doubt. Not that the pathway is important, but that we really have a good sense of how it functions, nor how antagonism of the pathway in patients will impact anti-tumor activity and baseline immune responses. Locally, Drs Vijay Kuchroo and Ana Anderson have done wonderful work on TIGIT biology, and no doubt one or more of the Cambridge immunotherapy companies is working on this target and exploring it’s utility in the tumor setting. Given the expression pattern of TIGIT in tumors – i.e. on PD-1+/TIM3+ “exhausted” T cells – it is certainly worth the effort to find out.

How to select patients who should respond to anti-TIGIT co-therapy (or anti-TIM-3 or anti-LAG-3) is a critical question, best left for another day.

stay tuned

AND HAPPY HOLIDAYS AND PEACE TO ALL

Tumor Neo-Epitopes

I’m asked a lot about the onco-vaccine field, and if immune checkpoint inhibitors will be the key to unlocking the potential of this long-suffering therapeutic class. The answer is never simple, since we are often looking at thin patient data that can contain compelling hints of efficacy – those immunized late-stage patients who not only regressed but stay in remission, month after month and year after year. The problem for companies and investors is that such observational data can be very misleading, and the vaccine candidates most often go on to fail in later and larger clinical trials, sometimes spectacularly. These big failures burden the field with a high evidentiary bar.

Data have emerged that suggest several issues with most vaccines, and these issues are both distinct and related.

At the end of November Nature published two interesting papers that asked a very simple question: what immunogenic antigens are present in common mouse tumor models. Yadav et al from Genentech and Immatics Biotechnologies (link 1) used a genome-wide exome and transcriptome sequence analyses, mass spectrometry and structural modeling to identify immunogenic neo-antigens in the widely used MC-38 and TRAMP-C1 mouse syngeneic tumor models. These models are considered poorly immunogenic in wild-type syngeneic (C57Bl6) mice. The sequencing analysis was used to identify mutated proteins that were present at >20% allelic frequency. From the MC-38 model, 1290 expressed mutations were identified of which 170 were considered to be neo-epitopes, that is, modeling suggested they would be expressed by MHCI and sufficient residues would be solvent exposed to allow immunogenicity. Only 67 expressed mutations were found in the TRAMP-C1 model, and of these 6 were considered to be potential neo-epitopes. Of this total of 170 (MC-38) and 6 (TRAMP-C1) only 6 bound MHC1 by Mass Spec, with a predicted IC50 for MHCI < 500nM. Of these, 3 were actually immunogenic in vivo (using C57Bl/6 mice) and could protect wild-type mice from tumor challenge. The neo-epitopes were found in the proteins Dpagt1, Reps1 and Adpgk. Here is a schematic of the filtering scheme:

 Screen Shot 2014-12-15 at 6.37.49 PM

Working the other way, the authors confirmed the immunogenicity of neo-epitope peptides by analyzing tumor-infiltrating lymphocytes (TIL) and staining with peptide–MHCI dextramers to identify bound T cells. CD8+ T cells specific for Reps1, Adpgk and Dpagt1 were enriched in the tumor. Using the Adpgk neo-epitope, the TIL were further investigated and found to express PD-1 and TIM-3, inhibitory receptors associated with anergic or “exhausted” CD8+ T cells, showing that the murine immune system had indeed recognized and responded to the neo-epitopes, a response that was then actively immunosuppressed in the tumor microenvironment. Importantly, none of the identified neo-epitopes would qualify as tumor-antigens, that is, they are not specifically overexpressed at a sufficient level to qualify. The neo-antigen-specific TIL are also pretty rare, suggesting that use of tumor lysate as an immunogen to elicit an anti-tumor response may “miss” by failing to present enough of the right antigen to the immune system.

We noted at the top that this paper came out of labs at Genentech and Immatics. An agreement between Roche/Genentech and Immatics will focus on the use of this technology. The two companies will develop new tumor-associated peptides (the neo-epitopes as cancer vaccine candidates, initially targeting gastric, prostate and non-small cell lung cancer. The most advanced candidate is IMA942, a peptide vaccine for the treatment of gastric cancer, in late preclinical development. Immatics CEO Paul Higham has publicly stated that a Phase I study of IMA942 with Roche’s PD-L1 inhibitor MPDL3280A in gastric cancer will be initiated soon. Immatics will also conduct research to identify neo-antigens for the additional indications. For those keeping score, Immatics received $17 million upfront, committed research funding, and potential milestones

The second work, led by Schreiber’s group at Wash U, used mouse models to ask a different but related question: what tumor antigens are recognized after immune checkpoint blockade with anti-PD-1 or anti-CTLA4 antibodies (link 2). The sarcoma lines d42m1-T3 and F244 were rejected in wild-type mice treated with either anti-PD-1 or anti-CTLA4 antibodies, in a CD4/CD8/IFNy/DC-dependent manner. As in the first paper, a filtering system built from diverse technologies was used to identify potential neo-epitopes. Mutations were identified by cDNA sequencing, translated to corresponding protein sequences, then tested against MHCI binding algorithms. Neo-epitopes were ranked by predicted median binding affinities and likelihood of productive immunoproteasome processing and antigen display. Using these methods, two MHCI restricted neo-epitopes were identified in Alg8 and Lama4.

As in the first paper, the authors then turned the system around, asking what neo-epitopes could be identified through analysis of TIL. Alg8 and Lama4 were found in tumor TIL and their frequency was increased by treatment with anti-PD-1 or anti-CTLA4. The neo-epitopes could successfully be used to induce anti-tumor immune responses. As in the first paper, these are not neo-epitopes that would qualify as tumor-antigens using the traditional criteria of selective and high expression.

So these are our two distinct but related issues with the current tumor vaccine landscape: those that have selected antigens have likely selected the wrong ones, while those that use lysates are likely too dilute.

Importantly, we can now compare these model systems to actual data from human patients treated with anti-CTLA4 antibody, as published recently in NEJM (link 3). The clinical group from Memorial Sloan Kettering Cancer Center  obtained tumor tissue from melanoma patients treated with anti-CTLA4 antibodies (ipilimumab or tremelimumab). As in the mouse study, whole-exome sequencing was performed, somatic mutations identified and potential neo-antigens were characterized. Here is their schematic:

Screen Shot 2014-12-16 at 9.42.56 AM

Baseline analyses showed that there was a significant difference in mutational load between patients with long-term clinical benefit and those with a minimal or no benefit, with higher mutational load associated with response. However the relationship was correlative, since some tumors with a high mutational burden were not responsive to anti-CLTA4 therapy. Using peptides predicted to bind to MHCI with a binding affinity ≤ 500 nM, the authors focused on mutated peptide sequences shared by multiple tumors and shared by patients having long-term clinical benefit. From this analysis a neo-epitope “signature” was derived, consisting of a distinct pattern of mutated peptide sequences. One of the peptide signatures identified matched an amino acid sequence in MART1, a known melanoma antigen. However the bulk of predicted neoantigens were tetrapeptide sequences shared across antigenic peptides, that is, they were encoded by diverse genes (you have to go into the huge supplemental data file to find this list, suffice to say it is very long). To make sense of this curious result the authors note that the some of the predicted sequences have high homology to viral and bacterial antigens, citing a CMV antigenic sequence as an example. They speculate, and here we quote from the paper: ” These data suggest that the neoepitopes in patients with strong clinical benefit from CTLA-4 blockade may resemble epitopes from pathogens that T cells are likely to recognize.”

The unstated null hypothesis is that there is no relationship between the shared tetrapeptide sequences and clinical response and that the association between the two phenomena is due to a productive immune system response to anti-CTLA4 antibody therapy which has released the anti-tumor response as well as many otherwise quiescent immune responses, such as those to pathogenic viruses and bacteria (and to self antigens, as shown by the autoimmune toxicity associated with anti-CTLA4 antibody treatment). The in vitro response assay data sheds no real light on this, since these assays cannot distinguish anti-tumor responses from other immune responses. So we are left with an intriguing correlation, and a nagging sense that only a very few of the vast number of predicted neo-epitopes will actually trigger bona-fide anti-tumor T cells responses. Indeed the weakness of the paper is the reliance on predictive rather than experimental identification of productive peptide/MHC interaction. As we say in the mouse studies the majority of predicted interactions are not confirmed experimentally.

Regardless, the paper is a remarkable and important step forward, and shows us (as do the mouse studies) the level of investigation required to identify neo-antigens that might expand be used to expand patient TIL populations, as we have discussed in other posts. Returning to onco-vaccines, these three papers together show us that neo-antigen anonymity, rarity and variability from patient to patient are critical issues that will need to be addressed if we are to efficiently develop this therapeutic class.

Side Effect Profiles of Immune Checkpoint Therapeutics – Parts 2 and 3

Part 2 – The Border Wars.

One of the fascinating aspects of the toxicity of immune checkpoint therapeutics is that it is a lot of is triggered at the border between self and non-self, where non-self is everything that the immune system must encounter and sort through continuously. The sorting serves to identify pathogens and ignore non-pathogens among the myriad components of the microfauna and flora that inhabit these borders. The “sampling” of these ecosystems is continuous and highly reactive – one glass of unpurified water taken on foreign soil will teach you this lesson pretty quickly. When the immune system is unrestrained by blockade of CTLA4 and/or PD-1 it is not surprising that we see the breakdown of immune tolerance in these border zones.

There are three major surfaces where toxicity has been an issue: the skin, the gut mucosa, and the airspaces of the lung. Ipilimumab treatment can cause pretty intense inflammation of the skin, generally dismissed in the clinical trial literature as “rash”. In a pooled analysis of nearly 1500 patients enrolled in various ipilimumab clinical trials, 45% developed dermatological AEs considered drug related, and 2.6% (so 39 people) developed severe symptoms rating a grade 3-4 (where grade 5 is lethal) (see Tarhani, A. Scientifica 2013, Article ID 857519). A fair amount of the milder skin AEs can be ascribed to an anti-melan-A response, as this antigen is abundant in melanoma, the setting for the clinical development trials. In the Phase 3 registrational trials dermatologic AEs were reported in more than 40% of patients in the ipilimumab arms, and there were very severe AEs that cannot be ascribed to an anti-melan-A (i.e melanocyte) immune response. This is from Tarhani’s review of patients in the ipilimumab + gp100 (vaccine) and ipilimumab monotherapy arms having dermatological irAEs,

“of these, 2.1% and 1.5%, respectively, were grade 3 or higher … Severe, life threatening, or fatal immune-mediated dermatitis (Stevens- Johnson syndrome, toxic epidermal necrolysis, … full thickness dermal ulceration, or necrotic, bullous, or hemorrhagic manifestations; grade 3–5) occurred in 13 of 511 (2.5%) patients treated with ipilimumab. One patient (0.2%) died as a result of toxic epidermal necrolysis, and one additional patient required hospitalization for severe dermatitis… .”

That’s some rash. We note in passing that dermatologic AEs were see in a phase 2 trial of ipilimumab plus chemotherapy in non-small cell lung cancer (NSCLC) and so this is certainly not limited to the melanoma setting. PD-1 pathway antagonists also cause skin inflammation in both the melanoma and other settings, similarly suggesting that what we are seeing here are immune responses to antigenic stimulation that is normally immunologically inert. Nivolumab-induced dermatologic toxicity can be severe, but is less common than seen with ipilimumab therapy.

The issue of skin toxicity is well known clinically, and there are established treatment protocols requiring cessation of therapy and treatment with anti-inflammatories, usually steroids (i.e the REMS protocols). The gastrointestinal (GI, “gut”) AEs are also common, can arise suddenly, be resistant to therapy (corticosteroids, and rarely, anti-TNF antibody), and are of significant concern. Returning to the pooled analysis of ~1500 ipilimumab patients we see roughly half of the patients developing GI symptoms (this includes diarrhea). If we focus on grade 3/4 SAEs we have 10-12% of patients with GI disorders that include colitis, enterocolitis, intestinal perforations etc that can proceed to lethal septic complications. Of note, inflammatory infiltrates in the intestines include abundant T cells and neutrophils, showing that acute ongoing inflammation is occurring. GI toxicity is less common and less severe in nivolumab-treated patients, and this is true also of Merck’s anti-PD-1 antibody pembrolizumab and the anti-PD-L1 antibody MPDL3280A from Roche. Colitis is generally not a big issue, for example, GI SAEs are seen in less than 1% of nivolumab-treated patients. We might conclude here that other pathways are maintaining tolerance in the gut mucosa when the PD-1 pathway is blocked.

A different picture emerges when we consider AEs in the lung. Pulmonary toxicity is rare in the context of ipilimumab monotherapy, with only scattered case reports in the literature (see Voskens et al for a review of rare ipilimumab-induced AEs: link). Anti-PD-1 pathway therapeutics, particularly nivolumab, are associated with pneumonitis, which is inflammation of the lung tissues. In the monotherapy setting, both nivolumab and pembrolizumab causes pneumonitis in 3-4% of patients – the condition is generally mild and treatable. Of note this AE rate is consistent across indications (e.g. melanoma, renal cell). The anti-PD-L1 antibodies (Roche’s MPDL3280A and Astra Zeneca’s MEDI4736) have not been associated with pneumonitis to date, perhaps reflecting a unique profile. The recent data from the anti-PD-L1 antibody MEDI4736 trial in NSCLC presented a tolerable profile. While response rate was low, significant numbers of patients remained on therapy with stable disease (ASCO 2014, Abstract #3002).

More worrisome is the pneumonitis rate and severity in combination therapy particularly in the NSCLC setting where diminished lung function is already a concern (smokers with lung cancer can’t breathe). When nivolumab was combined with platinum-based chemotherapy in NSCLC the SAE rate jumped to 45%, with notable findings of grade 3/4 pneumonitis (7%) and acute renal failure (5%) (ASCO 2014, Abstract #8113). Nivolumab plus erlotinib was not associated with pneumonitis (ASCO 2014, Abstract #8022) but response rates were low as well suggesting that these therapies were not particularly additive. The combination of nivolumab with ipilimumab was most worrisome, with grade 3/4 pneumonitis (6%) now seen along with grade 3/4 SAEs of skin (4%), GI (16%) and others (16%) (ASCO 2014, Abstract #8023). Most problematic is that 35% of patients discontinued, and between 3 to 5 patients died due to drug related SAEs including respiratory failure (caused by severe colitis), epidermal necrolysis (in a patient with multiple SAEs) and pulmonary hemorrhage (pneumonitis). As indicated above, the anti-PD-L1 antibody MEDI4736 may better suited for combination therapy. A combo trial in NSCLS with anti-CTLA4 mAb tremelimumab is enrolling, so we’ll wait and see.

It’s fair at this point to take a step back and say “so what?” These are close to terminal patients with deadly cancers usually highly refractory to treatment, and we cannot expect a free ride. The unmet need is acute and urgent, and these therapeutics offer potential cures and increase in life expectancy – as shown very clearly in last weeks early termination of the Phase 3 trial of nivolumab versus dacarbazine due to the obvious overall survival advantage offered by nivolumab (see John Carroll’s story in Fierce Biotech here: link)

The problem is that the response rates we are seeing are generally low, the discontinuation rates high, and for anti-CTLA4 and anti-PD-1 therapeutics there is no clear consensus regarding the use of biomarkers to select patients most likely to respond. Therefore the actual percent penetrance of therapy in the patient cohorts becomes quite low. For those relatively few patients who respond well the outcomes can be sustained and robust. It is critical however to get these response rates up. The blockbuster combination of nivolumab plus ipilimumab in metastatic melanoma gives us a sense of what is possible, if the drugs are tolerable. It is also critical to understand how and why immune therapy can make subsequent therapy intolerable, as we’ve seen in case reports, or conversely, how and why prior therapies can cause such problems for patients going onto an immune therapeutic (see that Voskens review mentioned above). We’ve seen some the issues that can bedevil combinations in metastatic melanoma (with vemurafenib) and in renal cell carcinoma clinical trials (pazopanib) When we look at all of the combination clinical trials underway with these agents we have to wonder what surprises lay in store.

Part 3 – The Fifth Column.

The fifth column refers to enemies lurking within the boundaries of the state, in this case the human body. These are a mixed collection of AEs that can be difficult to understand. While we are used to see liver and kidney inflammation in the setting of cancer therapy, it remains a bit mysterious that immune checkpoint therapy can cause severe inflammatory responses in these organs, the most notable is probably the induction of hepatitis in patients treated with ipilimumab. Even weirder (for me anyway) are the endocrinopathies, headlined by pituitary inflammation, seen with both CTLA4 and PD-1 directed immunotherapies. Primary thyroid inflammation is also seen although less frequently. These are of course autoimmune targets in this setting, but the triggers are obscure, as is also almost always true in autoimmune disease. Somewhat remarkable is the emergence of a sometimes fatal but normally very rare condition known as autoimmune hypophysitis or lymphocytic hypophysitis, which is inflammation of the pituitary gland. Hypophysitis is a unique toxicity of immune checkpoint inhibitors, and has been been seen in patients treated with ipilimumab, tremelimumab, and nivolumab. Because the pituitary sits in the middle of the limbic hypothalamic-pituitary-adrenal axis effects on the thymus and adrenal gland are also noted, with adrenal insufficiency being a severe and life-threatening complication. It must be stressed that the frequency of this AE is stunningly high, reaching 17% in some trials, as the disease has been described only very rarely, with a good deal less than 1000 cases ever known prior to the introduction of immune checkpoint therapeutics.

So we won’t dwell on this, as clinicians now know what to watch for, and treatment paradigms have been developed. As mentioned earlier, treatment generally involves initiation of steroids to control to autoimmune response, and cessation of immune checkpoint therapy.

Let’s return to the consideration of combination therapy, which I think we all agree is essential if we are really to expand use of immune therapeutics in the treatment of these difficult cancers. Great hope has been placed in the combination of CTLA4 and PD-1 targeting agents with “safe” immune checkpoint modulators, notably the IDO-inhibitor from Incyte. We have very little information to date, but it is notable that the dose limiting toxicity in the first combination trial of ipilimumab and INCB024360 from Incyte (INCY) was liver damage as measured by ATL elevation. It may be that merely piling on ways of disrupting Treg activity will not help with the toxicity profile; in fact, one might make the prediction that this approach will make things worse in some settings.

We’ve remarked in passing on the apparently mild safety profile of the anti-PD-L1 inhibitors compared to the PD-1 inhibitors. This makes some sense, as the ligands are expressed by the target tumor cells, and this may be the main sink for the injected antibody, i.e. antibody may not be evenly bio-distributed but rather predominantly localized to the tumors. The concordance of anti-PD-L1 antibody activity with tumor PD-L1 expression is consistent with a direct and localized effect. The fact that there is less consistent concordance of anti-PD-1 antibody activity with PD-1 expression by tumor-infiltrating T cells suggests less specificity in the induced immune response, and this may be why we see autoimmune toxicity in the nivolumab setting. As CTLA-4 is exclusively T cell expressed, the same seems to hold true for anti-CTLA4 antibody therapy. So combining these may not be the most ideal way forward.

We will discuss alternative approaches next time, but first there is some new data on novel immune checkpoint therapies to consider. These are the TNF receptor superfamily proteins that we discussed last month (link): 4-1BB, CD27, OX40 and GITR. There is admittedly very little data to date. Pfizer’s (PFE) anti-4-1BB antibody PF-05082566 reached a safe dose in Phase 1 without undue toxicity signals (ASCO 2014, Abstract #3007). Pfizer disclosed combination trials with rituximab in Non-Hodgkin Lymphoma (NHL) and pembrolizumab (anti-PD-1). The BMY antibody urelumab was tolerated through its’ dose escalation cohorts, and ex vivo analysis showed activation of CD8+ T cells and NK cells (ASCO 2014, Abstract #3017). The Celldex anti-CD27 mAb also has demonstrated safe dose escalation, although to date without signs of clinical activity (ASCO 2014, Abstracts #3024 and #3027). Celldex (CLDX) claims planned studies in combination with nivolumab, ipilimumab, and the targeted therapeutics darafenib and trametinib.

As we discussed in an earlier post, 4-1BB, CD27, OX40 and GITR are evolutionarily closely related receptors. Biomarker studies such as the one performed in the urelumab trial will be essential in understanding how these immune stimulatory pathways will differentiate clinically and which will be safe in combination settings. We’ve reviewed the biology of this superfamily recently (see these posts) so won’t do so again until we get some more clinical data.

Next we will introduce some novel targets in the TNF receptor superfamily, revisit some apoptotic pathway “influencers”, and will swing back around to PD-1 and PD-L1 in some other solid tumor settings (not necessarily in that order).

stay tuned.

PD-1 Pathway Inhibitors Reveal Unique Benefit/Risk Profiles Across Cancer Indications

Introduction

Anyone attending the immunotherapy sessions at ASCO earlier this month would have heard several distinct messages about PD-1 pathway inhibition in oncology. PD-1 appears to be a central control point for curtailing T cell responses in the peripheral tissues, similar to the role that CTLA4 plays in regulating initial T cell activation in secondary lymphoid organs such as the lymph nodes and spleen. Remarkable progress has been made in the 13 years since Gordon Freemen and colleagues first proposed in Nature Immunology that the PD-1 pathway was used by tumor cells as a shield against immune system attack (http://www.ncbi.nlm.nih.gov/pubmed/11224527).

It is clear that PD-1 pathway antagonists show tremendous promise in treating diverse cancers. Less clear is an understanding of why certain patients respond or don’t, what biomarkers might predict response, how to increase response rates, how to accurately measure response, and how to safely combine PD-1 pathway inhibition with other therapies.

Table 1 lists the PD-1 therapeutics in development (some of these therapeutics did not have updates at ASCO).

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As the table demonstrates, the PD-1 pathway inhibitors are being developed in diverse tumor types. As late Phase 2 data and Phase 3 data are coming out we can begin to see the real promise of these drugs in clinical responses measured in large numbers of patients. The amount of data presented at ASCO was a bit overwhelming so to simplify the landscape we can address each tumor type individually, when possible. Some terms we will use are given in the table below.

Table 2 defines the RECIST1.1 clinical response parameters and their abbreviations.

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To put these terms in perspective we can just consider that a meaningful clinical response is a measureable response to therapy (SD < PR < CR) that is durable and leads to an increase in PFS, which in turn allows a significant increase in OS. There are other terms used to describe clinical responses but these are the most common. We will start with some of the most recent data, and see where that takes us.

Part 1: Immune Checkpoint Combination Treatment of Melanoma 

The very first trials of PD-1 pathway inhibitors began with the investigation of nivolumab in metastatic melanoma. As such, there was an impressive amount of progress reported and we now have mature data on different therapeutics. To set the stage, we can consider the benefit shown by nivolumab monotherapy compared to standard of care treatment protocols, and also to ipilimumab (brand name Vervoy) an anti-CTLA4 antibody, also from Bristol-Myers Squibb (BMY). Ipilimumab is approved for the treatment of metastatic melanoma based on Phase 3 clinical trial data in metastatic melanoma patients that had failed prior therapy (a chemotherapy regimen). The trial compared ipilimumab to a tumor vaccine targeting the melanoma antigen gp100. Ipilimumab treatment improved median OS to 10 months versus 6 months with the vaccine treatment (which was no better than standard of care). The 1 year survival rate was 45%. ORR however was low, just about 10%. Also, adverse events (AEs) were a problem, and included autoimmune manifestations (colitis, pituitary inflammation) and some treatment-related deaths (2% of patients). In a separate study of treatment-naive metastatic melanoma patients, ipilimumab therapy was associated with an OS = 11.2 months and a 1 year survival rate of 47%, falling to 21% by year 3. Patients were given ipilimumab or placebo plus chemotherapy (dacarbazine), and then moved to ipilimumab or placebo alone if there was a response measured or if the initial therapy caused toxicity. One consequence of this scheme was that AEs went up dramatically, with 38% of patients experiencing an immune related, grade 3 or 4 severe AE (SAE). We dwell on the anti-CTLA4 antibody ipilimumab because it is the benchmark for other immunotherapies such as nivolumab.

Nivolumab therapy for advanced melanoma has produced impressive data, with median OS = nearly 17 months, and 1 and 2-year survival rates of 62% and 43%. ORR was 33%. AEs were significant if less severe than those seen with ipilimumab. Grade 3-4 treatment-related AEs were seen in 22% of nivolumab-treated patients. Immune-related adverse events (all grades) were seen in 54% of treated patients, and included skin, GI and endocrine disorders. However only 5% of patients experienced immune-related SAEs of grade 3 or 4 and there were no drug-related deaths. These data from Topalian, Sznol et al. from John Hopkins University School of Medicine were presented at ASCO last year and published earlier this year                       (http://jco.ascopubs.org/content/early/2014/03/03/JCO.2013.53.0105.full.pdf).

So with that as our backdrop lets update the state of PD-1 pathway antagonism in melanoma. One of the obvious next steps in the development of immunotherapy is to combine treatments and we saw dramatic long-term data from the combination trial of ipilimumab plus nivolumab in advanced melanoma. Early trial results presented at ASCO last year introduced 4 cohorts of patients given different doses of nivolumab and ipilimumab in combination, with an ORR across all four cohorts of 40% and a 1 year survival rate of 82%. Median OS had not been reached. SAE rate across the 4 cohorts was 53%. This quickly gets complicated so let’s define the cohorts. Numbers are doses of nivolumab and ipilimumab, respectively, in mg/kg: Cohort 1 (0.3 + 3), Cohort 2 (1 + 3), Cohort 3 (3 + 1), Cohort 4 (3 + 3). No data were presented for Cohorts 6 and 7 so we’ll skip those. Cohort 8 is designed to mimic the dose schedule chosen for later clinical trials.

Note that after the induction phase, patients are moved onto maintenance therapy, as show below.

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The slide is taken from the trial update presented at ASCO by Dr Sznol (Abstract #LBA9003). The data updates drove home several critical points. First, at the optimal dose rates of 1 + 3 and 3 + 1 the ORR ranged from 43-53%. The author’s introduce a new classification of clinical response to capture the observation that many patients are experiencing benefit while not strictly meeting RECIST1.1 criteria, this is termed “Aggregate Clinical Activity Rate” and reaches 81-83% in Cohorts 3 and 4 (note that Cohort 4 (3 + 3) was the maximum tolerated dose due to SAEs and will no longer be used). Perhaps more meaningfully, the percent of patients whose tumor burden was reduced by > 80% at 36 weeks was 42% across the cohorts. This is a remarkable number suggesting sustained clinical benefit. Indeed, in those patients who responded, the median DOR in Cohorts 1-3 plus Cohort 8 has not been reached. In Cohorts 1-3, 18/22 patients are still responding and 7 of those had discontinued therapy due to AEs (more on this below).

Dose cohorts were analyzed for impact on 1 and 2 year survival. In Cohorts 2-3 the 1 year OS = 94% and the 2 year OS = 88%. Most stunning of all was this data showing a median OS in Cohorts 1-3 of 40 months. Median OS in Cohort 3 (1 + 3) has not yet been reached.

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These data are best-in-class for treating advanced melanoma, and place ipilimumab plus nivolumab at the forefront of therapeutic options for these patients. The one outstanding issue remains that of toxicity. 23% of patients had to discontinue therapy due to toxicity, and one patient died of complications resulting from treatment. While Dr Sznol repeatedly pointed out that the toxicities observed are controlled by standard interventions, the problem is that these standard interventions include cessation of therapy. We have already learned from the ipilizumab experience that responses to immune checkpoint inhibition can take time, and for those patients who have to stop treatment after 1 – 2 doses due to toxicity, time may not be kind. It will certainly be beneficial to reduce SAEs so that more patients can remain on therapy.

Tomorrow we’ll look at other PD-1 pathway therapeutics and combinations in melanoma before moving on to other tumor types.

Biogen Idec, multiple sclerosis, and the anti-Lingo story

It’s AAN conference week, and we were looking around, trying to get caught up on multiple sclerosis after a few months dedicated to oncology. We stumbled across this analyst report, and just had to comment.

Credit Suisse (CS) recently released a deep-dive report on Biogen Idec’s (Nasdaq: BIIB) anti-Lingo antibody program, assigning between $5-10BB (billion) USD of the total relapsing/remitting Multiple Sclerosis (rrMS) market share to the program by 2020. The program is currently in Phase 2. This analysis, in part, supports CS’s current price target for BIIB stock at $400, leveraging presumed growth due to the view on continued success of the anti-Lingo program. In other words, positive news on this program will help support inflated multiples through 2018, when pivotal trials may actually read out. The analysis seems ill considered, misses key aspects of BIIB corporate strategy, and places undo pressure on an early Phase 2 program. Further, intense focus on the anti-Lingo antibody program in turn places pressure on two early phase clinical trials, one due to read out in 2H14. The implication is that the base case for the price target could be undermined if the very early clinical development of the anti-Lingo program falters. That’s an unfair burden for a single high-risk program to bear.

Let’s dive in. Our focus will be on the science, but we’ll first set the stage. Our driving goal when looking at any biotech company or program is to bet the science, not the hype.

Two years ago the company set an internal goal of “400 in 5″, essentially promising to drive EPS in support of a sustained stock price of $400 USD by 2017. They came close during the biotech bubble that burst earlier this year. The stock is holding its’ own at around $320 USD. The “400 in 5″ goal is in place irrespective of the success or failure of the anti-Lingo program, which cannot read out pivotal clinical trials until at least mid-2018. With that in mind we can deconstruct the CS analysis, and create our own. Importantly, our analysis drastically de-risks the impact of the anti-Lingo program on the trajectory of BIIB growth, while leaving room for very attractive upside if this program hits.

The CS analysis correctly estimates that oral MS drugs will take over an increasing % of market share running from 2014 through 2020. No argument there, and BIIB will take the bulk of this market with Tecfidera, per multiple analysts. But CS believes that the “pipeline focus” is on the anti-Lingo antibody program to will help drive the stock price as the program matures. A few comments:

1) Analyst and/or investor focus on the anti-Lingo program is a sign of pipeline weakness, not strength. Where, one might ask, is the rest of the pipeline?

2) The program is very high-risk (and thus high return) for multiple reasons beyond the inherent weakness of being in Phase 2.

3) Management recognizes the oversized risk of the program, and will not tether stock performance to this program, instead they will act to de-risk the pipeline and performance.

Let’s look at these points one by one. First, the portfolio and pipeline. We agree that top-line growth will continue to be robust, driven by Tecfidera in the expanding orals segment of the market. We believe that the Daclizumab program is likely to succeed (the data being shown at AAN this week is very good) but it seems likely that this drug will compete for the declining injectable biologics market share with Tysabri. Maybe not, if it is successfully positioned for JC virus antibody positive patients, and can hold off the orals. Ocrelizumab may successfully evolve into the successor for Rituxan, an anti-CD20 antibody pulled from the MS market by Genentech/Roche because of exposure to generics competition. STX-100, an excellent program for fibrosis, is emerging into a rapidly evolving IPF treatment landscape (pirfenidone, nintedanib), and we’ll see if the company can eventually steer this drug into other indications, such as systemic sclerosis. The hemophilia biologics Eloctate and Alprolix are approved and launch-ready, with a consensus view that these will pull in 500MM over the first full year of sales, rising to 1BB by 2018. That’s already baked into the current forecasts.  The rest of the programs are as high risk as the anti-Lingo program, so let’s be conservative and assume half or more of these programs eventually fail. Point #2 is that the anti-Lingo program is high risk and can fail for a variety of reasons. At least three can be articulated. First, the therapeutic hypothesis, that axonal regeneration can be induced by a therapeutic in the setting of MS, has never been demonstrated. So there is an inherent biology risk. Second, the preclinical data package supports the hypothesis that blocking Lingo will improve myelin sheath regeneration and axonal function after insult or injury. However the preclinical package using MS animal models is very weak. Finally, the technical hypothesis, that sufficient quantity of antibody can be delivered across the blood-brain barrier in a robust and reproducible manner, patient to patient, has not been demonstrated. So there is an inherent technical risk. It’s also critical to note that the optic neuritis trial, the first Phase 2 to read out, perhaps addresses the therapeutic hypothesis (we could debate this, but won’t) but simply fails to address the technical hypothesis. Focusing investor attention on a Phase 2 readout in optic neuritis as a surrogate for efficacy in MS is a shell game that will go bad quickly if that Phase 2 trials comes in with negative results.

So we agree with CS that anti-Lingo antibody might work in rrMS, and it might not. We disagree that this program should be the focus of interest in the pipeline. We disagree outright with a few of their more outlandish predictions, including the statement that anti-Lingo “has potential in SPMS” the progressive and untreated form of the disease. There is no support for this statement. And while we agree that anti-Lingo is likely to be used in combination with other BIIB MS drugs, trials supporting such use are a very long way away. There is no basis to evaluate such a statement at this time. Finally, instead of concluding that pipeline focus on the anti-Lingo program is a positive, as CS does, we see this as a sign of a fundamentally weak BIIB pipeline.

Should we be surprised? Let’s consider that BIIB has not successfully developed a novel internal program since Avonex and Amevive, well over 15 years ago (yes there is Peligry, but that’s just pegylated-interferon, still, they did develop it). What else? Rituxan came from Idec. Tysabri came from Elan. Tecfidera came from Fumapharm. Daclizumab came from PDL Biopharma/Abbvie. Ocrelizumab came from Genentech/Roche. Long acting Factors XIII and XI came from Syntonix Pharmaceuticals. STX-100 is a BIIB moelcule but had to leave for 5 years in order to be successfully developed by Stromedix. In the meantime the Immunology Department has produced no drugs since it’s inception in the mid-80s, well over 20 years ago. The oncology experiment (BIIB San Diego) produced no drugs. The BIIB hemophilia group will produce no new drugs (more on this below). The medicinal chemistry effort has produced no drugs (although we think they will). The BIIB neurology research group has produced no drugs outside of the interferon space, although they are getting closer (anti-Lingo, BIIB037). So why is this company even competitive, indeed dominant, in MS?

The answer is simple and compelling. BIIB excels in the development of in-licensed, clinical stage MS programs. Look at what they’ve brought in and then brought to registration: Tysabri is the single best MS drug available (nothing else is even close); Tecfidera is the single best oral MS drug, and again it’s not even close; Daclizumab will present an extraordinary efficacy/safety profile, and so on. Let’s also consider that while BIIB was accumulating and developing these assets, their competition was developing cladribine, alemtuzumab (campath), lemtrada, aubagio and other hideous potions. Even Novartis came razor close to missing with Gilenya, a nicely efficacious drug that has a challenging toxicity history

Perhaps anti-Lingo antibody will join the BIIB parade of success in MS, but company management is not counting on it. When management set a goal of “400 in 5″ in 2012, they meant it, which means they cannot wait for anti-Lingo or any other early Phase 2 program to mature. This is our final point from above, that management will de-risk the pipeline. This means they have 2 choices, and they have been excellent at executing on either or both of these choices:

1) Buy a late clinical stage MS asset/company.

2) Cut costs in order to manage EPS aggressively.

A third possible outcome of course is that they will do both. A very interesting question is: what attractive MS asset/company could BIIB buy? There are some very compelling answers, and maybe we’ll share these, but not today. A less interesting question, because the answer is so obvious, is where to cut. Let’s go back to those hemophilia drugs, brought in on a wave of enthusiasm for the much broader hematology space. What happened? When costs needed to be trimmed a “strategic review” quickly revealed that hematology was not so attractive after all. So the hemophilia R&D group was slashed, and only the clinical programs retained. Note further that those Factor XIII and Factor XI drugs are utlilizing very valuable and expensive bio-manufacturing capacity for the company. What might happen here? BIIB could sell the programs for 10-20x annual sales to Bayer or Novo Nordisk and keep the manufacturing rights for 5 years or more. We’re just guessing, but we also think it’s a very good bet.

The other obvious target is the Immunology group. A possible hint here is that a new department has been formed, carrying the name Remodeling and Repair or something similar. The department is built around the very interesting Phase 2 fibrosis program STX-100, mentioned above. A simple decision would be to move the few Immunology clinical assets (the anti-TWEAK and anti-CD40L antibodies) under this new department, and jettison the Immunology Research efforts. Such a move would mimic what was done in the hematology space, and would further move the company further away from basic Research, which historically has failed to move therapeutics forward, and further toward Development: in-licensing, clinical execution, regulatory execution and bio-manufacturing, the company’s true core competencies.

Will BIIB do any of these things? We have no idea. But we have watched this company for a long time, and if top-line results fail to drive EPS to the goals promised, the company will act decisively to control the bottom line. Personally, we expect to see an acquisition in short order, rather than further cuts. Just to reinforce what we said at the beginning: the proposed corporate strategy fundamentally de-risks the impact on the anti-Lingo program on the company fortunes, leaving intact the potential for a large upside if that program performs well in the clinic.

disclosures: PDR was a senior member of BIIB’s Immunology department for a long time, and retains both positive and negative biases. PDR is also long BIIB stock.

stay tuned

Immune checkpoint inhibitors – Part 2

In part 1 our focus was primarily on the PD-1 and CTLA4 pathways, where the biology is well understood and the drug development advanced. See that post here. In part 2 we look at drug development for some newer immune checkpoint targets, and this will drive us a little deeper into the scientific rationale for some of the less known pathways.

 I would argue that a good deal of the excitement around some recent deals (Novartis/CoStim and Agenus/4-Antibody) really is driven by the opportunity to get in early with novel targets. While the CoStim portfolio included PD-1 pathway related IP, I think the fact that this deal was so early stage suggests that novel LAG-3 and TIM-3 IP had a lot to do with driving interest. Similarly, emerging details from the BIOCIO conference indicate that Agenus (NASDAQ: AGEN), a somewhat obscure company, acquired novel LAG-3, TIM-3, OX40 and GITR antibodies as well as novel CTLA4 and PD-1 antibodies in its’ 4-Antibody acquisition. It would seem that this company, nominally a cancer vaccine company, is taking a huge leap forward by acquiring assets that could be combined with cancer vaccines. Barron’s labeled this a “genius move”, and I agree. This should make Agenus itself an attractive acquisition candidate. The Smith On Stocks Blog has much more on this (http://bit.ly/1ljmEzx).

 So I think it make sense to take on these targets one by one, do a quick update on the therapeutic rationale, and see who is leading the pack. Later we’ll fold this into a landscape analysis to try to understand where the large companies are heading.

We can start with a few targets that are represented by drugs in clinical development. Bristol-Myers Squib (NYSE: BMY), already loaded with anti-CTLA4 and anti-PD-1 programs, is moving their LAG-3 antibody ahead in both monotherapy and combination therapy trials. LAG-3 (lymphocyte activation gene, CD223) is a negative regulator of cell activation. It is expressed on various activated lymphoid cells, including T cells and NK cells that mediate tumor cell killing. The mechanism of action is the binding of LAG-3 to the MHC Class II complex expressed on antigen-presenting cells (B cells, monocytes, macrophages, dendritic cells, and other cell types). The high affinity binding event blocks cell proliferation and effector functions. LAG-3 is also an important mediator of the immune suppressive function of regulatory T cells. Of tremendous interest is the finding that LAG-3 is synergistic with other down-regulatory pathways, specifically PD-1 and TIM-3. As we will see this is driving much of the work on the design of combination therapy testing.

BMS-986016 is an anti-LAG-3 antibody from BMY currently in phase 1 testing in solid tumors and in B cell lymphomas. A very interesting study is NCT01968109: Safety Study of Anti-LAG-3 With and Without Anti-PD-1 in the Treatment of Solid Tumors. This is a Phase 1 dose escalation study of BMS-986016 alone or in combination of one of two defined doses of nivolumab (anti-PD-1). The primary endpoint is safety (AEs, SAEs, fatalities, lab abnormalities). There is also a cardiovascular risk assessment (QTc interval) among the secondary endpoints. Otherwise the secondary endpoints cover PK and exposure, immunogenicity, and RECIST defined tumor responses.

The point is that this is an instructive example of rational combination immunotherapy being investigated at Phase 1.

Other LAG-3 antibodies of potential use in oncology include Immutep’s IMP701, an antagonist antibody. IMP701 ought not to be confused with their depleting anti-LAG-3 antibody IMP731 (partnered with GSK for treatment of autoimmune disease) nor with their activating LAG-3-Fc fusion protein IMP321 (and how this thing works I have no idea). We have already mentioned that CoStim and 4-Antibody had LAG-3 programs and IP, but these would be preclinical. Somewhat better known for its’ anti-CD70 mAb (see below), arGEN-X also lists TIM-3, LAG-3 and VISTA antibodies in its’ preclinical portfolio. No doubt there are other early stage programs, they just are not readily visible yet. I wager that we will see many more of these popping up in the poster aisles at AACR and ASCO this year.

Two proteins related to PD-L1, B7-H3 and B7-H4, are also T cell inhibitory ligands. Both proteins are expressed on tumor cells and expression of B7-H3 or B7-H4 correlates with poor outcome for some tumor types. Both B7-H3 and B7-H4 are normally expressed on myeloid lineage cells including monocytes and dendritic cells. Preclinical tumor model data have supported efficacy with blocking antibodies to these ligands in vivo. The mechanism of action of these ligands is not well understood, as the receptors are not known, or at least cannot be confirmed across different laboratories

The Macrogenics (NASDAQ: MGNX) antibody to B7-H3 has reached clinical development. The phase 1 study in patients with advanced carcinoma, melanoma, or glioblastoma that overexpresses B7-H3. The antibody, MGA271, is licensed to Servier; Macrogenics recently received a milestone payment indicating that the expansion part of the Phase 1 trial had been initiated. Five Prime recently disclosed novel antibodies to B7-H3 and B7-H4 along with TIM-3 and VISTA, as mentioned previously.

With TIM-3 we have a landscape that is a bit earlier than LAG-3 – the excitement about this pathway is driven by the preclinical tumor model data and the translational medicine data. Like LAG-3, TIM-3 has been identified as co-expressed with PD-1, in particular on tumor infiltrating lymphocytes. Genetic data (knockout, transgenic, etc) clearly indicate that TIM-3 is an important immunoregulatory pathway. This is true as well of CTLA4, PD-1 and LAG-3 – the number of “brakes” on the system is remarkable and hints at how dangerous the immune system can be when it is unregulated, as it is in autoimmune, inflammatory, allergic and similar diseases. One of the interesting observations about TIM-3 is that it is ectopically expressed by some tumors and also by dendritic cells associated with tumors, i.e. within the tumor microenvironment. Therefore by blocking TIM-3 in the tumor setting, multiple responses may contribute to efficacy. A confounding issue in the TIM-3 field is the identification of the relevant ligand for TIM-3, with a number of ligands having been proposed (galectin-9, phosphatidylserine (PS), HMGB1). The binding motif for PS is well defined, while binding to the other proposed ligands is less well understood. In particular, TIM-3 and galectin-9 activities seem distinct, at least as far as we can understand from the published genetic data.

The proteins mentioned so far (CTLA4, CD28, CD80, CD86, PD-1, PD-L1, PD-L2, B7-H3, B7-H4, LAG-3, TIM-3, VISTA and TIGIT) are all members of the immunoglobulin (Ig) superfamily of proteins. Two additional protein families of critical importance in regulating immune responses are the TNF and TNF receptor families. Again the leader in this field, clinically at least, is BMY. The antibody BMS-663513 (urelumab) is an agonist anti-4-1BB antibody that functions by stimulating T cell activation. 4-1BB (CD137) is best known for contributing a signaling moiety to the CAR-T constructs (a discussion for another day). BMS-663513 is now in phase 1/2 testing in lymphoma patients. The antibody had previously completed a phase 2 study in melanoma, but that program was put on clinical hold following dose dependent liver toxicity. The new studies utilize lower doses, as a very low dose appears to be efficacious. An important differentiating feature of anti-4-1BB is the apparent ability to eradicate established tumors, at least in some patients. With this is mind it is encouraging to look forward to combination treatment studies. Pfizer also has an anti-4-1BB antibody in development, PF-05082566. This antibody is in a very interesting phase 1 clinical trial in solid tumors and B cell lymphomas, the latter patients being treated with and without rituximab co-therapy.

4-1BB biology is well understood, and agonist stimulation of this receptor induces CD8+ T cell activation, interferon gamma secretion, secretion of cytolytic compounds and recruitment of helper T cells. Of interest, 4-1BB is only expressed on T cells that have been activated through the T cell receptor and CD28, and so is specifically expressed on those T cells that would potentially have anti-tumor activity.

CD27 expression is also induced upon T cell activation, and the critical role of this receptor in immune responses is shown by patients who lack function CD27, as these patients are grossly immunosuppressed. The role of CD27 is subtly different from 4-1BB in that this receptor seems critical to activated T cell survival. Celldex (NASDAQ: CLDX) has developed an agonist anti-CD27 antibody, CDX-1127. In pre-clinical models, CDX-1127 had anti-tumor effects due to enhanced T cell activation. In addition various cancers, particularly B and T cell lymphomas, can express CD27 at high levels and the antibody may be able to such tumor cells directly and activate immune cell killing. Early data is promising, with no obvious toxicities.

The ligand for CD27 is CD70. Paradoxically (and stretching the limits of our understanding of these systems) CD70 is expressed at very high levels on a variety of tumor types, including solid tumors and hematopoietic cancers. Therefore, antibodies targeting CD70 to effect tumor cell killing have been developed. The most advanced of these are antibody drug conjugates, e.g. SGN-75 (SGEN) and MDX-1203 (BMY); there are other coming e.g. from Ambrx. In January. arGEN-X started a Phase 1b expansion study with ARGX-110, a novel cytotoxic anti-CD70 antibody. There are undoubtedly other antibodies in development.

A critical pathway found on cells that interact with T cells (dendritic cells, macrophages, B cells) is the CD40 pathway. Although early work is in the monotherapy setting, it is reasonable to speculate that agonists to CD40 would complement other approaches, such as cancer vaccines and modulators of T cell responses. Dacetuzumab, developed by Seattle Genetics (SGEN) was discontinued in phase 2b. The reason was unclear but appeared to involve both toxicity and futility analysis. Toxicities included cytokine release syndrome (common) and thrombosis (< 5% of patients), some liver toxicity and cytopenias. Most of these toxicities could be controlled with prophylactic agents. CP-870,893 (Pfizer) has completed Phase 1 clinical trials in melanoma, pancreatic cancer and other solid tumors. The current development in the US of CP-870,893 seems limited to trials being sponsored by U Penn’s Abramson Cancer Center. Of note, one of these trials is in combination with the anti-CTLA4 mAb, tremelimumab. The antagonist anti-CD40 antibody lucatumumab (NVS) competed a phase 1 trial in refractory follicular lymphoma in May of 2012. Here the hypothesis was that the bound antibody would activate cytotoxic killing of CD40+ tumor cells. This Phase 1 trial was in combination with chemotherapy (bendamustine).

At this point I would characterize the development of CD40 modulators in oncology as stalled, and awaiting a better understanding of the best antibody activity (and associated isotype) to use, the appropriate dose, and the most relevant tumor types.

Two final pathways to mention in this section are the OX40 and GITR pathways, the subject of headlines when Agenus bought out 4-Antibody. Several clinical stage therapeutics have been developed for these targets.

OX-40 (CD134) is another T cell survival pathway, activated downstream of CD28, and essential for the induction of anti-apoptotic proteins that keep activated T cells alive and functional. It may also be required for the establishment of the memory T cell pool. Stimulation of OX40 by the OX40-L or by agonist anti-OX40 antibodies enhances T cell responses.

AZN/Medimmune has developed a murine anti-OX40 agonist antibody designed to stimulate the immune system and block tumor suppression of the immune response. AZN’s OX40 collaborations are complex. AZN/Medimmune has partnered with AgonOx, a tech transfer spinoff from the Providence Cancer Center in Portland, OR. There are several clinical trials of anti-OX40 therapy underway at the Providence Cancer Center. AZN/Medimmune has also partnered with the Cancer Research Institute and Ludwig Institute for Cancer Research specifically to undertake clinical trials evaluating immunotherapy combinations including the MedImmune antibodies to OX40, and PD-L1 (MED14736), together with other agents within the CRI/Ludwig portfolio and the Cancer Vaccine Collaborative network of clinical immunologists and oncologists. There was one clinical trial co-sponsored by AgonOx and the Ludwig Institute, to study anti-OX40 in combination with ipilimumab. However, this trial has been suspended. According to AZN/Medimmune, the partnership trials are designed to complement their in-house clinical development effort.

GlaxoSmithKline (NYSE: GSK) gained rights to an OX40 antibody preclinical program from the MD Anderson Cancer Center’s Institute for Applied Cancer Sciences, as part of a deal focused on immune checkpoint antibodies that can trigger immune responses against cancer.

GITR was the other target grabbing headlines in light of the Agenus/4-Antibody deal. GITR is yet another cell surface receptor that is involved in amplifying T cell responses. It’s mechanism of action is distinct, in that GITR inhibits the suppressive activity of T-regulatory cells, thereby releasing effector T cells from active suppression. Secondarily GITR signaling is a pro-survival pathway for activated T cells.

GITR, Inc., is a biotech company spun out when Tolerx went under. The company is developing TRX518, an anti-GITR agonist antibody designed to enhance the immune response to cancer cells. A Phase 1 clinical trial in melanoma and solid tumors is currently recruiting after being released from clinical hold.

A few thoughts about these newer pathways. One is that some of them are very potent indeed (4-1BB, CD27) and we will have to watch carefully for toxicity issues. A second is that we can begin to outline rational combinations based on the biology of the pathways. For example, the CTLA4 and PD-1 antagonists may pair well with treatments that induce tumor cell death, thereby releasing novel tumor antigens that the newly stimulated immune system can then recognized. Some of the downstream T cell or antigen-presenting cell activators (CD40, OX40 as examples) may be better suited for use with cancer vaccine therapies.

There are two more classes of immune checkpoint modulators to consider. One consists of the IDO inhibitors. The second consists of the innate immune response modulators (TLRs, KIR, NKG2A). There are very exciting companies working in these areas, and these will be the subject of the next update.

as always please leave a comment or email me at rennertp@sugarconebiotech.com and follow @PDRennert

stay tuned.

Immunotherapy: Companies Chasing Immune Checkpoint Therapeutics

Excitement continues to build in the Immunotherapeutic drug development space following a recent flurry of deals. In the most recent, we saw Novartis acquire Costim Pharma(http://www.fiercebiotech.com/story/novartis-beefs-its-cancer-immunotherapy-pipeline-biotech-buyout/2014-02-17).

The deal making begs the question as to what, and who, is next. The immunotherapeutic space is very large and diverse so it’s important to focus. Lets start by defining the space broadly, using the following categories:

1) Immune checkpoint modulators. These are therapeutics specifically designed to alter the way the immune system interacts with a tumor. This field is exemplified by the anti-CTLA4 antibody ipilimumab (Vervoytm), from Bristol Myers Squibb and the anti-PD-1 antibody MK-3475, from Merck.

2) Tumor depleting antibodies. These are antibodies with inherent or engineered cell-killing (cytotoxic) activity. The first generation of cytotoxic antibodies is best illustrated by the anti-CD20 antibody rituximab (Rituxantm) from Roche. Engineered antibodies have increased cytotoxic activity (ofatumumab from GlaxoSmithKline being an important example). Other formats include bispecific antibodies that recognize 2 different tumor proteins (antigens) simultaneously. All of these antibodies act by recruiting the immune system to kill cells that they have bound. The antibodies do this by activating cell killing NK and CD8+ T cells and by activating the complement cascade.

3) Bispecific antibodies and fusion proteins that recruit T cells, NK cells or dendritic cells and bind tumor antigen, simultaneously. These molecules function similarly to tumor depleting antibodies, but have the added activity of specifically engaging relevant immune cell types.

4) Modified T cells. Made famous by the CAR-T (CAR-19) technology developed by Carl June at U Penn, this technology uses genetic engineering to take a patients T cells and repurpose them for high impact tumor cell recognition and killing.

5) Cancer vaccines. Exemplified by Provengetm from Dendrion, these are techniques designed to induce an immune response to the tumor by immunizing with tumor antigens along with immune stimulants. There are ex vivo approaches (like Provenge) and in vivo approaches.

Note that we have left out the antibody-drug conjugates (ADC) and radiolabeled antibodies since they theoretically do not require the immune system to attack the tumors. In this class the cytotoxic drug or radioactive payload is brought to the tumor by the antibody.

Today we will only discuss novel and next generation therapeutics in the first class: immune checkpoint modulators.

The field has been dominated by discussion of the clinical stage drugs being developed to target the CTLA4 and PD-1 pathways. Blocking CTLA4 shuts down this T cell inhibitory pathway by preventing interaction of CTLA4 with it’s ligands, called CD80 and CD86, which are expressed on B cells, dendritic cells, macrophages and related cell types. This then allows these ligands to productively interact with the stimulatory receptor CD28, also expressed on T cells, thereby promoting T cell activation. In the case of the PD-1 pathway, blocking PD-1 or its ligand (PD-1L) prevents another inhibitory pathway on T cells, although in this case the ligand is often found overexpressed on tumor cells, that is, this is an active pathway for immune evasion.

Just for review, these are the key late stage clinical therapeutics:

drug

target

phase

company

 
     ipilimumab      CTLA4      approved      Bristol Myers Squibb
     nivolumab      PD-1      3      Bristol Myers Squibb
     MK-3475      PD-1      3      Merck
     MPDL3280A      PD-L1      3 (not yet recruiting)      Roche/Genentech

These are all monoclonal antibodies (mAbs). The approval and phase 3 designations refer to advanced metastatic melanoma however all of these drugs are in multiple clinical trials for many tumor types. Of equal interest are the ipilimumab/nivolumab co-therapy trials also underway.

So these are very advanced drugs. Earlier clinical trials with agents targeting the CTLA4 and PD-1 pathways are shown here:

drug

target

phase

company

       
     tremelimumab    CTLA4   1 and 2, in various solid     tumors      Astra Zeneca          (AZN)/Medimmune
     MEDI4736    PD-L1   1 and 1/2 in various solid   tumors      AZN/Medimmune
     pidilizumab    PD-1   2: hematological cancers,   solid tumors      CureTech Ltd
     BMS-9365569    PD-L1   1: multiple cancers      Bristol Myers Squibb
     AMP-224    PD-1   1: advanced cancers      Amplimmune/AZN
     AMP-514    PD-1   1: advanced cancers      Amplimmune/AZN

Again these earlier stage drugs are all mAbs, except AMP-224, a Fc-PD-L2 fusion protein that serves as a soluble inhibitor of PD-1. Pidilizumab had been partnered with Teva, but was returned last year. According to Nature Reviews Drug Discovery (NRDD), CureTech is seeking a partner for this drug to advance its’ development (http://www.nature.com/nrd/journal/v12/n7/full/nrd4066.html). The NRDD report is free to read and download.

There are other immune checkpoint modulators in the clinic, and we’ll get to those in a bit. What has been really shocking is how aggressive large pharma and biotech have been in acquiring very early stage assets in the immune checkpoint area. The CoStim acquisition by Novartis is an excellent example. CoStim had no clinical assets, and probably not even any IND-enabled assets, and yet was scooped up. Why? And importantly, who is next?

“Why” is a pretty interesting question, and translates into “What did they own?” The answer in the case of CoStim was that they owned patents on novel antibody inhibitors of PD-1 and PD-L1/PD-L2. Possibly of greater importance, they owned intellectual property (IP) portfolios covering new checkpoint pathways, notably the LAG-3 pathway and the TIM-3 pathway. We have no clinical data yet on either of these pathways, but preclinical tumor models, and the expression profile of these pathways, suggests very strongly that they will be critical for the prosecution of specific tumor types. Therein lies the value of buying early into the science. Bruce Booth writing on the role of Atlas Venture in the CoStim deal, has a great take on this on the LifeSci VC blog (http://lifescivc.com/2014/02/immuno-oncology-startup-costim-pharmaceuticals-acquired-by-novartis/).

So are there other CoStim Pharmas just waiting to be scooped up? The question is critical for biopharma portfolio gurus trying to peer into the future, and for stock investors wondering who to bet on. That second category, stock investors, will be looking for public companies or venture owned companies about to go public. The recent surge in biotech IPOs has helped bring plenty of candidates into public view.

Lets have a look around, but as an organizing principal, we’ll let the biology of tumor immune evasion and response lead the way.

We briefly mentioned the ligands for CTLA4 (CD80 and CD86) and for PD-1 (PD-L1 and PD-L2). These proteins are all related by protein sequence, and are members of the B7 protein family. The receptors for these ligands are also related and can be considered members of the CD28 protein family. Lets start with these, and line them up:

Screen Shot 2014-02-23 at 4.27.58 PM

This image is from Drew Pardoll’s excellent review in Nature Reviews Cancer. This paper is free to read and download, and can be found here:                       http://www.nature.com/nrc/journal/v12/n4/full/nrc3239.html. At the top you see the PD-1 and CTLA4 pathways and corresponding ligands – note here that an activating receptor for PD-L1 and PD-L2 is proposed, although none has been found yet. At the bottom we see some newer members of the B7 family, B7RP-1 (ICOS-L), B7-H3 and B7-H4. There are both stimulatory and inhibitory pathways proposed. Not surprisingly, there have been a number of development deals across this spectrum of targets.

Novartis. We’ve already mentioned the CoStim/Novartis deal, which purportedly includes PD-1 and PD-L1/2 assets and IP.

Merck. Merck took the biopharma world by surprise a few weeks ago by announcing a suite of partnerships for MK-3475 anti-PD-1 mAb. The stance is bold and aggressive and shows that Merck recognizes the importance of anticipating combination therapy clinical practice and developing MK-3475 accordingly. The company is capitalizing on the momentum behind MK-3475 that has accelerated with FDA breakthrough therapy designation (for advanced melanoma) in April of last year and an aggressive rolling submission drug application, which should be completed by mid-year.

Merck plans to run clinical studies of MK-3475 in combination with axitinib, Pfizer’s small molecule kinase inhibitor for renal cell carcinoma. This deal is similar to the one that Merck did with GlaxoSmithKline (GSK) in December 2013, to pair MK-3475 with GSK’s kinase inhibitor, pazopanib, also in advanced renal cell carcinoma.

In a combination immunotherapy effort, MK-3475 will be paired with PF-05082566, Pfizer’s agonist mAb to the 4-1BB receptor. We’ll discuss 4-1-BB and related pathways later, as this is an interesting area. The combo therapy will be tested in multiple cancer types. In a similar effort, Merck will partner with Incyte to pair MK-3475 with INCB24360, an indoleamine 2, 3-dioxygenase (IDO) inhibitor, in patients with advanced or metastatic cancers. IDO inhibitors are a very hot subject, which we will tackle below. Finally, in collaboration with Amgen, Merck will combine MK-3475 treatment with Amgen’s investigational oncolytic immunotherapy talimogene laherparepvec, in patients with previously untreated advanced melanoma.

Merck also signed on with Ablynx in a very interesting deal to develop nanobody therapeutics to immune checkpoint targets. Nanobodies are derived from camelid (camels, llamas, etc) antibodies and have some nice intrinsic properties (small size, good pharmacodynamics). Of interest, the Merck deal specifies bi- and tri-specific nanobodies targeting different proteins.

Servier. In another very recent deal (February 13, 2014), French pharmaceutical firm Pierre Fabre licensed a peptide therapeutic directed to PD-1 from Biotech company Aurigene. This new therapeutic is IND-enabled, but clinical development has not begun. Servier also acquired rights to Macrogenic’s anti-B7-H3 mAb MGA271 in December 2011. B7-H3 is overexpressed by a variety of solid tumors (prostate, pancreatic, melanoma, renal cell, ovarian, colorectal, gastric, bladder, and NSCLC). It has been hypothesized that B7-H3 expression by tunors is a mechanism of immune evasion, however, since the receptor in unknown this remains a hypothesis. So, although an anti-B7-H3 antibody may have biological impact on the tumor, Macrogenics is taking no chances, and has engineered MGA271 for optimized interaction with cytotoxic immune cells, including NK cells, macrophages and CD8+ T cells. MGA271 is currently in phase 1, in patients with B7-H3+, refractory neoplasms.

Astra Zeneca. In October of 2013, AZN/Medimmune announced that it had acquired Amplimmune, a privately held company developing immune checkpoint modulators for oncology. This preclinical company’s assets included AMP-224, the Fc-PD-L2 fusion protein mentioned earlier, and AMP-514, an anti-PD1 mAb. In December of 2013, Amplimmune registered its first clinical trial for AMP-514, a phase 1 in patients with advanced solid tumors. As discussed in a column by FierceBiotech’s John Carroll “the widely acknowledged area for differentiation will be combinations … mAbs (anti-CTLA4 tremelimumab, anti-PD1 AMP514,  OX40 agonist MEDI6469) and … targeted therapies … AZN is gearing up for combination trials with Iressa & tremelimumab … AZN’s purchase of Amplimmune gained it access to other … targets … likely including another attractive checkpoint antibody to B7-H4″. You can see the article here:                     http://www.fiercebiotech.com/story/can-astrazeneca-catch-leaders-cancer-immunotherapy/2013-10-03

Amplimmune’s discovery portfolio covers many B7 family members and their patent portfolio includes both agonist and antagonist assets and IP. Within the database-visible patents there are claims to fusion proteins and antibodies targeting PD-1, PD-L1/2. B7-H3, B7-H4, “B7-H5″, ICOS and ICOS-L.

Bayer Healthcare. Late to the party is Bayer, who to date has not made a big play in immune modulatory drugs. The company took a step forward perhaps in a deal with Compugen (NASDAQ: CGEN), paying 10MM USD upfront in a collaboration/licensing agreement. The goal is to develop novel antibody based immune checkpoint regulators discovered by Compugen. While the company is secretive as to the specific targets, one may be TIGIT, a relatively new member immune regulatory protein with some very exciting preclinical biology.

Early stage assets like Compugen’s are hard to judge without the benefit of full due diligence. We can list some of the asset players however, and some are pretty easy to score just based on the prior reputation of the company:

-  Earlier this month Five Prime Therapeutics went on record as having novel ligands for B7-H3 and B7-H4 (http://www.biotech-now.org/business-and-investments/2014/02/bio-ceo-five-prime-therapeutics-company-snapshot#) among other targets. Five Prime has an antibody discovery and development deal with Adimab. As far as I can tell, none of these are visible in the patent databases to date. Five Prime recently went public (NASDAQ: FPRX).

-  Kadmon LLC, backed by the former head of Imclone, lists anti-PD-1 and anti-PD-L1 mAbs on its pipeline chart. However this company seems focused on other areas.

-  Locally, Third Rock funded Jounce Therapeutics is developing antibodies and proteins to undisclosed immune checkpoint targets. Jounce and Adimab have announced a collaboration to drive the antibody technology. It will of great interest to see if Jounce will take the IPO route over the next few years, or instead will be acquired while still private.

-  VISTA is another relatively new immune regulator being developed by privately held ImmuNext, in partnership with Johnson & Johnson.

-  In January of this year Johnson & Johnson’s Janssen unit agreed with BiocerOX Products to develop a new mAb to an immune checkpoint protein. The target was not released but is rumored to be PD-1.

-  By the way, J&J/Janssen really does seem to be taking a multi-pronged approach to get into this space. In late January J&J Innovation partnered with MD Anderson Cancer Center, as part of its “Moon Shots” oncology effort. The joint program will evaluate new combination therapies and identifying useful biomarkers for eight critical cancers. MD Anderson has a very similar agreement with Pfizer.

-  AnaptysBio, Inc has publicized a portfolio that includes an anti-PD-1 antibody, ANB011, and novel antibodies against other immune checkpoint receptors, including TIM-3 and LAG-3.

I’m going to assume that there are other CTLA4, PD-1, PD-L1 and PD-L2 assets out there in the hands of companies large and small. We’ll track the progress of these as they pop up, whether in the poster hall at AACR, or in press releases! Also, we will discuss companies targeting TIM-3 and LAG-3, along with 4-1BB, OX40, GITR, IDO, and various other interesting targets, next post.

 stay tuned.

The development of combination therapies for B cell lymphoma: ABT-199

The role of ABT-199 in the development of combination therapies in lymphoma.

Following yesterday’s blockbuster win for PCYC and JNJ – the Phase 3 trial versus Arezza was stopped early on clear PFS and OS benefit – it seems a little deflating to return to AbbVie, whose Bcl2 inhibitor ABT-199 has been dogged by Tumor Lysis Syndrome (TLS) problems, some fatal, and recent rumors of oversight problems at one clinical site. I stated the other day that ibrutinib would win the medical marketplace for B cell lymphoma treatment, based on its impressive suite of clinical trials, and the results announced yesterday support that opinion. I still believe that combo therapy is the critical path forward in this field, and ibrutinib and idelalisib are the clear leading candidates for combo treatment protocols.

However, ABT-199 remains a wildcard and could be transformative if developed carefully. The drug demonstrates ORR and CR responses in B cell lymphoma that are very dramatic, as detailed earlier. In the spirit of our earlier January posts, lets look at the clinical trial spectrum for ABT-199. There are five trials listed for ABT-199 monotherapy in oncology, including the phase 1 extension. These include trials in relapsed/resistant NHL, CLL, high-risk CLL (del17p), MM, and AML. The inclusion of acute myeloid leukemia (AML) distinguishes ABT-199 from the other lymphoma drugs, and is based on the mechanism of action and profiling of different tumor types for sensitivity to Bcl2 inhibition.

The combination trials are very narrow in scope and reflect the fact that the ABT-199 is partnered with Roche/Genentech, and therefore the anti-CD20 mAbs used are those developed by Roche, that is, rituximab and obinutuzumab (Gazyva). Obinutuzumab is already approved for the treatment of previously untreated CLL, i.e., as first line therapy. The obinutuzumab trial with ABT-199 is sponsored by Roche/Genentech, illustrating the depth of this collaborative effort. Roche has an ongoing preclinical BTK program, and it will be interesting to see if a combination trial with ABT-199 is eventually filed.

Here are the combination trials listed:

Trial Number
Phase
date filed
Combination
Indication
NCT0159422914/20/2012bendamustine/rituximabrrNHL and DLBCL
NCT0167190418/10/2012bendamustine/rituximabCLL (rr & untreated)
NCT016826161b6/26/2012rituximabrrCLL and SLL
NCT0168589219/12/2012ObinutuzumabCLL (rr & untreated)

The ultimate success of the program will depend in large measure on controlling the TLS issue. Its worth reminding ourselves that TLS did not suddenly become a toxicity concern in the treatment of B cell lymphoma. It occurs with anti-CD20 treatment and with chemotherapy treatment, as a result of triggering the death of a large number of tumor cells. The problem for ABBV and ABT-199 is that TLS does not seem to be related to dose given, remaining somewhat unpredictable (aside from worrying when patients present with bulky disease, which indicates huge number of tumor cells in the lymph nodes, bone marrow, etc). The recent outcry over moving one patient from one dose to another (150mg to 1200mg if I remember right) seems a little silly when a dose of 50mg can trigger TLS in a lymphoma patient. That said, the burden is on AbbVie to demonstrate that they can provide better efficacy than the competing drugs (ibrutinib and idelalisib), safely. If they can do this, I predict that ABT-199 will have a big role to play in the treatment of B cell lymphoma. If they continue to struggle then this drug will will still have a role, but may be relegated to second line or even salvage therapy status. Given the resources behind it, from both AbbVie and Roche, I imagine that a huge effort will be brought to bear on understanding and controlling the TLS toxicity.