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RN1-00550-1: Epigenetics in cancer stem cell initiation and clinical outcome prediction

Recommendation: Recommended for funding
Scientific Score: 61

First Year Funds Requested: $612,690
Total Funds Requested: $3,063,450

Public Abstract (provided by applicant)

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 (provided by applicant)

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.

Review

SYNOPSIS: The general goal of this proposal is to study epigenetic modifications in normal cells, human embryonic stem cells (hESCs) and human tumors. The Principal Investigator (PI) wishes to screen the drugable genome to identify new regulators of epigenetic modifications, probe chromatin alterations that mimic cancer, and correlate epigenetic patterns in epithelial cancers with outcome, ultimately to direct better therapy. Proteins that recognize specific epigenetic modifications will be identified in an effort to better understand how these modifications affect gene expression.

STRENGTHS AND WEAKNESSES OF THE RESEARCH PLAN: This is an ambitious proposal that will attempt to determine the role of histone modifications on cancer and stem cells. The amount of work proposed is massive and many of the experiments proposed are clearly goal oriented and weakly based on a sound hypothesis. More importantly, although the research plan has some strong components, its relevance to the stem cell field is minimal. Cancer seems to be the central goal of this proposal, but no specific analyses of cancer stem cells are proposed, and only few experiments using stem cells are planned. Some experiments explore how human ES cells respond to a specific viral protein, but they are of dubious relevance to stem cell biology. Clearly, the goal of the applicant is to study the control of epigenetic modifications and how this impacts tumorigenesis. Other funding mechanisms may be more appropriate to pursue that goal.

In Aim 1 the applicant will perform a whole genome screen to identify genes that affect global amounts of two specific histone modifications in two different cell types. Gene expression and biochemical/molecular analyses will then be used to address the mechanisms causing these changes in chromatin modification and the biological pathways that are affected. These are well-conceived experiments, and the preliminary results identifying one regulator of histone modification suggests that the approach will uncover new and unexpected pathways. However, nothing in this aim is directed at understanding stem cells in general or cancer stem cells in particular.

In Aim 2 the applicant will study the effect of a viral protein on histone modification. Previous results from the applicant have shown that this protein causes the global alteration of a specific histone modification, and changes in gene expression associated with both cell proliferation and differentiation. In this aim the applicant proposes to identify proteins that bind the viral protein in normal human lung fibroblasts and human ES cells, and map the sites of viral protein-induced chromatin modifications in these cells. Of all the experiments described in this proposal, these perhaps come closest to having stem cell relevance. The idea is that the ability of this viral protein to maintain an undifferentiated state may be dependent upon its effects on histone modification, and this process may be critical to the transformation of cancer stem cells. However, as part of this aim the applicant proposes to address whether the viral protein does indeed suppress the differentiation of human ES cells. The fact that this is not established already comes as a surprise, because the justification for one part of this aim is based on this being the outcome. Thus, it is remains uncertain whether this aim will lead to insights into bona-fide stem cells. One weakness in experimental design appears in another part of this aim where the applicant proposes to identify binding proteins for a particular epigenetic histone modification, in order to understand how this modification may affect gene activity. There is considerable concern about the specificity of the proposed approach, and important controls are not proposed. Some preliminary data are required here.

The PI has previously reported that the above-mentioned epigenetic mark is heterogeneous in cancers and its presence vs. absence correlates with outcome. In Aim 3 the applicant will study the utility of additional histone modifications as biomarkers for predicting clinical outcome in prostate cancer. The relevance of this work to stem cell biology is obscure. The applicant states that the results of Aim 2 will inform the choice of biomarkers in this aim, but it is very unclear how this will occur and no specific explanation is provided. Indeed, this aim apparently will proceed by using commercially available antibodies to the standard histone modifications. Nevertheless, this aim relates to more translational testing and would be clinically useful if Aim 1 were successful.

QUALIFICATIONS AND POTENTIAL OF THE PRINCIPAL INVESTIGATOR: The PI has a strong background and is a physician scientist. The applicant received an M.D. in 1999, followed by a residency and postdoctoral training. In 2004 the applicant was appointed an Assistant Professor at the applicant institution. The PI received two significant young investigator and early career awards and has numerous significant publications from postdoctoral work including first author papers in high-profile journals, and a senior author paper in a top-tier journal that appeared shortly after starting his/her own lab. Additional relevant senior author papers are either submitted for publication or in preparation. While it is clear that the PI is dedicated to an academic research career, the career development plan is rather limited as compared with that of other investigators in this competition. There is also a question as to whether the PI will be able to supervise this massive undertaking since significant time is already committed to other proposals.

INSTITUTIONAL COMMITMENT TO PRINCIPAL INVESTIGATOR: The applicant occupies adequate independent lab space, and has access to exceptional shared resources. These include a tissue microarray resource, a DNA microarray core, a molecular screening core, a stem cell culture service and a mass spectrometry core. The PI has been provided a substantial start-up package that can used for salaries, supplies and equipment. The intellectual environment is superb and supportive. The applicant institution has an outstanding track record in the development of junior faculty and a demonstrated commitment to stem cell research.

DISCUSSION: This young PI is one of the most promising candidates for a physician-scientist award, but in this case the candidate is much stronger than the proposal. The translational aspect of the proposal is the most likely to succeed, therefore this person may be a good fit for the physician-scientist track. Discussants noted the PI’s amazing training and tremendous publication record, but the project is only addressing a fundamental problem in biology and has little relevance to stem cells. Aim 2 is only one that uses stem cells, and the other 2 aims are not relevant to stem cells. Moreover, the proposal is a little weak scientifically as one of the cell types chosen is not the best to start a screen, and the relevance of the viral protein experiments to stem cells is unclear – this significantly dampened the enthusiasm of one reviewer.

PROGRAMMATIC DISCUSSION: A motion was made to recommend that this application be moved to Tier 1 – Recommended for Funding. One discussant noted that among the physician-scientists, this PI is a rising star with training from two top-notch institutions, and an interest in translational research. Another discussant pointed out that career development for physician-scientists is an objective of this RFA, and supported this motion because this applicant was the best of the physician-scientists in Tier 2. The motion to recommend that this application be moved carried.

The following Working Group members had a conflict of interest with this application and were therefore recused from participating in review of, discussion of, and voting on the application:

  • None