Posts filed under: Drug development

Our new website, and continuing R&D on antibody drugs for cancer immunotherapy

OX40 Protein Source: Emw http://bit.ly/1Fww0kP

OX40 Protein Source: Emw http://bit.ly/1Fww0kP

Haberman Associates has a new website, with the same URL as previously but with many improvements. This article is the first Biopharmconsortium Blog post to be posted after the new website has gone online. Please explore the new site, and send any comments on the site to us.

In addition to announcing our new website, this article is designed to outline several new areas of cancer immunotherapy R&D.

Research and development of novel checkpoint inhibitors for cancer immunotherapy

Our September 2014 book-length Insight Pharma Report, “Cancer Immunotherapy: immune checkpoint inhibitors, cancer vaccines, and adoptive T-cell therapies”  focused on agents that had reached the clinic. In the case of checkpoint inhibitors, the report did not cover the universe of immune checkpoints, but only those that have been addressed with late-stage agents, some of which had entered—or were about to enter—the market. However, as we stated in the report, researchers expect new experimental products to emerge from immune checkpoint research in the next 5-10 years.

In the report, we mentioned research on agents to target the lymphocyte-activation gene 3 (LAG-3, CD223) pathway. In a published study in mice, Bristol-Myers Squibb (BMS) researchers and their academic collaborators obtained evidence that dual treatment with an anti-PD-1 (such as BMS’ nivolumab) and an anti-LAG-3 monoclonal antibody (MAb) cured most mice of established tumors that were largely resistant to single antibody treatment. They concluded that dual blockade of PD-1 and LAG-3 might constitute a viable strategy for cancer immunotherapy, which might be superior to blocking PD-1 alone.

At the time of our report’s publication, BMS had initiated two Phase 1 safety studies with an investigational anti-LAG-3 MAb. These are a study of anti-LAG-3 with and without anti-PD-1 in treatment of solid tumors (clinical trial number NCT01968109), and a study of anti-LAG-3 in relapsed or refractory chronic lymphocytic leukemia (CLL), Hodgkin lymphoma (HL) and non-Hodgkin lymphoma (NHL) (clinical trial number NCT02061761). Both of these studies are still ongoing and recruiting patients.

Another checkpoint inhibitor target that is begin investigated (in preclinical studies) for potential use in cancer immunotherapy is TIM-3 (T-cell immunoglobulin domain and mucin domain 3). TIM-3 is is co-expressed on PD-1+ CD8 T cells in mouse models with solid tumors or hematologic malignancies. In a preclinical mouse melanoma model, combined blockade of TIM-3 and PD-1, or TIM-3 and CTLA4, was more effective in prolonging survival than blocking either protein alone. Moreover, the combination of anti-CTLA4, anti-TIM-3 and anti-LAG-3 produced further suppression of growth of the melanoma tumor. These data suggest that blockade of multiple inhibitory receptors—including TIM-3 and LAG-3—results in synergistic antitumor activity.

Research and development of agonist antibodies for use in cancer immunotherapy

Another approach to antibody-based cancer immunotherapy—in addition to targeting checkpoint inhibitors—is development of agonist antibodies. This is the subject of an upcoming conference in Boston—sponsored by Cambridge Healthtech Institute (CHI), on May 7-8, 2015. This conference is part of CHI’s annual PEGS Boston (Essential Protein Engineering Summit). Agonist antibodies target certain cell surface proteins on T cells, resulting in stimulation of the activity of the T cells. This contrasts with checkpoint inhibitors, which are designed to overcome blockages to T cell activity mediated by immune checkpoints.

Among the targets for agonist antibodies are two members of the tumor necrosis receptor (TNFR) superfamily—CD27 and OX40.

Celldex Therapeutics’ fully-human monoclonal antibody (MAb) agent varlilumab (CDX-1127) targets CD27. As discussed in our cancer immunotherapy report, activation of naïve T-cells requires both T-cell receptor (TCR) signaling and costimulation by a “second signal”. In our report, we used the example of CD28 (present on the surface of T cells) interacting with B7 [present of the surface of an antigen-presenting cell (APC) such as a dendritic cell] to deliver a “second signal”. CD27 is a member of the CD28 superfamily, and it interacts with CD70 to deliver a “second signal”. Varlilumab can substitute for CD70, and deliver a costimulatory signal to T cells whose TCRs are engaged. This can change a weak immune response into a strong, prolonged response. In preclinical models, immunostimuation by varlilumab has been shown to mediate antitumor effects.

In addition to the immunostimulatory activity of varlilumab, this agent may also exert direct therapeutic effects against tumors that express CD27 at high levels, such as human B and T cell lymphomas. Varlilumab has shown potent anti-tumor activity against these lymphomas in preclinical models. In these models, varlilumab may exert its therapeutic activity both via “second-signal” immune activation, and via direct antitumor activity against CD27-bearing lymphoma cells.

Varlilumab is now in ongoing Phase 1 clinical trials against solid and hematological tumors (clinical trial number NCT01460134), and in ongoing Phase 1 and Phase 2 trials in combination with the anti-PD-1 MAb agent nivolumab (BMS’ Opdivo) against advanced refractory solid tumors (clinical trial number NCT02335918). Reports of interim data from clinical trials of varlilumab at scientific meetings in 2013  and in 2014  indicate that this agent was very well tolerated and demonstrated biological activity and signs of clinical activity against advanced, treatment-refractory lymphoid malignancies and metastatic melanoma and renal cell carcinoma.

On March 17, 2015 Celldex announced that it had entered into an agreement with Roche to evaluate the safety, tolerability and preliminary efficacy of varlilumab in combination with Genentech/Roche’s investigational anti-PDL1 agent MPDL3280A in a Phase 1/2 study in renal cell carcinoma. This is based on preclinical studies that suggest that the combination of these two agents may be synergistic, and enhance anti-tumor immune response as compared to either agent alone. In Celldex’s Phase 1 study of varlilumab in multiple solid tumors, promising signs of clinical activity had been seen  in patients with refractory renal cell carcinoma. This included a durable partial response (11.0+ months) with decreases in tumor volume over time, and 4 patients with stable disease over periods ranging from 5.3 to 30.7+ months.

Another target for agonist MAbs in immuno-oncology is OX40. MedImmune (the global biologics R&D arm of AstraZeneca) is testing the OX40 agonist MAb MEDI6383 in an ongoing Phase 1 clinical trial (clinical trial number NCT02221960) against recurrent or metastatic solid tumors. MedImmune’s OX40 program is based on technology developed by AgonOx (Portland, OR). The two companies entered into an exclusive global partnership to develop OX40 agonists in 2011.

OX40 is a costimulatory receptor that can potentiate TCR signaling in T cells, leading to the activation of these cells by antigens recognized by their TCRs. Engagement of OX40 by its natural ligands on dendritic cells, or by anti-OX40 antibodies initiates a signal transduction cascade that enhances T cell survival, proliferation, and cytokine production, and can augment immune responses to tumors. Preclinical studies have shown that OX40 agonist antibodies increase antitumor immunity and improve tumor-free survival. A Phase 1 clinical study of an mouse anti-OX40 agonist MAb in patients with advanced cancer was carried out by researchers at the Providence Portland Medical Center in Portland, OR. (AgonOx is a spin-off of the Providence Portland Medical Center.) The study (clinical trial number NCT01644968), whose results were published in 2013, found that treatment with one course of the anti-OX40 MAb induced regression of at least one tumor metastasis in 12 of 30 patients, and exhibited an acceptable toxicity profile. Treatment with the agent also increased the antitumor reactivity of T and B cells in patients with melanoma.

In the upcoming CHI agonist antibody conference, Scott A. Hammond, Ph.D., Principal Scientist, Oncology Research at MedImmune will discuss the preclinical characterization of MedImmune’s OX40 agonists now in clinical trials.

Conclusions

The studies on novel immune checkpoint inhibitors and agonist antibodies illustrate that researchers are continuing to advance the frontiers of immuno-oncology beyond the late-stage MAb agents described in our report. Moreover, many of these studies involve clinical trials of combination therapies of the novel agents with other therapeutics discussed extensively in our report, including the CTLA-4 inhibitor ipilimumab (Medarex/BMS’s Yervoy), the PD-1 inhibitors nivolumab (BMS’ Opdivo) and pembrolizumab (Merck’s Keytruda), and the PD-L1 inhibitor MPDL3280A (Genentech/Roche). This is consistent with the idea that “the future of cancer immunotherapy is combination therapy”. In the survey that Insight Pharma Reports conducted in conjunction with our report, 80% of respondents agreed with this statement.
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As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to your company, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

Our New Year’s 2015 article: Notable researchers and breakthrough research of 2014

pre 1917 happy christmas and happy new year card

Pre-1917 Russian Happy Christmas and Happy New Year card

As is their customary practice, both Nature and Science ran end-of-year specials. The Nature special (in their 18 December issue) is entitled “365 days: Nature’s 10. Ten people who mattered this year.” The Science special (in their 19 December issue) is entitled, as usual “2014 Breakthrough of the Year.” As is also usual, there is a section for “Runners Up” to the year’s “Breakthrough”.

From the point of view of a consulting group—and a blog—that focuses on effective drug discovery and development strategies, we were disappointed with both end-of-year specials. Most of the material in these articles was irrelevant to our concerns.

Science chose the Rosetta/Philae comet-chasing mission as the “Breakthrough of the Year”, and its “runners up” included several robotics and space-technology items, as well as new “letters” to the DNA “alphabet” that don’t code for anything.

Nature also focused on comet chasers, robot makers, and space technologists, as well as cosmologist and mathematicians, and a fundraising gimmick—“the ice-bucket challenge”. Moreover, Nature was much too restrictive in titling its article “Ten people who mattered”. Every human being matters!

Nevertheless, these two special sections do contain a few gems that are both relevant to effective drug discovery and development, and are worthy of highlighting as “notable researchers of 2014” and “breakthrough research of 2014”. We discuss these in the remainder of this article.

Suzanne Topalian, M.D.

Suzanne Topalian is one of the researchers profiled in “Nature’s 10”. She is a long-time cancer immunotherapy clinical researcher who began her career in 1985 in the laboratory of cancer immunotherapy pioneer Steven Rosenberg at the National Cancer Institute (Bethesda MD). In the early days of the field, when cancer immunotherapy was scientifically premature, there was a great deal of skepticism that these types of treatments would even work. However, both Dr. Rosenberg and Dr. Topalian persevered in their research.

In 2006, Dr. Topalian moved to Johns Hopkins University (Baltimore, MD) to help launch clinical trials of Medarex/Bristol-Myers Squibb/Ono’s nivolumab, a PD-1 inhibitor. As noted in the Nature article, her work “led to a landmark publication in 2012 showing that nivolumab produced dramatic responses not only in some people with advanced melanoma but also in those with lung cancer [specifically, non–small-cell lung cancer, NSCLC].” We also discussed that publication on the Biopharmconsortium Blog, and in our recently published book-length Insight Pharma Report, Cancer Immunotherapy: immune checkpoint inhibitors, cancer vaccines, and adoptive T-cell therapies. Our report also includes discussions of Dr. Rosenberg’s more recent work in cellular immunotherapy.

As discussed in our report, nivolumab was approved in Japan as Ono’s Opdivo in July 2014 for treatment of unresectable melanoma, and a competitive PD-1 inhibitor, pembrolizumab (Merck’s Keytruda) was approved in the United States for advanced melanoma on September 5, 2014. More recently, on December 22, 2014, the FDA also approved nivolumab (BMS’ Opdivo) for advanced melanoma in the U.S. There are thus now two FDA-approved PD-1 inhibitors [in addition to the CTLA-4 inhibitor ipilimumab (BMS’ Yervoy)] available for treatment of advanced melanoma in the U.S.

Meanwhile, researchers continue to test both nivolumab and pembrolizumab for treatment of NSCLC and other cancers. And some analysts project that both of these agents are likely to be approved by the FDA for treatment of various populations of patients with NSCLC before the middle of 2015. Researchers are also testing combination therapies that include nivolumab or pembrolizumab in various cancers. And clinical trials of Genentech/Roche’s PD-L1 blocking agent MPDL3280A are also in progress.

Science’s 2013 Breakthrough of the Year was cancer immunotherapy, as we highlighted in our New Year’s 2014 blog article. Science could not make cancer immunotherapy the Breakthrough of the Year for 2014, too. Thus it chose to give physical scientists a turn in the limelight by highlighting the comet-chasing mission instead. Nevertheless, 2014 was the year in which cancer immunotherapy demonstrated its maturity by the regulatory approval of the two most advanced checkpoint inhibitor agents, pembrolizumab and nivolumab.

Implications for patients with terminal cancers

The clinically-promising results of cancer immunotherapy in a wide variety of cancers, coupled with the very large numbers of clinical trials in progress in this area, has also changed the situation for patients who have terminal cancers. Researchers who are conducting clinical trials of immunotherapies for these cancers are actively recruiting patients, of whom there are limited numbers at any one time. For example, there are now numerous clinical trials—mainly of immunotherapies—in pancreatic cancer, and most of these trials are recruiting patients. There are also active clinical trials of promising immunotherapies in the brain tumor glioblastoma. These are only two of many examples.

Recently, a 29-year-old woman with terminal glioblastoma ended her life using Oregon’s physician-assisted suicide law. Prior to her suicide, she became an advocate for “terminally ill patients who want to end their own lives”. We, however, are advocating that patients with glioblastoma and other types of terminal cancer for which there are promising immunotherapies seek out clinical trials that are actively recruiting patients. There is the possibility that some of these patients will receive treatments that will result in regression of their tumors or long-term remissions. (See, for example, the case highlighted in our September 16, 2014 blog article. There are many other such cases.) And it is highly likely that patients who participate in these trials will help researchers to learn how to better treat cancers that are now considered “incurable” or “terminal”, and thus help patients who contract these diseases in the future. From our point of view, that is a lot better than taking one’s own life via assisted suicide, and/or becoming an euthanasia advocate.

Masayo Takahashi, M.D., Ph.D.

Another researcher profiled in “Nature’s 10” is Masayo Takahashi, an ophthalmologist at the RIKEN Center for Developmental Biology (CDB) in Kobe, Japan who has been carrying out pioneering human stem cell clinical studies. We also discussed Dr. Takahashi’s research in our March 14, 2013 article on this blog.

At the time of our article, Dr. Takahashi and her colleagues planned to submit an application to the Japanese health ministry for a clinical study of induced pluripotent stem cell (iPS)-derived cells, which would constitute the first human study of such cells. They planned to treat approximately six people with severe age-related macular degeneration (AMD). The researchers planned to take an upper arm skin sample the size of a peppercorn, and transform the cells from this sample into iPS cells by using specific proteins. They were then to add other factors to induce differentiation of the iPS cells into retinal cells. Then a small sheet of these retinal cells were to be placed under the damaged area of the retina, where they were expected to grow and repair the damaged retinal pigment epithelium (RPE). Although the researchers would like to demonstrate efficacy of this treatment, the main focus of the initial studies was to be on safety.

According to the “Nature’s 10” article, such an autologous iPS-derived implant was transplanted into the back of a the damaged retina of one patient in September 2014. This patient, a woman in her 70s, had already lost most of her vision, and the treatment is unlikely to restore it. However, Dr. Takahashi and her colleagues are determining whether the transplant is safe and prevents further retinal deterioration. So far, everything has gone smoothly, and the transplant appears to have retained its integrity. However, the researchers will not reveal whether the study has been a success until a year after the transplantation.

The “Nature’s 10” article discusses how this technology might be moved forward into clinical use if the initial study is successful. It also discusses how Dr. Takahashi has been carrying her research forward in the face of a major setback that has plagued stem cell research at the CDB in 2014, as the result of the withdrawal of two once highly-regarded papers and the suicide of one of their authors.

Generation of insulin-producing human pancreatic β cells from embryonic stem (ES) cells or iPS

Another stem cell-related item, which was covered in Science’s end-of-2014 “Runners Up” article, concerned the in vitro generation of human pancreatic β cells from embryonic stem (ES) cells or iPS. For over a decade, researchers have been attempting to accomplish this feat, in order to have access to autologous β cells to treat type 1 diabetes, in which an autoimmune attack destroys a patient’s own β cells. In vitro generated β cells might also be used to screen for drugs that can improve β cell function, survival, and/or proliferation in patients with type 2 diabetes.

As reported in the Science article, two research groups—one led by Douglas A. Melton, Ph.D. (Harvard Stem Cell Institute, Cambridge, MA), and the other by Alireza Rezania, Ph.D. at BetaLogics Venture, a division of Janssen Research & Development, LLC.–developed protocols to produce unlimited quantities of β cells, in the first case from IPS cells, and in the other from ES cells.

However, in order to use the β cells to treat type 1 diabetes patients, researchers need to develop means (for example, some type of encapsulation) to protect the cells from the autoimmune reaction that killed patients’ own natural β cells in the first place. For example, Dr. Melton is collaborating with the laboratory of Daniel Anderson, Ph.D. (MIT Koch Institute for Integrative Cancer Research). Dr. Anderson and his colleagues have developed a chemically modified alginate that can be used to coat and protects clusters of β cells, thus forming artificial islets. Dr. Melton estimates that such implants would be about the size of a credit card.

The 2014 Boston biotech IPO boom

Meanwhile, the Boston area biotechnology community has seen a boom in young companies holding their initial public offerings (IPOs). 17 such companies were listed in a December 24 article in the Boston Business Journal. Among these companies are three that have been covered in the Biopharmconsortium Blog—Zafgen, Dicerna, and Sage Therapeutics.

We hope that 2015 will see at least the level of key discoveries, drug approvals, and financings seen in 2014.

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As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to your company, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

Immune checkpoint inhibitors work by reactivating tumor-infiltrating T cells (TILs)

cancer cell

Cancer Cell

The 27 November issue of Nature contains a wealth of new studies on how immune checkpoint inhibitors target various types of cancer, and how researchers and physicians might be able to identify the patients who are most likely to benefit from treatment with these agents.

These studies are described in five papers published in that issue of Nature. This issue also contains a “News & Views” commentary on these articles by Drs. Jedd D. Wolchok and Timothy A. Chan (both at the Memorial Sloan Kettering Cancer Center). This article serves as an introduction to the five research articles.

In addition, Science Magazine published a commentary on these articles, entitled “Multiple boosts for cancer immunotherapy”, by contributing correspondent Mitch Leslie.

Checkpoint inhibitors can be used to treat several types of cancer

One important result of these studies is the expansion of the range of cancers that can be treated via immunotherapy beyond melanoma, kidney cancer, and non-small cell lung cancer (NSCLC). The papers by Powles et al. and Herbst et al. contain results from a Phase 1 clinical trial of Genentech’s monoclonal antibody (MAb) PD-L1 blocker MPDL3280A. Herbst et al. reported that MPDL3280A showed therapeutic responses in patients with NSCLC, melanoma, renal cancer, and head and neck cancer. Powles et al. focused on the effects of this agent in a larger group of patients with metastatic urothelial bladder cancer (UBC). In both reports, researchers documented that a subset of patients experienced durable responses, and that the treatment showed low toxicity.

We discussed earlier presentations of the results of the Phase 1 trial of MPDL3280A in our Insight Pharma Report (IPR), Cancer Immunotherapy: Immune Checkpoint Inhibitors, Cancer Vaccines, and Adoptive T-Cell Therapies. As we discussed in this report, the FDA granted breakthrough therapy designation for MPDL3280A for treatment of UBC. Roche/Genentech has initiated a Phase 2 clinical trial (clinical trial number NCT02108652) of MPDL3280A in UBC. UBC is the ninth most common cancer in the world. Metastatic UBC is associated with a poor prognosis, and has few treatment options. There have been no new treatment advances in nearly 30 years.

Checkpoint inhibitors work by reactivating tumor-infiltrating T cells (TILs)

Perhaps the most important finding of the research published in the November 27th issue of Nature is that checkpoint inhibitors work via reactivating endogenous tumor-infiltrating T cells. (These T cells are often called “TILs”, which is an acronym for “tumor-infiltrating lymphocytes”.)

For example, as described in the Powles et al. report, Genentech’s PD-L1 blocker MPDL3280A was found to be especially effective in treating patients whose tumors contained PD-L1-positive TILs. As we discussed in our IPR report, Genentech researchers found that MPDL3280A not only targets PD-L1 on the surface of tumor cells, but also PD-L1 on the surface of TILs. PD-L1 on activated T cells interacts not only with PD-1, but also with B7 on the surface of antigen presenting cells, sending a negative signal to the T cells. MPDL3280A targets the PD-L1-B7 interaction, thus enabling reactivation of PD-L1-bearing TILs so that they can attack the tumor.

As we also discuss in our report, targeting PD-1, PD-L1, and CTLA-4 may also be important in reversing immunosuppression by regulatory T cells (Tregs), which typically heavily infiltrate tumors. This provides another mechanism by which checkpoint inhibitors can reactivate TILs and thus induce anti-tumor immune responses.

As described in Powles et al, MPDL3280A was engineered with a modification in the Fc domain that eliminates antibody-dependent cellular cytotoxicity (ADCC). Genentech researchers did this because PD-L1 is expressed on activated T cells, and they wanted an anti-PD-L1 MAb agent that would reactivate these T cells, not destroy them via ADCC.

In the studies described by Herbst et al., researchers showed that Genentech’s PD-L1 blocker MPDL3280A gives antitumor response across multiple types of cancer, in tumors that expressed high levels of PD-L1. These responses especially occurred when PD-L1 was expressed by TILs. The studies suggest that MPDL3280A is most effective against tumors in which endogenous TILs are suppressed by PD-L1, and are reactivated via anti-PD-L1 MAb targeting.

In the Tumeh et al. study, the researchers found that patients responding to treatment with Merck’s MAb PD-1 blocker pembrolizumab (Keytruda) showed proliferation of intratumoral CD8+ T cells that correlated with reduction in tumor size. Pretreatment tumor samples taken from responding patients showed higher numbers of CD8, PD-1, and PD-L1 expressing cells at the invasive tumor margin and within tumors, with a close proximity between PD-1 and PD-L1, and a clonal TCR repertoire.

Based on this information, the researchers developed a predictive model based on CD8 expression at the invasive tumor margin. They validated this model in an independent 15-patient cohort. The researchers concluded that tumor regression due to treatment with the PD-1 blocker pembrolizumab requires preexisting CD8+ T cells whose activity has been blocked by PD-1/PD-L1 adaptive resistance. This study, like those of Powles et al. and Herbst et al., thus indicate that checkpoint inhibitors work against cancer by reactivating TILs. The Tumeh et al. study also indicates that CD8 expression at the invasive tumor margin is a predictive biomarker for sensitivity of patient tumors to treatment with anti-PD-1 checkpoint inhibitors.

The Powles, Herbst, and Tumeh reports all involved studies in human patients. However, the other two papers—Yadav et al. and Gubin et al. involve studies in mouse tumor models.

In the study of Yadav et al., the researchers used their mouse model to develop a method for discovering immunogenic mutant peptides in cancer cells that can serve as targets for T cells. They sequenced the exomes of two mouse cancer cell lines, and looked for differences with the corresponding normal mouse exomes. They also identified which of the neoantigens that they identified via exome sequencing could bind to histocompatibility complex class I (MHCI) proteins, and thus could be presented to T cells. They then modeled the MHC1/peptide complexes, and used these models to predict which of these neoantigens were likely to be immunogenic.

These methods identified only a few candidate neoantigens. Vaccination of tumor-bearing mice with these neoantigens resulted in therapeutically active T-cell responses. In addition, the researchers developed methods for monitoring the antitumor T cell response to peptide vaccination.

In the study of Gubin et al., the researchers used similar genomic and bioinformatic approaches to those of Yadav et al., and identified two neoantigens that were targeted by T cells following therapy with anti-PD-1 and/or anti-CTLA-4 antibodies. [Human CTLA-4 is the target of the checkpoint blockade inhibitor ipilimumab (Medarex/ Bristol-Myers Squibb’s Yervoy).] As with PD-1 and PD-L1 blockers, we discussed this agent in our IPR report. T cells specific for these neoantigens (in the context of MHCI proteins expressed by the mice) were present in the tumors. These T cells were reactivated by anti-PD-1 and/or anti-CTLA-4 antibodies, enabling the mice to reject the tumors.

As in the study of Yadav et al., the Gubin et al. researchers performed experiments in which they vaccinated tumor-bearing mice with peptides that incorporated the mutant epitopes. This vaccination induced specific tumor rejection that was comparable to treatment with checkpoint blockade inhibitors. As in the case of Yadav et al, the Gubin et al. researchers concluded that specific mutant antigens were targets of checkpoint inhibitor therapy in their mouse models, and that the mutant antigens could also be used to develop personalized cancer vaccines.

Since the studies of Yadav et al. and Gubin et al. were carried out using mouse tumor models, the results are not directly applicable to cancer in human patients. However, the studies suggest that immune checkpoint inhibitors work by reactivating endogenous TILs, and that anti tumor TILs work by attacking specific neoantigens on the tumors.

As we discussed in our IPR report, Dr. Steven Rosenberg (National Cancer Institute, Bethesda, MD) identified specific antigens that were the targets of TILs, both in metastatic melanoma and in metastatic cholangiocarcinoma (a type of epithelial bile duct cancer). However, these target antigens were from human cancers, and they were targets of TILs that has been isolated from patient tumors, cultured and expanded ex vivo, and used in adoptive cellular immunotherapy.

Moreover, the antigens were targets of TIL therapies that resulted in a durable compete remission in the case of the melanoma patient, and long-term tumor regression in the case of the metastatic cholangiocarcinoma patient. The metastatic cholangiocarcinoma case was highlighted in our September 16, 2014 Biopharmconsortium Blog article.

The Yadav et al. paper referenced the Rosenberg group’s work. However, this paper stated that “few mutant epitopes have been described because their discovery required the laborious screening of patient tumour-infiltrating lymphocytes for their ability to recognize antigen libraries constructed following tumour exome sequencing.”

The methods of Yadav et al. (and of Gubin et al.) are thus designed to simplify and accelerate the discovery of immunogenic mutant peptides. They carried out their studies in mouse models, which helped these researchers to develop methods that could potentially discover greater numbers of neoantigens more efficiently. However, it remains to be seen to what extent they can apply their methods to human patients.

Unifying the field of immuno-oncology

As can be seen, for example, from the title of our IPR report, the three major approaches to immuno-oncology in 2014/2015 are development of immune checkpoint inhibitors, of cancer vaccines, and of adoptive T-cell therapies.

In the immuno-oncology papers published in the 27 November issue of Nature, researchers show that checkpoint inhibitors work via reactivating of endogenous TILs. They also (in mouse tumor models) identified neoantigens that are targets of these reactivated TILs, and designed peptide vaccines that were as effective as checkpoint inhibitor therapy in the mouse models. In principle, one can isolate TILs that are reactive to particular neoantigens in the mouse tumors, culture and expand them ex vivo, and infuse them back into the mice to target their tumors. Thus the studies in the 27 November issue of Nature serve as a template for the unification of the immuno-oncology field as it now exists.

However, it will be necessary to apply the methodologies developed by Yadav et al. and Gubin et al. to human patients. And at least so far, peptide vaccines have not been very successful in treating patients, as compared to TIL therapy (in the subset of patients in whom TIL therapy can be done). It is thus possible that once these methods of neoantigen identification are applied to human patients, it will be found that targeting the neoantigens with ex vivo-expanded TILs will be more successful than therapy with peptide vaccines. However, whether this is true awaits the application of the new methodologies to neoantigen identification in human tumors.

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As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to your company, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

The Genentech/NewLink alliance, the IDO/TDO pathway, and targeting metabolism for immuno-oncology

Indoleamine 2,3-dioxygenase 1

Indoleamine 2,3-dioxygenase 1

On October 20, 2014, New Link Genetics Corporation (Ames, IA) announced that it had entered into an exclusive worldwide license agreement with Genentech/Roche for the development of NLG919, an IDO (indoleamine-pyrrole 2,3-dioxygenase) inhibitor under development by NewLink. The two companies also initiated a research collaboration for the discovery of next generation IDO/TDO (tryptophan-2,3-dioxygenase) inhibitors.

Under the terms of the agreement, NewLink will receive an upfront payment of $150 million, and may receive up to over $1 billion in milestone payments, as well as royalties on any sales of drugs developed under the agreement. Genentech will also provide research funding to NewLink in support of the collaboration. Other details of the agreement are outlined in NewLink’s October 20, 2014 press release.

The target of NewLink’s iDO/TDO program, and of its collaboration with Genentech, is cancer immunotherapy. As we discussed in our September 2014 report, Cancer Immunotherapy: Immune Checkpoint Inhibitors, Cancer Vaccines, and Adoptive T-cell Therapies (published by Cambridge Healthtech Institute), Genentech is developing the PD-L1 inhibitor MPDL3280A, which is in Phase 2 trials in renal cell carcinoma and urothelial bladder cancer, and in Phase 1 trials in several other types of cancer. PD-L1 inhibitors such as MPDL3280A constitute an alternative means to PD-1 inhibitors of blocking The PD-1/PD-L1 immune checkpoint pathway.

Two PD-1 inhibitors, pembrolizumab (Merck’s Keytruda) and nivolumab (Medarex/Bristol-Myers Squibb’s Opdivo) are in a more advanced stage of development than MPDL3280A and other PD-L1 inhibitors. The FDA approved pembrolizumab for treatment of advanced melanoma in September 2014, and nivolumab was approved in Japan in July 2014, also for treatment of advanced melanoma.

MPDL3280A, pembrolizumab, and nivolumab are monoclonal antibody (MAb) drugs. Another MAb immune checkpoint inhibitor, ipilimumab (Medarex/BMS’s Yervoy) was approved for treatment of advanced melanoma in 2011. Ipilimumab, which was the first checkpoint inhibitor to gain regulatory approval, targets CTLA-4.

As summarized in the October 20, 2014 New Link press release, IDO pathway inhibitors constitute another class of immune checkpoint inhibitors. However, they are small-molecule drugs. The IDO pathway is active in many types of cancer both within tumor cells and within antigen presenting cells (APCs) in tumor draining lymph nodes. This pathway can suppress T-cell activation within tumors, and also promote peripheral tolerance to tumor associated antigens. Via both of these mechanisms, the IDO pathway may enable the survival, growth, invasion and metastasis of malignant cells by preventing their recognition and destruction by the immune system.

As also summarized in this press release, NewLink has several active IDO inhibitor discovery and development programs, and has also discovered novel tryptophan-2,3-dioxygenase (TDO) inhibitors. As with IDO, TDO is expressed in a significant proportion of human tumors, and also functions in immunosuppression. TDO inhibitors are thus potential anti-cancer compounds that might be used alone or in combination with IDO inhibitors.

The kynurenine pathway and its role in tumor immunity and in neurodegenerative diseases

IDO and TDO are enzymes that catalyze the first and rate-limiting step of tryptophan catabolism through the kynurenine pathway (KP). The resulting depletion of tryptophan, an essential amino acid, inhibits T-cell proliferation. Moreover, the tryptophan metabolite kynurenine can induce development of immunosuppressive regulatory T cells (Tregs), as well as causing apoptosis of effector T cells, especially Th1 cells.

A 2014 review by Joanne Lysaght Ph.D. and her colleagues on the role of metabolic pathways in tumor immunity, and the potential to target these pathways in cancer immunotherapy also highlights the role of IDO and kynurenine in upregulation of Tregs and in the phenomenon of T-cell exhaustion, in which T cells chronically exposed to antigen become inactivated or anergic.

In our cancer immunotherapy report, we discuss the role of Tregs and T-cell exhaustion in immune suppression in tumors, and the role of anti-PD-1 agents in overcoming these immune blockades. Targeting the IDO and TDO-mediated tryptophan degradation pathway may thus complement the use of anti-PD-1 (and/or anti-PD-L1) MAb drugs, and potentially lead to the development of combination therapies.

We have discussed the kynurenine pathway of tryptophan catabolism in another context in our July 11, 2011 article on this blog. This article discusses the potential role of kynurenine pathway metabolites in such neurodegenerative diseases as Alzheimer’s disease (AD) and Huntington’s disease (HD).

As discussed in that article, HD and AD patients have elevated levels of two metabolites in the KP–quinolinic acid (QUIN) and 3-hydroxykynurenine (3-HK)–in their blood and brains. Both of these metabolites have been implicated in pathophysiological processes in the brain. In contrast, kynurenic acid (KYNA), which is formed in a side arm of the KP by conversion of kynurenine by the enzyme kynurenine aminotransferase, appears to be neuroprotective.

Researchers have been targeting kynurenine 3-monooxygenase (KMO) in order to induce a more favorable ratio of KYNA to QUIN. As a result, they have discovered a drug candidate, JM6. They proposed to first conduct clinical trials in HD, since the cause of HD is much better understood than for AD, and disease progression in placebo controls is better characterized than for AD. Moreover, clinical trials in AD are notoriously long and expensive.

A 2014 review of targets for future clinical trials in HD lists JM6 as a “current priority preclinical therapeutic targets in Huntington’s disease”. It also contains an updated discussion of the mechanism of action of JM6.

NewLink’s IDO inhibitor development program

NewLink presented progress posters on its IDO inhibitor development program at the American Society for Clinical Oncology (ASCO) 2014 annual meeting. These described trials in progress, which did not yet have any results. As described in these presentations, NewLink’s most advanced IDO inhibitor, indoximod is in:

  • a Phase 1/2 clinical trial in combination with ipilimumab in advanced melanoma
  • a Phase 1/2 study in combination with the alkylating agent temozolomide (Merck’s Temodar) in primary malignant brain tumors
  • a Phase 2 study in combination with the antimitotic agent docetaxel (Sanofi’s Taxotere) in metastatic breast cancer
  • a Phase 2 study in which indoximod is given subsequent to the anticancer vaccine sipuleucel-T (Dendreon’s Provenge) in metastatic castration-resistant prostate cancer.
The company also presented a progress poster on a first-in-humans Phase 1 study of NLG919, in solid tumors. NLG919, the focus of NewLink’s alliance with Genentech, is the second product candidate from NewLink’s IDO pathway inhibitor technology platform.

The major theme of NewLink’s ASCO meeting presentations is thus the development of the company’s IDO inhibitors as elements of combination immuno-oncology therapies with MAb immune checkpoint inhibitors, cancer vaccines, and cytotoxic chemotherapies.

In this connection, NewLink also hosted a panel discussion on combination therapies entitled “Points to Consider in Future Cancer Treatment: Chemotherapy, Checkpoint Inhibitors and Novel Synergistic Combinations” at the ASCO meeting. The collaboration of NewLink with Genentech will provide the opportunity for the two companies to test combinations of IDO inhibitors with Genentech’s PD-L1 inhibitor MPDL3280A.

Might targeting T-cell metabolism be used to enhance cancer immunotherapy?

In their 2014 review, Dr. Lysaght and her colleagues outline changes in metabolism as T-cells become activated, and differences in metabolism between various T-cell subsets (e.g., effector T cells, Tregs, exhausted or anergic T cells, and memory T cells). These researchers propose devising means to modulate T-cell metabolism in order to enhance anti-tumor immunity. However more research needs to be done in order to make such approaches a reality. In the meantime, development of IDO and TDO inhibitors is already in the clinic, providing the possibility of a metabolic approach to cancer immunotherapy.

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As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or an initial one-to-one consultation on an issue that is key to your company’s success, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

Vertex cystic fibrosis therapeutics update

 

CFTR protein: A. normal B. gating mutant. Source: Lbudd14 http://bit.ly/1rGrzJ1

CFTR protein: A. normal B. gating mutant.
Source: Lbudd14 http://bit.ly/1rGrzJ1

As we said in our September 10, 2014 article, we intended to post updates on companies that we had been following on our blog, and that have achieved significant progress in recent months. So far, we have covered Agios and Zafgen. Both of these companies were featured in Boston-area meetings in October—Zafgen in Xconomy Xchange: Boston’s Life Science Disruptors on October 8, and Agios in the New Approaches to Cancer Drug Discovery symposium at Harvard Medical School on October 14.

Now we turn to the small-molecule cystic fibrosis (CF) therapeutics program at Vertex Pharmaceuticals (Boston, MA).

We covered Vertex’ CF program in our articles of January 24, 2013 and February 15, 2013. As a result of the publication of these articles, I was interviewed for and quoted in an article in the March 11, 2013 issue of Elsevier Business Intelligence’s The Pink Sheet entitled “Cystic Fibrosis Market Snapshot: Disease-Modifying Drugs Elusive 24 Years After Discovery Of Root Cause”. (A subscription is required to view the full text of this article.)

To summarize our discussions of CF in these earlier articles, CF causes a suite of symptoms that affect the skin, the lungs and sinuses, and the digestive, endocrine, and reproductive systems. The most important results of CF is that patients accumulate thick, sticky mucus in the lungs. This results in clogging of the airways with mucus. This leads to inflammation and bacterial infections. Lung transplantation is often necessary as the disease worsens. With proper management, patients can live into their late 30s or 40s.

The gene that is affected in cystic fibrosis encodes the cystic fibrosis transmembrane conductance regulator (CFTR).  CFTR is an ion channel that regulates the movement of chloride and sodium ions across epithelial membranes, including the epithelia of lung alveoli. CF is an autosomal recessive disease, which is most common in Caucasians. The most common mutation that causes CF, ΔF508, is a deletion of three nucleotides that causes the loss of the amino acid phenylalanine at position 508 of the CFTR protein. The ΔF508 mutation accounts for approximately two-thirds of CF cases worldwide and 90% of cases in the United States. However, there are over 1500 other mutations that can cause CF.

Ion channels constitute an important class of drug targets, which are targeted by numerous currently marketed drugs. These compounds were developed empirically by traditional pharmacology before knowing anything about the molecular nature of their targets. However, discovery of novel ion channel modulators via modern molecular methods has proven to be challenging.

The ΔF508 mutation results in defective cellular processing, and the mutant CTFR protein is retained in the endoplasmic reticulum. Some other mutations in CTFR (which affect a small percentage of CF patients) result in mutant proteins that reach the cell membrane, but are ineffective in chloride-channel function.

After a long discovery and development program (which we outlined in our February 15, 2013 article), Vertex identified two types of candidate small-molecule CF therapeutics:

  • CFTR potentiators, which potentiate the chloride channel activity of mutant CFTR molecules at the cell surface;
  • CFTR correctors, which partially correct the folding and/or trafficking defect of such mutant CFTRs as ΔF508, thus enabling a portion of these mutant proteins to exit from the endoplasmic reticulum and to deposit in the cell membrane.
Vertex’ CTFR potentiator ivacaftor (Kalydeco, formerly known as VX-770) was approved by the FDA in January 2012, and approved in Europe in July 2012. At that time, ivacaftor was only indicated for treatment of CF patients age 6 and over carrying the CFTR G551D mutation (Gly551Asp). Although the G551D mutation only affects approximately 4% of CF patients, it is the most common CFTR gating mutation (i.e., a mutation that affects transport of sodium and chloride ions across epithelial membranes).

New indications for ivacaftor (Kalydeco)

On July 31, 2014, Vertex announced that the European Commission had approved ivacaftor for treatment of CF patients age 6 and over who have one of eight non-G551D gating mutations in the CFTR gene. The eight additional gating mutations included in the new approval affect approximately 250 people ages 6 and older in the European Union.

The approval was based on data from a Phase 3 randomized, double-blind, placebo-controlled study of 39 people with CF ages 6 and older who have a non-G551D gating mutation.

The European approval followed the February 21, 2014 announcement that the FDA had approved ivacaftor for treatment of CF patients 6 and older who have one of the same additional eight mutations in the CFTR gene. In the U.S., approximately 150 people ages 6 and older have one of the additional eight mutations.

On October 21, 2014, the FDA’s Pulmonary Allergy Drugs Advisory Committee (PADAC) voted 13-2 to recommend approval of ivacaftor in CF patients age 6 and older who have the R117H mutation in the CTFR gene. This new indication is now under review by the FDA.

Thus Vertex has been pursuing a strategy of testing and seeking approval of ivacaftor for treatment of CF patients with gating mutations in the CTFR gene other than the G551D mutation, in a systematic, step-by-step fashion. As a result of this strategy, ivacaftor is currently approved to treat over 2,600 people ages 6 and older in North America, Europe and Australia.

Vertex’ development of the CFTR correctors lumacaftor (VX-809) and VX-661

Meanwhile, Vertex has also been pursuing approval for its CFTR correctors lumacaftor (VX-809) and VX-661. We have discussed these agents in our February 15, 2013 blog article.

As we discussed in that article, as of February 2013 Vertex had completed Phase 2 studies of a combination of ivacaftor and lumacaftor in CF patients who were homozygous for the CFTR ΔF508 mutation. They then planned pivotal phase 3 trials of the combination therapy in this patient population. The rationale for the combination treatment was that VX-809 potentates the deposition of CFTR ΔF508 in the cell membrane, and invacaftor potentiates the function of cell-surface CFTR ΔF508.

As of February 2013, Vertex was also conducting Phase 2 trials of another CTFR corrector, VX-661, alone and in combination with ivacaftor in CF patients homozygous for CFTR ΔF508.

On June 24, 2014, Vertex announced that results from two Phase 3 studies of lumacaftor in combination with ivacaftor showed statistically significant improvements in lung function in people ages 12 and older with cystic fibrosis (CF) who were homozygous for CFTR ΔF508. All four 24-week combination treatment arms in the studies, known as TRAFFIC and TRANSPORT, met their primary endpoint of mean absolute improvement in lung function from baseline compared to placebo at the end of treatment. The combination treatments were also generally well tolerated.

Data from a pre-specified pooled analysis also showed improvements in multiple key secondary endpoints, including lowering pulmonary exacerbations.

On October 9, 2014, Vertex announced updates of the results of the TRAFFIC and TRANSPORT studies, in conjunction with the company’ presentations at the 28th Annual North American Cystic Fibrosis Conference (NACFC). Patients who completed 24 weeks of treatment in TRAFFIC or TRANSPORT were eligible to enter a Phase 3 rollover study to receive a combination regimen of lumacaftor and ivacaftor. The first interim data from the rollover study (presented at NACFC) showed that the improvements in lung function observed in the 24-week TRAFFIC and TRANSPORT studies were sustained through 48 weeks of treatment with the combination treatment. At the time of the interim analysis, safety and tolerability results were also consistent with those observed in the initial Phase 3 TRAFFIC and TRANSPORT studies.

In the October 9, 2014 press release, Vertex also announced the submission of an NDA in the U.S. and an MAA in Europe for the approval of ivacaftor in children with CF ages 2 to 5 with one of the same 9 CTFR gene mutations for which the drug is approved in patients 6 or older. These line extension submissions are based on further Phase 3 studies, which were also presented at the NACFC.

On November 5, 2014, the company announced that it had submitted an NDA to the FDA and an MAA to the European Medicines Agency (EMA) for a fully co-formulated combination of lumacaftor and ivacaftor for CF patients age 12 and older who are homozygous for CFTR ΔF508. There are approximately 22,000 people with CF ages 12 and older who are homozygous for CFTR ΔF508 in North America, Europe and Australia. This includes approximately 8,500 people in the United States and 12,000 people in Europe. These new submissions are based on data from TRAFFIC and TRANSPORT, and on the first interim data from the subsequent rollover study.

Meanwhile, as also announced on October 9, 2014, clinical studies of VX-661 are continuing. Vertex presented data from Phase 2 studies of VX-661 in combination with ivacaftor at the 2014 NACFC. In the October 9 press release, Vertex announced that it plans to initiate a pivotal Phase 3 development program for VX-661 in combination with ivacaftor in CF patients who have one or two copies of the CFTR ΔF508 mutation, including patients with a second CFTR mutation that causes a defect in the gating of the CFTR protein. The initiation of this study is pending regulatory discussions and data from a fully enrolled 12-week Phase 2b study of VX-661 in combination with ivacaftor in patients who are homozygous for CFTR ΔF508.

The high cost of Kalydeco causes controversy

Kalydeco (ivacaftor) costs nearly $300,000 a year. These costs are usually borne by insurers and governments, and Vertex has pledged to provide the drug free to any U.S. patient who is uninsured or whose insurance won’t cover it.

However, the high cost of this drug—and the anticipated higher cost of combination therapies for treatment of CF—has generated controversy in some circles. This issue has been discussed, for example, in 2013 articles in the M.I.T. Technology Review and in MedPage Today. (MedPage Today is a peer-reviewed online medical news service for clinicians, which provides breaking medical news, professional medical analysis and continuing medical education (CME) credits to its physician readers.)

According to the Technology Review article, by Barry Werth, doctors and patients enthusiastically welcomed Kalydeco because it offers life-saving health benefits and there is no other treatment. Insurers and governments readily paid the cost. However, commentators quoted in the MedPage Today article said that the price of Kalydeco is exorbitant, and the increasing numbers of high-priced life-saving drugs to treat rare diseases (although nor usually borne directly by patients themselves) is unsustainable. Vertex—as quoted in the MedPage Today article—said that the price of Kalydeco reflects its high degree of efficacy, the time and cost [and risk] it took to develop the drug, and the company’s commitment to reinvest in continued development of newer drugs to help other CF patients.

The discussions of the high cost of Kalydeco echoes the discussions of the cost of novel drugs for life-threatening cancers, as mentioned in our October 2, 2014 article, “Late-breaking cancer immunotherapy news”, on this blog.

With respect to the development of Kalydeco and other small-molecule CF drugs, the publicly-funded—and successful—research to determine the molecular cause of CF was of little help in enabling researchers to develop disease-modifying drugs. (See our January 24, 2013 blog article, “Determining the molecular cause of a disease does not necessarily enable researchers to develop disease-modifying drugs”.) As outlined in our February 15, 2013 blog article, Vertex’ own drug discovery and development program (partially funded by the nonprofit Cystic Fibrosis Foundation, which now receives royalties on sales of Kalydeco) was long (beginning in 1998), expensive, risky, and involved considerable ingenuity.

Given the high barrier between the knowledge of the molecular biology of CF and its use in discovering and developing safe and efficacious small-molecule drugs, the development of such agents as ivacaftor, lumacaftor, and VX-661 is almost miraculous. Vertex’ arguments that justify the high cost of the drug thus have considerable merit. However, discussions in the medical community and beyond on how the costs of novel life-saving drugs for rare diseases and cancer may be sustained will and should continue.

Conclusions

The goal of Vertex’ CF program as a whole is the development, approval and marketing of multiple combinations of small-molecule therapeutics that will have disease-modifying efficacy in the great majority of CF patients. Especially with the recent progress with clinical studies of the ivacaftor/lumacaftor combination in patients with CFTR ΔF508 mutations, and with line extensions of ivacaftor, Vertex appears to be well on its way to accomplishing this, pending regulatory approvals.

________________________________

As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or an initial one-to-one consultation on an issue that is key to your company’s success, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.