Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer

Colon tumors from four independent mouse models and 100 human colorectal cancers all exhibited striking recapitulation of embryonic colon gene expression from embryonic days 13.5-18.5

Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer

Abstract Background The expression of carcino-embryonic antigen by colorectal cancer is an example of oncogenic activation of embryonic gene expression. Hypothesizing that oncogenesis-recapitulating-ontogenesis may represent a broad programmatic commitment, we compared gene expression patterns of human colorectal cancers (CRCs) and mouse colon tumor models to those of mouse colon development embryonic days 13.5-18.5. Results We report here that 39 colon tumors from four independent mouse models and 100 human CRCs encompassing all clinical stages shared a striking recapitulation of embryonic colon gene expression. Compared to normal adult colon, all mouse and human tumors over-expressed a large cluster of genes highly enriched for functional association to the control of cell cycle progression, proliferation, and migration, including those encoding MYC, AKT2, PLK1 and SPARC. Mouse tumors positive for nuclear β-catenin shifted the shared embryonic pattern to that of early development. Human and mouse tumors differed from normal embryonic colon by their loss of expression modules enriched for tumor suppressors (EDNRB, HSPE, KIT and LSP1). Human CRC adenocarcinomas lost an additional suppressor module (IGFBP4, MAP4K1, PDGFRA, STAB1 and WNT4). Many human tumor samples also gained expression of a coordinately regulated module associated with advanced malignancy (ABCC1, FOXO3A, LIF, PIK3R1, PRNP, TNC, TIMP3 and VEGF). Conclusion Cross-species, developmental, and multi-model gene expression patterning comparisons provide an integrated and versatile framework for definition of transcriptional programs associated with oncogenesis. This approach also provides a general method for identifying pattern-specific biomarkers and therapeutic targets. This delineation and categorization of developmental and non-developmental activator and suppressor gene modules can thus facilitate the formulation of sophisticated hypotheses to evaluate potential synergistic effects of targeting within- and between-modules for next-generation combinatorial therapeutics and improved mouse models

Comparative Effectiveness of Anti-TNF in Combination With Low-Dose Methotrexate vs Anti-TNF Monotherapy in Pediatric Crohn\u27s Disease: A Pragmatic Randomized Trial

BACKGROUND & AIMS: Tumor necrosis factor inhibitors, including infliximab and adalimumab, are a mainstay of pediatric Crohn\u27s disease therapy; however, nonresponse and loss of response are common. As combination therapy with methotrexate may improve response, we performed a multicenter, randomized, double-blind, placebo-controlled pragmatic trial to compare tumor necrosis factor inhibitors with oral methotrexate to tumor necrosis factor inhibitor monotherapy. METHODS: Patients with pediatric Crohn\u27s disease initiating infliximab or adalimumab were randomized in 1:1 allocation to methotrexate or placebo and followed for 12-36 months. The primary outcome was a composite indicator of treatment failure. Secondary outcomes included anti-drug antibodies and patient-reported outcomes of pain interference and fatigue. Adverse events (AEs) and serious AEs (SAEs) were collected. RESULTS: Of 297 participants (mean age, 13.9 years, 35% were female), 156 were assigned to methotrexate (110 infliximab initiators and 46 adalimumab initiators) and 141 to placebo (102 infliximab initiators and 39 adalimumab initiators). In the overall population, time to treatment failure did not differ by study arm (hazard ratio, 0.69; 95% CI, 0.45-1.05). Among infliximab initiators, there were no differences between combination and monotherapy (hazard ratio, 0.93; 95% CI, 0.55-1.56). Among adalimumab initiators, combination therapy was associated with longer time to treatment failure (hazard ratio, 0.40; 95% CI, 0.19-0.81). A trend toward lower anti-drug antibody development in the combination therapy arm was not significant (infliximab: odds ratio, 0.72; 95% CI, 0.49-1.07; adalimumab: odds ratio, 0.71; 95% CI, 0.24-2.07). No differences in patient-reported outcomes were observed. Combination therapy resulted in more AEs but fewer SAEs. CONCLUSIONS: Among adalimumab but not infliximab initiators, patients with pediatric Crohn\u27s disease treated with methotrexate combination therapy experienced a 2-fold reduction in treatment failure with a tolerable safety profile. CLINICALTRIALS: gov, Number: NCT02772965

An integrated view of colon cancer transcriptional programs provides novel insight into neoplasia

Murine colon tumor adenomas and human CRCs both show adoption and dysregulation of signatures tightly controlled during embryonic mouse colon development. The use of etiologically distinct mouse models of colon cancer allows for the identification of models that resemble different stages of embryonic mouse colon development and that are recapitulated by specific tumor types. All tumors exhibit large-scale activation of developmental patterns. Nuclear β-catenin-positive (and AOM) tumors map more strongly to early development stages during (more proliferative, less differentiated), whereas nuclear β-catenin-negative (and ) tumors map more strongly to later stages consistent with increased epithelial differentiation. Overall representation of the relationship of mouse colon tumor models and human CRC to development and non-developmental expression patterns. Gene expression clusters mapped to the progression of adenomatous and carcinomatous transformation identified in Figures 5 and 6 are shown as the clusters of genes whose expression is either gained or lost associated with the stage of progression. For example normal development could be considered as 'subverted' if there is an absence of expression of genes normally expressed at high level in the developing colon that fail to be expressed in tumors (for example, C18, C19), or that are activated in tumor but not normally expressed in development (C20). Upregulated clusters are enriched for genes with known oncogenic functions and down-regulated clusters for genes associated with tumor suppression. Both mouse colon tumor models and human CRC share in the activation of embryonic colon expression (C22), or partially overlap (C23, dotted lines) the loss or repression of adult differentiation-associated genes (C19), and the loss of tumor suppressor genes (C18). Many human CRCs also lack the expression of additional tumor suppressor programs and gain the expression of oncogenes that are not over-expressed during normal developmental morphogenesis (C21).<p><b>Copyright information:</b></p><p>Taken from "Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer"</p><p>http://genomebiology.com/2007/8/7/R131</p><p>Genome Biology 2007;8(7):R131-R131.</p><p>Published online 5 Jul 2007</p><p>PMCID:PMC2323222.</p><p></p

Both human CRCs and mouse colon tumors reactivate an embryonic gene signature

When human and murine tumors are compared, they both broadly re-express an embryonic gene expression pattern. Gene expression profiles from the mouse tumor models and human CRC samples were combined into a single non-redundant gene ortholog genome table structure and subjected to comparative profile analysis. Informative probe-sets from human and mouse platforms were selected, mapped to corresponding ortholog genes, and used to populate a table in which normalized expression for each gene is relative to normal adult colon. Heatmap plot for all cross-species gene orthologs both present and successfully measured on both the Affymetrix Hg-U133 and Vanderbilt Mouse NIA 20 K microarrays (= 8,621 features). This representation suggests that a large number of human CRC signatures exhibit similar behaviors in the mouse tumors and during embryonic mouse colon development (sidebar: 1,080 (red) and 431 (green) gene lists from (b)). Based on results in (a), four separate gene lists were generated with criteria of over- or under-expression in development or over-expression or under-expression in human CRCs (2,718, 2,365, 2,212, and 737, respectively, with the overlaps shown as a sidebar in (a); red, 1,080 transcripts, and green, 431 transcripts). Genes over-expressed and under-expressed in embryonic mouse colon and human CRCs were found to be over-represented as determined by Fisher's exact test analysis (*< 7 × 10, **< 1 × 10, ***< 5 × 10, ****< 1 × 10). Heatmap plot of all genes co-regulated in human CRCs and during early (ED) and late (LD) mouse embryonic colon development (= 2,216 features). Six predominant clusters (C18-C23) characterize the transcriptional relationship between human CRC and mouse colon tumor models and embryonic development. Two clusters (C20 and 21) primarily distinguish human CRCs from murine tumors (A, M, S and T). For example, CRC up-regulated transcripts that are either developmentally up- or down-regulated are represented by cluster C22 (= 860 features) and clusters C21/C23 (= 142 features), respectively. Conversely, CRC down-regulated transcripts that are either down- or up-regulated during development are shown in clusters C18/C19 (= 258 features) and cluster C20 (= 42 features), respectively. Interestingly, while approximately 80% and approximately 60% of genes up- and down-regulated in both human CRCs and mouse development were also up- and down-regulated in tumors from the various mouse models, several clusters provide very interesting exceptions: cluster C20 comprises genes down-regulated in human CRCs that are routinely over-expressed in mouse tumors and development; cluster C21 comprises genes robustly expressed in human CRC that are rarely expressed in embryonic colon or murine tumors. Sample groups: ED, early development (E13.5-E15.5); LD, late development (E16.5-E18.5); A, AOM-induced; M, ; T, ; S, . Tissue groups: AC, adult colon; CRC, human CRC. Staging: nAC, normal colon.<p><b>Copyright information:</b></p><p>Taken from "Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer"</p><p>http://genomebiology.com/2007/8/7/R131</p><p>Genome Biology 2007;8(7):R131-R131.</p><p>Published online 5 Jul 2007</p><p>PMCID:PMC2323222.</p><p></p

All four murine tumor models exhibit reactivation of embryonic gene expression

The expression level of each gene in each sample was calculated relative to that in adult colon. Genes and samples were subjected to unsupervised hierarchical tree clustering for similarities among genes and tumors. Heatmap shows the relative behaviors of 20,393 transcripts that passed basic signal quality filters with gene transcripts shown as separate rows and samples as separate columns. Note that the majority of genes over-expressed in tumors (red) are also over-expressed in embryonic colon; similarly, the genes under-expressed in tumors (blue) are under-expressed in embryonic colon. The color bars to the right indicate the position of 4,693 transcripts over-expressed in both tumors and development (red) or under-expressed in both (green). In addition, there are genes over-expressed in embryonic colon that are under-expressed in tumors and vice versa (asterisks). The genes represented in (a) were divided into those over-expressed and under-expressed in embryonic colon and in the tumors, respectively. Fisher's exact test was used to calculate expected overlaps between lists and confirmed significant over-representation of development-regulated signatures among the tumors (*< 1, **< 1.3, ***< 4, ****< 1). Heatmap showing the behavior of a subset of the transcripts in (a) (= 4,693 features) that were over-expressed in both embryonic colon and tumor samples. Refer to Table 2 for a complete description of the genes associated with these clusters. Embryonic gene expression can be further refined into genes expressed differentially during early (ED; E13.5-15.5) and late (LD; E16.5-18.5) embryonic development. Heatmap showing the relative behaviors of 750 transcripts that are highest-ranked for early versus late embryonic regulation. Overall, transcripts with the highest early embryonic expression were expressed at higher levels in nuclear β-catenin-positive tumors (A and M), whereas nuclear β-catenin-negative tumors (S and T) were representative of later stages of embryonic development. Sample groups: ED, early development (E13.5-E15.5); LD, late development (E16.5-E18.5); A, AOM-induced; M, ; T, ; S, . Staging: nAC, normal colon. Clusters C8-C10 to the right of the heatmap correspond to the K-means functional clusters listed in Table 2.<p><b>Copyright information:</b></p><p>Taken from "Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer"</p><p>http://genomebiology.com/2007/8/7/R131</p><p>Genome Biology 2007;8(7):R131-R131.</p><p>Published online 5 Jul 2007</p><p>PMCID:PMC2323222.</p><p></p

Active canonical WNT signaling (as determined by nuclear β-catenin) stratifies the four murine colon tumor models into two groups

Hierarchical clustering of gene transcripts separates the four models into two groups. The upper panel shows 1,798 gene transcripts identified as differentially expressed among any of the four mouse tumor models (Kruskal-Wallis test + Student-Newman-Keuls test + FDR < 5.10). Results demonstrate that AOM (A) and (M) tumors are transcriptionally more similar to each other than to tumors from (S) and (T) mice. Five clusters have been identified (C1-C5) that correspond to the K-means functional clusters listed in Table 1. Please refer to Table 1 for an in-depth description of the functional classification of the genes found in these clusters. The lower panel illustrates the extent of the similarity between A/M and S/T tumors by identifying the top-ranked 1,265 transcripts of the 1,798 that were higher or lower in the two tumor super-groups (rank based on Wilcoxon-Mann-Whitney test for between-group differences with a FDR < 5.10cutoff). Up-regulated transcripts in A/M tumors are highly enriched for genes associated with canonical WNT signaling activity, cell proliferation, chromatin remodeling, cell cycle progression and mitosis; transcripts over-expressed in S/T tumors are highly enriched for genes related to immune and defense responses, endocytosis, transport, oxidoreductase activity, signal transduction and metabolism. Representative histologies for each of the four tumor models. The lower panel illustrates the model-dependent localization of β-catenin. Tumors from M (bottom left) and A (not shown) mice exhibited prominent nuclear β-catenin accumulation and reduced cell surface staining. Conversely, tumors from S (bottom right) and T(not shown) mice exhibited retention of plasma membrane β-catenin immunoreactivity. A and M in top panel 100× magnification; S and T 200× magnification. M and S in lower panel both 400× magnification.<p><b>Copyright information:</b></p><p>Taken from "Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer"</p><p>http://genomebiology.com/2007/8/7/R131</p><p>Genome Biology 2007;8(7):R131-R131.</p><p>Published online 5 Jul 2007</p><p>PMCID:PMC2323222.</p><p></p

Stratification of murine colon tumor models by localization of β-catenin and plan for analysis

Colon tumors from four etiologically distinct mouse models of CRC were subjected to microarray gene expression profiling. The gene expression profiles from the different mouse model tumors were compared and contrasted to each other, as well as to those from embryonic mouse colon development and 100 human CRCs.<p><b>Copyright information:</b></p><p>Taken from "Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer"</p><p>http://genomebiology.com/2007/8/7/R131</p><p>Genome Biology 2007;8(7):R131-R131.</p><p>Published online 5 Jul 2007</p><p>PMCID:PMC2323222.</p><p></p

Human CRCs exhibit gene expression profile complexity consistent with significant tumor subclasses

Genes potentially able to distinguish cancer subtypes were identified from Affymetrix HG-U133 plus2 Genechip expression profiles by filtering for 3,285 probe sets that were top-ranked by raw expression and their differential regulation in at least 10 out of 100 human colorectal cancer tumors. Coordinately regulated transcripts and similarly behaving samples were identified via hierarchical tree clustering. Seven different gene clusters (C11-17) were identified that distinguished ten or more tumors from the other tumors. Gene clusters were found to be highly enriched for gene functions listed in Table 3. Data were processed using Robust Microarray Analysis (RMA) with expression value ratios depicted as the relative expression per probe set in each sample relative to the median of its expression across the 100 CRCs. A striking heterogeneity of gene expression was observed, including metallothionein genes in cluster C15 previously shown to be predictive of microsatellite instability (indicated by asterisk), and C17 represented by 734 probesets rich in genes associated with extracellular matrix and connective tissue, tumor invasion and malignancy. Tissue groups: AC, adult colon; CRC, human CRC. Staging: nAC, normal colon; Dukes A-D, human tumors obtained from individuals. Clusters C11-C17 labeled to the right of the heatmap correspond to the K-means functional clusters listed in Table 3.<p><b>Copyright information:</b></p><p>Taken from "Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer"</p><p>http://genomebiology.com/2007/8/7/R131</p><p>Genome Biology 2007;8(7):R131-R131.</p><p>Published online 5 Jul 2007</p><p>PMCID:PMC2323222.</p><p></p