Periodic Reporting for period 1 - GBM_Cellular_States (Deciphering and targeting cellular states in glioblastoma)
Reporting period: 2022-05-01 to 2024-10-31
Intra-tumor heterogeneity (ITH), the diversity of cells within a tumor, has been recognized for decades as a fundamental property of cancer and as a major barrier for successful therapies. However, our understanding of ITH and our ability to eradicate heterogeneous tumors remain poor. One of the cancer types in which such heterogeneity is well known and thought to be highly important is glioblastoma (GBM) and other types of glioma such as IDH-mutant glioma. Over the last decade, single cell RNA sequencing (scRNA-seq) and other technologies enabled significant advances in defining ITH, opening up new avenues in cancer research. We previously applied scRNA-seq to GBM and other gliomas and found that similar cellular states (as defined by large-scale expression programs) are observed across patients. Two GBMs would typically differ from one another by the expression levels of hundreds of genes, yet beyond those differences they share an internal pattern of ITH: each GBM is likely to contain multiple malignant subpopulations reflecting four stereotypic cellular states, one with upregulation of astrocyte (AC) genes, another expressing mesenchymal markers (e.g. VIM, FN1), and two additional subpopulations with increased expression of genes of neural progenitor cells (NPC) and oligodendrocyte progenitor cells (OPC). Each of these states were found in many glioblastomas, but with variable cellular frequencies, and with the potential to proliferate and interconvert. Together, these “core” cellular states define a central aspect of GBM biology that may dictate many phenotypes and clinical features. Thus, it is now crucial to better understand how these states are regulated, and most notably how they relate to invasion and drug resistance.
Apart from these common and previously defined states, we speculate that additional states of functional and clinical significance might also exist and have yet to be fully described and appreciated. For example, previous studies examined the tumor samples that were surgically removed, but were unable to evaluate cells that diffuse from the tumor and invade the brain parenchyma. Such cells are of immense clinical significance as they cannot be surgically removed and ultimately lead to recurrence. Whether such invasive cells differ from the cells in the core of the tumor remains unknown, and if so, it would motivate new therapeutic strategies to specifically eliminate the invading cells. Thus, in addition to the core cellular states, we propose to identify and study rare and invasive cellular states.
Apart from these common and previously defined states, we speculate that additional states of functional and clinical significance might also exist and have yet to be fully described and appreciated. For example, previous studies examined the tumor samples that were surgically removed, but were unable to evaluate cells that diffuse from the tumor and invade the brain parenchyma. Such cells are of immense clinical significance as they cannot be surgically removed and ultimately lead to recurrence. Whether such invasive cells differ from the cells in the core of the tumor remains unknown, and if so, it would motivate new therapeutic strategies to specifically eliminate the invading cells. Thus, in addition to the core cellular states, we propose to identify and study rare and invasive cellular states.
During the last two years we have extensively analyzed the relationship between glioma cell states and their location within the tumor. We used new methods for profiling the transcriptome and proteome of cells while maintaining the information of their location within the tumor. This allowed us to discover that some tumor samples are highly structured while others are disorganized and chaotic. We found that the main parameter that distinguishes these two types of samples is the presence of hypoxia. hypoxia appears to generate an organization, such that some cell state tend to be close to the hypoxic region and other cell states are located in multiple "layers" of cells around the hypoxic regions. Thus, hypoxia is a central driver of the organization of glioma and the state of cells depends on its location in the tumor and specifically its distance from the hypoxic regions.
In another effort, we examined how the states of cancer cells change following several types of treatments, including standard of care treatments and others that are examined in clinical trials. In one such project that was recently completed, we discovered that a new treatment (inhibitors of mutant IDH) is causing the cells to switch from a progenitor state to a more differentiated state and that this reduces the proliferation of the cancer cells and therefore decreases the growth of the tumor and leads to clinical benefit.
In another effort, we examined how the states of cancer cells change following several types of treatments, including standard of care treatments and others that are examined in clinical trials. In one such project that was recently completed, we discovered that a new treatment (inhibitors of mutant IDH) is causing the cells to switch from a progenitor state to a more differentiated state and that this reduces the proliferation of the cancer cells and therefore decreases the growth of the tumor and leads to clinical benefit.
Our discovery that mutant IDH inhibitors lead to clinical benefit by inducing the differentiation of glioma cells has potential clinical implications. First, it suggests that rather than assessing the shrinkage of the tumor, as expected when cancer cells die, it might instead be relevant to assess the differentiation of cancer cells in order to evaluate response to such treatment. Second, it might enable a strategy to stratify patients for this treatment based on the capacity of cancer cells to differentiate. some tumors have lost this ability, for example due to mutations that disrupt their differentiation potential, and our analysis already suggests one such mutation. Third, this result might direct future efforts to improve the treatment by combining it with another treatment that would improve the inducting of differentiation. in future research we will attempt to further establish these possibilities and aim to use this understanding to develop improved teatments for IDH mutant glioma.