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Additional file 5 Figure S3. Flow Cytometry Analysis: A The experimental outline is illustrated describing the incubation of (i) DC preparations for the specified time and (ii) the conditions to which the cells were exposed, specifically IL-4 and GM-CSF cytokines to derive the DCs, conditioned media from the TCM to precondition the DCs and LPS to mature the DCs. Finally, DCs were analyzed by flow cytometry and DC supernatants were analyzed by ELISA. B-C The gating strategy of the monocyte-derived DCs is shown of singlet, monogate cells which are CD11c + (B) and the Fluorescence Minus One staining controls (C).

Additional file 1 Table S1. Patient characteristics including surgical details, and Tumor-Nodal-Metastasis (TNM) stage. The median age at the time of surgery 74.5 years (range: 62–82 years), with an equal number of males [4] & females [4]

Additional file 5 Figure S3. Flow Cytometry Analysis: A The experimental outline is illustrated describing the incubation of (i) DC preparations for the specified time and (ii) the conditions to which the cells were exposed, specifically IL-4 and GM-CSF cytokines to derive the DCs, conditioned media from the TCM to precondition the DCs and LPS to mature the DCs. Finally, DCs were analyzed by flow cytometry and DC supernatants were analyzed by ELISA. B-C The gating strategy of the monocyte-derived DCs is shown of singlet, monogate cells which are CD11c + (B) and the Fluorescence Minus One staining controls (C).

The identification and use of “privileged structures” can increase the reliability and shorten the process in the drug discovery and drug design (a-b). Indane scaffolds occur in various natural products and they constitute the privileged structure that is ubiquitous in many biologically and pharmaceutically active molecules (c-e). Our research group has been working on the synthesis and pharmacological activity of nature identical and synthetically modified indanes and indanones for 20 years. In the current study, the molecular design is centred on elaboration of a fern derived bioactive pharmacophore. The fern is used in traditional Taiwanese medicine to treat inflammation, allergy, stomach cramps and fever (f). Using a synthetic approach we have designed a novel chemical scaffold which can be modified to inhibit angiogenesis and 5-lipoxygenase activity. The parent scaffold and a number of strategically modified derivatives were initially screened using the Zebra fish (Danio rerio) model of tumour angiogenesis (g). This screen led to the identification of two lead molecules, which were then further evaluated in in vitro cell lines and colorectal explants. Results from these experiments establish that the lead compounds affect inter-segmental vessel formation. These molecules also inhibit cell invasion and tube formation. When evaluated in ex vivo colorectal cancer explants where the molecules significantly affected angiogenic and inflammatory protein secretions. These small molecules also alter gene expression. Modification of the scaffold can inhibit 5-lipoxygenase activity. These data suggest that the new scaffold may have significant potential in the treatment of angiogenesis and inflammatory related diseases.

Additional file 1 Supplementary Table 1. Patient demographics. Supplementary Fig. 1. Experimental outline and flow cytometry gating strategy and staining controls. Supplementary Fig. 2. ex vivo TCM from distinct gastrointestinal adenocarcinoma types induced differential effects on LPS-induced DC maturation. Supplementary Fig. 3. ex vivo TCM from distinct gastrointestinal adenocarcinoma types induced differential effects on unstimulated DC marker levels. Supplementary Fig. 4. in vitro TCM of 2Gy-irradiated cell lines from gastrointestinal cancers induced significant inhibition of DC markers compared to mock irradiation. Supplementary Fig. 5. ex vivo TCM of 2Gy-irradiated TME from gastrointestinal cancers inhibited DC markers compared to mock irradiation

Additional file 3 Figure S1. Expression of angiogenic mediators in tumor conditioned media from resected CRC tissue. The MSD V-plex Angiogenesis panel 1 was used to determine the expression level of angiogenic markers in tumor conditioned media generated from resected patient CRC tissue (n = 8). Following drug treatment, no significant difference in expression level was observed for (A) bFGF, (B) PGF, (C) FLT-1, and (D) VEGF-C.

Additional file 2 Table S2. Summary of significant results including fold-change.

Additional file 3 Figure S1. Expression of angiogenic mediators in tumor conditioned media from resected CRC tissue. The MSD V-plex Angiogenesis panel 1 was used to determine the expression level of angiogenic markers in tumor conditioned media generated from resected patient CRC tissue (n = 8). Following drug treatment, no significant difference in expression level was observed for (A) bFGF, (B) PGF, (C) FLT-1, and (D) VEGF-C.

Additional file 4 Figure S2. Expression of pro-inflammatory mediators in TCM from resected CRC tissue. The MSD V-plex Proinflammatory panel 1 was used to determine the expression level of proinflammatory markers in tumor conditioned media generated from resected patient CRC tissue. Following drug treatment, no significant difference in expression level was observed for (A) IL-1β, IL-2, IL-4, IL-8, IL-12p70, and TNF-α.

Additional file 2 Table S2. Summary of significant results including fold-change.

Additional file 4 Figure S2. Expression of pro-inflammatory mediators in TCM from resected CRC tissue. The MSD V-plex Proinflammatory panel 1 was used to determine the expression level of proinflammatory markers in tumor conditioned media generated from resected patient CRC tissue. Following drug treatment, no significant difference in expression level was observed for (A) IL-1β, IL-2, IL-4, IL-8, IL-12p70, and TNF-α.

Background & Aims\ud Barrett's esophagus (BE) increases the risk of esophageal adenocarcinoma (EAC). We found the risk to be BE has been associated with single nucleotide polymorphisms (SNPs) on chromosome 6p21 (within the HLA region) and on 16q23, where the closest protein-coding gene is FOXF1. Subsequently, the Barrett's and Esophageal Adenocarcinoma Consortium (BEACON) identified risk loci for BE and esophageal adenocarcinoma near CRTC1 and BARX1, and within 100 kb of FOXP1. We aimed to identify further SNPs that increased BE risk and to validate previously reported associations.\ud \ud Methods\ud We performed a genome-wide association study (GWAS) to identify variants associated with BE and further analyzed promising variants identified by BEACON by genotyping 10,158 patients with BE and 21,062 controls.\ud \ud Results\ud We identified 2 SNPs not previously associated with BE: rs3072 (2p24.1; odds ratio [OR] = 1.14; 95% CI: 1.09–1.18; P = 1.8 × 10−11) and rs2701108 (12q24.21; OR = 0.90; 95% CI: 0.86–0.93; P = 7.5 × 10−9). The closest protein-coding genes were respectively GDF7 (rs3072), which encodes a ligand in the bone morphogenetic protein pathway, and TBX5 (rs2701108), which encodes a transcription factor that regulates esophageal and cardiac development. Our data also supported in BE cases 3 risk SNPs identified by BEACON (rs2687201, rs11789015, and rs10423674). Meta-analysis of all data identified another SNP associated with BE and esophageal adenocarcinoma: rs3784262, within ALDH1A2 (OR = 0.90; 95% CI: 0.87–0.93; P = 3.72 × 10−9).\ud \ud Conclusions\ud We identified 2 loci associated with risk of BE and provided data to support a further locus. The genes we found to be associated with risk for BE encode transcription factors involved in thoracic, diaphragmatic, and esophageal development or proteins involved in the inflammatory response.

BACKGROUND & AIMS: Barrett's esophagus (BE) increases the risk of esophageal adenocarcinoma (EAC). We found the risk to be BE has been associated with single nucleotide polymorphisms (SNPs) on chromosome 6p21 (within the HLA region) and on 16q23, where the closest protein-coding gene is FOXF1. Subsequently, the Barrett's and Esophageal Adenocarcinoma Consortium (BEACON) identified risk loci for BE and esophageal adenocarcinoma near CRTC1 and BARX1, and within 100 kb of FOXP1. We aimed to identify further SNPs that increased BE risk and to validate previously reported associations. METHODS: We performed a genome-wide association study (GWAS) to identify variants associated with BE and further analyzed promising variants identified by BEACON by genotyping 10,158 patients with BE and 21,062 controls. RESULTS: We identified 2 SNPs not previously associated with BE: rs3072 (2p24.1; odds ratio [OR] = 1.14; 95% CI: 1.09-1.18; P = 1.8 × 10(-11)) and rs2701108 (12q24.21; OR = 0.90; 95% CI: 0.86-0.93; P = 7.5 × 10(-9)). The closest protein-coding genes were respectively GDF7 (rs3072), which encodes a ligand in the bone morphogenetic protein pathway, and TBX5 (rs2701108), which encodes a transcription factor that regulates esophageal and cardiac development. Our data also supported in BE cases 3 risk SNPs identified by BEACON (rs2687201, rs11789015, and rs10423674). Meta-analysis of all data identified another SNP associated with BE and esophageal adenocarcinoma: rs3784262, within ALDH1A2 (OR = 0.90; 95% CI: 0.87-0.93; P = 3.72 × 10(-9)). CONCLUSIONS: We identified 2 loci associated with risk of BE and provided data to support a further locus. The genes we found to be associated with risk for BE encode transcription factors involved in thoracic, diaphragmatic, and esophageal development or proteins involved in the inflammatory response.