Cancer

Coding Dimension ID: 
280
Coding Dimension path name: 
Cancer

Targeting glioma cancer stem cells with receptor-engineered self-renewing memory T cells

Funding Type: 
Early Translational III
Grant Number: 
TR3-05641
ICOC Funds Committed: 
$5 217 004
Disease Focus: 
Cancer
Brain Cancer
Stem Cell Use: 
Adult Stem Cell
Cell Line Generation: 
Cancer Stem Cell
oldStatus: 
Active
Public Abstract: 
While current treatment strategies for high-grade glioma can yield short term benefits, their inability to eradicate the highly tumorigenic cancer stem cell population results in disease recurrence in the vast majority of patients. Stem cells and some cancer cells (the targets of our therapy) share many common characteristics, including the ability to self-renew and grow indefinitely. These cancer stem cells are also resistant to many standard therapies including radiation and chemotherapy, creating a critical need for novel therapies that will efficiently eliminate this cell population. We propose here to develop and optimize a therapeutic strategy, termed “adoptive T cell therapy", that will eliminate the brain tumor stem cell population by re-directing a patient’s immune cells, specifically T cells, to recognize and destroy tumor stem cells. Our goal is a therapy in which a single administration of tumor-specific T cells results in long-term anti-glioma protection. Our approach builds on previous findings that T cells, when reprogrammed, can potently kill glioma stem cells. Furthermore, we will exploit the self-renewing stem cell-like properties of a defined T cell population (central memory T cells) to establish reservoirs of long-lasting tumor-directed T cells in patients with glioma, and thereby achieve durable tumor regression with a glioma-specific T cell product. Our findings can then be applied to cancers besides glioma, including tumors that metastasize to brain.
Statement of Benefit to California: 
The goal of this project is to develop a novel and promising immunotherapy utilizing genetically modified T cells to target glioma stem cells in order to improve cure rates for patients with high-grade malignant glioma. Our strategy, in which a single administration of tumor-specific T cells results in long-term anti-glioma protection, has the potential to provide significant therapeutic benefit to patients with brain tumors, for which there is a dearth of effective treatment options. Further, the tumor-specificity of this therapy is intended to improve the quality of life for patients with high-grade gliomas by reducing treatment related side-effects of conventional therapies. Moreover, due to the high cost hospital stays and treatments usually required for patients with advanced disease, this therapy, by generating long-lasting anti-cancer immunity, has the potential to significantly reduce the costs of health care to California and its citizens. Carrying out these proposed studies will have further economic benefit for California through the creation and maintenance of skilled jobs, along with the purchasing of equipment and supplies from in-state companies. This project will also yield long-reaching benefit through continuing to build the larger CIRM community that is establishing California as a leader in stem-cell and biomedical research both nationally and internationally.
Progress Report: 
  • While current treatment strategies for high-grade glioma can yield short term benefits, their inability to eradicate the highly tumorigenic cancer stem cell population results in disease recurrence in the vast majority of patients. Stem cells and some cancer cells (the targets of our therapy) share many common characteristics, including the ability to self-renew and grow indefinitely. These stem cell-like cancer cells are also resistant to many standard therapies including radiation and chemotherapy, creating a critical need for novel therapies that will efficiently eliminate this cell population. The goal of this project is to develop and optimize a therapeutic strategy, termed “adoptive T cell therapy,” that will eliminate the brain tumor stem cell population by re-directing a patient’s immune cells, specifically T cells, to recognize and destroy tumor stem cells. Our goal is a therapy in which a single administration of tumor-specific T cells results in long-term anti-glioma protection. Our approach builds on our previous pre-clinical and clinical findings that T cells, when reprogrammed, can potently kill glioma stem cells.
  • Over the past year, our group has developed and characterized an optimized next-generation adoptive T cell therapy platform for targeting the glioma-associated antigen IL13Rα2. As such, T cells were modified to express a chimeric antigen receptor (CAR) to recognize and kill IL13Rα2-expressing glioma cells. This T cell platform incorporates several improvements in CAR design and T cell engineering, including improved receptor signaling and the utilization of central memory T cells (Tcm) as the starting cell population for CAR-engineering for enhanced long-term persistence of the cells after they are administered to patients. Importantly, we now demonstrate that this optimized IL13Rα2-specific CAR Tcm therapeutic product mediates superior antitumor efficacy and improved T cell persistence as compared to our previous first-generation IL13Rα2-specific T cells. These findings are significant as they suggest the potential for improving the transient anti-glioma responses for patients, as observed in two Phase I clinical trials by our group at City of Hope, with this optimized next-generation platform.
  • The variability of gliomas, including the known differences between populations of glioma stem-like cells, is a critical barrier to the development of a therapy with the potential to mediate complete and durable remission of this disease. We have therefore hypothesized that a multi-targeted therapeutic approach will be required to achieve elimination of glioma stem-like cells and achieve longer lasting regression of high-grade glioma. To devise an effective multi-target therapy, one must first identify the potentially useful T cell target antigens and variations in their expression between patients and within individual tumors. The ideal target will be highly expressed on tumor cells, including stem-like cells, and not found on normal brain or other tissues. To this end, we have assembled a cohort of 35 patient samples in commercial tissue arrays and 45 patient specimens from the CoH Department of Pathology. Within this group of 80 patient tumors we have begun to examine expression of potential T cell targets, such as IL13Rα2, HER2, EGFR, and others. The goal is to find a set of target antigens that would encompass the maximum number of tumors and, in particular, the cancer stem-like cells within an individual tumor.
  • Our progress thus far has set the stage for our team to develop a potent multi-antigen specific T cell therapy that can “box-in” tumor variability. This clinically translatable platform has the potential to provide new treatment options for this devastating disease.

A Phase I dose escalation and expansion clinical trial in patients with advanced solid tumors

Funding Type: 
Disease Team Therapy Development III
Grant Number: 
DR3-07067
ICOC Funds Committed: 
$6 924 317
Disease Focus: 
Cancer
oldStatus: 
Active
Public Abstract: 
Cancer is a major cause of morbidity and mortality worldwide. Many believe that progress in drug development has not been as rapid as one would have predicted based on the significant technological advancements that have led to improved molecular understanding of this disease. There are numerous explanations for the lag in clinical success with new therapeutics. However, work in the past decade has provided support for what has become known as the cancer stem cell hypothesis. This model suggests that there is a class of cells that are the main drivers of tumor growth that are resistant to standard treatments. In one model the cancer stem cells inhabit an anatomical “niche” that prevents drug efficacy. Another view is one in which tumors can achieve resistance by cell fate decisions in which some tumor cells are killed by therapeutics, while other cells avoid this fate by choosing to become cancer stem cells. These stem cells are thought to be capable of both cancer stem cell renewal and repopulation of the tumor. Our proposal aims to conduct a Phase I clinical trial of a first-in-class mitotic inhibitor. The target is a serine/threonine kinase that was originally selected because blocking this target affects both tumor cell lines and tumor initiating cells (TICs). Our data suggest that the target kinase functions at the intersection of mitotic regulation, DNA damage and repair, and cell fate decisions associated with stem cell renewal. Preclinical work has begun to segregate “sensitive” and “resistant” groups of tumor cell lines and TICs after treatment with the drug candidate as a single agent and in combination with standard-of-care therapeutics. Our data also support the model in which cancer stem cell resistance is likely to arise, at least in some cases, due to stem cell fate decisions that happen in response to therapeutic intervention. This grant is a natural progression of work partially funded by CIRM that enabled the isolation of Tumor Initiating Cells (TICs)from tumors in different tissue types. This facilitated the development and assessment of drug candidates that target both bulk tumor cells and TICs and has now led to the development of a potential anti-cancer drug which we are now preparing to test in humans. The goal of the Phase I trial is to determine the maximum tolerated dose, the recommended Phase II dose, and any dose-limiting toxicities. We will also characterize safety, pharmacokinetic, and pharmacodynamic profiles along with any antitumor activity. Once the maximum tolerated dose has been identified, a biomarker expansion cohort will be opened in order to determine whether appropriately selected biomarkers are associated with a predictable patient response. This will allow a rational approach to study single agent and combination studies that perturb this network and allow us the opportunity to facilitate a targeted clinical development plan.
Statement of Benefit to California: 
It has been estimated, by the California Department of Public Health, that in 2013 about 145,000 Californians will be diagnosed with cancer and more than 55,000 of these will ultimately succumb to their disease. Furthermore, more than 1.3 million Californians are living today with a history of cancer. Therefore, innovative research programs that are able to impact this devastating disease burden are likely to have a large potential benefit to the state of California and its residents. This grant application proposes a Phase I clinical trial for a first-in-class inhibitor of a target that has never been tested in patients. The aim of this trial is to determine the maximum tolerated dose in humans, the recommended dose for phase II trials, and evaluate any dose-limiting toxicities. The trial will also characterize safety, pharmacokinetics, and pharmacodynamic properties. It will also provide early insight into any antitumor activity. Our group has developed a comprehensive unbiased platform that facilitates the segregation of sensitive and resistant populations of cancer based on their molecular subtypes. This capability has the promise to improve the success rate and reduce the cost of oncology clinical trials by focusing on the subsets that are most likely to benefit while avoiding unnecessarily treating patients that would otherwise benefit from alternative treatments. Our preliminary pre-clinical work, funded by CIRM in the context of a Disease Team I award, suggests that this approach can be successfully applied to the networks associated with mitotic regulation, DNA repair, and stem-cell fate decisions. Our ongoing research has tested a number of chemical compounds that are able to block pathways that are critical to the growth and proliferation of many cancer models. These compounds have all been tested in multiple in vitro and in vivo systems and have been found to inhibit the ability of the cancer stem cell to repopulate. Now that our pre-clinical enabling studies have been completed, we have submitted an Investigational New Drug (IND) application to the FDA for a first-in-human phase I clinical trial. In the current proposal, we will be able to test our hypotheses in a clinical setting, which if successful will lead to confirmation of safety and the establishment of the appropriate dose with which to test in later stage trials. This trial will set the stage for a new class of agents that has not yet been tested in clinical settings. We believe that the proposal described herein has the promise to expand the reach of targeted therapies into mechanisms that in most cases have been resistant to innovation. Finally, it is reasonable to expect that our preclinical work and the proposed clinical trials will validate a number of potential biomarkers that will identify susceptible patient subpopulations.

Therapeutic Eradication of Cancer Stem Cells

Funding Type: 
Disease Team Therapy Development III
Grant Number: 
DR3-06924
ICOC Funds Committed: 
$4 179 600
Disease Focus: 
Cancer
Blood Cancer
oldStatus: 
Active
Public Abstract: 
Cancer is a leading cause of death in California. Research has found that many cancers can spread throughout the body and resist current anti-cancer therapies because of cancer stem cells, or CSC. CSC can be considered the seeds of cancer; they can resist being killed by anti-cancer drugs and can lay dormant, sometimes for long periods, before growing into active cancers at the original tumor site, or at distant sites throughout the body. Required are therapies that can kill CSC while not harming normal stem cells, which are needed for making blood and other cells that must be replenished. We have discovered a protein on the surface of CSC that is not present on normal cells of healthy adults. This protein, called ROR1, ordinarily is found only on cells during early development in the embryo. CSC have co-opted the use of ROR1 to promote their survival, proliferation, and spread throughout the body. We have developed a monoclonal antibody that is specific for ROR1 and that can inhibit these functions, which are vital for CSC. Because this antibody does not bind to normal cells, it can serve as the “magic bullet” to deliver a specific hit to CSC. We will conduct clinical trials with the antibody, first in patients with chronic lymphocytic leukemia to define the safety and best dose to use. Then we plan to conduct clinical trials involving patients with other types of cancer. To prepare for such clinical trials, we will use our state-of-the-art model systems to investigate the best way to eradicate CSC of other intractable leukemias and solid tumors. Finally, we will investigate the potential for using this antibody to deliver toxins selectively to CSC. This selective delivery could be very active in killing CSC without harming normal cells in the body because they lack expression of ROR1. With this antibody we can develop curative stem-cell-directed therapy for patients with any one of many different types of currently intractable cancers.
Statement of Benefit to California: 
The proposal aims to develop a novel anti-cancer-stem-cell (CSC) targeted therapy for patients with intractable malignancies. This therapy involves use of a fully humanized monoclonal antibody specific for a newly identified, CSC antigen called ROR1. This antibody was developed under the auspices of a CIRM disease team I award and is being readied for phase I clinical testing involving patients with chronic lymphocytic leukemia (CLL). Our research has revealed that the antibody specifically reacts with CSC of other leukemias and many solid-tumor cancers, but does not bind to normal adult tissues. Moreover, it has functional activity in blocking the growth and survival of CSC, making it ideal for directing therapy intended to eradicate CSC of many different cancer types, without affecting normal adult stem cells or other normal tissues. As such, treatment could avoid the devastating physical and financial adverse effects associated with many standard anti-cancer therapies. Also, because this therapy attacks the CSC, it might prove to be a curative treatment for California patients with any one of a variety different types of currently intractable cancers. Beyond the significant benefit to the patients and families that are dealing with cancer, this project will also strengthen the position of the California Institute of Regenerative Medicine as a leader in cancer stem cell biology, and will deliver intellectual property to the state of California that may then be licensed to pharmaceutical companies. In summary, the benefits to the citizens of California from the CIRM disease team 3 grant are: (1) Direct benefit to the thousands of patients with cancer (2) Financial savings through definitive treatment that obviates costly maintenance or salvage therapies for patients with intractable cancers (3) Potential for an anti-cancer therapy with a high therapeutic index (4) Intellectual property of a broadly active uniquely targeted anti-CSC therapeutic agent.

[REDACTED]: A New Cancer Therapeutic to Reduce CSC Frequency

Funding Type: 
Disease Team Therapy Planning I
Grant Number: 
DR2-05352
ICOC Funds Committed: 
$65 120
Disease Focus: 
Cancer
oldStatus: 
Closed
Public Abstract: 
A important benefit of the tremendous progress in stem cell research has been the recognition that stem cell pathways are frequently re-activated in cancer cells conferring stem cell-like properties on a subset of tumor cells. This understanding is the basis for the emerging field of cancer stem cell (CSC) research. The cancer stem cell paradigm is a new approach in cancer research that has profound implications for new anti-cancer drug development. It is now widely understood that tumors are comprised of different cell types. Experimental evidence has accumulated from many laboratories indicating that different tumor cells vary dramatically in their ability to grow a new tumor. The tumor cells capable of re-growing a new tumor are the CSCs, whereas the bulk of the tumor cells lack this capacity. This property of seeding new tumor growth is analogous to the growth of distant metastases that is a major cause of mortality in cancer patients. The highly tumorigenic cells CSCs share certain properties with normal stem cells, but have accumulated cancer causing mutations clearly making them abnormal. It is now widely appreciated that may current therapies fail to effectively target the CSC population, and thus the CSCs mediate recurrence of disease after treatment. New drugs that target CSCs to kill them or cause them to differentiate into less dangerous, non-tumorigenic cells have the potential to provide significant benefit to patients and to dramatically improve cancer treatment. This project is focused on developing a new anti-cancer drug that has been shown to effectively block CSC self renewal in a variety of common types of cancer. New therapeutic agents that are effective in targeting cancer stem cells may reduce metastases and relapse after treatment thus providing a chance for improved long term survival of cancer patients. In the first phase of the project, we will complete the manufacturing of the drug for subsequent use in clinical trial and also execute safety studies that are necessary before initiating clinical trials. Next, we will test the safety of the drug in patients in Phase 1 clinical trials. Lastly, we will determine the efficacy in breast cancer patients in Phase 2 trials. This project will utilize innovative clinical trial designs to identify the patient populations most likely to benefit from treatment with this new treatment. We intend to focus our clinical testing on an important subset of women with breast cancer for whom effective therapies are currently lacking. Our project is a unique partnership of industry and academic researchers and clinicians dedicated to bringing new medicines to patients most in need of effective therapy.
Statement of Benefit to California: 
This project will benefit the state of California and its citizens in several significant ways. The goal of the work funded by this grant is to develop a new cancer treatment. This agent attacks cancer stem cells - the most dangerous type of tumor cells because they have the unique ability to resist many current therapies and re-grow and metastasize to distant sites in the body. The funds from this study will be used to support innovative drug development and clinical testing in women with advanced breast cancer. Thus, this therapy will benefit cancer patients with a critical need for new treatment options. We have observed that agents that reduce cancer stem cells in tumors also inhibit the spread of metastatic disease. Patients with advanced cancers which have disseminated to distant organs typically require high cost hospital stays. Our new treatment is intended to ameliorate the incidence and relapse of metastatic cancer, thus reducing the requirement for hospitalization and associated specialized care for this class of advanced cancer patients. In addition to the medical benefits of this project, funds from this grant will create and maintain high quality jobs in the state of California. California has been a recognized leader in biomedical research over the past several decades because of its excellent academic institutions and innovative companies attracting researchers from all over the country and the world. Many companies have made significant investments in establishing research facilities in California. Thus, biomedical research generates significant economic activity in the state. Continued leadership in the life sciences field relies on being at the forefront of cutting edge fields that are focal points of research interest and investment. Novel anti-cancer therapeutics, in general, and cancer stem cell-based therapeutic approaches, in particular, are excellent examples of important and innovative directions in drug development. CIRM will provide an important source of funding to support cancer stem cell therapeutics which hold the promise of becoming breakthrough medications in cancer treatment.
Progress Report: 
  • Our project is focused on developing a new anti-cancer drug that has been shown to effectively block cancer stem cell (CSC) self renewal in a variety of major tumor types. During the reporting period our group made significant advances on several fronts in advancing our novel stem cell directed therapy toward clinical development. In particular, we have associated cancer causing mutations in breast cancer in the molecular target of our therapeutic and shown that tumors bearing this type of mutation are exquisitely sensitive to our treatment. Based on this discovery, we have developed methodologies and reagents to identify patients who are most likely to benefit from treatment with our agent. Thus, this project is an excellent example of how "personalized medicine" is becoming a reality in cancer drug development. Furthermore, our results highlight the promise of targeting inappropriate activation of stem cell pathways as new strategy in cancer treatment.
  • During the reporting period we have assembled an experienced team of scientists and clinicians at our institution and also at collaborating institutions to execute the pre-clinical and clinical development of our new anti-cancer treatment. We have developed a detailed clinical strategy which involves a close collaboration between academic medical centers and the biotech industry. We have planned a series of clinical trials which will test the safety and efficacy of our anti-cancer drug and also test our hypothesis regarding selecting patients most likely to respond to treatment. This trials will take place at multiple sites including several in California.
  • In addition, we have made tremendous and tangible progress in advancing our therapeutic toward clinical testing. These steps include the completion of GMP manufacture of the drug for IND-enabling safety studies and for use in subsequent Phase 1 clinical trials and the initiation of IND-enabling safety studies.

Combinatorial Chemistry Approaches to Develop LIgands against Leukemia Stem Cells

Funding Type: 
New Faculty I
Grant Number: 
RN1-00561
ICOC Funds Committed: 
$2 392 397
Disease Focus: 
Blood Cancer
Cancer
Stem Cell Use: 
Adult Stem Cell
Cancer Stem Cell
Cell Line Generation: 
Cancer Stem Cell
oldStatus: 
Active
Public Abstract: 
Various cells and organs in the human body originate from a small group of primitive cells called stem cells. Human cancer cells were also recently found to arise from a group of special stem cells, called cancer stem cells (CSCs). At present, cancer that has spread throughout the body (metastasized) is difficult to treat, and survival rates are low. One major reason for therapeutic failure is that CSCs are relatively resistant to current cancer treatments. Although most mature cancer cells are killed by treatment, resistant CSCs will survive to regenerate additional cancer cells and cause a recurrence of cancer. As opposed to other human stem cells, CSCs have their own unique molecules on their cell surface. This project aims to develop agents that specifically target the unique cell surface molecules of CSCs. These agents will have the potential to eradicate cancer from the very root, i.e., from the stem cells (CSCs) that produce mature cancer cells. In this project, we will develop agents that specifically target leukemia stem cells to determine the feasibility of our approach. Leukemia is the fourth most common cause of cancer death in males and the fifth in females. If our approach is successful, we can use the same approach for other cancer types. To develop these specific agents, we will screen a library of billions of molecules to identify those that specifically target the unique cell surface molecules of leukemia stem cells (LSCs). After we identify these specific molecules, we will optimize their structure to increase their specific binding to LSCs. Specific binding to LSCs is crucial, as the optimized molecules will be able to uniquely kill LSCs and spare normal blood cells. Many leukemia patients need stem cell transplantation during treatment. There are two approaches to harvesting stem cells for transplantation: those harvested from patients themselves and those harvested from healthy donors. Stem cells harvested from healthy donors need to genetically match patients’ cells. Otherwise, these transplanted cells from the donor recognize the recipient’s (host or patient) cells as non-self cells and attack these cells. This response leads to a serious disease called graft-versus-host disease (GVHD). It is often difficult to find matched donors. Stem cells harvested from patients are usually not used for the treatment of acute leukemia because they are contaminated with LSCs that will lead to recurrence of leukemia after transplantation. If this project is successful, the targeting agents developed in this project can be used to eliminate the contaminating LSCs and decrease the leukemia recurrence after transplantation.
Statement of Benefit to California: 
Acute leukemia is the sixth most common cause of cancer death in males and females in California. The outcome for acute leukemia is poor and over 70% of patients will die from this disease. This project aims to develop therapeutic agents that specifically target leukemia stem cells and therefore eradicate leukemia from its root. These agents can also be used for stem cell transplantation. Many leukemia patients need stem cell transplantation during treatment. There are two approaches to harvesting stem cells for transplantation: those harvested from patients themselves and those harvested from healthy donors. Stem cells harvested from healthy donors need to genetically match patients’ cells. Otherwise, these transplanted cells from the donor recognize the recipient’s (host or patient) cells as non-self cells and attack these cells. This response leads to a serious disease called graft-versus-host disease (GVHD). It is often difficult to find matched donors. This is especially true in California because of the genetically diversified population. Stem cells harvested from patients are usually not used because they are contaminated with leukemia stem cells that will lead to recurrence of leukemia after transplantation. If this project is successful, the targeting agents developed in this project can be used to eliminate the contaminated leukemia cells and decrease the likelihood of leukemia recurrence after transplantation. The ligands developed in this project can be used for targeted therapy for leukemia. Since no such ligands have been identified so far that specifically target leukemia stem cells, these ligands can be patented and eventually commercialized. This may have huge financial benefits to California. If this project is successful, the same approach can be used to treat other cancers and for the development of more commercialized drugs. If this grant is funded, it will secure my career as a physician-scientist in stem cell and cancer research. The physician-scientist is a diminishing breed in that it is difficult for physicians to do research while meeting the huge demands of the clinic. However, there is a huge gap between basic research and clinical applications. This gap is in part traced to the fact that it is difficult to find researchers who know and can integrate clinical needs with basic research. I consider myself a promising physician-scientist who has received extensive, rigorous and systematic training in medical science and basic research ([REDACTED]). If this grant is funded, I will not only carry out this important research, but this will also give me protected time for this research.
Progress Report: 
  • Human cancer cells were recently found to arise from a group of special stem cells, called cancer stem cells (CSCs). At present, cancer that has spread throughout the body (metastasized) is difficult to treat, and survival rates are low. One major reason for therapeutic failure is that CSCs are relatively resistant to current cancer treatments. Although most cancer cells are killed by treatment, resistant CSCs will survive to regenerate additional cancer cells and cause a recurrence of cancer. As opposed to other human stem cells, CSCs may have some unique molecules that can be targeted for cancer treatment. This project is to use such technologies as our patented one-bead one-compound technology (OBOC) to develop small molecules that can specifically target cancer stem cells. With OBOC, trillions copies of small molecules are synthesized in tiny beads around 90 microns. During development, millions of molecules can be screened against cancer stem cells with hours to days. So far, we have identified six molecules that target CSC. Currently, we are optimizing these molecules to increase their efficiency of these molecules on CSC. Once fully developed, these molecules will have the potential to eradicate cancer from the very root, i.e., from the stem cells (CSCs) that produce mature cancer cells.
  • Acute myeloid leukemia is a group of serious blood malignant diseases. The treatment outcome is poor, in large part, to the fact that a small group of cells named leukemia stem cells can survive treatment, regenerate more leukemic cells and cause recurrence. This project aims to improve the treatment outcomes of acute leukemia by eradicating leukemia stem cells. During the previous two years, we identified several small molecules that can specifically bind to leukemia stem cells. Over the last one year, we determined that one of these small molecules has the potential to work like a “smart missile” to guide the delivery of chemotherapeutic drugs to leukemia stem cells. More specifically, we linked this small molecule on the surface of nanoparticles that are small particles with the size of about 1/100th of one micron (much smaller than the width of a human hair). Inside of these nanoparticles, we can load chemotherapeutic drugs. We found that our small molecules can specifically attach the nanoparticles to leukemia stem cells, and deliver the drug load to the inside of the cells. Therefore, these “smart” nanoparticles can potentially target leukemia stem cells, and eradicate leukemia from the very root. Furthermore, chemotherapeutic drugs formulated in these nanoparticles are less toxic, suggesting that high-dose chemotherapeutic drugs can be given to patients to treat leukemia without increasing the horrendous toxicity associated with regular chemotherapy.
  • Acute myeloid leukemia is a group of serious blood malignant diseases. The treatment outcome is poor, in large part, due to the fact that a small group of cells named leukemia stem cells can survive treatment, regenerate more leukemic cells and cause recurrence. This project aims to improve the treatment outcomes of acute leukemia by eradicating leukemia stem cells. We identified one molecule that can specifically bind to leukemia stem cells. We also developed nanoparticles that are small particles with the size of about 1/100th of one micron (much smaller than the width of a human hair). Inside of these nanoparticles, we can load chemotherapeutic drugs, such as daunorubicin that is one of the two drugs used for the upfront treatment of acute leukemia. When we attached the stem cell-targeting molecules on the surface of nanoparticles, these nanoparticles work like “small missiles” that can seek and delivery daunorubicin into leukemia stem cells. We have shown that these “smart” nanoparticle can delivery chemotherapeutic drug daunorubicin to leukemia cells directly isolated from clinical patient specimens, and kills these cells more efficient that the regular nanoparticles. Therefore, these “smart” nanoparticles can potentially target leukemia stem cells, and eradicate leukemia from the very root. Furthermore, chemotherapeutic drugs formulated in these nanoparticles are less toxic, suggesting that high-dose chemotherapeutic drugs can be given to patients to treat leukemia without increasing the horrendous toxicity associated with regular chemotherapy.
  • Acute myeloid leukemia (AML) is the most common acute leukemia in adults and a very serious disease. Most AML cells arise from a group of special stem cells, named leukemia stem cells (LSCs). One major reason for treatment failure is that LSCs are relatively resistant to current treatments. Although most leukemia cells are killed by treatment, resistant LSCs will survive to regenerate additional leukemia cells and cause a recurrence of leukemia. Recently, we have developed a small molecule that can recognize and bind to AML LSCs. We have also developed tiny particles named nanomicelles. These nanomicelles have a size of about 1-2/100th of one micron (one millionth of a meter), and can be loaded with chemotherapy drug called daunorubicin that can kill LSCs. In this project, we will coat the drug-loaded nanomicelles with small molecules that specifically bind and kill LSCs. In patient’s body, these drug-loaded nanomicelles will work like “smart bombs”, and deliver a high concentration of daunorubicin to kill LSCs. Over the last one year, we found that these LSC-targeting nanomicelles could target and kill LSC more efficiently that free daunorubicin or nanomicelles that do not target LSC. We also found that, compared to free daunorubicin commonly used in the treatment of AML now, daunorubicin in nanomicelles could raise the blood daunorubicin concentration by more than 20 times. This is clinically significant as leukemia cells and LSC are located inside blood vessels and bone, and have direct contact with blood. Therefore, increase in blood daunorubicin concentration may represent more efficiency in killing leukemia and LSC.
  • Acute myeloid leukemia (AML) is the most common acute leukemia in adults and a very serious disease. Most AML cells arise from a group of special stem cells, named leukemia stem cells (LSCs). One major reason for treatment failure is that LSCs are relatively resistant to current treatments. Although most leukemia cells are killed by treatment, resistant LSCs will survive to regenerate additional leukemia cells and cause a recurrence of leukemia. Recently, we have developed a small molecule that can recognize and bind to AML LSCs. We have also developed tiny particles named nanomicelles. These nanomicelles have a size of about 1-2/100th of one micron (one millionth of a meter), and can be loaded with chemotherapy drug called daunorubicin that can kill LSCs. In this project, we will coat the drug-loaded nanomicelles with small molecules that specifically bind and kill LSCs. In patient’s body, these drug-loaded nanomicelles will work like “smart bombs”, and deliver a high concentration of daunorubicin to kill LSCs. Over the last one year, we found that daunorubicin-loaded nanomicelles could significantly increase the blood daunorubicin concentration by 20-35 times after intravenous administration. This is clinically significant as leukemia cells and leukemia stem cells are mainly located inside blood vessels. Therefore, increase in blood daunorubicin concentration by nanomicelles means leukemia and leukemia stem cells are exposed to 20-35 times more daunorubicin than regular chemotherapy. one of the major toxicity of daunorubicin is toxicity to the heart. As acute myeloid leukemia usually occurs in elderly patients, many of them already have heart diseases that prevent them from receiving the most effective chemotherapeutic drug daunorubicin. We found that, when compared to the standard daunorubicin, daunorubicin in nanomicelle has 3-5 folds less toxicity to the heart. In addition, the toxicity to other vital organs, such as liver and spleen, is significantly decreased. Compared to the standard daunorubicin, daunorubicin in nanomicelles dramatically increases the drug efficacy in killing cancer cells and prolonging the survival in animal models.

Mechanisms of Hematopoietic stem cell Specification and Self-Renewal

Funding Type: 
New Faculty I
Grant Number: 
RN1-00557
ICOC Funds Committed: 
$2 286 900
Disease Focus: 
Blood Cancer
Cancer
Anemia
Stem Cell Use: 
Adult Stem Cell
Embryonic Stem Cell
oldStatus: 
Active
Public Abstract: 
During an individual’s lifetime, blood-forming cells in the bone marrow called hematopoietic stem cells (HSCs) supply all the red and white blood cells needed to sustain life. These blood stem cells are unique because they can make an identical copy of themselves (self-renew). Disorders of the blood system can be terminal, but such diseases may be cured when patients are treated with a bone marrow transplant. Unfortunately, bone marrow is in short supply due to limited availability of donors, and it is not yet possible to expand HSCs outside of the human body; HSCs that are removed from their native environment, or niche, rapidly lose their ability to self-renew and thus cannot sustain hematopoiesis in a transplant recipient. Furthermore, attempts to make blood stem cells from embryonic stem cells (ESCs) have also proved unsuccessful to date because these “tailored HSCs” are defective in self-renewal as well. These problems suggest that our understanding of the biology of HSCs is not sufficient to foster their maintenance or generation. To address this issue, we propose to study hematopoietic stem cells in the context of mammalian development; the entire complement of a person’s HSCs is made in a very short time window during the first trimester of pregnancy. By increasing our understanding of how HSCs are made and acquire self-renewal in vivo, we hope to develop better methods of generating HSCs in vitro and learn to provide the missing cues to coax them into becoming fully functional, self-renewing hematopoietic stem cells. Specifically, we plan to investigate how the fate decision that delineates blood cells from their embryonic precursor, called specification, is maintained at the molecular level. Second, we are interested in what cell type human HSCs descend from so as to understand what precursor to look for when attempting to differentiate ESCs into blood stem cells. Finally, we plan to apply molecular analyses to the property of self-renewal by looking at cell populations that cover a spectrum with regards to self-renewal: HSCs, cultured HSCs (not self-renewing), HSC precursors (not self-renewing), and ESCs differentiated to non-self-renewing HSCs. These comparisons will help define the molecular regulation of self-renewal, and place ESC-derived progenitors on the spectrum of self-renewal. Through these studies, we hope to better understand blood stem cells as they are made and maintained during human development with the ultimate goal to provide wider access to stem cell-based therapies.
Statement of Benefit to California: 
Funding of research to understand hematopoietic stem cell (HSC) biology offers rewards beyond the pursuit of knowledge. HSCs are responsible for providing all of the blood cells in the body, including both red cells that carry oxygen and white cells that mediate immunity. Inherited disorders affecting HSCs and their progeny are responsible for diseases such as sickle cell anemia, Severe Combined Immunity Disorder (SCID), and leukemia; these devastating ailments change the lives of thousands of people in California every year, and currently most are incurable without a bone marrow or cord blood transplant. Due to the limited availability of donors, other alternatives, such as differentiating embryonic stem cells (ESCs) into HSCs, are being explored. One critical fault of ESC-derived progenitors is their inability to “self-renew”, i.e. produce more of themselves, thus eliminating their usefulness for transplantation. However, a deeper understanding of the developmental and molecular processes that create functional HSCs that can self-renew may ultimately make the goal of deriving HSCs from ESCs attainable. Research into the mechanisms of self-renewal may also improve treatments of cancers such as leukemia, as these diseases are a function of over-proliferation of cells caused by uncontrolled self-renewal; targeting genes or proteins involved in abnormal self-renewal programs may provide more specific cancer fighting drugs, and would likely foster collaborations with biotechnology companies. Furthermore, as all stem cells in the body have the ability to self-renew, a clear understanding of self-renewal mechanisms will benefit all stem cell research, and could have a positive effect in a wide range of biomedical specialties.
Progress Report: 
  • The goal of this grant is to investigate the cell intrinsic mechanisms that govern hematopoietic stem cell specification and self-renewal. During the second year of this award, we have further elucidated the regulatory mechanisms that dictate hematopoietic fate specification by validating the target genes that Scl/tal1 activates and represses in vivo (Aim 1). We have also shown that loss of Scl results not only results in loss of all blood cells, but also causes defective arterio-venous identity that precludes generation of hemogenic endothelium and hematopoietic stem cells. We have defined the phenotype of hemogenic endothelium and emerging HSCs in both mouse and human embryos (Aim 2), and identified novel markers that can be used to isolate developing HSCs at distinct stages, as well as to purify functional HSCs further (Aim 3). We have also established an inducible lentiviral based expression system that will now be used to test functionally candidate HSC regulators that were identified by comparing gene expression profiles between freshly isolated HSCs and dysfunctional HSCs that were expanded in culture or generated from human ES cells. We hope that these studies will provide better understanding of the key regulatory mechanisms that govern HSC properties, and ultimately lead to development of improved methods for generation of functional HSCs in culture.
  • Our work has focused on defining mechanisms that govern the specification and self-renewal of hematopoietic stem cells during mouse and human development. Using gene targeted mouse ES cells and mouse embryos, we defined the transcriptional programs that are regulated by Scl, the master regulator for blood formation. We discovered that Scl not only establishes the transcriptional programs that are critical for specifying hemogenic endothelium and hematopoietic stem cells, but it also represses heart development. Strikingly, in the absence of Scl, hemogenic endothelium in embryonic hematopoietic tissues becomes converted to cardiogenic fate, and gives rise to fully functional, beating cardiomyocytes.
  • In order to define the key programs that distinguish self-renewing HSCs from their downstream progenitors or the compromised HSPCs (hematopoietic stem/progenitor cells) that were generated in vitro, we performed microarray analysis for human phenotypic HSCs from various sources. We identified novel markers for human HSCs that can be used to purify transplantable HSCs to a higher purity. We have identified key molecular defects in HSCs that are expanded in culture, or generated from human ES cells. We have further validated that dysregulation of certain Hox genes is a major bottleneck for generating functional HSCs from human ES cells. Future studies are focused on establishing methods that would allow correction of the compromised HSC regulatory networks in cultured HSCs.
  • We have defined key regulatory mechanisms that are required for generation and maintenance of blood forming stem cells. We showed that transcription factor Scl is critical for specifying hemogenic endothelium from where blood stem cells emerge, and moreover, we discovered and unexpected repressive function for Scl to suppress cardiomyogenesis; in the absence of Scl, the blood vessels in start to generate beating cardiomyocytes. We have also identified factors that are critical for blood stem cells to maintain the unique properties: to self-renew (make more of themselves) and engraft (interact with the niche cells that support them). We will now continue to define how these key regulators act so that we can design better strategies to generate blood stem cells as well as heart muscle precursors for therapeutic applications.
  • The goal of this grant was to define mechanisms that govern blood stem cell specification and self-renewal. We have completed the studies on hematopoietic fate specification by defining how Scl/tal1 establishes hemogenic endothelium. We documented that, in addition to Scl’s critical function in activating blood cell regulators, Scl also has to repress heart factors to prevent the misspecification of blood precursors to heart muscle. We documented that Scl controls blood and heart regulators through enhancers that have been primed for activation prior to Scl action (Aim 1). We identified a new surface marker that is expressed in hemogenic endothelium and blood forming cells in the yolk sac (Lyve1), which provides new tools to investigate the origin of blood stem and progenitor cells during development (Aim 2). We identified GPI-80 as a novel marker for transplantable blood stem cells during human fetal development (Aim 2, 3). Taking advantage of this new marker for blood stem cells, we narrowed down the critical defects in the dysfunctional blood precursors that are generated from human ES cells, or expanded in culture from fetal liver blood stem cells (Aim 3). We showed that the inability to induce HOXA cluster genes and other novel blood stem cell regulators that cannot be sustained in culture hinder the generation of blood stem cells from pluripotent cells, and further validated these novel regulators using lentiviral knockdown and overexpression. These findings will now be used to develop novel strategies to generate blood stem cells in culture.

Epigenetics in cancer stem cell initiation and clinical outcome prediction

Funding Type: 
New Faculty I
Grant Number: 
RN1-00550
ICOC Funds Committed: 
$3 063 450
Disease Focus: 
Solid Tumor
Cancer
Stem Cell Use: 
Embryonic Stem Cell
oldStatus: 
Active
Public Abstract: 
Cancer is responsible for approximately 25% of all deaths in the US and other developed countries. For women, breast and lung cancers and for men, cancers of prostate and lung are the most prevalent and the most common cause of deaths from cancer. While a large number of treatment modalities such as surgery, chemotherapy, radiation therapy, etc. have been developed, we still are far from finding a cure for most cancers. So, more research is needed to understand the basic processes that are subverted by cancer cells to gain a proliferative advantage. In addition, cancer patients show a great deal of heterogeneity in the course and outcome of the disease. Therefore it is important to be able to predict the clinical outcome of the patients so that appropriate therapies can be administered. Clinical outcome prediction is based generally on tumor burden and degree of spread with additional information provided by histological type and patient demographics. However, patients with similar tumor characteristics still show heterogeneity in the course and outcome of disease. Thus, accurate sub-classification of patients with similar clinical outcomes is required for development of more efficacious therapies. One important molecular process that is altered in cancer is the epigenetic regulation of gene expression. In humans, DNA is tightly wrapped around a core of proteins called histones to form chromatin—the physiologically relevant form of the genome. The histones can be modified by small chemical molecules which can affect the structure of chromatin, allowing for a level of control on gene expression. The patterns of occurrences of the histone modifications throughout chromatin are highly regulated and affect all molecular processes that are based on DNA. This information which is heritable but not encoded in the sequence of DNA is referred to as ‘epigenetics.’ A challenge in biology is to understand how histone modifications which can number to more than 150, contribute to normal gene regulation and how their alterations contribute to development of cancer stem cells. These cells are thought to be responsible for maintain the bulk of the tumor and need to be completely eradicated if we were to cure a given cancer. By studying primary cancer tissues and viruses that cause tumor, we have found that one histone modification plays a critical role in transforming a normal call to a tumor cell, potentially generating a cancer stem cell. We have found that he same histone modifications can be used as a biomarker to predict clinical outcome of patients. We now propose to study this process in more depth, discover other important histone modifications that contribute to cancer development and progression and use this knowledge to develop standard, simple and robust assays for predicting clinical outcome of cancer patients. Our work may also lead to identification important molecules that can be targeted for cancer therapy.
Statement of Benefit to California: 
Cancer is a devastating disease that is becoming more prevalent as the population ages. While scientists have developed a general framework of how cancer initiates, there remains significant gaps in our knowledge about how cancer arises from a normal cell. One difficulty with studying cancer is the heterogeneity in the types of cells that exist within a given cancer tissue. Some of these cells have recently been shown to have stem cell-like properties and when isolated can reestablish the original tumor. These ‘cancer stem cells’ are thought to be responsible for maintaining the bulk of the tumor and need to be completely eradicated if we were to cure a given cancer. There is also a great deal of differences in the course and outcome of cancers with seemingly similar attributes, making application of appropriate therapies difficult. Our proposal aims to understand some of the basic processes that may contribute to development of cancer stem cells and to use this knowledge to develop proper clinical tests for prediction of cancer patients’ clinical outcome. This would be beneficial for people of California as it may lead to personalization of cancer therapy. Our work may also lead to identification of critical molecules that need to be therapeutically targeted to improve rates of cancer therapy. Identification of such molecules may lead to innovative discoveries and patents that may be exploited by the biotech industry in California, and thereby improve the economy of California as well.
Progress Report: 
  • Cancer is a genetic disease but epigenetic processes also contribute to cancer development and progression. Epigenetic processes include molecular pathways that modify the DNA itself or the proteins that are associated with DNA (i.e. histones), thereby affecting how the genetic information is used to maintain cellular states. Cancer cells exploit the normal epigenetic processes to their advantage to support uncontrolled growth and evade host defense mechanisms. Our proposal aims to understand the epigenetic requirements for cancer initiation and progression and how they can be used to develop prognostic assays that can predict cancer clinical outcome or response to therapeutics. We have made significant progress in all of our aims. We are discovering new basic principles governing epigenetic processes in human embryonic stem cells versus more differentiated cell types and understanding how these principles are implemented and regulated by the different types of cells. We have also shown that epigenetics can be used for cancer prognostic purposes as well as for prediction of response to specific cancer chemotherapeutics.
  • The goal of this proposal is to understand the dynamics of chromatin in various cellular differentiation states and how alteration of this dynamic may contribute to cancer development and progression. Our major findings are outlined as follows and further elaborated below.
  • 1) Among the various acetylation sites of histones, H3K18ac has a unique distribution in hESCs and is specifically affected during oncogenic transformation. As part of a screen to discover upstream regulators of this modification site (described in previous reports), we identified a non-coding RNA that is required for maintenance of H3K18ac, expression of SOX2 and its target genes, and growth of hESCs.
  • 2) We have discovered a highly novel and unanticipated role for histone acetylation. We have found that global histone acetylation and deacetylation coupled with flux of acetic acid in and out of the cells acts as a buffering system for regulation of intracellular pH. This phenomenon is a fundamental biological process and occurs in hESCs, cancer cells as well as normal differentiated human cells. (A paper reporting this finding is currently being reviewed at Nature.)
  • 3) We are continuing our efforts on the role of linker histone H1.5 in transcriptional regulation of terminally differentiated cells vs hESCs. This is a continuation project from a CIRM SEED grant. A manuscript on this project was submitted to Cell but was not accepted. We have performed additional experiments and preparing a new manuscript.
  • I. A non-coding RNA is required for hESC growth.
  • This aim was designed to understand how the global levels of histone modifications are regulated. As reported in previous progress reports, we carried out a kinase screen in which ~800 kinases were knocked down individually using siRNAs and the levels of two histone modifications were examined. We validated the top hits which were reported last year. The most significant effect on histone modifications, especially H3K18ac, was observed in knockdown of TPRXL (tetra-peptide repeat homeobox-like). We found that knockdown of TPRXL causes ~50-70% reductions in the global levels of H3K18ac specifically, suggesting that TPRXL is required for maintenance of a portion of H3K18ac throughout the genome. It turned out that the identification of TPRXL was a fortuitous finding. TPRXL is not a kinase but has been mis-annotated as a kinase in certain databases, hence its inclusion in the kinase siRNA library. TPRXL is a member of the TPRX homeobox gene family and is designated as a non-functional retrotransposed pseudogene (Booth and Holland, 2007). It is suggested that TPRXL was generated by reverse transcription of TPRX1 mRNA which was then integrated near an enhancer active in placenta. Consistently, TPRXL has a very high expression in placenta compared to other tissues. Subsequent to integration, TPRXL sequence has diverged from that of TPRX1 in an unusual way. In certain regions, such as over the homebox domain, TPRXL has retained 81% nucleotide identity but only 66% amino acid identity compared to TPRX1 (Booth and Holland, 2007). Despite its designation, TPRXL could possibly be a functional retrogene as it is transcribed and contains two potential open reading frames (ORFs). One ORF can code for a short protein (139 a.a.) that would contain the homeodomain and a polyglutamine stretch. Another ORF codes for a longer protein that would consist mostly of a long polyserine/proline stretch.
  • Epigenetic processes include molecular pathways that modify the DNA or the proteins that are associated with DNA (i.e. histones), thereby affecting how the genetic information is used to maintain cellular states. Thus epigenetics plays an important role in normal biology and disease. When deregulated, epigenetic processes could contribute to disease development and progression. Since embryonic stem cells (ESCs) and cancer cells share the capacity to divide indefinitely, our proposal aims to understand the epigenetic requirements for such capacity. We have found that a particular epigenetic process, which we previously linked to cancer progression, may contribute to regulation of DNA replication in human ESCs. We have also discovered how epigenetic processes could in novel ways exert control over metabolic state of the cell. Finally, we have discovered how chromatin – the complex of DNA and histones – at specific sets of gene families is differentially compacted in differentiated cell types vs. human ESCs. Altogether, we are providing novel insights into the functions of various epigenetic processes and how they may differ in stem cells vs. other normal and cancer cell types.
  • Epigenetic processes include molecular pathways that modify the DNA or the proteins that are associated with DNA (i.e. histones), thereby affecting how the genetic information is read. Epigenetics plays an important role in normal biology and disease because it can affect how genes are turned on and off. Deregulation of epigenetic processes indeed contributes to disease development and progression including cancer. Our proposal has aimed to understand how the epigenome exerts its control over gene regulation. We have found that in addition to gene regulation, on epigenetic process is unexpectedly linked to control of cellular physiology. We have shown that dynamic acetylation of histone proteins regulates intracellular level of acidity, providing an unprecedented function for the epigenome. Our data provides plausible explanations for why ESCs contain in general higher levels of histone acetylation than other cell types and why certain cancers with low levels of histone acetylation are more aggressive. In a separate study, we have found that replication of DNA in ESCs is associated with a unique epigenetic signature that is not found in differentiated cells or other rapidly dividing cell types such as cancer. We have proposed that this molecular property of replication in ESCs may be an important determinant of continual cell division without malignancy, fundamentally distinguishing ESC-specific from cancer-like cell division. Altogether, we are providing novel insights into the functions of various epigenetic processes and how they may be similar or differ in stem cells vs. other normal and cancer cell types.

Mechanisms Underlying the Responses of Normal and Cancer Stem Cells to Environmental and Therapeutic Insults

Funding Type: 
New Faculty II
Grant Number: 
RN2-00934
ICOC Funds Committed: 
$2 274 368
Disease Focus: 
Blood Cancer
Cancer
Trauma
oldStatus: 
Active
Public Abstract: 
Adult stem cells play an essential role in the maintenance of tissue homeostasis. Environmental and therapeutic insults leading to DNA damage dramatically impact stem cell functions and can lead to organ failure or cancer development. Yet little is known about the mechanisms by which adult stem cells respond to such insults by repairing their damaged DNA and resuming normal cellular functions. The blood (hematopoietic) system provides a unique experimental model to investigate the behaviors of specific cell populations. Our objective is to use defined subsets of mouse hematopoietic stem cells (HSCs) and myeloid progenitor cells to investigate how they respond to environmental and therapeutic insults by either repairing damaged DNA and restoring normal functions; accumulating DNA damage and developing cancer; or undergoing programmed cell death (apoptosis) and leading to organ failure. These findings will provide new insights into the fundamental mechanisms that regulate stem cell functions in normal tissues, and a better understanding of their deregulation during cancer development. Such information will identify molecular targets to prevent therapy-related organ damage or secondary cancers. These are severe complications associated with current cancer treatments and are among the leading causes of death worldwide. Originally discovered in blood cancers (leukemia), cancer stem cells (CSCs) have now been recognized in a variety of solid tumors. CSCs represent a subset of the tumor population that has stem cell-like characteristics and the capacity for self-renewal. CSCs result from the transformation of either stem or progenitor cells, which then generate the bulk of the cancer cells. Recent evidence indicates that CSCs are not efficiently killed by current therapies and that CSC persistence could be responsible for disease maintenance and cancer recurrence. Developing interventions that will specifically target CSCs is, therefore, an appealing strategy for improving cancer treatment, which is dependent on understanding how they escape normal regulatory mechanisms and become malignant. Few mouse models of human cancer are currently available in which the CSC population has been identified and purified. This is an essential prerequisite for identifying pathways and molecules amenable to interventional therapies in humans. We have previously developed a mouse model of human leukemia in which we have identified the CSC population as arising from the HSC compartment. We will use this model to understand how deregulations in apoptosis and DNA repair processes contribute to CSC formation and function during disease development. These results will provide new insights into the pathways that distinguish CSCs from normal stem cells and identify ways to prevent their transformation. Such information will be used to design novel and much-needed therapies that will specifically target CSCs while sparing normal stem cells.
Statement of Benefit to California: 
This application investigates how environmental and therapeutic insults leading to DNA damage impact stem cell functions and can lead to organ failure or cancer development. The approach is to study how specific population of blood (hematopoietic) stem, progenitor, and mature cells respond to DNA damaging agents and chose a specific cellular outcome. Such information could identify molecular pathways that are available for interventional therapies to prevent end-organ damage in patients who are treated for a primary cancer and reduce the risk of a subsequent therapy-induced cancer. These are severe complications associated with current mutagenic cancer treatments (radiation or chemotherapeutic agents) that comprise a substantial public health problem in California and in the rest of the developed world. The hematopoietic system is the first to fail following cancer treatment and the formation of therapy-related blood cancer (leukemia) is a common event. The development of novel approaches to prevent therapy-related leukemia will, therefore, directly benefit the health of the Californian population regardless of the type of primary cancer. This application also investigates a novel paradigm in cancer research, namely the role of cancer stem cells (CSCs) in the initiation, progression and maintenance of human cancer. The approach is to study how dysregulations in important cancer-associated pathways (apoptosis and DNA repair processes) contribute to CSC aberrant properties using one of the few established mouse model of human cancer where the CSC population has already been identified. Leukemia, the disease type investigated in this application, has been the subject of many landmark discoveries of basic principles in cancer research that have then been shown to be applicable to a broad range of other cancer types. Accordingly, this research should benefit the people of California in at least two ways. First, the information gained about the properties of CSCs should improve the ability of our physicians and scientists to design, develop and evaluate the efficacy of innovative therapies to target these rare disease-initiating cells for death. This would place Californian cancer research at the forefront of translational science. Second, an average of 11.55 out of 100,000 Californian inhabitants are diagnosed with primary leukemia each year. Thus, in California, leukemia occurs at approximately the same frequency as brain, liver and endocrine cancers. As is true for many types of cancer, most cases of leukemia occur in older adults. At this time, the only treatment that can cure leukemia is allogeneic stem cell transplantation, which is a high-risk and expensive procedure that is most successful in younger patients. The development of novel and safe curative therapies for leukemia would, therefore, particularly benefit the health of our senior population and the economy of the state of California by realizing savings in the healthcare sector.
Progress Report: 
  • Escape from apoptosis and increased genomic instability resulting from defective DNA repair processes are often associated with cancer development, aging and stem cell defects. Adult stem cells play an essential role in the maintenance of normal tissue. Removal of superfluous, damaged and/or dangerous cells is a critical process to maintain tissue homeostasis and protect against malignancy. Yet much remains to be learned about the mechanisms by which normal stem and progenitor cells respond to environmental and therapeutic genotoxic insults. Here, we have used the hematopoietic system as a model to investigate how cancer-associated mutations affect the behaviors of specific stem and progenitor cell populations. Our work during the first year of the CIRM New Faculty award has revealed the differential use of DNA double-strand break repair pathways in quiescent and proliferative hematopoietic stem cells (HSCs), which has clear implications for human health. Most adult stem cell populations, including HSCs, remain in a largely quiescent (G0), or resting, cell cycle state. This quiescent status is widely considered to be an essential protective mechanism stem cells use to minimize endogenous stress caused by cellular respiration and DNA replication. However, our studies demonstrate that quiescence may also have detrimental and mutagenic effects. We found both quiescent and proliferating HSCs to be similarly protected from DNA damaging genotoxic insults due to the expression and activation of cell type specific protective mechanisms. We demonstrate that both quiescent and proliferating HSCs resolve DNA damage with similar efficiencies but use different repair pathways. Quiescent HSCs preferentially utilize nonhomologous end joining (NHEJ) - an error-prone DNA repair mechanism - while proliferating HSCs essentially use homologous recombination (HR) - a high-fidelity DNA repair mechanism. Furthermore, we show that NHEJ-mediated repair in HSCs is associated with acquisition of genomic rearrangements. These findings suggest that the quiescent status of HSCs can, on one hand, be protective by limiting cell-intrinsic stresses but, on the other hand, be detrimental by forcing HSCs to repair damaged DNA with an error-prone mechanism that can generate mutations and eventually cause hematological malignancies. Our results have broad implications for cancer development and provide the beginning of a molecular understanding of why HSCs, despite being protected, are more likely than other cells in the hematopoietic system (i.e., myeloid progenitors) to become transformed. They also partially explain the loss of function occurring in HSCs with age, as it is likely that over a lifetime HSCs have acquired and accumulated numerous NHEJ-mediated mutations that hinder their cellular performance. Finally, our findings may have direct clinical applications for minimizing secondary cancer development. Many solid tumors and hematological malignancies are currently treated with DNA damaging agents, which may result in therapy-induced myeloid leukemia. Our results suggest that it might be beneficial to induce HSCs to cycle before initiating treatment, to avoid inadvertently mutating the patient's own HSCs by forcing them to undergo DNA repair using an error-prone mutagenic mechanism.
  • Our work during the second year of the CIRM New Faculty award has lead to the discovery of at least one key reason why blood-forming stem cells can be susceptible to developing genetic mutations leading to adult leukemia or bone marrow failures. Most adult stem cells, including hematopoietic stem cells (HSCs), are maintained in a quiescent or resting state in vivo. Quiescence is widely considered to be an essential protective mechanism for stem cells that minimizes endogenous stress associated with cellular division and DNA replication. However, we demonstrate that HSC quiescence can also have detrimental effects. We found that HSCs have unique cell-intrinsic mechanisms ensuring their survival in response to ionizing irradiation (IR), which include enhanced pro-survival gene expression and strong activation of a p53-mediated DNA damage response. We show that quiescent and proliferating HSCs are equally radioprotected but use different types of DNA repair mechanisms. We describe how nonhomologous end joining (NHEJ)-mediated DNA repair in quiescent HSCs is associated with acquisition of genomic rearrangements, which can persist in vivo and contribute to hematopoietic abnormalities. These results demonstrate that quiescence is a double-edged sword that, while mostly beneficial, can render HSCs intrinsically vulnerable to mutagenesis following DNA damage. Our findings have important implications for cancer biology. They indicate that quiescent stem cells, either normal or cancerous, are particularly prone to the acquisition of mutations, which overturns the current dogma that cancer development absolutely requires cell proliferation. They help explain why quiescent leukemic stem cells (LSC), which currently survive treatment in most leukemia, do in fact represent a dangerous reservoir for additional mutations that can contribute to disease relapse and/or evolution, and stress the urgent need to develop effective anti-LSC therapies. They also have direct clinical applications for minimizing the risk of therapy-related leukemia following treatment of solid tumors with cytotoxic agents. By showing that proliferating HSCs have significantly decreased mutation rates, with no associated change in radioresistance, they suggest that it would be beneficial to induce HSCs to enter the cycle prior to therapy with DNA-damaging agents in order to enhance DNA repair fidelity in HSCs and thus reduce the risk of leukemia development. While this possibility remains to be tested in the clinic using FDA approved agents such as G-CSF and prostaglandin, it offers exciting new directions for limiting the deleterious side effects of cancer treatment. Our findings also have broad biological implications for tissue function. While the DNA repair mechanism used by quiescent HSCs can indeed produce defective cells, it is likely not detrimental for the organism in evolutionary terms. The blood stem cell system is designed to support the body through its sexually reproductive years, so the genome can be passed along. The ability of quiescent HSCs to survive and quickly undergo DNA repair in response to genotoxic stress supports this goal, and the risk of acquiring enough damaging mutations in these years is minimal. The problem occurs with age, as these long-lived cells have spent a lifetime responding to naturally occurring insults as well as the effects of X-rays, medications and chemotherapies. In this context, the accumulation of NHEJ-mediated DNA misrepair and resultant genomic damages could be a major contributor to the loss of function occurring with age in HSCs, and the development of age-related hematological disorders. We are now using this work on normal HSCs as a platform to understand at the molecular level how the DNA damage response and the mechanisms of DNA repair become deregulated in leukemic HSCs during the development of hematological malignancies.
  • Our work during the third year of the CIRM New Faculty award has extended and broaden up our investigations in two novel directions that are still within the scope of our initial Aims: 1) identifying novel stress-response mechanisms that preserve hematopoietic stem cells (HSC) fitness during periods of metabolic stress; and 2) understanding how deregulations in DNA repair mechanisms contribute to the aberrant functions of old and transformed HSCs. Blood development is organized hierarchically, starting with a rare but well-defined population of HSCs that give rise to a series of committed progenitors and mature cells with exclusive functional and immunophenotypic properties. HSCs are the only cells within the hematopoietic system that self-renew for life, whereas other hematopoietic cells are short-lived and committed to the transient production of mature blood cells. Under steady-state conditions, HSCs are a largely quiescent, slowly cycling cell population, which, in response to environmental cues, are capable of dramatic expansion and contraction to ensure proper homeostatic replacement of all blood cells. While considerable work has deciphered the molecular networks controlling HSC activity, still little is known about how these mechanisms are integrated at the cellular level to ensure life-long maintenance of a functional HSC compartment. HSCs reside in hypoxic niches in the bone marrow microenvironment, and are mostly kept quiescent in order to minimize stress and the potential for damage associated with cellular respiration and cell division. Last year, we showed that HSCs can also engage specialized response mechanisms that protect them from the killing effect of environmental stresses such as ionizing radiation (IR) (Mohrin et al., Cell Stem Cell, 2010). We demonstrated that long-lived HSCs, in contrast to short-lived myeloid progenitors, have enhanced expression of pro-survival members of the bcl2 gene family and robust induction of p53-mediated DNA damage response, which ensures their specific survival and repair following IR exposure. We reasoned that HSCs have other unique protective features, which allow them to contend with a variety of cellular insults and damaged cellular components while maintaining their life-long functionality and genomic integrity. Now, we show that HSCs use the self-catabolic process of autophagy as an essential survival mechanism in response to metabolic stress in vitro or nutriment deprivation in vivo. Last year, we also reported that although HSCs largely survive genotoxic stress their DNA repair mechanisms make them intrinsically vulnerable to mutagenesis (Mohrin et al., Cell Stem Cell, 2010). We showed that their unique quiescent cell cycle status restricts them to the use of the error-prone non-homologous end joining (NHEJ) DNA repair mechanism, which renders them susceptible to genomic instability and transformation. These findings provide the beginning of an understanding of why HSCs, despite being protected at the cellular level, are more likely than other hematopoietic cells to initiate blood disorders (Blanpain et al., Cell Stem Cell, review, 2011). Such hematological diseases increase with age and include immunosenescence (a decline in the adaptive immune system) as well as the development of myeloproliferative neoplasms, leukemia, lymphoma and bone marrow failure syndromes. Many of these features of aging have been linked to changes in the biological functions of old HSCs. Gene expression studies and analysis of genetically modified mice have suggested that errors in DNA repair and loss of genomic stability in HSCs are driving forces for aging and cancer development. However, what causes such failures in maintaining HSC functionality over time remains to be established. We therefore asked whether the constant utilization of error-prone NHEJ repair mechanism and resulting misrepair of DNA damage over a lifetime could contribute to the loss of function and susceptibility to transformation observed in old HSCs. Similarly, we started investigating how mutagenic DNA repair could contribute to the genomic instability of HSC-derived leukemic stem cells (LSC).
  • Our work during the fourth year of the CIRM New Faculty award has been focused on achieving the goals set forth last year for the two first aims of the grant: 1) identifying the stress-response mechanisms that preserve hematopoietic stem cells (HSC) fitness during periods of metabolic stress; and 2) understanding how deregulations in DNA repair mechanisms contribute to the aberrant functions of old HSCs and the aging of the blood system.
  • Blood development is organized hierarchically, starting with a rare but well-defined population of HSCs that give rise to a series of committed progenitors and mature cells with exclusive functional and immunophenotypic properties. HSCs are the only cells within the hematopoietic system that self-renew for life, whereas other hematopoietic cells are short-lived and committed to the transient production of mature blood cells. Under steady-state conditions, HSCs are a largely quiescent, slowly cycling cell population, which, in response to environmental cues, are capable of dramatic expansion and contraction to ensure proper homeostatic replacement of all needed blood cells. While considerable work has deciphered the molecular networks controlling HSC activity, still little is known about how these mechanisms are integrated at the cellular level to ensure life-long maintenance of a functional HSC compartment.
  • HSCs reside in hypoxic niches in the bone marrow microenvironment, and are mostly kept quiescent in order to minimize stress and the potential for damage associated with cellular respiration and cell division. Previously, we found that HSCs also have a unique pro-survival wiring of their apoptotic machinery, which contribute to their enhanced resistance to genotoxic stress (Mohrin et al., Cell Stem Cell, 2010). Now, we identified autophagy as an essential mechanism protecting HSCs from metabolic stress (Warr et al., Nature, in press). We show that HSCs, in contrast to their short-lived myeloid progeny, robustly induce autophagy following ex vivo cytokine withdrawal and in vivo caloric restriction. We demonstrate that FoxO3a is critical to maintain a gene expression program that poise HSCs for rapid induction of autophagy upon starvation. Notably, we find that old HSCs retain an intact FoxO3a-driven pro-autophagy gene program, and that ongoing autophagy is needed to mitigate an energy crisis and allow their survival. Our results demonstrate that autophagy is essential for the life-long maintenance of the HSC compartment and for supporting an old, failing blood system.
  • Previous studies have also suggested that increased DNA damage could contribute to the functional decline of old HSCs. Therefore, we set up to investigate whether the reliance on the error-prone non-homologous end-joining (NHEJ) DNA repair mechanism we previously identified in young HSCs (Mohrin et al., Cell Stem Cell, 2010) could render old HSCs vulnerable to genomic instability. We confirm that old HSCs have increased numbers of γH2AX DNA foci but find no evidence of associated DNA damage. Instead, we show that γH2AX staining in old HSCs entirely co-localized with nucleolar markers and correlated with a significant decrease in ribosome biogenesis. Moreover, we observe high levels of replication stress in proliferating old HSCs leading to severe functional impairment in condition requiring proliferation expansion such as transplantation assays. Collectively, our results illuminate new features of the aging HSC compartment, which are likely to contribute to several facets of age-related blood defects (Flach et al, manuscript in preparation).
  • Our work during the fifth and last year of our CIRM New Faculty award has been essentially focused on understanding how deregulations in DNA repair mechanisms contribute to the aberrant functions of old hematopoietic stem cells (HSC) and the aging of the blood system.

Derivation and Characterization of Myeloproliferative Disorder Stem Cells from Human ES Cells

Funding Type: 
New Faculty II
Grant Number: 
RN2-00910
ICOC Funds Committed: 
$3 065 572
Disease Focus: 
Blood Cancer
Cancer
Stem Cell Use: 
Cancer Stem Cell
Embryonic Stem Cell
oldStatus: 
Active
Public Abstract: 
Cancer is the leading cause of death for people younger than 85. High cancer mortality rates related to resistance to therapy and malignant progression underscore the need for more sensitive diagnostic techniques as well as therapies that selectively target cells responsible for cancer propagation. Compelling studies suggest that human cancer stem cells (CSC) arise from aberrantly self-renewing tissue specific stem or progenitor cells and are responsible for cancer propagation and resistance to therapy. Although the majority of cancer therapies eradicate rapidly dividing cells within the tumor, the rare CSC population may be quiescent and then reactivate resulting in disease progression and relapse. We recently demonstrated that CSC are generated in chronic myeloid leukemia by activation of beta-catenin, a gene that allows cells to reproduce themselves extensively. However, relatively little is known about the sequence of events responsible for leukemic transformation in more common myeloproliferative disorders (MPDs) that express an activating mutation in the JAK2 gene. Because human embryonic stem cells (hESC) have robust self-renewal capacity and can provide a potentially limitless source of tissue specific stem and progenitor cells, they represent an ideal model system for generating and characterizing human MPD stem cells. Thus, hESC cell research harbors tremendous potential for developing life-saving therapy for patients with cancer by providing a platform to rapidly and rationally test new therapies that specifically target CSC. To provide a robust model system for screening novel anti-CSC therapies, we propose to generate and characterize BCR-ABL+ and JAK2+ MPD stem cells from hESC. We will investigate the role of genes that are essential for initiation of these MPDs such as BCR-ABL and JAK2 V617F as well as additional mutations in beta-catenin or GSK3betaï€ implicated in CSC propagation. The efficacy of a selective BCR-ABL and JAK2 inhibitors at blocking BCR-ABL+ and JAK2+ human ES cell self-renewal, survival and proliferation alone and in combination with a potent and specific beta-catenin antagonist will be assessed in robust in vitro and in vivo assays with the ultimate aim of developing highly active anti-MPD stem cell therapy that may halt progression to acute leukemia and obviate therapeutic resistance.
Statement of Benefit to California: 
Although much is known about the genetic and epigenetic events involved in CSC production in a Philadelphia chromosome positive MPD like chronic myeloid leukemia (CML), comparatively little is known about the molecular pathogenesis of the five-fold more common Philadelphia chromosome negative (Ph-) MPDs. MPD patients have a moderately increased risk of fatal thrombotic events as well as a striking 36-fold increased risk of death from transformation to acute leukemia. Recently, a point mutation, JAK2 V617F(JAK2+), resulting in constitutive activation of the JAK2 cytokine signaling pathway was discovered in a large proportion of MPD patients. A critical barrier to developing potentially curative therapies for both BCR-ABL+ and JAK2+ MPDs is a comprehensive understanding of relative contribution of BCR-ABL and JAK2 V617F to disease initiation versus transformation to acute leukemia. We recently discovered that JAK2 V617F is expressed at the hematopoietic stem cell level in PV, ET and MF and that JAK2 skewed ifferentiation in PV is normalized with a selective JAK2 inhibitor, TG101348. However, a detailed molecular pathogenetic characterization has been hampered by the paucity of stem and progenitor cells in MPD derived blood and marrow samples. Because hESC have robust self-renewal capacity and can provide a potentially limitless source of tissue specific stem and progenitor cells in vitro, they represent an ideal model system for generating human MPD stem cells. Thus, California hESC research harbors tremendus potential for understanding the MPD initiating events that skew differentiation versus events that promote self-renewal and thus, leukemic transformation. Moreover, a more comprehensive understanding of primitive stem cell fate decisions may yield key insights into methods to expand blood cell production that may have major implications for blood banking. Clinical Benefit Generation of MPD stem cells from hESC would provide an experimentally amenable and relevant platform to expedite the development ofsensitive diagnostic techniques to predict disease progression and to develop potentially curative anti-CSC therapies. Economic Benefit The translational research performed in the context of this grant will not only speed the delivery of innovative MPD targeted therapies for Californians, it will help to train Californiaís future R&D workforce in addition to developing leaders in translational medicine. This grant will provide the personnel working on the project with a clear view of the importance of thir research to cancer therapy and a better perspective on future career opportunities in California as well as directly generate revenue through development and implementation of innovative therapies aimed at eradicating MPD stem cells that may be more broadly applicable to CSC in other malignances.
Progress Report: 
  • Summary of Overall Progress
  • This grant focuses on generation of MPN stem cells from hESC or CB and correlates leukemic potential with MPN patient samples. In the first year of this grant, we have demonstrated that 1) hESC differentiate on AGM stroma to the CD34+ stage, which is associated with increased GATA-1, Flk2, GATA-2 and ADAR1 expression; 2) hESC CD34+ differentiation is enhanced in vitro and in vivo in the presence of a genetically engineered mouse stroma, which produces human stem cell factor, IL-3 and G-CSF; 3) hESC CD34+ cells can be transduced with our novel lentiviral BCR-ABL vector, which, unlike retroviral BCR-ABL, can transduce quiescent stem cells; 4) BCR-ABL expression by CP CML progenitors does not sustain engraftment but rather leukemic transformation is predicated, in part, on bcl-2 overexpression; 5) JAK2V617F expression in hES or CB stem cells is insufficient to induce leukemic transformation; 6) BCR-ABL transduced hESC CD34+ cells have significantly higher BCR-ABL transplantation potential than CP CML progenitors suggesting that they have higher survival capacity; 7) lentiviral -catenin transduction of BCR-ABL hESC CD34+ cells leads to serial transplantation indicative of LSC formation; 8) CML BC LSC persist in vivo despite potent BCR-ABL inhibition with dasatinib therapy and will likely require combined inhibitor therapy to eradicate. Currently, HEEBO arrays and phospho-flow studies are underway to detect bcl-2 family members and self-renewal protein expression in BCR-ABL and JAK2 V617F transduced hESC and CB CD34+ cells compared with MPN patient derived progenitors. This will aid in development of combined MPN stem cell inhibitor strategies in this grant.
  • This grant focuses on generation of myeloproliferative disorder or neoplasm (MPN) stem cells from pluripotent (hESC) or multipotent (CB) stem cells and seeks to correlate their leukemic potential with that of MPN patient sample-derived stem cells. To provide a platform for testing induction of stem cell differentiation, survival and self-renewal by BCR-ABL versus JAK2, hESC were utilized in the first year and as more patient samples and cord blood became available these were utilized.
  • In the first year of this grant, we found that hESC undergo hematopoietic differentiation on AGM stroma to the CD34+ stage resulting in increased GATA-1, Flk2, ADAR1 and GATA-2 expression. Moreover, CD34+ differentiation was enhanced on a genetically engineered mouse stroma (SL/M2) secreting human SCF, IL-3 and G-CSF. Lentiviral BCR-ABL transduced hESC-derived CD34+ cells had higher BCR-ABL+ cellular transplantation potential than chronic phase (CP) CML progenitors, indicative of a higher survival capacity. However, they sustained self-renewal only when co-transduced with lentiviral -catenin (Rusert et al, manuscript in preparation) suggesting that blast crisis evolution requires acquisition of both enhanced survival and self-renewal potential. Similarly, lentiviral mouse mutant JAK2 expression in hESC or CB stem cells was insufficient to produce self-renewing MPN stem cells, indicating that the cellular context, nature of the genetic driver and responses to extrinsic cues from the microenvironment play seminal roles in regulating therapeutically resistant MPN stem cell properties such as aberrant survival, differentiation, self-renewal and dormancy.
  • In the second year of this five year grant, we have focused on human cord blood (CB) stem cells compared with a large number of MPN patient samples propagated on SL/M2 stroma or in RAG2-/-c-/- mice to more adequately recapitulate the human MPN stem cell niche. Also, to more faithfully recapitulate human (rather than the previously published lentiviral mouse JAK2 vectors, Cancer Cell 2008) JAK2 driven MPNs, we cloned human wild-type JAK2 and human JAK2 V617F from MPN patient samples into lentiviral-GFP vectors (Court Recart A*, Geron I* et al, manuscript in preparation). We also incorporated full transcriptome RNA (ABI SOLiD 4.0) sequencing, PCR array and nanofluidic phosphoproteomics technology to better gauge the impact of JAK2 versus BCR-ABL on stem cell fate, survival, self-renewal and dormancy in the context of specific malignant microenvironments and the relative susceptibility of MPN stem cells in these niches to single agent molecularly targeted inhibitors.
  • This grant focuses on generation of myeloproliferative disorder or neoplasm (MPN) stem cells from pluripotent human embryonic stem cells (hESC) or multipotent cord blood (CB) stem cells, and seeks to correlate their leukemic potential with that of disease progression in MPN patient sample-derived stem cells. In the first and second years of this grant, we found that lentiviral BCR-ABL transduced hESC-derived CD34+ cells had higher leukemic transplantation potential than chronic phase (CP) chronic myeloid leukemia (CML) progenitors. However, they sustained self-renewal only when co-transduced with lentiviral beta-catenin suggesting that blast crisis (BC) evolution requires acquisition of both enhanced survival and self-renewal potential. Similarly, we have shown using lentiviral vectors that mouse and human mutant JAK2 were insufficient to produce self-renewing MPN stem cells. New results in Year 3 demonstrate that BCR-ABL and JAK2 activation drive differentiation of hematopoietic progenitors towards an erthyroid/myeloid lineage bias. We have used full transcriptome RNA-Sequencing (RNA-Seq) technology to evaluate the genetic and epigenetic status of BCR-ABL and JAK2-transduced normal progenitor cells as well as patient-derived MPN progenitors. This has allowed us to probe the mechanisms of aberrant differentiation and self-renewal of MPN progenitors and identify unique gene expression signatures of disease progression.
  • We previously found that overexpression and splice isoform switching of a key RNA editing enzyme – adenosine deaminase acting on dsRNA (ADAR), and splice isoform changes in pro-survival BCL2 family members, correspond with disease progression in CML. In the current reporting period, RNA-Seq analyses revealed that ADAR1-driven activation of RNA editing contributed to malignant progenitor reprogramming, promoting aberrant differentiation and self-renewal of MPN stem cells. Knocking down ADAR1 using lentiviral shRNA vectors reduced the self-renewal potential of CML progenitors. This work has culminated in a manuscript that has now been submitted to PNAS (Jiang et al.). Recent results also show that ADAR1 is activated in progenitors from patients with JAK2-driven MPNs. Thus, ADAR1 may be an important factor that works in concert with BCR-ABL or JAK2 to facilitate disease progression in MPNs.
  • Our results show that another self-renewal factor that may drive BCR-ABL or JAK2-mediated propagation of disease from quiescent MPN progenitors is Sonic hedgehog (Shh). We have examined the expression patterns of this pathway in MPN progenitors using qRT-PCR and RNA-Seq, and have tested a pharmacological inhibitor of this pathway in a robust stromal co-culture model of MPN progression to Acute Myeloid Leukemia (AML).
  • In sum, we have utilized full transcriptome RNA-Seq and qRT-PCR coupled with hematopoietic progenitor assays and in vivo studies to evaluate the impact of JAK2 versus BCR-ABL on stem cell fate, survival, self-renewal and dormancy. These techniques have allowed us to investigate in more detail the role of genetic and epigenetic alterations that drive disease progression in the context of specific malignant microenvironments, and the relative susceptibility of MPN stem cells in these niches to single agent molecularly targeted inhibitors.
  • The main objectives of this project are generation of myeloproliferative disorder or neoplasm (MPN) stem cells from pluripotent human embryonic stem cells (hESC) or multipotent stem cells, and identification of crucial leukemia stem cell (LSC) survival and self-renewal factors that contribute to the development and progression of BCR-ABL and JAK2-driven hematopoietic disorders. A key finding of our work thus far is that in addition to activation of BCR-ABL or JAK2 oncogenes, generation of self-renewing MPN LSC requires stimulation of other pro-survival and self-renewal factors such as β-catenin, Sonic hedgehog (SHH), BCL2, and in particular the RNA editing enzyme ADAR1, which we identified as a novel regulator of LSC differentiation and self-renewal.
  • We have now completed comprehensive gene expression analyses from next-generation RNA-sequencing studies performed on normal and leukemic human hematopoietic progenitor cells from primary cord blood samples and adult normal peripheral blood samples, along with normal cord blood transduced with BCR-ABL or JAK2 oncogenes, and primary samples from patients with BCR-ABL+ chronic phase and blast crisis chronic myeloid leukemia (CML). These studies revealed that gene expression patterns in survival and self-renewal pathways (SHH, JAK2, ADAR1) clearly distinguish normal and leukemic progenitor cells as well as MPN disease stages. These data provide a vast resource for identification of LSC-specific biomarkers with diagnostic and prognostic clinical applications, as well as providing new potential therapeutic targets to prevent disease progression.
  • New results from RNA-sequencing studies reveal high levels of expression of inflammatory mediators in human blast crisis CML progenitors and in BCR-ABL transduced normal cord blood stem cells. Moreover, expression of the inflammation-responsive form of ADAR1 correlated with generation of an abnormally spliced GSK3β gene product that has been previously linked to LSC self-renewal. These results have now been published in the journal PNAS (Jiang et al.). Together, we have demonstrated that ADAR1 drives hematopoietic cell fate by skewing cell differentiation – a trend which occurs during normal bone marrow aging – and promotes LSC self-renewal through alternative splicing of critical survival and self-renewal factors. Notably, inhibition of ADAR1 through genetic knockdown strategies reduced self-renewal capacity of CML LSC, and may have important applications in treatment of other disorders that transform to acute leukemia. Thus, these results suggest that RNA editing (ADAR1) and splicing represent key therapeutic targets for preventing LSC self-renewal – a primary driver of leukemic progression.
  • Whole transcriptome profiling studies coupled with qRT-PCR, hematopoietic progenitor assays and in vivo studies have shown that combined inhibition of BCR-ABL and JAK2 is another effective method to reduce LSC self-renewal in pre-clinical models. New results show that lentivirus-enforced BCR-ABL or JAK2 expression in normal cord blood stem cells drives generation of distinct splice isoforms of STAT5a. While inhibition of JAK2/STAT5a signaling or BCR-ABL tyrosine kinase activity alone did not eradicate self-renewing LSC, combined JAK2 and BCR-ABL inhibition dramatically impaired LSC survival and self-renewal in the protective bone marrow niche, and increased the lifespan of serial transplant recipients. These effects were associated with reduction in STAT5a isoform expression – which represents a novel molecular marker of response to combined BCR-ABL/JAK2 inhibition – and altered expression of cell cycle genes in human progenitor cells harvested from the bone marrow of transplanted mice. These results are the subject of a new manuscript currently under review (Court et al.). Moreover, this work has led to the development of new experimental tools that will facilitate study of LSC maintenance and cell cycle status in the context of normal versus diseased bone marrow microenvironments. In sum, studies completed thus far have uncovered a role for RNA editing and splicing alterations in leukemic progression, particularly in specific microenvironments. Using specific inhibitors targeting BCR-ABL and JAK2, along with strategies to block RNA editing and aberrant splicing activities, we have been able to establish the relative susceptibility of MPN stem cells to molecular inhibitors with activity against LSC residing in select hematopoietic niches that are difficult to treat with conventional chemotherapeutic agents.
  • In the final year of this project, we focused on elucidating the mechanisms of leukemia stem cell (LSC) generation in JAK2 compared with BCR-ABL1 initiated myeloproliferative neoplasms (MPN, previously called myeloproliferative disorders). To this end, we investigated the MPN stem cell propagating effects of BCR-ABL1 or JAK2 alone or in combination with activation of the human embryonic stem cell RNA editase, ADAR1. Recently, we discovered that ADAR1, which edits adenosine to inosine bases in the context of primate specific Alu sequences, leads to GSK3β missplicing and β-catenin activation in chronic phase (CP) CML progenitors leading to blast crisis (BC) transformation and LSC generation. In addition, variant isoform expression of a Wnt/β-catenin target gene, CD44, was also characteristic of LSC. In a previous report (Jiang et al., PNAS 2013), identification of ADAR1 as a malignant reprogramming factor represented the first description of RNA editing as a regulator of reprogramming. When lentivirally overexpressed, ADAR1 endows committed CP myeloid progenitors with self-renewal capacity. Further studies revealed that JAK2/STAT5a activates ADAR1 leading to deregulation of cell cycle progression and global down-regulation of microRNA expression thereby uncovering two additional key mechanisms of LSC generation in MPNs. This is consistent with our findings from gene expression profiling studies performed in the previous year, along with functional classification and network analysis using Ingenuity Pathway Analysis (IPA), showing that cell cycle-related genes were significantly altered in human progenitors from xenografted mice treated with combination JAK2 and BCR-ABL inhibitor therapy compared with single agent therapies alone. Together these data suggest that combined BCR-ABL and JAK2 inhibition impairs LSC survival and self-renewal via cell cycle modulation. ADAR1 and other stem cell regulatory pathways such as CD44 represent novel targets to detect and eradicate the self-renewing LSC. We also performed new studies that elucidate the stem cell-intrinsic genetic changes that occur during human bone marrow aging, which may contribute to BCR-ABL or JAK2-dependent functional alterations.
  • This work has led to discovery of a novel role for embryonic stem cell genes and splice isoforms, including ADAR1 p150 and a transcript variant of CD44, in the maintenance of LSC that promote MPN progression. In addition, through the course of this research we have 1) developed novel lentiviral tools for investigating normal hematopoietic stem and progenitor (HSPC) and malignant LSC survival, differentiation, self-renewal, and cell cycle regulation, and 2) devised innovative LSC diagnostic strategies and 3) tested therapeutic strategies targeting LSC-associated RNA editing and splice isoform generation that selectively inhibit LSC self-renewal.

Stem Cells in Lung Cancer

Funding Type: 
New Faculty II
Grant Number: 
RN2-00904
ICOC Funds Committed: 
$2 381 572
Disease Focus: 
Lung Cancer
Cancer
Respiratory Disorders
Stem Cell Use: 
Adult Stem Cell
Cancer Stem Cell
oldStatus: 
Active
Public Abstract: 
Lung cancer is the most deadly cancer worldwide and accounts for more deaths than prostate cancer, breast cancer and colon cancer combined. Non small cell lung cancer (NSCLC) accounts for about 85% of all lung cancers. The current 5-year survival rate for all stages of NSCLC is only 15%. Although early stage lung cancer has a much better survival rate. Current therapeutic strategies of chemotherapy, radiation therapy and trials with new targeted therapies have only demonstrated, at best, extension in survival by a few months. Clearly, a novel approach is required to develop new therapies for this devastating disease and to detect the disease at an early stage. Cancer stem cells have been identified as the initial cell in the formation of carcinomas. Chemotherapy, radiation and even targeted therapies are all designed to eliminate dividing cells. However, cancer stem cells “hide out” in the quiescent phase of growth. This provides an explanation as to why our cancer therapies may produce an initial response but are often unsuccessful in curing patients. Lung cancer develops through a series of step wise changes that result in the progression of pre-malignant lesions to invasive lung cancer. The mechanisms of how lung cancer develops are not known and if we can prevent the formation of pre-malignant lesions, we will likely be able to prevent lung cancer. We have discovered a subpopulation of stem cells that circulates in the blood and is essential for normal lung repair. Blocking these cells from entering the lung results in a pre-malignant condition in the lungs. We have also identified a subpopulation of stem cells in the lung that is responsible for generating pre-malignant lung cancer lesions. We hypothesize that the interaction between the stem cells in the blood and the stem cells in the lung are critical to prevent lung cancer. We plan to use cutting edge technologies to characterize these different stem cell populations in the lung, and determine how they form pre-malignant lung cancer lesions. We also plan to use preclinical models to try to prevent lung cancer by giving additional stem cells derived from the blood as a therapy. Lastly, we plan to determine whether levels of stem cells in the blood in patients may be used as a blood test to measure the chance of recurrence of lung cancer after therapy. The long term goals of our work are to develop a screening test for lung cancer stem cells that can predict which patients are at high risk for developing lung cancer in order to diagnose lung cancer at an early stage, and to potentially develop a new stem cell based therapy for preventing and treating lung cancer.
Statement of Benefit to California: 
According to the Center for Health Statistics, California Department of Health Services, 13,427 people died of lung cancer in the state of California in 2005. This is more than the deaths attributed to breast, prostate and colon cancers combined. The devastating effects of this disease on the citizens of California and the health care costs involved are enormous. Most cases of lung cancer occur in smokers, but non smokers, people exposed to second hand smoke and ex-smokers are also at risk. In addition, of special concern to California residents, is that exposure to air pollution is associated with an increased risk of lung cancer. Current therapeutic strategies for lung cancer are in general only able to prolong survival by a few months, especially for late stage disease. One reason for this may be that the cancer initiating stem cell is resistant to these therapies. Understanding the stem cell populations involved in repair of the lung and how these cells may give rise to lung cancer is important for potentially generating new therapeutic targets for lung cancer. We propose to study the stem cell populations of the lung that are crucial for normal airway repair and characterize the putative cancer initiating stem cell in the lung. We have also found stem cells in the blood that are critical for normal airway repair and we plan to test their role in the prevention of premalignant lung cancer lesions. We also plan to test whether levels of these stem cells in the blood may be used as a biomarker of lung cancer. Ultimately, the ability to perform a screening test to detect lung cancer at an early stage, and the development of new therapies for lung cancer will be of major benefit to the citizens of California.
Progress Report: 
  • We identified a putative tumor-initiating stem/progenitor cell that goes rise to smoking-associated non small cell lung cancer (NSCLC). We examined 399 NSCLC samples for this tumor-initiating stem/progenitor cell and found that the presence of this cell in the tumor gave rise to a significantly worse prognosis and was associated with metastatic disease. This stem/progenitor cell is known to be important for repair of the airway and is present in precancerous lesions. We believe that this cell undergoes aberrant repair after smoking injury, which leads to lung cancer. We are currently trying to identify the genetic and epigenetic mechanisms involved in this aberrant repair as a means to identify a novel therapy to prevent the development of lung cancer. The presence of these stem/progenitor cells may also be used as a biomarker of poor prognostic NSCLC even in early stage disease.
  • We have identified markers on these stem/progenitor tumor-initiating cells and identified sub-populations of these cells. We are now determining the stem cell capabilities of each of these sub-populations. We are using a model of the development of lung cancer to determine if giving a stem/progenitor cell sub-population for repair can prevent NSCLC from developing.
  • We examined the blood of patients diagnosed with a lung nodule for circulating epithelial stem/progenitor cells. We found that the presence of these cells in the blood of patients predicted the presence of a subtype of NSCLC as compared to a benign lung nodule. We are currently obtaining many more blood samples from patients to further determine whether circulating epithelial stem/progenitor cells could be used as a biomarker of early NSCLC.
  • We have found a stem cell that is important for lung repair after injury that is located in a protected niche in the airway. After repeated injury, for example in smokers, these stem cells persist in an abnormal location on the surface of the airway and replicate and form precancerous areas in the lung. The presence of these stem cells in lung cancer tumors was associated with a poor prognosis with an increased chance of relapse and metastasis.This was especially true in current and former smokers. We therefore believe we have found a putative stem cell that is a tumor initiating cell for lung cancer. We developed a method to isolate these lung stem cells and to profile these cells and developed in vitro and in vivo models to assess their stem cell properties. Finally, we examined human blood samples to assess levels of surrogate markers of these stem cells to assess whether we could use this as a biomarker to predict the presence or absence of lung cancer in patients with a lung nodule.
  • We found a stem cell that is important for lung repair after injury that we believe may form precancerous areas in the lung. We are characterizing these stem cells and identifying pathways involved in normal repair and aberrant repair that leads to lung cancer. We are also isolating this stem cell population and other cell populations from the airway and inducing genetic changes to determine the tumor initiating cell/s for lung cancer. We are also examining the effect the environment may have on the regulation of genes in these stem cells, in precancerous areas and in lung cancers. Finally, we are examining human blood samples to assess levels of surrogate markers of these stem cells to assess whether we could use this as a biomarker to predict the presence or absence of lung cancer in patients with a lung nodule.
  • During this period of funding we discovered a method to reproducibly recover stem cells from human airways and grow them in a dish into mature airway cells. We also discovered the role that certain metabolic cell processes play in regulating the repair after airway injury. We believe that an inability to shut off these processes leads to abnormal repair and lung cancer and are actively investigating this. We are also determining whether the stem cells we isolate from the airways are the stem cells for lung cancer and how they might give rise to lung cancer.
  • In the last year of funding we identified a novel mechanism that tightly controls airway stem cell proliferation for repair after injury. We found that perturbing this pathway results in precancerous lesions that can ultimately lead to lung cancer. Correcting the abnormalities in this pathway that are seen in smokers could allow the development of targeted chemoprevention strategies to prevent the development of precancerous lesions and therefore lung cancer in at risk populations. We also continued our work on trying to identify a cell of origin for squamous lung cancer and identifying the critical drive mutations that are required for squamous lung cancer to develop.

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