Periodic Reporting for period 4 - StroMaP (Stromal stress networks underlying phenotypic plasticity and tumor fitness)
Período documentado: 2022-04-01 hasta 2022-09-30
Though originally studied as a disease of genetically mutated cells, it is now widely accepted that cancers are evolving ecosystems, in which functionally distinct cell types and subpopulations engage in complex interactions that drive tumor progression and metastasis. Defining the principles that govern the division of labor inside the tumor is an open challenge in cancer biology, with vast implications for the development of novel cancer treatments.
Cells in our body constantly acquire mutations and alterations to their DNA. But these events are usually controlled by various protective mechanisms, and are not sufficient to cause cancer. Tumors expand, evade and metastasize only when these protective mechanisms fail, and normal cells are recruited and reprogrammed to support the growing mass of cancer cells instead of trying to kill it. These reprogrammed cells are collectively termed the tumor microenvironment (TME). Cells of the TME support essential tumor functions, and the tumor cannot survive without them. Importantly, though reprogrammed to support the growing tumor, these cells do not harbor mutations to their DNA. Rather, they are transcriptionally reprogrammed, changing the RNA and the regulating phenotypes and functions they exert. These features make the tumor microenvironment an attractive therapeutic target. Eradicating, or re-educating cells of the microenvironment is expected to inhibit tumor growth, and evolving resistance would be harder in cells that have normal DNA.
Our overarching objective is to define the principles that govern phenotypic plasticity in the TME and to understand how heterogeneity in the TME enables the evolution of aggressive cancer phenotypes. Our hypothesis is that this heterogeneity is driven by activation of a network of stress responses that transcriptionally reprograms cells of the TME. Our aim in this project was to map the transcriptional landscape of the TME and define the network of stress responses activated in different cell types and subpopulations of cells in the TME.
In this project, we made a substantial advance in our understanding of transcriptional programs and stress networks underlying phenotypic plasticity in the TME, and tumor fitness. We focused our studies on cancer-associated fibroblasts (CAFs), the most abundant cell type in many carcinomas. We characterized distinct subset of CAF in the TME, we provided evidence that distinct cancer mutations lead to distinct CAF compositions, we established the central protumorigenic role of the stress-activated transcription factor HSF1 in the TME of multiple carcinomas, and we unraveled a new layer of epigenetic regulation of cancer stroma.
Cells in our body constantly acquire mutations and alterations to their DNA. But these events are usually controlled by various protective mechanisms, and are not sufficient to cause cancer. Tumors expand, evade and metastasize only when these protective mechanisms fail, and normal cells are recruited and reprogrammed to support the growing mass of cancer cells instead of trying to kill it. These reprogrammed cells are collectively termed the tumor microenvironment (TME). Cells of the TME support essential tumor functions, and the tumor cannot survive without them. Importantly, though reprogrammed to support the growing tumor, these cells do not harbor mutations to their DNA. Rather, they are transcriptionally reprogrammed, changing the RNA and the regulating phenotypes and functions they exert. These features make the tumor microenvironment an attractive therapeutic target. Eradicating, or re-educating cells of the microenvironment is expected to inhibit tumor growth, and evolving resistance would be harder in cells that have normal DNA.
Our overarching objective is to define the principles that govern phenotypic plasticity in the TME and to understand how heterogeneity in the TME enables the evolution of aggressive cancer phenotypes. Our hypothesis is that this heterogeneity is driven by activation of a network of stress responses that transcriptionally reprograms cells of the TME. Our aim in this project was to map the transcriptional landscape of the TME and define the network of stress responses activated in different cell types and subpopulations of cells in the TME.
In this project, we made a substantial advance in our understanding of transcriptional programs and stress networks underlying phenotypic plasticity in the TME, and tumor fitness. We focused our studies on cancer-associated fibroblasts (CAFs), the most abundant cell type in many carcinomas. We characterized distinct subset of CAF in the TME, we provided evidence that distinct cancer mutations lead to distinct CAF compositions, we established the central protumorigenic role of the stress-activated transcription factor HSF1 in the TME of multiple carcinomas, and we unraveled a new layer of epigenetic regulation of cancer stroma.
In the first part of our project we surveyed the activation of different stress responses in tumors rich with cancer-associated fibroblasts (CAFs). Based on this survey we decided to focus on Gi-tract tumors, and on breast cancer.
In aim 1, we characterized the network of stress responses in the TME. We analyzed patient samples, and found co-activation of a network of stress responses with a particular role for heat-shock factor 1 (HSF1) in driving CAF transcriptional reprogramming in gastrointestinal tract cancers. In the colon, we explored the role of HSF1 in colitis-associated cancer (CAC). We discovered that HSF1 promotes extracellular matrix remodeling and inflammatory programs, leading to the development of CAC (Nature Comm. 2020). We characterized the underlying transcriptional changes and confirmed the clinical relevance of our findings by showing similar pathways activated in colitis-associated cancer patient samples. In parallel, we combined the targeted analysis of stress responses with unbiased transcriptional profiling from patient samples (Aim 2) to characterize the first stromal transcriptional signature of gastric cancer (Cancer Research 2021). We defined a stromal gene signature associated with poor disease outcome and found that components of this signature are regulated by HSF1, and delivered via CAF-derived exosomes to the TME to promote cancer.
In aim 2, we set to dissect the transcriptional landscape of CAFs. To dissect CAF compositions and dynamic changes, we profiled CAFs using single cell RNA-sequencing (in collaboration with Amit lab, WIS) in a mouse model breast cancer. We revealed distinct subpopulations, the transcriptional programs of which changed over time and in metastases (Nature Cancer 2020). We developed imaging and analytic tools to probe these changes in patients, and discovered CAF compositions that associated with disease outcome, and correlated with BRCA mutations. Our findings raised the concept of a dynamic TME that changes in tandem with the evolving tumor ecosystem.
In aim 3, we integrated our stress network data with the stromal transcriptome data to discover actionable nodes for intervention. This approach was implemented in our work in gastric cancer (mentioned above), and in pancreatic cancer. We assembled and analyzed a cohort of pancreatic cancer patient samples, and discovered different CAF compositions in germline BRCA-mut vs. BRCA-WT tumors (BioRxiv 2021 & Nature Comm. in press). This study unraveled a new dimension of stromal heterogeneity, influenced by germline mutations in cancer cells.
Together, our findings in this project provide maps and tools that allow deeper dissection and understanding of basic cancer biology. Importantly, our findings can be used to develop new therapeutic strategies to fight cancer.
In aim 1, we characterized the network of stress responses in the TME. We analyzed patient samples, and found co-activation of a network of stress responses with a particular role for heat-shock factor 1 (HSF1) in driving CAF transcriptional reprogramming in gastrointestinal tract cancers. In the colon, we explored the role of HSF1 in colitis-associated cancer (CAC). We discovered that HSF1 promotes extracellular matrix remodeling and inflammatory programs, leading to the development of CAC (Nature Comm. 2020). We characterized the underlying transcriptional changes and confirmed the clinical relevance of our findings by showing similar pathways activated in colitis-associated cancer patient samples. In parallel, we combined the targeted analysis of stress responses with unbiased transcriptional profiling from patient samples (Aim 2) to characterize the first stromal transcriptional signature of gastric cancer (Cancer Research 2021). We defined a stromal gene signature associated with poor disease outcome and found that components of this signature are regulated by HSF1, and delivered via CAF-derived exosomes to the TME to promote cancer.
In aim 2, we set to dissect the transcriptional landscape of CAFs. To dissect CAF compositions and dynamic changes, we profiled CAFs using single cell RNA-sequencing (in collaboration with Amit lab, WIS) in a mouse model breast cancer. We revealed distinct subpopulations, the transcriptional programs of which changed over time and in metastases (Nature Cancer 2020). We developed imaging and analytic tools to probe these changes in patients, and discovered CAF compositions that associated with disease outcome, and correlated with BRCA mutations. Our findings raised the concept of a dynamic TME that changes in tandem with the evolving tumor ecosystem.
In aim 3, we integrated our stress network data with the stromal transcriptome data to discover actionable nodes for intervention. This approach was implemented in our work in gastric cancer (mentioned above), and in pancreatic cancer. We assembled and analyzed a cohort of pancreatic cancer patient samples, and discovered different CAF compositions in germline BRCA-mut vs. BRCA-WT tumors (BioRxiv 2021 & Nature Comm. in press). This study unraveled a new dimension of stromal heterogeneity, influenced by germline mutations in cancer cells.
Together, our findings in this project provide maps and tools that allow deeper dissection and understanding of basic cancer biology. Importantly, our findings can be used to develop new therapeutic strategies to fight cancer.
Our study in breast cancer (Aim 2) was a breakthrough in our understanding of CAF heterogeneity, with direct clinical implications. In this study we discovered a previously unknown subset of CAFs in breast cancer – antigen presenting CAFs, and showed that this subset is associated with favorable outcome in breast cancer patients. This study also highlighted the dynamic and plastic nature of CAFs – changing with tumor progression and metastasis, and exhibiting not only temporal but also spatial heterogeneity (Nature Cancer, 2020).
Our studies on HSF1 in the tumor microenvironment (Aim 1, 3) significantly advanced the research field of stress responses. Cellular stress responses have been studied for decades, however the notion that stress responses serve to promote cell-cell communication was scarcely explored. Our work established a central role for HSF1 in CAFs, and showed that stress responses can act in a non-cell autonomous manner (Nature Communications 2020, Advances in Experimental Medicine and Biology 2020, Cancer Research 2021).
Our study in breast cancer mentioned above (Nature Cancer 2020) led to an unexpected finding that the CAF composition of BRCA-mutated tumors is distinct from the CAF composition of BRCA-WT tumors. This study opened up a new avenue of research in my lab and led to our study of stromal composition of BRCA-mutated cancers in the pancreas (BioRxiv 2021 & Nature Communication, in press).
Together, these studies provide transcriptional and functional maps of CAFs in breast, pancreas, gastric and colon cancer, and highlight potential diagnostic and therapeutic targets in the genomically stable tumor microenvironment.
Our studies on HSF1 in the tumor microenvironment (Aim 1, 3) significantly advanced the research field of stress responses. Cellular stress responses have been studied for decades, however the notion that stress responses serve to promote cell-cell communication was scarcely explored. Our work established a central role for HSF1 in CAFs, and showed that stress responses can act in a non-cell autonomous manner (Nature Communications 2020, Advances in Experimental Medicine and Biology 2020, Cancer Research 2021).
Our study in breast cancer mentioned above (Nature Cancer 2020) led to an unexpected finding that the CAF composition of BRCA-mutated tumors is distinct from the CAF composition of BRCA-WT tumors. This study opened up a new avenue of research in my lab and led to our study of stromal composition of BRCA-mutated cancers in the pancreas (BioRxiv 2021 & Nature Communication, in press).
Together, these studies provide transcriptional and functional maps of CAFs in breast, pancreas, gastric and colon cancer, and highlight potential diagnostic and therapeutic targets in the genomically stable tumor microenvironment.