SOX17 enables immune evasion of early

Pelka, K. et al. Spatially organized multicellular immune hubs in human colorectal cancer. Cell 184, 4734–4752.e4720 (2021).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Lin, J. R. et al. Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer. Cell 186, 363–381.e319 (2023).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Tauriello, D. V. F. et al. TGFβ drives immune evasion in genetically reconstituted colon cancer metastasis. Nature 554, 538–543 (2018).

ADS 
CAS 
PubMed 

Google Scholar 

Shankaran, V. et al. IFNγ and lymphocytes prevent primary tumour development and shape tumour immunogenicity. Nature 410, 1107–1111 (2001).

ADS 
CAS 
PubMed 

Google Scholar 

Koebel, C. M. et al. Adaptive immunity maintains occult cancer in an equilibrium state. Nature 450, 903–907 (2007).

ADS 
CAS 
PubMed 

Google Scholar 

Beyaz, S. et al. Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis. Cell Stem Cell 28, 1922–1935 e1925 (2021).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Roper, J. et al. In vivo genome editing and organoid transplantation models of colorectal cancer and metastasis. Nat. Biotechnol. 35, 569–576 (2017).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Roper, J. et al. Colonoscopy-based colorectal cancer modeling in mice with CRISPR–Cas9 genome editing and organoid transplantation. Nat. Protoc. 13, 217–234 (2018).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Barker, N. et al. Crypt stem cells as the cells-of-origin of intestinal cancer. Nature 457, 608–611 (2009).

ADS 
CAS 
PubMed 

Google Scholar 

Goto, N. et al. Lymphatics and fibroblasts support intestinal stem cells in homeostasis and injury. Cell Stem Cell 29, 1246–1261 e1246 (2022).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Spence, J. R. et al. Sox17 regulates organ lineage segregation of ventral foregut progenitor cells. Dev. Cell 17, 62–74 (2009).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Shivdasani, R. A. Molecular regulation of vertebrate early endoderm development. Dev. Biol. 249, 191–203 (2002).

CAS 
PubMed 

Google Scholar 

Kanai-Azuma, M. et al. Depletion of definitive gut endoderm in Sox17-null mutant mice. Development 129, 2367–2379 (2002).

CAS 
PubMed 

Google Scholar 

Schepers, A. G. et al. Lineage tracing reveals Lgr5+ stem cell activity in mouse intestinal adenomas. Science 337, 730–735 (2012).

ADS 
CAS 
PubMed 

Google Scholar 

The Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330–337 (2012).

ADS 

Google Scholar 

Westcott, P. M. K. et al. Low neoantigen expression and poor T-cell priming underlie early immune escape in colorectal cancer. Nat. Cancer 2, 1071–1085 (2021).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Heide, T. et al. The co-evolution of the genome and epigenome in colorectal cancer. Nature 611, 733–743 (2022).

ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Fordham, R. P. et al. Transplantation of expanded fetal intestinal progenitors contributes to colon regeneration after injury. Cell Stem Cell 13, 734–744 (2013).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Mustata, R. C. et al. Identification of Lgr5-independent spheroid-generating progenitors of the mouse fetal intestinal epithelium. Cell Rep. 5, 421–432 (2013).

CAS 
PubMed 

Google Scholar 

Nusse, Y. M. et al. Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche. Nature 559, 109–113 (2018).

ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Llosa, N. J. et al. The vigorous immune microenvironment of microsatellite instable colon cancer is balanced by multiple counter-inhibitory checkpoints. Cancer Discov. 5, 43–51 (2015).

CAS 
PubMed 

Google Scholar 

Beltra, J. C. et al. Developmental relationships of four exhausted CD8+ T cell subsets reveals underlying transcriptional and epigenetic landscape control mechanisms. Immunity 52, 825–841.e828 (2020).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Miller, B. C. et al. Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade. Nat. Immunol. 20, 326–336 (2019).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Khan, O. et al. TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion. Nature 571, 211–218 (2019).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Di Pilato, M. et al. CXCR6 positions cytotoxic T cells to receive critical survival signals in the tumor microenvironment. Cell 184, 4512–4530.e4522 (2021).

PubMed 
PubMed Central 

Google Scholar 

Ikeda, H., Old, L. J. & Schreiber, R. D. The roles of IFNγ in protection against tumor development and cancer immunoediting. Cytokine Growth Factor Rev. 13, 95–109 (2002).

CAS 
PubMed 

Google Scholar 

Pan, D. et al. A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science 359, 770–775 (2018).

ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Miao, D. et al. Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors. Nat. Genet. 50, 1271–1281 (2018).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Reschke, R. & Gajewski, T. F. CXCL9 and CXCL10 bring the heat to tumors. Sci. Immunol. 7, eabq6509 (2022).

CAS 
PubMed 

Google Scholar 

Fearon, E. R. & Vogelstein, B. A genetic model for colorectal tumorigenesis. Cell 61, 759–767 (1990).

CAS 
PubMed 

Google Scholar 

Shimokawa, M. et al. Visualization and targeting of LGR5+ human colon cancer stem cells. Nature 545, 187–192 (2017).

ADS 
CAS 
PubMed 

Google Scholar 

de Sousa e Melo, F. et al. A distinct role for Lgr5+ stem cells in primary and metastatic colon cancer. Nature 543, 676–680 (2017).

ADS 
PubMed 

Google Scholar 

Fumagalli, A. et al. Plasticity of Lgr5-negative cancer cells drives metastasis in colorectal cancer. Cell Stem Cell 26, 569–578.e567 (2020).

CAS 
PubMed 
PubMed Central 

Google Scholar 

He, S., Kim, I., Lim, M. S. & Morrison, S. J. Sox17 expression confers self-renewal potential and fetal stem cell characteristics upon adult hematopoietic progenitors. Genes Dev. 25, 1613–1627 (2011).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Kim, I., Saunders, T. L. & Morrison, S. J. Sox17 dependence distinguishes the transcriptional regulation of fetal from adult hematopoietic stem cells. Cell 130, 470–483 (2007).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Agudo, J. et al. Quiescent tissue stem cells evade immune surveillance. Immunity 48, 271–285 e275 (2018).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Drukker, M. et al. Human embryonic stem cells and their differentiated derivatives are less susceptible to immune rejection than adult cells. Stem Cells 24, 221–229 (2006).

PubMed 

Google Scholar 

Li, L. et al. Human embryonic stem cells possess immune-privileged properties. Stem Cells 22, 448–456 (2004).

CAS 
PubMed 

Google Scholar 

Manguso, R. T. et al. In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target. Nature 547, 413–418 (2017).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Patel, S. J. et al. Identification of essential genes for cancer immunotherapy. Nature 548, 537–542 (2017).

ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Gao, J. et al. Loss of IFN-γ pathway genes in tumor cells as a mechanism of resistance to anti-CTLA-4 therapy. Cell 167, 397–404.e399 (2016).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Zaretsky, J. M. et al. Mutations Associated with acquired resistance to PD-1 blockade in melanoma. N. Engl. J. Med. 375, 819–829 (2016).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Baldominos, P. et al. Quiescent cancer cells resist T cell attack by forming an immunosuppressive niche. Cell 185, 1694–1708.e1619 (2022).

CAS 
PubMed 

Google Scholar 

Zhang, W. et al. Epigenetic inactivation of the canonical Wnt antagonist SRY-box containing gene 17 in colorectal cancer. Cancer Res. 68, 2764–2772 (2008).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Wang, L. et al. SOX17 antagonizes the WNT signaling pathway and is epigenetically inactivated in clear-cell renal cell carcinoma. OncoTargets Ther. 14, 3383–3394 (2021).

Wang, M. et al. Loss-of-function mutations of SOX17 lead to YAP/TEAD activation-dependent malignant transformation in endometrial cancer. Oncogene 42, 322–334 (2023).

CAS 
PubMed 

Google Scholar 

Delgiorno, K. E. et al. Identification and manipulation of biliary metaplasia in pancreatic tumors. Gastroenterology 146, 233–244.e235 (2014).

CAS 
PubMed 

Google Scholar 

Tan, D. S., Holzner, M., Weng, M., Srivastava, Y. & Jauch, R. SOX17 in cellular reprogramming and cancer. Semin. Cancer Biol. 67, 65–73 (2020).

CAS 
PubMed 

Google Scholar 

Barker, N. et al. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 449, 1003–1007 (2007).

ADS 
CAS 
PubMed 

Google Scholar 

el Marjou, F. et al. Tissue-specific and inducible Cre-mediated recombination in the gut epithelium. Genesis 39, 186–193 (2004).

CAS 
PubMed 

Google Scholar 

Kuraguchi, M. et al. Adenomatous polyposis coli (APC) is required for normal development of skin and thymus. PLoS Genet. 2, e146 (2006).

PubMed 
PubMed Central 

Google Scholar 

Johnson, L. et al. Somatic activation of the K-ras oncogene causes early onset lung cancer in mice. Nature 410, 1111–1116 (2001).

ADS 
CAS 
PubMed 

Google Scholar 

Marino, S., Vooijs, M., van Der Gulden, H., Jonkers, J. & Berns, A. Induction of medulloblastomas in p53-null mutant mice by somatic inactivation of Rb in the external granular layer cells of the cerebellum. Genes Dev. 14, 994–1004 (2000).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Hogquist, K. A. et al. T cell receptor antagonist peptides induce positive selection. Cell 76, 17–27 (1994).

CAS 
PubMed 

Google Scholar 

Chu, V. T. et al. Efficient generation of Rosa26 knock-in mice using CRISPR/Cas9 in C57BL/6 zygotes. BMC Biotechnol. 16, 4 (2016).

PubMed 
PubMed Central 

Google Scholar 

Madisen, L. et al. A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat. Neurosci. 13, 133–140 (2010).

CAS 
PubMed 

Google Scholar 

Hao, Z. & Rajewsky, K. Homeostasis of peripheral B cells in the absence of B cell influx from the bone marrow. J. Exp. Med. 194, 1151–1164 (2001).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Dow, L. E. et al. Apc restoration promotes cellular differentiation and reestablishes crypt homeostasis in colorectal cancer. Cell 161, 1539–1552 (2015).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Boutin, A. T. et al. Oncogenic Kras drives invasion and maintains metastases in colorectal cancer. Genes Dev. 31, 370–382 (2017).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Fujii, M., Matano, M., Nanki, K. & Sato, T. Efficient genetic engineering of human intestinal organoids using electroporation. Nat. Protoc. 10, 1474–1485 (2015).

CAS 
PubMed 

Google Scholar 

Miyoshi, H. & Stappenbeck, T. S. In vitro expansion and genetic modification of gastrointestinal stem cells in spheroid culture. Nat. Protoc. 8, 2471–2482 (2013).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Schwank, G. & Clevers, H. CRISPR/Cas9-mediated genome editing of mouse small intestinal organoids. Methods Mol. Biol. 1422, 3–11 (2016).

CAS 
PubMed 

Google Scholar 

Matano, M. et al. Modeling colorectal cancer using CRISPR–Cas9-mediated engineering of human intestinal organoids. Nat. Med. 21, 256–262 (2015).

CAS 
PubMed 

Google Scholar 

Drost, J. et al. Sequential cancer mutations in cultured human intestinal stem cells. Nature 521, 43–47 (2015).

ADS 
CAS 
PubMed 

Google Scholar 

Koo, B. K. et al. Controlled gene expression in primary Lgr5 organoid cultures. Nat. Methods 9, 81–83 (2011).

PubMed 

Google Scholar 

Pelossof, R. et al. Prediction of potent shRNAs with a sequential classification algorithm. Nat. Biotechnol. 35, 350–353 (2017).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Dow, L. E. et al. A pipeline for the generation of shRNA transgenic mice. Nat. Protoc. 7, 374–393 (2012).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Fellmann, C. et al. An optimized microRNA backbone for effective single-copy RNAi. Cell Rep. 5, 1704–1713 (2013).

CAS 
PubMed 

Google Scholar 

Mana, M. D. et al. High-fat diet-activated fatty acid oxidation mediates intestinal stemness and tumorigenicity. Cell Rep. 35, 109212 (2021).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Cheng, C. W. et al. Ketone body signaling mediates intestinal stem cell homeostasis and adaptation to diet. Cell 178, 1115–1131.e1115 (2019).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Beyaz, S. et al. High-fat diet enhances stemness and tumorigenicity of intestinal progenitors. Nature 531, 53–58 (2016).

ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Sheridan, B. S. & Lefrancois, L. Isolation of mouse lymphocytes from small intestine tissues. Curr. Protoc. Immunol. 99, 3.19.1–3.19.11 (2012).

Google Scholar 

Buenrostro, J. D., Wu, B., Chang, H. Y. & Greenleaf, W. J. ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr. Protoc. Mol. Biol. 109, 21.29.21–21.29.29 (2015).

Google Scholar 

Skene, P. J., Henikoff, J. G. & Henikoff, S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat. Protoc. 13, 1006–1019 (2018).

CAS 
PubMed 

Google Scholar 

Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

PubMed 
PubMed Central 

Google Scholar 

Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome. BMC Bioinform. 12, 323 (2011).

Bullard, J. H., Purdom, E., Hansen, K. D. & Dudoit, S. Evaluation of statistical methods for normalization and differential expression in mRNA-seq experiments. BMC Bioinform. 11, 94 (2010).

Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417–419 (2017).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Soneson, C., Love, M. I. & Robinson, M. D. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Res 4, 1521 (2015).

PubMed 

Google Scholar 

Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

PubMed 
PubMed Central 

Google Scholar 

Zhu, A., Ibrahim, J. G. & Love, M. I. Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences. Bioinformatics 35, 2084–2092 (2019).

CAS 
PubMed 

Google Scholar 

Mootha, V. K. et al. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 34, 267–273 (2003).

CAS 
PubMed 

Google Scholar 

Han, T. et al. Lineage reversion drives WNT independence in intestinal cancer. Cancer Discov. 10, 1590–1609 (2020).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).

ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

PubMed 
PubMed Central 

Google Scholar 

Feng, J., Liu, T., Qin, B., Zhang, Y. & Liu, X. S. Identifying ChIP-seq enrichment using MACS. Nat. Protoc. 7, 1728–1740 (2012).

CAS 
PubMed 

Google Scholar 

Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Wang, Q. et al. Exploring epigenomic datasets by ChIPseeker. Curr. Protoc. 2, e585 (2022).

CAS 
PubMed 

Google Scholar 

Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Meers, M. P., Tenenbaum, D. & Henikoff, S. Peak calling by sparse enrichment analysis for CUT&RUN chromatin profiling. Epigenetics Chromatin 12, 42 (2019).

PubMed 
PubMed Central 

Google Scholar 

Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e3529 (2021).

CAS 
PubMed 
PubMed Central 

Google Scholar 

You May Also Like

More From Author

+ There are no comments

Add yours