Lecture Summaries

WEEK # TOPICS LECTURE SUMMARIES
Unit 1: The Ins and Outs of Cancer: We will begin the course by gaining a basic understanding of what cancer is and how normal cells turn malignant. We will read papers that describe the fundamentals of cancer biology: the role of oncogenes and tumor suppressors in tumorigenesis, and the concept of cancer stem cells and minimal residual disease, which present as a major hurdle in achieving complete eradication of cancer in the clinic.
1 Introduction The first session will begin with instructor and student introductions. We will then go over the syllabus, including expectations and goals of the class, an overview of the course and the two assignments. We will also discuss strategies for reading and deconstructing primary scientific papers. At the end of the session, the instructor will provide a brief summary of the humanized mouse field and its place in cancer research followed by an introduction to the first two papers.
2 Of tumor suppressors and oncogenes At its core, cancer is a disease of uncontrolled growth of abnormal cells. Normal cells rely on external stimuli and internal cell intrinsic cues to control their rate of proliferation and differentiation: pro-growth cues will induce growth in response to external signals, whereas cellular stress or DNA damage cues will activate networks in the cell that halt its growth. In cancer cells these networks are often bypassed, allowing malignant cells to grow uncontrollably. An analogy of these pro and anti-growth networks can be made with the gas and brake pedal of a car, respectively, which control opposing actions on the vehicle. Activation of pro-growth genes, also known as oncogenes (analogous to pressing on the gas pedal), or inactivation of anti-growth genes, also known as tumor suppressors (uncoupling the brakes), results in aberrant growth of cancer cells. In this session, we will discuss two papers, one highlighting the enhanced expression of the oncogene Myc in neuroblastoma and the other covering the role of the p53 tumor suppressor as a growth inhibitor. These papers will address the two tenets of Cancer Biology and serve as an introduction to the field.
3 Cancer stem cells and minimal residual disease Most cancers are difficult to eradicate due to the presence of residual cells that are resistant to conventional therapy and eventually repopulate the disease. These cells are referred to as cancer stem cells (CSCs), and the residual disease that causes relapses is referred to as minimal residual disease (MRD). CSCs are a quiescent population of cells that share certain characteristics with normal stem cells. MRD is postulated to arise from CSC, which are primitive, have a relatively finite proliferative capacity and are able to differentiate into progenitor, disease-causing cells. While the CSC hypothesis had been proposed for many years now, it was only recently that support for the presence of CSCs in hematopoietic malignancies and solid tumors was documented. In hematologic cancers, the CSC is also referred to as the leukemia stem cell (LSC). The CSC hypothesis was first tested and proven in Acute Myeloid Leukemia (AML) by John Dick and colleagues and this paper will be the first for this session. Our second paper will investigate the role of AML LSCs in MRD and disease relapse. In this session we will use AML as a model to understand CSCs and MRD.
Unit 2: The Mouse as a Model Organism to Study Human Cancer: In Unit 2, we will begin addressing the idea of modeling human cancer in a model organism, namely the mouse. The first session will introduce us to xenograft mouse models, i.e. transplanting human cancer cells in immunocompromised mice. From there we will explore the efforts of improving the immunocompromised mouse host to allow better human tumor engraftment. Finally, we will learn about ways to develop a de novo human tumor in mice, thus generating a mouse with a matched human tumor and human immune system. At the end of this session we will have the opportunity to visit the Chen laboratory, which implements the technologies discussed to develop humanized mouse models.
4 Can we model human cancers in mice? Since the dawn of Cancer Biology, scientists have been studying ways to model human cancer in model organisms. Mice, due to their availability, ease of manipulation and short gestation periods have been the mammal of choice for these studies. Two obvious approaches to model human cancer in mice, or to "humanize" mice, are by i) introducing human cells into tolerant hosts, and ii) modifying the mouse genetically to resemble the lesion of interest (oncogene or tumor suppressor). We will begin this class by discussing a paper by Ishikawa et al. that utilizes the first approach. This paper describes a xenograft model of human Acute Myeloid Leukemia (AML) in immunocompromised mice. This work builds upon decades of xenograft models with patient AML cells and provides an improved system for AML cell engraftment by using the latest strains of immunocompromised mice. The next paper focuses on the second strategy: introducing a commonly-occurring cancer lesion into the mouse genome and monitoring tumor development. The lesion modeled in this paper is the Myc-Ig translocation found in Burkitt's lymphoma. We will compare and contrast the approaches taken in the two papers and discuss the implications of these studies.
5 Making a better Mouse Man—Recent developments in humanized mouse technologies

"Humanization" can occur by genetic means, whereby a human gene is inserted into the mouse locus, or by the engraftment of human cells in immunocompromised mice. For this class, we will use the term humanized mice to refer to the latter: immunocompromised mice engrafted with human cells and/or tissues. As we discovered in Session 4, the earliest attempts to create mouse models of human cancer relied on the engraftment of human cancer cells in immunocompromised mice. Several different genetic backgrounds of immunocompromised mice have been used for xenograft assays. However, there are several limitations to these models, e.g. i) the presence of residual mouse innate and adaptive immune cells, and ii) the lack of functional human T cells. The absence of functional human T cells that are selected on human major histocompatibility complex-I (MHC-I) molecules is a major disadvantage for the development of models that rely on T cells as a mode of therapeutic intervention. During T cell development in the thymus, naïve thymocytes undergo several rounds of selection by thymic epithelial cells, which express MHC-I molecules in complex with peptide antigens. This interaction, also referred to as the education of the T cells, is important to select for T cells that are able to differentiate between self and non-self peptide antigens.

In humanized mouse strains that do not express human MHC-I molecules, the engrafted human T cells are selected on mouse MHC-I molecules. This is not ideal, as these T cells are a suboptimal model to study the role of human T cells, via interaction with human MHC-I: Peptide complexes, on disease progression and therapy efficacy. To address this problem, several research groups have attempted to generate improved humanized mouse strains that allow the development and education of human T cells by human MHC-I molecules. Lan et al. reasoned that the engraftment of human thymic tissue along with human hematopoietic stem cells in immunocompromised mice should allow for the development of T cells that are selected on human thymic epithelial cells. The model they developed is commonly referred to as the BLT (blood-liver-thymus) model and marks a momentous step forward in the field of humanized mice. Shultz and colleagues took a different approach by introducing the human MHC-I locus into an immunocompromised mouse strain that is devoid of mouse adaptive immunity and natural killer cells (NSG strain). This new strain of mice, known as HLA-A2-NSG, is a powerful tool to study the development and function of human T cells in an MHC-matched environment. We will compare and contrast the different approaches taken by the two groups to develop a better humanized mouse model.

6 Sophisticated models of de novo human tumors in humanized mice In this session we will explore the concept of generating de novo human tumors in immunocompromised mice. One of the strengths of this approach when compared to xenograft models (e.g. Ishikawa et al., from Session 4) is the ability to study all steps of human tumorigenesis: initiation, development and propagation of cancer. In addition, these models allow the development of tumors alongside a matched human immune system, which is important to study the role of the immune system in cancer progression and also to develop novel immune-based therapies. The first paper is by Moriya et al. and reports the development of a human Mixed Lineage Leukemia in humanized mice by viral transduction of human hematopoietic stem cells (CD34+ HSCs). The second report, from Professor Lishan Su's group, is an elegant demonstration of the development of human hepatocytes alongside an intact human immune system in immunocompromised mice. This model is then used to study Hepatitis C virus pathogenesis, a frequent precursor to hepatocellular carcinoma in humans.
7 Visit to Chen Research Lab

Students will have the opportunity of visiting the Chen research lab to learn about some of the techniques used to generate humanized mice with de novo human cancer and a matching immune system.

Reminder: Written assignment due at the start of class

Unit 3: Cancer Immunotherapy and Mouse Avatars: The final Unit of the course aims at introducing students to the emerging field of cancer immunotherapy and highlighting the power of humanized mouse models in developing and testing such therapies. We will begin this unit by learning about the interaction between cancer and the immune system followed by examples of how the immune system can be manipulated to attack cancer. The last two sessions will focus on two new concepts that are making headway in the cancer therapy field: mouse avatars and co-clinical trials. Both of these new areas of research are booming rapidly and have given promising results in fighting the battle against cancer.
8 The immune system and cancer—Cancer Immunoediting hypothesis

In the early 1900s, Paul Ehrlich was one of the first people to hypothesize that organisms with a long lifespan would have a high cancer burden if not for the protective mechanisms imposed by the body's natural defense, the immune system. This led to the development of the cancer immunosurveillance concept, which was later refined into the cancer immunoediting hypothesis by Robert Schreiber and colleagues in the early 2000s. In its most basic form, cancer immunoediting can be defined as an extrinsic tumor suppressive role of the immune system. There are three stages to immunoediting: Elimination, equilibrium and escape. In the first stage, a tumor is recognized and eliminated by the immune system before disease onset. In the event that there are malignant cells that survive the elimination stage, the adaptive immune system steps in and keeps these cells in a dormant state constituting the second stage–equilibrium. A person can remain cancer free as long as this equilibrium phase is unperturbed and the tumor is not allowed to grow. However, upon external cues, environmental stressors and changes in the tumor, the immune system becomes suppressed and the tumor escapes dormancy and grows uncontrollably, also known as escape, which manifests as apparent disease.

We will start today's class with a discussion of a seminal paper by Shankaran et al. that helped shaped the cancer immunoediting hypothesis by proving, using mouse models, that the long-held concept that the immune system can control cancer was indeed true. We will then discuss a second, older paper that shows evidence for cancer immunoediting in patients, providing evidence for the presence of an immune response against melanoma in patients. The Muul et al. paper describes the discovery of tumor-infiltrating lymphocytes capable of specifically lysing melanoma cells, thus proving that the immune system elicits a response against tumor cells.

9 T cell mediated immunotherapy

In this session we will be delving deeper into the phenomenon of immune escape of tumors by investigating the interaction between tumors and immune cells in the tumor microenvironment. Tumors can create a microenvironment that suppresses the function of infiltrating immune cells and new immunotherapies are being developed to reverse this suppression and thus enabling the immune system to eliminate cancer. There are many mechanisms by which tumors can create suppressive microenvironments. One of the best-studied is the suppression of function of tumor-infiltrating lymphocytes, particularly T cells, by increasing the expression of immune checkpoint molecules, such as CTLA-4 on infiltrating T cells and PD-L1 on tumor and stromal cells. Immune checkpoints refer to inhibitory pathways that modulate the amplitude and duration of an immune response. Immune checkpoint molecules are signaling molecules that suppress the activity of T cells, thus rendering them unable to kill target cells, which in this case would be cancer cells. Years of research in relieving the inhibition of immune checkpoints to treat cancer has proven promising with the approval of an antibody therapy against CTLA-4 for melanoma several years ago and the even more exciting FDA approval in 2014 of antibodies targeting the PD-1 signaling axis in several cancers. Antibodies are proteins naturally produced by the adaptive arm of the immune system to combat invading pathogens. These proteins have two main domains, a variable antigen recognition domain and a constant domain. Antibodies function by binding to a cell-surface molecule on target cells via the variable domain and inducing the killing of the target cells by recruiting other immune cells via its constant domain. Because antibodies can be manufactured to recognize specific molecules on the cell surface, they have become a powerful treatment modality in cancer.

Today, we will discuss the development of Ipilimumab, an anti-CTLA-4 antibody for treatment of melanoma and the adverse effects associated with it. The paper by Attia et al. describes one of the first clinical trials of Ipilimumab that eventually led to its FDA approval. This paper documents the efficacy and autoimmune side effects associated with the therapy. Importantly, despite significant autoimmune side effects, the therapy was approved due to a lack of targeted therapies. Most of the work that led to the initial clinical trials was done in mouse models which showed no such toxicity profiles. The second paper by Vudattu et al., uses a humanized mouse model (with an intact human immune system) to profile the effect of Ipilimumab on a human immune system. Interestingly, the therapy is not very well tolerated and mirrors the side effects seen in patients. These two papers taken together, highlight the importance of better models to test therapies prior to rolling them out in the clinic to avoid unwanted side effects.

10 Improving combination chemotherapy and immune-based therapies based on lessons learned from humanized mice

Most of the chemotherapeutic agents used in the clinic today are decades old DNA-damaging agents that lack specificity for the tumor and work by attacking rapidly dividing cells, including tumor cells. However, due to this lack of targeting, these agents also cause a large amount of collateral damage in the form of unwanted side effects. Recently, several targeted immune-based therapies have been developed that aim to preferentially eliminate tumor cells. As we discussed in Session 9, of these therapies, antibody-based therapies have been the most promising. In this session, we will be discussing two papers that use antibody based therapies in conjunction with conventional chemotherapy to eliminate minimal residual disease in the bone marrow. Recall from Session 2 the concept of minimal residual disease: in most patients, disease relapse is due to a reservoir of cells that are highly resistant to conventional chemotherapy.

The first paper from Rambaldi et al. introduces us to a combination chemotherapy regimen, R-CHOP, which is widely used in the treatment of a type of B cell lymphoma. R-CHOP comprises of an antibody therapy (Rituximab) and four conventional chemotherapeutic agents (cyclophosphamide, doxorubicin hydrochloride, oncovin and prednisone). The second paper attempts to improve on this highly toxic chemotherapy regimen by testing new combination strategies in a humanized mouse model of B cell lymphoma. Pallasch and colleagues demonstrate that a lower dose of the highly toxic cyclophosphamide is effective at eliminating MRD in this humanized mouse model. This work was instrumental in altering the dose and administration strategy of R-CHOP in the clinic, and clinical trials are currently underway to implement this new strategy in the treatment of B cell lymphomas.

11 Personalized mice—Part 1: Mouse Avatars

The last two sessions of this Unit will be devoted to a new paradigm in cancer research—Mouse Avatars and Co-clinical trials. Mouse Avatars allow for personalized cancer therapy and are generated by implanting a patient's tumor in an immunocompromised mouse host, similar to the xenograft models we have previously discussed. The difference here is that the resultant tumor that develops is used to test new drug combinations based on the molecular and genetic makeup of the individual tumor. Development of the human tumor in an in vivo setting allows for personalized therapy regimens to be tested, thus reducing toxicity and improving efficacy from conventional non-targeted chemotherapies.

The paper by Villaroel and colleagues reports the exciting finding of modeling a patient's surgically resected pancreatic tumor in mice to determine the most effective chemotherapy regimen against this tumor. This regimen was then given to the patient in the clinic, resulting in a long-lasting response that was markedly better than that seen in most pancreatic cancer patients with standard chemotherapy. The second paper builds upon this concept with a larger cohort of patients and layers on top of it whole-exome sequencing technology. Exome sequencing provides information on the unique molecular profile of tumors that arises due to their genetic diversity. These two technologies combined would allow for complete personalization of cancer therapy based on the genetic makeup of the individual's tumor. In this paper they demonstrate the feasibility and challenges of this approach.

12 Personalized mice—Part 2: Co-clinical trials

Traditionally, clinical trials are initiated based on the efficacy of drugs on tumors generated either in genetically engineered mouse models (GEMM) or xenograft models with patient tumor or cell lines. While both models have their downsides, several advances in developing sophisticated GEMMs with complex mutational backgrounds have suggested the feasibility of this approach in accurately predicting the efficacy of drug or drug combinations for human cancers. About 15 years ago, Pandolfi and colleagues found a combination of drugs that could eradicate acute promyelocytic leukemia in a GEMM that recapitulates the human disease and tested this combination in the clinic in 2004. Remarkably, the drug combination was successful in eradication of a leukemia that until then was deemed uncurable. This success prompted the conception of the co-clinical trial to speed up the discovery process and uncover new combinations of therapies to eradicate various cancers. A co-clinical trial is a GEMM drug trial run in parallel with a human clinical trial with similar drug regimens. Co-clinical trials can be held in parallel with Phase I, II or III clinical trials and aim at fine-tuning the clinical trials based on data obtained from GEMMs treated with similar chemotherapy regimens.

The co-clinical trial concept is relatively new, and these papers are by pioneers in the field setting the stage for future studies. It is important to note that as we have previously discussed, engineered mouse models have their limitations, especially the lack of human cells and a human immune system. Therefore, while these models will be important for the idenfitication of drug combinations for non-immune based therapies, their utility in developing and testing immunotherapies will remain limited. Today we will review two papers describing co-clinical trials, both of non-small cell lung cancer (NSCLC) but with different genetic lesions and different drug combinations.

13 Class presentation and course evaluation Students will present a paper of choice in a 15-minute PowerPoint presentation, followed by a 5 minute Q&A session. The objective is to distill the research paper down to its most important experiment(s), controls and conclusion(s) and present it in a coherent manner.