Barker, N. (2014). Adult intestinal stem cells: critical drivers of epithelial homeostasis and regeneration. Nat. Rev. Mol. Cell Biol. 15, 19–33.
Barker, N., van Es, J.H., Kuipers, J., Kujala, P., van den Born, M., Co- zijnsen, M., Haegebarth, A., Korving, J., Begthel, H., Peters, P.J., et al. (2007). Identification of stem cells in small intestine and co- lon by marker gene Lgr5. Nature 449, 1003–1007.
Bedard, P.L., Hansen, A.R., Ratain, M.J., and Siu, L.L. (2013). Tumour heterogeneity in the clinic. Nature 501, 355–364.
Birkbak, N.J., and McGranahan, N. (2020). Cancer genome evolu- tionary trajectories in metastasis. Cancer Cell 37, 8–19.
Blanco, S., Bandiera, R., Popis, M., Hussain, S., Lombard, P., Aleksic, J., Sajini, A., Tanna, H., Cortes-Garrido, R., Gkatza, N., et al. (2016). Stem cell function and stress response are controlled by protein synthesis. Nature 534, 335–340.
Boj, S.F., Hwang, C.I., Baker, L.A., Chio, I.I., Engle, D.D., Corbo, V., Jager, M., Ponz-Sarvise, M., Tiriac, H., Spector, M.S., et al. (2015). Organoid models of human and mouse ductal pancreatic cancer. Cell 160, 324–338.
Clevers, H. (2013). The intestinal crypt, a prototype stem cell compartment. Cell 154, 274–284.
Cortina, C., Turon, G., Stork, D., Hernando-Momblona, X., Sevil- lano, M., Aguilera, M., Tosi, S., Merlos-Suarez, A., Stephan-Otto At- tolini, C., Sancho, E., et al. (2017). A genome editing approach to study cancer stem cells in human tumors. EMBO Mol. Med. 9, 869–879.
Dalerba, P., Kalisky, T., Sahoo, D., Rajendran, P.S., Rothenberg, M.E., Leyrat, A.A., Sim, S., Okamoto, J., Johnston, D.M., Qian, D., et al. (2011). Single-cell dissection of transcriptional heteroge- neity in human colon tumors. Nat. Biotechnol. 29, 1120–1127.
de Sousa e Melo, F., Kurtova, A.V., Harnoss, J.M., Kljavin, N., Hoeck, J.D., Hung, J., Anderson, J.E., Storm, E.E., Modrusan, Z., Koeppen, H., et al. (2017). A distinct role for Lgr5(+) stem cells in primary and metastatic colon cancer. Nature 543, 676–680.
Drost, J., and Clevers, H. (2018). Organoids in cancer research. Nat. Rev. Cancer 18, 407–418.
Eide, P.W., Bruun, J., Lothe, R.A., and Sveen, A. (2017). CMScaller: an R package for consensus molecular subtyping of colorectal can- cer pre-clinical models. Sci. Rep. 7, 16618.
Engel, R.M., Chan, W.H., Nickless, D., Hlavca, S., R ichards, E., Kerr, G., Oliva, K., McMurrick, P.J., Jarde, T., and Abud, H.E. (2020). Pa- tient-derived colorectal cancer organoids upregulate revival stem cell marker genes following chemotherapeutic treatment. J. Clin. Med. 9, 128.
Fujii, M., Shimokawa, M., Date, S., Takano, A., Matano, M., Nanki, K., Ohta, Y., Toshimitsu, K., Nakazato, Y., Kawasaki, K., et al. (2016). A colorectal tumor organoid library demonstrates progres- sive loss of niche factor requirements during tumorigenesis. Cell Stem Cell 18, 827–838.
Fumagalli, A., Oost, K.C., Kester, L., Morgner, J., Bornes, L., Bruens, L., Spaargaren, L., Azkanaz, M., Schelfhorst, T., Beerling, E., et al. (2020). Plasticity of Lgr5-negative cancer cells drives metastasis in colorectal cancer. Cell Stem Cell 26, 569–578.e7.
Guinney, J., Dienstmann, R., Wang, X., de Reynies, A., Schlicker, A., Soneson, C., Marisa, L., Roepman, P., Nyamundanda, G., Angel- ino, P., et al. (2015). The consensus molecular subtypes of colo- rectal cancer. Nat. Med. 21, 1350–1356.
Haber, A.L., Biton, M., Rogel, N., Herbst, R.H., Shekhar, K., Smillie, C., Burgin, G., Delorey, T.M., Howitt, M.R., Katz, Y., et al. (2017). A single-cell survey of the small intestinal epithelium. Nature 551, 333–339.
Huang, L., Holtzinger, A., Jagan, I., BeGora, M., Lohse, I., Ngai, N., Nostro, C., Wang, R., Muthuswamy, L.B., Crawford, H.C., et al. (2015). Ductal pancreatic cancer modeling and drug screening us- ing human pluripotent stem cell- and patient-derived tumor orga- noids. Nat. Med. 21, 1364–1371.
Ikehara, Y., Kojima, N., Kurosawa, N., Kudo, T., Kono, M., Nishi- hara, S., Issiki, S., Morozumi, K., Itzkowitz, S., Tsuda, T., et al. (1999). Cloning and expression of a human gene encoding an N- acetylgalactosamine-alpha2,6-sialyltransferase (ST6GalNAc I): a candidate for synthesis of cancer-associated sialyl-Tn antigens. Glycobiology 9, 1213–1224.
Ishaque, N., Abba, M.L., Hauser, C., Patil, N., Paramasivam, N., Huebschmann, D., Leupold, J.H., Balasubramanian, G.P., Klein- heinz, K., Toprak, U.H., et al. (2018). Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer. Nat. Commun. 9, 4782.
Iusuf, D., Teunissen, S.F., Wagenaar, E., Rosing, H., Beijnen, J.H., and Schinkel, A.H. (2011). P-Glycoprotein (ABCB1) transports the primary active tamoxifen metabolites endoxifen and 4-hy- droxytamoxifen and restricts their brain penetration.
J. Pharmacol. Exp. Ther. 337, 710–717.
Johnson, K.A., DeStefanis, R.A., Emmerich, P.B., Grogan, P.T., Kratz, J.D., Makkar, S.K., Clipson, L., and Deming, D.A. (2020). Hu- man colon organoids and other laboratory strategies to enhance patient treatment selection. Curr. Treat. Options Oncol. 21, 35.
Karthaus, W.R., Iaquinta, P.J., Drost, J., Gracanin, A., van Boxtel, R., Wongvipat, J., Dowling, C.M., Gao, D., Begthel, H., Sachs, N., et al. (2014). Identification of multipotent luminal progenitor cells in human prostate organoid cultures. Cell 159, 163–175.
Kiyotani, K., Mushiroda, T., Imamura, C.K., Hosono, N., Tsunoda, T., Kubo, M., Tanigawara, Y., Flockhart, D.A., Desta, Z., Skaar, T.C., et al. (2010). Significant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adjuvant tamoxifen therapy for breast cancer patients. J. Clin. Oncol. 28, 1287–1293.
Koslow, M., O’Keefe, K.J., Hosseini, Z.F., Nelson, D.A., and Larsen, M. (2019). ROCK inhibitor increases proacinar cells in adult sali- vary gland organoids. Stem Cell Res 41, 101608.
Lambert, A.W., Pattabiraman, D.R., and Weinberg, R.A. (2017). Emerging biological principles of metastasis. Cell 168, 670–691.
Lee, J.R., Kwon, C.H., Choi, Y., Park, H.J., Kim, H.S., Jo, H.J., Oh, N., and Park do, Y. (2016). Transcriptome analysis of paired primary colorectal carcinoma and liver metastases reveals fusion transcripts and similar gene expression profiles in primary carcinoma and liver metastases. BMC Cancer 16, 539.
Lenos, K.J., Miedema, D.M., Lodestijn, S.C., Nijman, L.E., van den Bosch, T., Romero Ros, X., Lourenco, F.C., Lecca, M.C., van der Heijden, M., van Neerven, S.M., et al. (2018). Stem cell function- ality is microenvironmentally defined during tumour expansion and therapy response in colon cancer. Nat. Cell Biol. 20, 1193– 1202.
Li, H., Courtois, E.T., Sengupta, D., Tan, Y., Chen, K.H., Goh, J.J.L., Kong, S.L., Chua, C., Hon, L.K., Tan, W.S., et al. (2017). Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Nat. Genet. 49, 708–718.
Liakath-Ali, K., Mills, E.W., Sequeira, I., Lichtenberger, B.M., Pisco, A.O., Sipila, K.H., Mishra, A., Yoshikawa, H., Wu, C.C., Ly, T., et al. (2018). An evolutionarily conserved ribosome-rescue pathway maintains epidermal homeostasis. Nature 556, 376–380.
Magee, J.A., Piskounova, E., and Morrison, S.J. (2012). Cancer stem cells: impact, heterogeneity, and uncertainty. Cancer Cell 21, 283– 296.
Massague, J., and Obenauf, A.C. (2016). Metastatic colonization by circulating tumour cells. Nature 529, 298–306.
Meacham, C.E., and Morrison, S.J. (2013). Tumour heterogeneity and cancer cell plasticity. Nature 501, 328–337.
Munoz, J., Stange, D.E., Schepers, A.G., van de Wetering, M., Koo, B.K., Itzkovitz, S., Volckmann, R., Kung, K.S., Koster, J., Radulescu, S., et al. (2012). The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent ’+4’ cell markers. EMBO J. 31, 3079–3091.
Nanki, K., Toshimitsu, K., Takano, A., Fujii, M., Shimokawa, M., Ohta, Y., Matano, M., Seino, T., Nishikori, S., Ishikawa, K., et al. (2018). Divergent routes toward Wnt and R-spondin niche inde- pendency during human gastric carcinogenesis. Cell 174, 856– 869 e817.
Ohata, H., Ishiguro, T., Aihara, Y., Sato, A., Sakai, H., Sekine, S., Ta- niguchi, H., Akasu, T., Fujita, S., Nakagama, H., et al. (2012). Induc- tion of the stem-like cell regulator CD44 by Rho kinase inhibition contributes to the maintenance of colon cancer-initiating cells. Cancer Res. 72, 5101–5110.
Ooft, S.N., Weeber, F., Dijkstra, K.K., McLean, C.M., Kaing, S., van Werkhoven, E., Schipper, L., Hoes, L., Vis, D.J., van de Haar, J., et al. (2019). Patient-derived organoids can predict response to chemo- therapy in metastatic colorectal cancer patients. Sci. Translational Med. 11, eaay2574.
Sachs, N., de Ligt, J., Kopper, O., Gogola, E., Bounova, G., Weeber, F., Balgobind, A.V., Wind, K., Gracanin, A., Begthel, H., et al. (2018). A living biobank of breast cancer organoids captures dis- ease heterogeneity. Cell 172, 373–386 e310.
Sakahara, M., Okamoto, T., Oyanagi, J., Takano, H., Natsume, Y., Yamanaka, H., Kusama, D., Fusejima, M., Tanaka, N., Mori, S., et al. (2019). IFN/STAT signaling controls tumorigenesis and the drug response in colorectal cancer. Cancer Sci. 110, 1293–1305.
Sato, T., Vries, R.G., Snippert, H.J., van de Wetering, M., Barker, N., Stange, D.E., van Es, J.H., Abo, A., Kujala, P., Peters, P.J., et al. (2009). Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 459, 262–265.
Schepers, A.G., Snippert, H.J., Stange, D.E., van den Born, M., van Es, J.H., van de Wetering, M., and Clevers, H. (2012). Lineage tracing reveals Lgr5+ stem cell activity in mouse intestinal ade- nomas. Science 337, 730–735.
Schlicker, A., Ellappalayam, A., Beumer, I.J., Snel, M.H.J., Mittem- pergher, L., Diosdado, B., Dreezen, C., Tian, S., Salazar, R., Loupa- kis, F., et al. (2020). Investigating the concordance in molecular subtypes of primary colorectal tumors and their matched synchro- nous liver metastasis. Int. J. Cancer 147, 2303–2315.
Schweiger, T., Liebmann-Reindl, S., Glueck, O., Starlinger, P., Laen- gle, J., Birner, P., Klepetko, W., Pils, D., Streubel, B., and Hoetze- necker, K. (2018). Mutational profile of colorectal cancer lung me- tastases and paired primary tumors by targeted next generation sequencing: implications on clinical outcome after surgery. J. Thorac. Dis. 10, 6147–6157.
Sensorn, I., Sirachainan, E., Chamnanphon, M., Pasomsub, E., Tra- chu, N., Supavilai, P., Sukasem, C., and Pinthong, D. (2013). Asso- ciation of CYP3A4/5, ABCB1 and ABCC2 polymorphisms and clin- ical outcomes of Thai breast cancer patients treated with tamoxifen. Pharmgenomics Pers Med. 6, 93–98.
Sensorn, I., Sukasem, C., Sirachainan, E., Chamnanphon, M., Pa- somsub, E., Trachu, N., Supavilai, P., Pinthong, D., and Wongwai- sayawan, S. (2016). ABCB1 and ABCC2 and the risk of distant metastasis in Thai breast cancer patients treated with tamoxifen. Onco Targets Ther. 9, 2121–2129.
Shimokawa, M., Ohta, Y., Nishikori, S., Matano, M., Takano, A., Fu- jii, M., Date, S., Sugimoto, S., Kanai, T., and Sato, T. (2017). Visual- ization and targeting of LGR5(+) human colon cancer stem cells. Nature 545, 187–192.
Signer, R.A., Magee, J.A., Salic, A., and Morrison, S.J. (2014). Hae- matopoietic stem cells require a highly regulated protein synthesis rate. Nature 509, 49–54.
Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S., et al. (2005). Gene set enrichment analysis: a knowl- edge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U S A 102, 15545–15550.
Suzuki, K., Tsunekawa, Y., Hernandez-Benitez, R., Wu, J., Zhu, J., Kim, E.J., Hatanaka, F., Yamamoto, M., Araoka, T., Li, Z., et al. (2016). In vivo genome editing via CRISPR/Cas9 mediated homol- ogy-independent targeted integration. Nature 540, 144–149.
Taniguchi, K., Wada, M., Kohno, K., Nakamura, T., Kawabe, T., Ka- wakami, M., Kagotani, K., Okumura, K., Akiyama, S., and Kuwano, M. (1996). A human canalicular multispecific organic anion trans- porter (cMOAT) gene is overexpressed in cisplatin-resistant human cancer cell lines with decreased drug accumulation. Cancer Res. 56, 4124–4129.
Tieng, F.Y.F., Baharudin, R., Abu, N., Mohd Yunos, R.I., Lee, L.H., and Ab Mutalib, N.S. (2020). Single cell transcriptome in colorectal cancer-current updates on its application in metastasis, chemore- sistance and the roles of circulating tumor cells. Front. Pharmacol. 11, 135.
Tuveson, D., and Clevers, H. (2019). Cancer modeling meets hu- man organoid technology. Science 364, 952–955.
van de Wetering, M., Francies, H.E., Francis, J.M., Bounova, G., Iorio, F., Pronk, A., van Houdt, W., van Gorp, J., Taylor-Weiner, A., Kester, L., et al. (2015). Prospective derivation of a living orga- noid biobank of colorectal cancer patients. Cell 161, 933–945.
van der Flier, L.G., Haegebarth, A., Stange, D.E., van de Wetering, M., and Clevers, H. (2009a). OLFM4 is a robust marker for stem cells in human intestine and marks a subset of colorectal cancer cells. Gastroenterology 137, 15–17.
van der Flier, L.G., van Gijn, M.E., Hatzis, P., Kujala, P., Haegebarth, A., Stange, D.E., Begthel, H., van den Born, M., Guryev, V., Oving, I., et al. (2009b). Transcription factor achaete scute-like 2 controls intestinal stem cell fate. Cell 136, 903–912.
Vermeulen, L., De Sousa, E.M.F., van der Heijden, M., Cameron, K., de Jong, J.H., Borovski, T., Tuynman, J.B., Todaro, M., Merz, C., Ro- dermond, H., et al. (2010). Wnt activity defines colon cancer stem cells and is regulated by the microenvironment. Nat. Cell Biol. 12, 468–476.
Vignot, S., Lefebvre, C., Frampton, G.M., Meurice, G., Yelensky, R., Palmer, G., Capron, F., Lazar, V., Hannoun, L., Miller, V.A., et al. (2015). Comparative analysis of primary tumour and matched me- tastases in colorectal cancer patients: evaluation of concordance between genomic and transcriptional profiles. Eur. J. Cancer 51, 791–799.
Vlachogiannis, G., Hedayat, S., Vatsiou, A., Jamin, Y., Fernandez- Mateos, J., Khan, K., Lampis, A., Eason, K., Huntingford, I., Burke, R., et al. (2018). Patient-derived organoids model treatment response of metastatic gastrointestinal cancers. Science 359, 920– 926.
Weeber, F., van de Wetering, M., Hoogstraat, M., Dijkstra, K.K., Krijgsman, O., Kuilman, T., Gadellaa-van Hooijdonk, C.G., van der Velden, D.L., Peeper, D.S., Cuppen, E.P., et al. (2015). Preserved genetic diversity in organoids cultured from biopsies of human colorectal cancer metastases. Proc. Natl. Acad. Sci. U S A 112, 13308–13311.
Xie, S.M., Fang, W.Y., Liu, T.F., Yao, K.T., and Zhong, X.Y. (2010). Association of ABCC2 and CDDP-resistance in two sublines resis- tant to CDDP derived from a human nasopharyngeal carcinoma cell line. J. Oncol. 2010, 915046.
Xie, T., Cho, Y.B., Wang, K., Huang, D., Hong, H.K., Choi, Y.L., Ko, Y.H., Nam, D.H., Jin, J., Yang, H., et al. (2014). Patterns of somatic alterations between matched primary and metastatic colorectal tu- mors characterized by whole-genome sequencing. Genomics 104, 234–241.
Yan, K.S., Janda, C.Y., Chang, J., Zheng, G.X.Y., Larkin, K.A., Luca, V.C., Chia, L.A., Mah, A.T., Han, A., Terry, J.M., et al. (2017). Non-equivalence of Wnt and R-spondin ligands during Lgr5(+) intesti- nal stem-cell self-renewal. Nature 545, 238–242.
Yang, Q., Bermingham, N.A., Finegold, M.J., and Zoghbi, H.Y. (2001). Requirement of Math1 for secretory cell lineage commit- ment in the mouse intestine. Science 294, 2155–2158.