Metabolic alterations play an important role in cancer and yet, few metabolic cancer driver genes are known. Here we perform a combined genomic and metabolic modeling analysis searching for metabolic drivers of colorectal cancer. Our analysis predicts FUT9, which catalyzes the biosynthesis of Ley glycolipids, as a driver of advanced‐stage colon cancer. Experimental testing reveals FUT9's complex dual role; while its knockdown enhances proliferation and migration in monolayers, it suppresses colon cancer cells expansion in tumorspheres and inhibits tumor development in a mouse xenograft models. These results suggest that FUT9's inhibition may attenuate tumor‐initiating cells (TICs) that are known to dominate tumorspheres and early tumor growth, but promote bulk tumor cells. In agreement, we find that FUT9 silencing decreases the expression of the colorectal cancer TIC marker CD44 and the level of the OCT4 transcription factor, which is known to support cancer stemness. Beyond its current application, this work presents a novel genomic and metabolic modeling computational approach that can facilitate the systematic discovery of metabolic driver genes in other types of cancer.

Individual response to radiochemotherapy (RCT) in rectal cancer patients is highly variable and the underlying mechanisms of treatment resistance of cancer cells are poorly understood. Recent studies revealed a considerable degree of genomic tumor heterogeneity. We hypothesize that this heterogeneity has a direct impact on treatment response as subpopulations of cancer cells are resistant to currently used RCT and facilitate tumor growth under treatment. To address this highly relevant clinical issue, patient-derived rectal cell lines were established. The tissue was derived from a 59-year-old male presenting with an adenocarcinoma of lower rectum (T3,N1,M0), who was treated by neoadjuvant RCT (50.4 Gy plus 5-FU) and low anterior resection. The neoadjuvant treatment induced a shrinkage of the tumor (staging of the surgical specimen: ypT3,N0), suggesting a partial response to RCT. A biopsy of the treatment naïve tumor was implanted heterotopically into an immunodeficient nude mouse. After in vivo growth, the tumor was dissociated and introduced to an in vitro culture where murine stromal cells were depleted using antibody-based columns. The cell line proved to be of human origin by immunofluorescence for human Keratin 20 as well as genotyping using short tandem repeat profiling. The characterization of the genome by array CGH and spectral karyotyping (SKY) revealed a highly complex near-triploid karyotype with numerous chromosomal imbalances, which are specific for colorectal cancers, including gains in chromosomes 7, 13 and 20. We also observed other structural abnormalities including an isochromosome 1q. Multiplex-FISH by consecutive hybridization of probes for 15 gene loci, which are known to be relevant in colorectal cancer genesis, revealed a significant degree of clonal heterogeneity of the cell line. Single cell sorting was then performed to establish single cell derived cell lines from the genomically well characterized parental cell line. Exposure of the single cell derived cell lines to irradiation in combination with 3 uM 5-FU revealed substantial differences in treatment response. Analyses of the genome by array CGH and transcriptome by RNA-Seq of the respective single cell derived cell lines are currently underway. This will allow the comparison of the respective sensitivities to RCT to the identified aberration profiles. These data will facilitate the understanding of therapy resistance and potentially allow a reliable prediction of the patient’s response. A tailored therapy is an important step towards individualized treatment in colorectal cancer patients to avoid therapy resistance. Citation Format: Rüdiger Meyer, Nicole E. McNeil, Darawalee Wangsa, Lena Anthuber, Noam Auslander, Danny Wangsa, Zhongqiu Zhang, Daniel Rosenberg, Eytan Ruppin, Jens K. Habermann, Thomas Ried. Intratumor heterogeneity impacts treatment response in rectal carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3947. doi:10.1158/1538-7445.AM2017-3947