Browsing by Subject "Colorectal cancer"

Non-genetic reprogramming, including but not limited to metabolomic and epigenetic, play an equally significant role in cancer development compared to genetic mutations. In most scenarios, non-genetic alterations of tumor cells are associated with their tumor microenvironment, which is highly related to tumor progress and efficiency of the treatment. Nevertheless, how cancer cells adapt their microenvironment by metabolomic or epigenetic reprogramming remains largely unknown. This dissertation started with exploring two scenarios in colorectal cancer (CRC) studies: the metabolic reprogramming of CRC liver metastasis and the epigenetic remodeling of CRC patient-derived models of cancer. In the study of CRC liver metastasis (Chapter 2), we found that metastatic CRC cells promote their fructose metabolism in the liver by upregulating ALDOB. Knocking down ALDOB or restricting the dietary fructose can suppress CRC liver metastasis. In addition, we examined the potential therapeutic approach for liver metastasis with a KHK inhibitor. For the patient-derived models of cancer (PDMC) project (Chapter 3), we developed six matched PT-PDMC sets and performed ATAC-seq and mRNA to study the chromatin accessibilities of CRC cells. We found two-axis chromatin remodeling separating PDMC from the original patient sample (axis #1) as well as the different cancer models (axis #2). PDOX is more similar to PDX than organoids suggesting the chromatin remodeling of CRC cells is under the pressure of tumor microenvironment in PDMC. We also identified the two transcript factors, KLF14 and EGR2, which respond to the xenografts’ environment by footprinting analysis. These two TFs and their downstream gene, EPHA4, altered CRC tumor growth and drug sensitivities. Therefore, chromatin remodeling of different PDMC may interfere with their ability to predict therapeutic outcomes. In the last part of the dissertation (Chapter 4), I developed a novel system that can label and manipulate the tumor niche in situ. This method provides tools for studying the non-genetic alterations of CRC cells when they interact with the tumor microenvironment. Taken together, this dissertation presents a comprehensive understanding of the non-genetic reprogramming of colorectal cancer and its tumor microenvironment. It advances both the knowledge of non-genetic reprogramming in colorectal cancer and technologies to study the tumor microenvironment.

Colorectal cancer (CRC) is the third most diagnosed type of cancer, and the 5-year survival rate drops significantly once the patient develops liver metastases. Notably, over the past decade, multiple patient-derived models of cancer (PDMC) have been developed and are widely accepted as preclinical models. Current chemotherapy does not distinguish the primary and metastatic loci, and there lack a direct comparison between different PDMC (e.g., patient-derived organoids (PDO), patient-derived xenografts (PDX) and PDO-derived xenografts (PDOX)) and the patient tumor (PT). Therefore, understanding the differences between the cells from metastasized CRC and the primary site, as well as the differences between the PDMC and the original patient specimen is of critical importance.In CRC, many conventional studies have focused on associating genetic mutations with clinical phenotypes. However, non-genetic alterations including changes in chromatin accessibility, transcriptome and histone modification markers provide an alternative and even faster way for the tumor cells to adapt to their microenvironment. In this dissertation, we first focused on how the liver microenvironment can affect the epigenetic transformations of the metastasized CRC. Using high-throughput sequencing such as ATAC-seq, RNA-seq and Mint-ChIP, we identified an HGF-PU.1-DPP4 epigenetic reprogramming axis that facilitates the metastatic tumor cells to adapt to the liver microenvironment. The results were validated by extensive numbers of patient samples and the precision epigenetic modification tools CRISPR/dCas9KRAB/HDAC. We identified several FDA approved drugs including Sitagliptin and Norleual, which can be repurposed to treat CRC liver metastases. Furthermore, using the similar set of tools, we revealed that each PDMC undergo distinctive epigenetic reprogramming following two modeling axes. The first axis delineates PDX and PDO from patient, while the second axis distinguishes PDX and PDO. We further identified that the transcription factors KLF14 and EGR2 are collectively more active in the PDOX than in PDO. Moreover, we demonstrated that the varied expression level of their common downstream targets EPHA4 led to distinct drug responses in PDO to 147 FDA approved compounds. We concluded that there are differences in growth and drug sensitivity between PDOX and PDO, which should be taken into consideration when using PDMC to predict clinical outcomes.

The intestine is the home for trillions of microbes, collectively called microbiota. The mutualism of commensal microbes benefits intestinal health. To establish mutualism, intestinal immunity must equip with mechanisms to tolerate innocent microbiota while responding to pathogens. Intestinal immunity is coordinated by specialized and complicated mononuclear phagocytes subsets. The constitution of complex mononuclear phagocytes are thought to be similar in both small intestine and colon, however, these two organs are distinct in anatomy, microbiota abundance and composition, and immunological requirement. However, whether those distinctions require organ-specific mononuclear phagocytes to exert organ-specific immunity is unknown. To address whether there are organ-specific demands, we implement a novel mononuclear phagocyte subsetting strategy in the murine intestine and found two novel colon-specific mononuclear phagocytes: a macrophage population and a Th17-inducing dendritic cell (DC) subset. Those colon-specific DCs and macrophages surprisingly both required the transcription factor IRF4 and co-expressed DC marker CD24 and macrophage marker CD14. Novel IRF4-dependent CD14+CD24+ macrophages were markedly different from conventional macrophages in the way that novel CD14+CD24+ macrophages did not express macrophage markers CX3CR1, CD64, and CD88, and surprisingly not expressed cytokine IL-10, which is known to expressed in intestinal macrophages. Furthermore, we found that novel colon-specific CD14+CD24+ mononuclear phagocytes promote Th17 immunity in the colon and showed definitive evidence of differential requirement of mononuclear phagocytes in small intestine and colon for Th17 immunity. Our research discovered the diversity of mononuclear phagocytes with organ specificity and the organ-specific requirements for Th17 immunity.

While we found the requirement of organ-specific mononuclear phagocytes for Th17 immunity, regulation of innate-like IL-17 producing gd T cells, constituting a large source of IL-17 in intestine, is not addressed. It has been widely known that effector functions of gd T cells were pre-committed in the thymus, however, emerging evidence shows that environmental cues further re-programed gd T cell effectors. In the intestine, the major environmental cues are derived from the microbiota. Nevertheless, the microbiota-dependent regulation is controversial that some reports hold that microbiota provide immune activation signals while other reports conclude the suppressive function of microbiota. It remains unknown whether the impact of microbiota on gd T cells is activated, suppressive, or binary and whether microbiota shape gd T cells immune dynamics in distinct physiological conditions. Here, we identify that microbiota concomitantly upregulate IL-17-production and expression of the inhibitory receptor programmed cell death protein (PD-1) in gd17 T cells. The requirement of microbiota to preferentially upregulate PD-1 is conserved in gd17 T cells across multiple mucosal tissues. We determined the microbiota-driven PD-1 inhibits IL-17 production by endogenous gd17 effectors. We further show that microbiota-driven PD-1 and IL-17 phenotype are dynamics, wherein both PD-1 and IL-17 are downregulated once microbiota is depleted and is concomitantly upregulated during gut inflammation. Additionally, we found subset-specific metabolic shift in gd17 T cells that elevated lipid uptake in gd17 cells in response to intestinal inflammation linking to enhanced IL-17 production.

The coordination between adaptive and innate immune responses is essential for eradicating cancer cells. Among immune cells, DCs are the most powerful cells connecting innate and adaptive immune responses. Especially, Batf3-dependent DCs subset are thought to be key to anti-tumor immunity. The anti-tumor functions of Batf3-dependent DCs have been well reported in skin cancer, however, whether these DCs have the similar anti-tumor functions in colorectal cancer is largely unknown. Here, we investigated the roles of Batf3-dependent DCs in a spontaneous colorectal cancer and surprisingly found that these DCs promoted colon tumorigenesis. We identified an unconventional function of Batf3-dependent DCs to promote tumor infiltrating gd17 T cells in colon tumor instead of expanding anti-tumor IFNg-producing T cells. Proinflammatory cytokine IL-17 is known to promote colon tumor and the pro-tumor role of gd17 T cells have been proposed in several cancers including colorectal cancer. Mechanistically, we determined that Batf3-dependent DCs promote recruitment of gd17 T cells in colon tumor but are not required for gd17 T cells survival or proliferation. As we found that microbiota drives IL-17 production in gd17 T cells, the production of tumor infiltrating endogenous effector gd17 T cells and colon tumor growth were microbiota-dependent. Our study revealed a requirement of Batf3-dependent DCs to regulate tumor infiltrating gd17 T cells and the effector function is modulated by microbiota in colon tumor.