CICON17 Day 1 Recap: Neoantigens, Vaccines, and Overcoming Immunotherapy Resistance

The third International Cancer Immunotherapy Conference (CICON17) organized by the Cancer Research Institute (CRI), the Association for Cancer Immunotherapy (CIMT), the European Academy of Tumor Immunology (EATI), and the American Association for Cancer Research (AACR), began on September 6, 2017, in Mainz, Germany along the banks of the Rhine River just thirty minutes away from bustling Frankfurt. More than 1,400 scientists from around the world are in attendance to hear the latest laboratory and clinical research in cancer immunotherapy.

SESSION 1: NEOANTIGENS

Opening the first session on Day 1 was The Netherlands Cancer Institute’s Ton N. Schumacher, PhD, with a talk on how immune cells called T cells recognize cancer. Specifically, how they recognize cancer neoantigens (neo = new, antigen = something the immune system detects), tumor markers that arise from mutations that T cells recognize via the T cell receptor (TCR).

Unfortunately, tumors can escape immune elimination and “exhaust” T cells by expressing another molecule, PD-L1, which activates the PD-1 immune checkpoint, a key pathway for deactivating T cells. As revealed in his recent Nature paper with Chong Sun, PhD, Schumacher explained how with genome-wide screening he identified CMTM6 along with a related “backup” molecule CMTM4 as important regulators of PD-L1 expression. Without CMTM6, the stability and presence of the PD-L1 protein was significantly diminished. Furthermore, a talk later in the day by Marian Burr, PhD, of the Peter MacCallum Cancer Centre and the Cambridge Institute for Medical Research, showed in mice that surface PD-L1 is rapidly degraded in cells lacking CMTM6, which was shown to protect PD-L1 from degradation. Thus, CMTM6’s maintenance of PD-L1 expression also regulated anti-tumor immunity, at least in mice.

Dr. Schumacher also investigated the ability of T cells in patients’ tumors to recognize cancer cells, and highlighted a new technique his team developed that enables them to accurately evaluate the tumor-targeting potential of T cells inside patient tumors, known as tumor infiltrating lymphocytes. With this, he showed that not all T cells that target tumor neoantigens are “equal” in their ability to attack tumors, and stressed the need for more sophisticated tests, or assays, to properly determine which neoepitopes—smaller bits of neoantigenic proteins that are actually “seen” by the T cell receptor—are most likely to lead to effective anti-tumor responses. Building on that, he pointed out that some of the “exhausted” T cells found in tumors might be irrelevant when it comes to these anti-tumor responses, and that strategies to reinvigorate exhausted T cells should take this into consideration.

Following Schumacher was BioNTech’s Ugur Sahin, MD, the morning session chair, who discussed the challenges facing personalized cancer vaccines: namely, that every patient is different, and even within a single patient the tumor cells can vary widely in their identity and behavior over time. He made the case, however, that we must confront this complexity by uncovering more information relevant to immunotherapy strategies, which would—borrowing from a modern manufacturing term for maximizing efficiencies and lowering costs— allow for the “just in time” design and production of individually tailored treatments.

In a clinical trial involving patients with stage 3 or 4 melanoma, Sahin demonstrated that personalized RNA vaccines enhanced tumor-specific T cell responses (against at least 3 tumor targets) within 2-4 weeks, and led to the presence of important memory T cells that can help provide long-term protection. Additionally, he showed that the majority of neoantigens (57%) were recognized by CD4+ T cells, while only 17% were recognized by CD8+ T cells and 26% were recognized by both.

Thus far, 5 of the 19 patients treated have experienced objective responses: two patients had complete responses to the vaccine alone, while one had a complete response to the vaccine in combination with anti-PD-1 checkpoint immunotherapy. Furthermore, there was evidence of vaccine-induced antigen spread, meaning that the immune system recognized and responded against tumor-specific neoantigens that weren’t even targeted by the vaccine. Antigen spreading is believed to be an important factor in the immune system’s ability to adapt to changes in cancer and provide durable protection.

Finally, Sahin discussed his team’s use of liposomes (essentially hollow fatty spheres) to deliver these RNA vaccines directly to dendritic cells, which can coordinate systemic immune responses. Already the approach—which can overcome the weak immune-stimulating ability of some antigens—has been successful in mice, and is now being evaluated in a first-in-human clinical trial. Preliminary results from the trial have been promising in terms of preventing relapse in disease-free patients as well as inducing therapeutic responses in checkpoint immunotherapy-treated patients with measurable disease. These liposomal vaccines have also shown synergy in combination with anti-PD-1 checkpoint immunotherapy.

Next, Stephen P. Schoenberger, PhD, who co-directs (with Ezra Cohen, MD) the San Diego Center for Precision Immunotherapy at the University of California, San Diego (UCSD), highlighted an improved way to discover the best patient-specific neoantigens to target through immunotherapy, which revealed that spontaneously occurring T cell responses against tumors are readily detectable. Additionally, T cells that react against both driver (those that fuel cancerous behavior) and passenger (those “along for the ride”) mutations were also found, and proteins resulting from DNA frameshift mutations were found to be especially immunogenic.

Building on previous approaches that rely on biopsies, genome sequencing, and T cell assays, Schoenberger’s platform enables sorting of tumor-infiltrating T cells (also referred to as TILs) according to what types of antigens they target. This allows isolation of only the TILs that are reactive against tumor antigens and provides an improved product for adoptive cell [immuno]therapy (ACT). Thus far, these “TIL 2.0” have led to improved tumor control in mice, and worked even better in combination with anti-PD-1 checkpoint immunotherapy.

Following Schoenberger, Catherine Wu, MD, of Harvard Medical School and the Dana-Farber Cancer Institute, discussed current cancer vaccine approaches and sought to address critical questions in cancer immunotherapy. In short, by expanding and broadening patients’ repertoires of tumor-specific T cells, doctors can aim to stimulate highly specific anti-tumor immune responses that also spare healthy tissues from autoimmune attacks.

Putting this concept into practice, Wu used vaccines containing SLPs (synthetic long peptides) against 20 personalized tumor neoantigens per patient, along with the immune stimulant poly-ICLC. This was able to induce responses in both CD4+ (helper) and CD8+ (killer) T cells. Vaccination was also associated with major shifts in T cell gene expression, producing T cells that were “very energetic and excited to go forward.”

In two previously-untreated metastatic melanoma patients who progressed after vaccination, subsequent treatment with anti-PD-1 immunotherapy was able to induce complete responses. While melanomas are typically heavily mutated, Wu also treated glioblastoma patients whose tumors were less mutated and observed successful induction of T cells against tumor-specific neoantigens. Finally, Wu stressed how the improved genome-mining and next-generation sequencing will allow for not only improved vaccination targets, but also (returning to the personalization theme) improved combination strategies tailored for individual patients.

Sine Reker Hadrup, PhD, of the Technical University of Denmark, spoke next on the field’s inability to predict which neoantigens actually stimulate immune responses in the body, and then discussed her experiments that sought to learn what determines the immunogenicity of neoantigens (and their corresponding neoepitopes, the molecules actually targeted by T cells within the context of Major Histocompatibility Complex (MHC), a cellular apparatus that presents antigens to the immune system. To do so, she took an MHC-loaded epitope that contained 10 amino acids (AAs) and altered it by substituting different AAs into each of the 10 positions. By doing this, she produced almost 200 variants and made interesting observations concerning how these single AA changes influenced the ability of T cells to recognize the epitope.

Next up was Memorial Sloan Kettering’s Timothy Chan, MD, PhD, who explained how large scale technologies that can predict neoantigens as well as the targets of TCRs theoretically allow doctors to build a better foundation for precision immunotherapy strategies. However, “how to really put this all together still eludes the field.” Using MSKCC’s IMPACT Platform to perform a pan-cancer analysis of mutational load and its influence on checkpoint immunotherapy responses, Chan showed that all cancers (with the exception of glioma) had a baseline number of mutations, above which more mutations were associated with improved survival after immunotherapy.

When it comes to resistance to checkpoint immunotherapy, Dr. Chan also demonstrated that—in addition to inactivating mutations in genes involved in antigen processing and presentation—mutations in two genes associated with a protein-cleaving enzyme called serine protease were found in melanoma patients and were associated with improved survival after anti-CTLA-4 checkpoint immunotherapy. Out of 18 patients with these mutations, 11 had complete responses (CR) to immunotherapy.

Lastly, Chan highlighted how tumors can evolve during treatment and provided potential evidence for the existence of immunoediting in human tumors. Immunoediting is a central concept in modern tumor immunology, described by Robert D. Schreiber, PhD, along with Gavin Dunn, MD, PhD, and Lloyd J. Old, MD, that characterizes the interaction over time between cancer and the immune system and how through a Darwinian type of selection the immune system shapes tumor “appearance” and behavior. Interestingly, the tumors of melanoma patients who responded anti-PD-1 checkpoint immunotherapy (and had improved overall and progression-free survival) were associated with tumor genomes that became less heterogeneous after treatment. This contrasted with the persistence of tumors’ genomic landscapes in patients who didn’t respond.

Céline Laumont, a PhD candidate at the University of Montreal, followed up Chan’s talk with her work that involved the development of a novel profiling approach which she used to identify five tumor-specific antigens (TSA) targets that were derived from the non-coding regions of the genome. Furthermore, she was able to delay or prevent the development of cancer in mice through the use of a prophylactic dendritic cell vaccine against the TSAs she identified.

Finishing up the first session on neoantigens was Memorial Sloan Kettering’s Vinod Balachandran, MD, who discussed the unique qualities of neoantigens found in rare long-term survivors of pancreatic cancer, a notoriously hard-to-treat tumor type with a historically low survival rate. Compared to short-term survivors, these long-term survivors had twelve times as many CD8+ killer T cells in their tumors and had enriched activity in the genes that control adaptive immunity as well as antigen processing and presentation.

Dr. Balachandran also developed a computational model to quantify a given tumor’s immunogenicity, which takes into account the quality of its neoantigens as well as the tumor’s heterogeneity (what proportion of the tumor cells express neoantigens). He found that the quality of neoantigens—not the quantity—could be used to stratify these long-term survivors and demonstrated prognostic survival value. In all seven of the long-term pancreatic cancer survivors he tested, he found reactivity against high quality neoantigens.

SESSION 2: NOVEL MECHANISMS OF IMMUNOSUPPRESSION AND IMMUNE EVASION

Nicholas Restifo, MD, of the National Cancer Institute Center for Cancer Research, began the second session of Day 1 by discussing his use of genome-scale CRISPR-Cas9 editing—a tool used to target and modify DNA with great precision—to identify the genes that, when deleted, allow tumor cells to escape T cell recognition and elimination. Using three independent analysis methods that reproducibly overlapped, his team was able to identify four novel “weird” genes—APLNR, BBS1, COL17A1, and SOX10—that were crucial for the ability of T cells to target and eliminate tumors. Importantly, the top hits from their analysis also correlated with cancer-killing T cell activity in multiple cancer subtypes.

Next up was Padmanee Sharma, MD, PhD, of the University of Texas MD Anderson Cancer Center, who sought to understand why some patients respond to checkpoint immunotherapy while others do not. To do so, she’s turned to “reverse translation,” or taking insights learned from patients and then going back to the lab to test hypotheses derived from them.

She focused especially on insights related to ICOS (Inducible CO–Stimulator), which belongs to the same family as the immune checkpoint CTLA-4, and revealed that ICOS expression in CD8+ killer T cells increased after they recognized their corresponding antigen in melanoma-bearing mice. Additionally, when the ICOS gene was deleted in T cells, it decreased their production of the important cytokine IFNg as well as Eomes. Because of this, Sharma hypothesized that the ICOS pathway could be targeted (activated, not blocked) through combination immunotherapy approaches to improve patient responses, and it did when combined with anti-CTLA-4 checkpoint immunotherapy in melanoma-bearing mice.

Furthermore, Sharma showed that treating patients with a combination of hormonal therapy and anti-CTLA-4 immunotherapy before surgery could convert “cold,” non-immunogenic prostate tumors into “hot” tumors full of immune cells. However, as the tumors became more infiltrated by immune cells, they also increased expression of immune checkpoints such as PD-L1 and VISTA that can suppress the activity of those immune cells, thus providing a rationale for combination strategies targeting these checkpoints.

Jesse Zaretsky, a PhD student in the lab of Antoni Ribas, MD, PhD, at the University of California, Los Angeles (UCLA), spoke next and discussed the mechanisms of acquired resistance to anti-PD-1 checkpoint immunotherapy in melanoma. He showed that even during tumor relapse, there can still be tumor-targeting T cells present in the tumor, but the tumor cells have evolved to escape detection. Ribas and Zaretsky then used whole exome sequencing and (in separate cases) identified two mutations that disrupted signaling through the JAK pathway and one in B2M, which is involved in antigen presentation. While T cells could still recognize cancer cells that had lost JAK function, it’s likely that it made the cancer cells more resistant to apoptosis, a form of programmed cell death.

Finally, AstraZeneca’s Yumeng Mao, PhD, capped off the Day 1 talks by revealing how two enzymes—AXL and MerTK—associated with myeloid immune cells can suppress immune responses against tumors. Through experiments involving co-culture of tumor cells and immune cells, he showed that deficiency in either of these two proteins was able to improve activation of anti-tumor immune cells, including CD4+ T cells, CD8+ T cells, and natural killer cells. This could lead to new therapeutic targets to improve patient responses to immunotherapy.

The day concluded with a reception and poster session featuring more than 250 abstracts covering topics such as neoantigens and cancer mutations, oncolytic viruses, adoptive cell therapy, checkpoint blockade therapy, immunomonitoring and biomarkers, and cancer-mediated immune suppression.

That’s it for our Day 1 coverage from CICON17. Check back tomorrow to see our coverage of Day 2 of the conference.