Predictive gene signatures: molecular markers distinguishing colon adenomatous polyp and carcinoma

SLC9A2, suppressing by the transcription suppressor ETS1, restrains growth and invasion of osteosarcoma via inhibition of aerobic glycolysis

Recent studies have shown that Solute Carrier Family 9 Member A2 (SLC9A2) could serve as a biomarker for cancer. However, its mechanism of action in osteosarcoma (OS) was still unclear. In this study, the data sets GSE154530 and GSE99671 were downloaded from the Gene Expression Omnibus (GEO) database, and 31 differentially expressed genes (DEGs) related to methylation were screened by bioinformatics analysis tools. Subsequently, SLC9A2 was screened as a candidate gene from DEGs, which was significantly downregulated in OS. CCK-8, transwell, western blotting and Seahorse XFe24 Cell Metabolic Analyzer assays demonstrated that overexpression of SLC9A2 could constrain OS cell proliferation, invasion, and aerobic glycolysis. Dual-luciferase reporter gene assay and chromatin immunoprecipitation (ChIP) assays indicated ETS proto-oncogene 1 (ETS1) was a transcription suppressor of SLC9A2, and overexpression of ETS1 could promote methylation levels in specific regions of the SLC9A2 promoter. ETS1 could promote the proliferation, invasion, and aerobic glycolysis ability of OS cells, as well as tumor growth in vivo by inhibiting the expression of SLC9A2. In addition, SLC9A2, suppressing by ETS1, restrains growth and invasion of OS via inhibition of aerobic glycolysis. Thus, SLC9A2 can function as a key inhibitory factor in the aerobic glycolysis to inhibit proliferation and invasion of OS. This indicated that SLC9A2 has a potential targeted therapeutic effect on OS.

Usefulness of COL11A1 as a Prognostic Marker of Tumor Infiltration

BACKGROUND

Determining the infiltration of carcinomas is essential for the proper follow-up and treatment of cancer patients. However, it continues to be a diagnostic challenge for pathologists in multiple types of tumors. In previous studies (carried out in surgical specimens), the protein COL11A1 has been postulated as an infiltration marker mainly expressed in the extracellular matrix (ECM). We hypothesized that a differential expression of COL11A1 may exist in the peritumoral stroma of tumors that have acquired infiltrating properties and that it may be detected in the small biopsies usually available in normal clinical practice.

MATERIAL AND METHODS

In our study, we performed immunohistochemical staining in more than 350 invasive and noninvasive small samples obtained via core needle biopsy (CNB), colonoscopy, or transurethral resection of bladder tumor (TURBT) of breast, colorectal, bladder, and ovarian cancer.

RESULTS

Our results revealed that COL11A1 immunostaining had a sensitivity to classify the samples into infiltrative vs. noninfiltrative tumors of 94% (breast), 97% (colorectal), >90% (bladder), and 74% (ovarian); and a specificity of 97% (breast), 100% (colorectal), and >90% (bladder). In ovarian cancer, the negative predictive value (0.59) did not present improvement over the usual histopathological markers. In all samples tested, the cumulative sensitivity was 86% and the specificity 96% (p < 0.0001).

CONCLUSIONS

COL11A1-positive immunostaining in small biopsies of breast, colon, bladder and ovarian cancer is an accurate predictive marker of tumor infiltration that can be easily implemented in daily clinical practice.

A Reddish Nodule on the Scalp: A Quiz

Abstract is missing (Quiz)

Mendelian randomization study of causal link from gut microbiota to colorectal cancer

Recent studies have shown the relevance of gut microbiota in the occurrence and development of colorectal cancer (CRC), but the causal relationship remains unclear in the human population. The present study aims to assess the causal relationship from the gut microbiota to CRC and to identify specific causal microbe taxa via genome-wide association study (GWAS) summary statistics based two-sample Mendelian randomization (MR) analyses. Microbiome GWAS (MGWAS) in the TwinsUK 1,126 twin pairs was used as discovery exposure sample, and MGWAS in 1,812 northern German participants was used as replication exposure sample. GWAS of CRC in 387,156 participants from the UK Biobank (UKB) was used as the outcome sample. Bacteria were grouped into taxa features at both family and genus levels. In the discovery sample, a total of 30 bacteria features including 15 families and 15 genera were analyzed. Five features, including 2 families (Verrucomicrobiaceae and Enterobacteriaceae) and 3 genera (Akkermansia, Blautia, and Ruminococcus), were nominally significant. In the replication sample, the genus Blautia (discovery beta=-0.01, P = 0.04) was successfully replicated (replication beta=-0.18, P = 0.01) with consistent effect direction. Our findings identified genus Blautia that was causally associated with CRC, thus offering novel insights into the microbiota-mediated CRC development mechanism.

Game-theoretic link relevance indexing on genome-wide expression dataset identifies putative salient genes with potential etiological and diapeutics role in colorectal cancer

Diapeutics gene markers in colorectal cancer (CRC) can help manage mortality caused by the disease. We applied a game-theoretic link relevance Index (LRI) scoring on the high-throughput whole-genome transcriptome dataset to identify salient genes in CRC and obtained 126 salient genes with LRI score greater than zero. The biomarkers database lacks preliminary information on the salient genes as biomarkers for all the available cancer cell types. The salient genes revealed eleven, one and six overrepresentations for major Biological Processes, Molecular Function, and Cellular components. However, no enrichment with respect to chromosome location was found for the salient genes. Significantly high enrichments were observed for several KEGG, Reactome and PPI terms. The survival analysis of top protein-coding salient genes exhibited superior prognostic characteristics for CRC. MIR143HG, AMOTL1, ACTG2 and other salient genes lack sufficient information regarding their etiological role in CRC. Further investigation in LRI methodology and salient genes to augment the existing knowledge base may create new milestones in CRC diapeutics.

Aberrantly methylated-differentially expressed genes and related pathways in cholangiocarcinoma

This study aimed to explore aberrantly methylated-differentially expressed genes and related pathways in cholangiocarcinoma (CCA).The mRNA expression data (GSE26566) and methylation profiling data (GSE44965) were collected from the Gene Expression Omnibus (GEO) Datasets. Differentially expressed genes and differentially methylated genes were identified using GEO2R. Gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using clusterprofiler in R. MCODE clustering tool was used to screen modules of the protein-protein interaction network in Cytoscape. Related pathways of hub gene by using gene set enrichment analysis.Eighty-one hypermethylated, lowly expressed genes (Hyper-LGs) and 76 hypomethylated, highly expressed genes (Hypo-HGs) were identified in this study. Hyper-LGs were enriched in ion channel binding and transcription factor activity, which was associated with Mineral absorption and Cell adhesion molecules. Hypo-HGs were enriched in cysteine-type endopeptidase activity, which was associated with Sphingolipid signaling pathway and T cell receptor signaling pathway. Based on protein-protein interaction networks, MYC and VWF were identified as hub genes for Hyper-LGs, and no hub genes for Hypo-HGs.This study found methylated-differentially expressed genes and signaling pathways that are connected with the CCA by using a series of bioinformatics databases and tools. MYC and VWF act as hub genes of CCA, which can be used as biomarkers based on aberrant methylation for the accurate diagnosis and treatment of CCA.

Identification of TPM2 and CNN1 as Novel Prognostic Markers in Functionally Characterized Human Colon Cancer-Associated Stromal Cells

Simple Summary

Non-transformed cells of tumor microenvironment also impact on cancer outgrowth and progression. In colon cancer, a leading cause of cancer-related death worldwide, a high abundance of a heterogeneous cell population generally referred to as cancer-associated fibroblasts (CAFs) or tumor-associated stromal cells (TASCs) is associated with poor prognosis. The identification of TASC-specific markers could help to select patients for additional treatments and may provide novel targets for innovative therapies. Some markers have been proposed, but their prognostic significance is modest. We successfully expanded TASCs from human colon cancers and demonstrated their capacity to promote tumor growth and metastatic spread in vitro and in in vivo models. By comparing TASC whole protein expression, the so-called “proteome”, with that of stromal cells derived from matched healthy colon tissues, we identified two novel markers highly significantly associated with severe prognosis. Our results might help to identify patients at risk and might suggest new treatment options.

Abstract

Stromal infiltration is associated with poor prognosis in human colon cancers. However, the high heterogeneity of human tumor-associated stromal cells (TASCs) hampers a clear identification of specific markers of prognostic relevance. To address these issues, we established short-term cultures of TASCs and matched healthy mucosa-associated stromal cells (MASCs) from human primary colon cancers and, upon characterization of their phenotypic and functional profiles in vitro and in vivo, we identified differentially expressed markers by proteomic analysis and evaluated their prognostic significance. TASCs were characterized by higher proliferation and differentiation potential, and enhanced expression of mesenchymal stem cell markers, as compared to MASCs. TASC triggered epithelial–mesenchymal transition (EMT) in tumor cells in vitro and promoted their metastatic spread in vivo, as assessed in an orthotopic mouse model. Proteomic analysis of matched TASCs and MASCs identified a panel of markers preferentially expressed in TASCs. The expression of genes encoding two of them, calponin 1 (CNN1) and tropomyosin beta chain isoform 2 (TPM2), was significantly associated with poor outcome in independent databases and outperformed the prognostic significance of currently proposed TASC markers. The newly identified markers may improve prognostication of primary colon cancers and identification of patients at risk.

Hsa-miR-186-3p suppresses colon cancer progression by inhibiting KRT18/MAPK signaling pathway

This study aimed to determine the effect of miR-186-3p and KRT18 interaction on the biological behavior of colon cancer cells. A biotin-microRNA pull-down assay was performed to identify potential miRNAs. qRT-PCR was used to verify the KRT18 and miR-186-3p levels. In addition, Western blotting was used to detect the KRT18 protein levels. The functional connection between KRT18 and miR-186-3p was confirmed using a dual luciferase reporter assay. BrdU incorporation, MTT assay, and flow cytometry were performed to verify the biological function coupled with in vivo assays. A significant decrease in miR-186-3p expression was observed in colon carcinoma tissues and cells. Functionally, overexpression of miR-186-3p displayed an obvious suppressive action on cell proliferation and viability, and a stimulatory action on the apoptotic ability of SW620 and SW480 cells. Conversely, reduced miR-186-3p had a marked stimulatory effect on proliferation and viability, and a suppressive apoptotic effect. Inhibition of tumorigenesis was observed in mice treated with the miR-186-3p agomir. Furthermore, we identified that miR-186-3p regulated KRT18 levels in colon carcinoma, where silenced KRT18 suppressed proliferation and viability and promoted apoptosis. However, the addition of a miR-186-3p inhibitor weakened the effects of si-KRT18. Additionally, the activation of MAPK signaling pathway upon miR-186-3p silencing was antagonized by the combined transfection of si-KRT18 and miR-186-3p inhibitor. miR-186-3p suppresses proliferation and viability, but facilitates apoptosis in colon cancer cells by targeting KRT18 and negatively regulating the MAPK signaling pathway, indicating that the miR-186-3p/KRT18 axis may be a promising therapeutic target for colon carcinoma.Abbreviations: KRT18: keratin 18; NC: negative control; si‑: small interfering RNA; inhibitor: miR-186-3p inhibitor; OD: optical density; PI: propidium iodide; FITC: fluorescein isothiocyanate; 3'UTR: 3'untranslated region; WT: wild-type; MUT: mutant-type; miR: microRNA.

Identification of hub genes and pathways in bladder cancer using bioinformatics analysis

Bladder cancer (BC) is the most common malignant tumor of urinary tract system. The aim of this study was to investigate the genetic signatures of bladder cancer (BC) and identify its potential molecular mechanisms. The gene expression profiles of GSE3167 (50 samples, including 41BC and 9 non-cancerous urothelial cells) was downloaded from the GEO database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) were performed to identify enriched pathways, and a protein-protein interaction (PPI) network was used to identify hub genes and for module analysis. Moreover, we conducted expression and survival analyses to screen and validate hub genes. In total, 1528 DEGs were identified in bladder cancer (BC), including 1212 up-regulated genes and 316 down-regulated genes. Up-regulated differentially expressed genes (DEGs) were significantly enriched in negative regulation of macromolecule metabolic process, macromolecule catabolic process, proteolysis and regulation of cell death, while the down-regulated differentially expressed genes (DEGs) were mainly involved in cell surface receptor linked signal transduction, ion transport, cell-cell signaling and defense response. The top 10 hub genes with the highest degrees were selected from the PPI network. These genes included HSP90AA1, MYH11, MYL9, CNN1, ACTC1, RAN, ENO1, HNRNPC, ACTG2 and YWHAZ. From sub-networks, we found these genes were involved in the proteasome, pathways in cancer and cell cycle. Hence, the identified DEGs and hub genes may be beneficial to elucidate the mechanisms underlying BC.

Update of the keratin gene family: evolution, tissue-specific expression patterns, and relevance to clinical disorders

Intermediate filament (IntFil) genes arose during early metazoan evolution, to provide mechanical support for plasma membranes contacting/interacting with other cells and the extracellular matrix. Keratin genes comprise the largest subset of IntFil genes. Whereas the first keratin gene appeared in sponge, and three genes in arthropods, more rapid increases in keratin genes occurred in lungfish and amphibian genomes, concomitant with land animal-sea animal divergence (~ 440 to 410 million years ago). Human, mouse and zebrafish genomes contain 18, 17 and 24 non-keratin IntFil genes, respectively. Human has 27 of 28 type I "acidic" keratin genes clustered at chromosome (Chr) 17q21.2, and all 26 type II "basic" keratin genes clustered at Chr 12q13.13. Mouse has 27 of 28 type I keratin genes clustered on Chr 11, and all 26 type II clustered on Chr 15. Zebrafish has 18 type I keratin genes scattered on five chromosomes, and 3 type II keratin genes on two chromosomes. Types I and II keratin clusters-reflecting evolutionary blooms of keratin genes along one chromosomal segment-are found in all land animal genomes examined, but not fishes; such rapid gene expansions likely reflect sudden requirements for many novel paralogous proteins having divergent functions to enhance species survival following sea-to-land transition. Using data from the Genotype-Tissue Expression (GTEx) project, tissue-specific keratin expression throughout the human body was reconstructed. Clustering of gene expression patterns revealed similarities in tissue-specific expression patterns for previously described "keratin pairs" (i.e., KRT1/KRT10, KRT8/KRT18, KRT5/KRT14, KRT6/KRT16 and KRT6/KRT17 proteins). The ClinVar database currently lists 26 human disease-causing variants within the various domains of keratin proteins.

LINC00337 promotes tumor angiogenesis in colorectal cancer by recruiting DNMT1, which suppresses the expression of CNN1

Colorectal cancer (CRC) is one of the most common human malignancies. An increasing body of evidence has revealed the important roles long noncoding RNA (lncRNA) plays in the growth dynamics of CRC cells. In this study, we aimed to define the role of LINC00337 in the malignant phenotypes, especially angiogenesis, of CRC and clarify the underlying molecular basis. Bioinformatic analyses identified promoter region methylation of CNN1 in CRC, which was further validated by BSP and MSP assays. Loss- and gain- of function approaches were used to determine the roles of CNN1 and LINC00337 in vitro and in vivo. MTT-based method, Transwell migration/invasion assays, and tube formation assay were adopted to evaluate the cancer cell proliferation, migration/invasion, and proangiogenetic potency respectively in vitro. The tumor growth, microvascular density (MVD) and markers of proliferation (Ki67) and angiogenesis (VEGF) were quantified in nude mice xenografted with CRC cells. It was found that CNN1 downregulation and LINC00337 overexpression occurred in CRC tissues and cells. Besides, the CNN1 promoter region was hypermethylated in CRC. CNN1 overexpression or LINC00337 knockdown restricted CRC cell proliferation, migration/invasion, and proangiogenetic potency in vitro, which was substantiated by the in vivo experiments evidenced by facilitated tumor growth and MVD as well as elevated Ki67 and VEGF. Furthermore, our mechanistic evidence revealed that LINC00337 recruited DNMT1 to the promoter region of CNN1 and restricted the transcription of CNN1. Taken together, this study indicates that LINC00337 facilitates the tumorigenesis and angiogenesis in CRC via recruiting DNMT1 to inhibit the expression of CNN1.

Identification of potential biomarkers with colorectal cancer based on bioinformatics analysis and machine learning

Colorectal cancer (CRC) is one of the most common malignancies worldwide. Biomarker discovery is critical to improve CRC diagnosis, however, machine learning offers a new platform to study the etiology of CRC for this purpose. Therefore, the current study aimed to perform an integrated bioinformatics and machine learning analyses to explore novel biomarkers for CRC prognosis. In this study, we acquired gene expression microarray data from Gene Expression Omnibus (GEO) database. The microarray expressions GSE103512 dataset was downloaded and integrated. Subsequently, differentially expressed genes (DEGs) were identified and functionally analyzed via Gene Ontology (GO) and Kyoto Enrichment of Genes and Genomes (KEGG). Furthermore, protein protein interaction (PPI) network analysis was conducted using the STRING database and Cytoscape software to identify hub genes; however, the hub genes were subjected to Support Vector Machine (SVM), Receiver operating characteristic curve (ROC) and survival analyses to explore their diagnostic values. Meanwhile, TCGA transcriptomics data in Gene Expression Profiling Interactive Analysis (GEPIA) database and the pathology data presented by in the human protein atlas (HPA) database were used to verify our transcriptomic analyses. A total of 105 DEGs were identified in this study. Functional enrichment analysis showed that these genes were significantly enriched in biological processes related to cancer progression. Thereafter, PPI network explored a total of 10 significant hub genes. The ROC curve was used to predict the potential application of biomarkers in CRC diagnosis, with an area under ROC curve (AUC) of these genes exceeding 0.92 suggesting that this risk classifier can discriminate between CRC patients and normal controls. Moreover, the prognostic values of these hub genes were confirmed by survival analyses using different CRC patient cohorts. Our results demonstrated that these 10 differentially expressed hub genes could be used as potential biomarkers for CRC diagnosis.

Development of a multiplex assay to determine the expression of mitochondrial genes in human skeletal muscle

NEW FINDINGS

What is the central question of this study? Can a custom-designed multiplex gene expression assay be used to quantify expression levels of a targeted group of mitochondrial genes in human skeletal muscle? What is the main finding and its importance? A custom-designed GeXP multiplex assay was developed, and the ability to accurately quantify expression of a targeted set of mitochondrial genes in human skeletal muscle was demonstrated. It holds distinct methodological and practical advantages over other commonly used quantification methods.

ABSTRACT

Skeletal muscle is an important endocrine tissue demonstrating plasticity in response to external stimuli, including exercise and nutrition. Mitochondrial biogenesis is a common hallmark of adaptations to aerobic exercise training. Furthermore, altered expression of several genes implicated in the regulation of mitochondrial biogenesis, substrate oxidation and nicotinamide adenine dinucleotide (NAD⁺ ) biosynthesis following acute exercise underpins longer-term muscle metabolic adaptations. Gene expression is typically measured using real-time quantitative PCR platforms. However, interest has developed in the design of multiplex gene expression assays (GeXP) using the GenomeLab GeXP™ genetic analysis system, which can simultaneously quantify gene expression of multiple targets, holding distinct advantages in terms of throughput, limiting technical error, cost effectiveness, and quantifying gene co-expression. This study describes the development of a custom-designed GeXP assay incorporating the measurement of proposed regulators of mitochondrial biogenesis, substrate oxidation, and NAD⁺ biosynthetic capacity in human skeletal muscle and characterises the resting gene expression (overnight fasted and non-exercised) signature within a group of young, healthy, recreationally active males. The design of GeXP-based assays provides the capacity to more accurately characterise the regulation of a targeted group of genes with specific regulatory functions, a potentially advantageous development for future investigations of the regulation of muscle metabolism by exercise and/or nutrition.

Plasma Membrane Localized GCaMP-MS4A12 by Orai1 Co-Expression Shows Thapsigargin- and Ca2+-Dependent Fluorescence Increases

Uniquely expressed in the colon, MS4A12 exhibits store-operated Ca2+ entry (SOCE) activity. However, compared to MS4A1 (CD20), a Ca2+ channel and ideal target for successful leukaemia immunotherapy, MS4A12 has rarely been studied. In this study, we investigated the involvement of MS4A12 in Ca2+ influx and expression changes in MS4A12 in human colonic malignancy. Fluorescence of GCaMP-fused MS4A12 (GCaMP-M12) was evaluated to analyse MS4A12 activity in Ca2+ influx. Plasma membrane expression of GCaMP-M12 was achieved by homo- or hetero-complex formation with no-tagged MS4A12 (nt-M12) or Orai1, respectively. GCaMP-M12 fluorescence in plasma membrane increased only after thapsigargin-induced depletion of endoplasmic reticulum Ca2+ stores, and this fluorescence was inhibited by typical SOCE inhibitors and siRNA for Orai1. Furthermore, GCaMP-MS4A12 and Orai1 co-transfection elicited greater plasma membrane fluorescence than GCaMP-M12 co-transfected with nt-M12. Interestingly, the fluorescence of GCaMP-M12 was decreased by STIM1 over-expression, while increased by siRNA for STIM1 in the presence of thapsigargin and extracellular Ca2+. Moreover, immunoprecipitation assay revealed that Orai1 co-expression decreased protein interactions between MS4A12 and STIM1. In human colon tissue, MS4A12 was expressed in the apical region of the colonic epithelium, although its expression was dramatically decreased in colon cancer tissues. In conclusion, we propose that MS4A12 contributes to SOCE through complex formation with Orai1, but does not cooperate with STIM1. Additionally, we discovered that MS4A12 is expressed in the apical membrane of the colonic epithelium and that its expression is decreased with cancer progression.

Clinical significance of enterocyte-specific gene polymorphisms as candidate markers of oxaliplatin-based treatment for metastatic colorectal cancer

Colorectal cancer (CRC) can be classified into subtypes based on gene expression signatures. Patients with stage III enterocyte subtype of the CRC Assigner classifier have been shown to benefit from oxaliplatin adjuvant therapy. Here, we investigated whether single nucleotide polymorphisms (SNPs) in two enterocyte subtype-related genes, MS4A12 and CDX2, could predict the efficacy of oxaliplatin in first-line treatment for patients with metastatic CRC (mCRC). Three cohorts of patients were included: a discovery cohort receiving FOLFOX ± bevacizumab (BEV) (n = 146), a validation cohort receiving FOLFOXIRI + BEV (n = 230), and a control cohort receiving FOLFIRI + BEV (n = 228). SNPs were analyzed by PCR-based direct sequencing. In the discovery cohort, MS4A12 rs4939378 and CDX2 rs3812863 were identified as potential markers of efficacy. In the validation cohort, any G allele of MS4A12 rs4939378 was associated with longer progression-free survival (PFS) than the A/A variant in both univariate analysis (12.4 vs. 10.9 months, hazard ratio [HR] 0.70, 95% confidence interval [CI] 0.49-0.99, P = 0.033) and multivariable analysis (HR 0.65, 95%CI 0.44-0.97, P = 0.035) in patients expressing wild-type KRAS, but not mutant KRAS. In contrast, longer PFS was observed for patients expressing the CDX2 rs3812863 G/G variant than any A allele in univariate analysis (32.3 vs. 10.3 months, HR 0.39, 95%CI 0.19-0.81, P = 0.004) only in patients expressing mutant KRAS. These findings were not observed in the control cohort. Thus, MS4A12 and CDX2 SNPs may have utility as predictive biomarkers of response to oxaliplatin-based treatment in mCRC patients.

Role of enterocyte-specific gene polymorphisms in response to adjuvant treatment for stage III colorectal cancer

OBJECTIVES

The enterocyte subtype of colorectal cancer (CRC) responds favorably to oxaliplatin-based adjuvant treatment for stage III CRC. We examined the clinical significance of single-nucleotide polymorphisms (SNPs) in enterocyte-related genes MS4A12 and CDX2 in response to adjuvant treatment for stage III CRC.

PATIENTS AND METHODS

A total of 350 patients with stage III CRC were included: 274 received adjuvant treatment with surgical resection (discovery cohort) and 76 received surgery alone (control cohort). In the discovery cohort, 68 patients received FOLFOX and 206 received oral fluoropyrimidine. SNPs were analyzed by PCR-based direct sequencing.

RESULTS

In the discovery cohort, the MS4A12 rs4939378 G/G variant was associated with lower 5-year survival than any A allele [70% vs. 90%, univariate: hazard ratio (HR) 2.29, 95% confidence interval (CI) 1.03-5.06, P = 0.035; multivariate: HR 2.58, 95% CI 1.15-5.76, P = 0.021]. Patients with the CDX2 rs3812863 G/G variant had better overall survival than those with any A allele, although this was not significant in multivariate analysis (5 year-survival: 95% vs. 82%, univariate: HR 0.34, 95% CI 0.12-0.97, P = 0.034; multivariate: HR 0.39, 95% CI 0.13-1.11, P = 0.078). The SNPs did not show significant association with overall survival in the control cohort, and significant interaction was observed between MS4A12 genotypes and groups (P = 0.007).

CONCLUSIONS

Our findings suggest that MS4A12 and CDX2 gene polymorphisms may predict outcome in stage III CRC. However, the clinical significance of SNPs for response to oxaliplatin may differ by tumor stage.

Comprehensive analysis of biomarkers for prostate cancer based on weighted gene co-expression network analysis

BACKGROUND

Prostate cancer (PCa) is one of the leading causes of cancer-related death. In the present research, we adopted a comprehensive bioinformatics method to identify some biomarkers associated with the tumor progression and prognosis of PCa.

METHODS

Differentially expressed genes (DEGs) analysis and weighted gene co-expression network analysis (WGCNA) were applied for exploring gene modules correlative with tumor progression and prognosis of PCa. Clinically Significant Modules were distinguished, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used to Annotation, Visualization and Integrated Discovery (DAVID). Protein-protein interaction (PPI) networks were used in selecting potential hub genes. RNA-Seq data and clinical materials of prostate cancer from The Cancer Genome Atlas (TCGA) database were used for the identification and validation of hub genes. The significance of these genes was confirmed via survival analysis and immunohistochemistry.

RESULTS

2688 DEGs were filtered. Weighted gene co-expression network was constructed, and DEGs were divided into 6 modules. Two modules were selected as hub modules which were highly associated with the tumor grades. Functional enrichment analysis was performed on genes in hub modules. Thirteen hub genes in these hub modules were identified through PPT networks. Based on TCGA data, 4 of them (CCNB1, TTK, CNN1, and ACTG2) were correlated with prognosis. The protein levels of CCNB1, TTK, and ACTG2 had a degree of differences between tumor tissues and normal tissues.

CONCLUSION

Four hub genes were identified as candidate biomarkers and potential therapeutic targets for further studies of exploring molecular mechanisms and individual therapy on PCa.

CpG-methylation-based risk score predicts progression in colorectal cancer

Aim: To identify patients with colorectal cancer (CRC) who are at a truly higher risk of progression, which is key for individualized approaches to precision therapy. Materials & methods: We developed a predictor associated with progression-free interval (PFI) using The Cancer Genome Atlas CRC methylation data. Results: The risk score was associated with PFI in the whole cohort (p < 0.001). A nomogram consisting of the risk score and other significant clinical features was generated to predict the 3- and 5-year PFI in the whole set (area under the curve: 0.79 and 0.71, respectively). Conclusion: The risk score based on 23 DNA-methylation sites may serve as the basis for improved prediction of progression in patients with CRC in future clinical practice.

Weighted gene co-expression network analysis identified MYL9 and CNN1 are associated with recurrence in colorectal cancer

Colorectal cancer (CRC) is one of the most common carcinomas and the fourth leading cause of cancer-related death worldwide. One of the obstacles in the successful treatment of CRC is a high rate of recurrence. We aimed to construct weighted gene co-expression network analysis (WGCNA) to identify key modules and hub genes in association with recurrence in CRC patients. We firstly used the microarray data, GSE41258, to construct a co-expression network and identify gene modules. Furthermore, protein and protein interaction (PPI) network was also performed to screen hub genes. To validate the hub genes, an independent dataset GSE17536 was used for survival analyses. Additionally, another two databases were also performed to investigate the survival rates and expression levels of hub genes. Gene set enrichment analyses (GSEA) combined with gene ontology (GO) were performed to further explore function and mechanisms. In our study, the midnightblue module was identified to be significant, 15 hub genes were screened, four of which were identified as hub nodes in the PPI network. In the test dataset, we found higher expression of MYL9 and CNN1 were significantly associated with shorter survival time of CRC patients. GO analyses showed that MYL9 and CNN1 were enriched in “muscle system process” and “cytoskeletal protein binding”. GSEA found the two hub genes were enriched in “pathways in cancer” and “calcium signaling pathway”. In conclusion, our study demonstrated that MYL9 and CNN1 were hub genes associated with the recurrence of CRC, which may contribute to the improvement of recurrence-free survival time of CRC patients.

PBMCs transcriptome profiles identified breed-specific transcriptome signatures for PRRSV vaccination in German Landrace and Pietrain pigs

Porcine reproductive and respiratory syndrome (PRRS) is a devastating viral disease affecting the swine industry worldwide. Genetic variation in host immunity has been considered as one of the potential determinants to improve the immunocompetence, thereby resistance to PRRS. Therefore, the present study aimed to investigate the breed difference in innate immune response to PRRSV vaccination between German Landrace (DL) and Pietrain (Pi) pigs. We analyzed microarray-based transcriptome profiles of peripheral blood mononuclear cells (PBMCs) collected before (0 h) and 24 h after PRRSV vaccination from purebred DL and Pi pigs with three biological replicates. In total 4,269 transcripts were identified to be differentially expressed in PBMCs in at least any of four tested contrast pairs (i.e. DL-24h vs. DL-0h, Pi-24h vs. Pi-0h, DL-0h vs. Pi-0h and DL-24h vs. Pi-24h). The number of vaccine-induced differentially expressed genes (DEGs) was much higher (2,459) in DL pigs than that of Pi pigs (291). After 24 h of PRRSV vaccination, 1,046 genes were differentially expressed in PMBCs of DL pigs compared to that of Pi (DL-24h vs. Pi-24h), indicating the breed differences in vaccine responsiveness. The top biological pathways significantly affected by DEGs of both breeds were linked to immune response functions. The network enrichment analysis identified ADAM17, STAT1, MMS19, RPA2, BAD, UCHL5 and APC as potential regulatory genes for the functional network of PRRSV vaccine response specific for DL; while FOXO3, IRF2, ADRBK1, FHL3, PPP2CB and NCOA6 were found to be the most potential hubs of Pi specific transcriptome network. In conclusion, our data provided insights of breed-specific host transcriptome responses to PRRSV vaccination which might contribute in better understanding of PPRS resistance in pigs.

KRT18 is correlated with the malignant status and acts as an oncogene in colorectal cancer

Keratin 18 (KRT18) has been suggested to be overexpressed in most types of human tumor, but the expression pattern of KRT18 in colorectal cancer (CRC) remained unknown. In our research, KRT18 protein expression was markedly increased in CRC cancer tissues and cell lines compared with adjacent normal colorectal tissues and normal colonic epithelial cell line, respectively. Meanwhile, we observed high KRT18 expression was associated with advanced clinical stage, deep tumor invasion, lymph node metastasis, distant metastasis, poor differentiation and unfavorable prognosis in CRC patients. Multivariate Cox regression analysis showed high expression of KRT18 was an unfavorable independent predictor for overall survival in CRC patients. The in vitro studies indicated down-regulation of KRT18 expression depressed CRC cell viability, migration and invasion. In conclusion, KRT18 serves as an oncogenic role in CRC progression and may be a therapeutic target for promoting CRC patients' prognosis.

Differentially expressed genes ASPN, COL1A1, FN1, VCAN and MUC5AC are potential prognostic biomarkers for gastric cancer

Gastric cancer (GC) is one of the most common malignancies worldwide. To the best of our knowledge, no biomarkers have been widely accepted for the early diagnosis and prognostic prediction of GC. This study aimed to identify potential novel prognostic biomarkers for GC. The dataset GSE29272, which originates from the public database Gene Expression Omnibus, was employed in the present study. The online tool GEO2R was used to calculate the differentially expressed genes (DEGs) in GSE29272 between tumour tissues and adjacent tissues. CytoHubba and MCODE plugins of Cytoscape software were used to obtain hub genes and modules of DEGs. The online tools Database for Annotation, Visualisation and Integrated Discovery and Search Tool for the Retrieval of Interacting Genes were employed to conduct Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis, and to construct protein-protein interaction networks. A total of 117 DEGs were extracted from GSE29272. In addition, 15 hub genes and seven modules were identified in the 117 DEGs. The enrichment analysis revealed that they were mainly enriched in GO biological process and cellular component domains, and the 'ECM-receptor interaction', 'focal adhesion', 'metabolism of xenobiotics by cytochrome P450' and 'drug metabolism' pathways. The hub genes asporin (ASPN), collagen type I α1 chain (COL1A1), fibronectin 1 (FN1), versican (VCAN) and mucin 5AC (MUC5AC) were demonstrated to have prognostic value for patients with GC. The ASPN and VCAN genes were significantly associated with overall survival and disease-free survival (log-rank P=0.025, 0.038, 0.0014 and 0.015, respectively). COL1A1 and FN1 were significantly associated with overall survival (log-rank P=0.013 and 0.05, respectively), and MUC5AC was significantly associated with disease-free survival (log-rank P=0.027). Results from the present study suggested that ASPN, COL1A1, FN1, VCAN and MUC5AC may represent novel prognostic biomarkers for GC.

Radiogenomic Analysis of F-18-Fluorodeoxyglucose Positron Emission Tomography and Gene Expression Data Elucidates the Epidemiological Complexity of Colorectal Cancer Landscape

Purpose

Transcriptomic profiling has enabled the neater genomic characterization of several cancers, among them colorectal cancer (CRC), through the derivation of genes with enhanced causal role and informative gene sets. However, the identification of small-sized gene signatures, which can serve as potential biomarkers in CRC, remains challenging, mainly due to the great genetic heterogeneity of the disease.

Methods

We developed and exploited an analytical framework for the integrative analysis of CRC datasets, encompassing transcriptomic data and positron emission tomography (PET) measurements. Profiling data comprised two microarray datasets, pertaining biopsy specimen from 30 untreated patients with primary CRC, coupled by their F-18-Fluorodeoxyglucose (FDG) PET values, using tracer kinetic analysis measurements. The computational framework incorporates algorithms for semantic processing, multivariate analysis, data mining and dimensionality reduction.

Results

Transcriptomic and PET data feature sets, were evaluated for their discrimination performance between primary colorectal adenocarcinomas and adjacent normal mucosa. A composite signature was derived, pertaining 12 features: 7 genes and 5 PET variables. This compact signature manifests superior performance in classification accuracy, through the integration of gene expression and PET data.

Conclusions

This work represents an effort for the integrative, multilayered, signature-oriented analysis of CRC, in the context of radio-genomics, inferring a composite signature with promising results for patient stratification.

CALD1, CNN1, and TAGLN identified as potential prognostic molecular markers of bladder cancer by bioinformatics analysis

BACKGROUND

Bladder cancer (BC) is one of the most common malignant neoplasms in the genitourinary tract. We employed the GSE13507 data set from the Gene Expression Omnibus (GEO) database in order to identify key genes related to tumorigenesis, progression, and prognosis in BC patients.

METHODS

The data set used in this study included 10 normal bladder mucosae tissue samples and 165 primary BC tissue samples. Differentially expressed genes (DEGs) in the 2 types of samples were identified by GEO2R. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the online website DAVID. The online website STRING was used to construct a protein-protein interaction network. Moreover, the plugins in MCODE and cytoHubba in Cytoscape were employed to find the hub genes and modules in these DEGs.

RESULTS

We identified 154 DEGs comprising 135 downregulated genes and 19 upregulated genes. The GO enrichment results were mainly related to the contractile fiber part, extracellular region part, actin cytoskeleton, and extracellular region. The KEGG pathway enrichment results mainly comprised type I diabetes mellitus, asthma, systemic lupus erythematosus, and allograft rejection. A module was identified from the protein-protein interaction network. In total, 15 hub genes were selected and 3 of them comprising CALD1, CNN1, and TAGLN were associated with both overall survival and disease-free survival.

CONCLUSION

CALD1, CNN1, and TAGLN may be potential biomarkers for diagnosis as well as therapeutic targets in BC patients.

DCLK1 Expression in Colorectal Polyps Increases with the Severity of Dysplasia

BACKGROUND

The expression of doublecortin-like kinase 1 (DCLK1) has been investigated in cancer; however not in precancerous adenomatous polyps.

MATERIALS AND METHODS

Immunohistological expression of DCLK1 was evaluated in various grades of adenomas, cancerous polyps, and hyperplastic polyps in resected human tissue specimens.

RESULTS

Ninety-two specimens were positive for DCLK1 and 134 were negative. Cancerous polyps showed a high DCLK1 positivity rate compared to adenomas (68.4% vs. 36.8%; p<0.01). The rate of DCLK1 positivity was not significantly different among the three grades of adenomas (mild, moderate, and severe). DCLK1 was highly positive in advanced adenomas than low risk adenomas (49.6% vs. 29.3%; p<0.01).

CONCLUSION

The expression of DCLK1 was found in low-grade adenomas and increased with worsening severity of dysplasia. DCLK1 expression was highly observed in advanced adenomas, which had a clinically higher malignant potential.

Hierarchical investigating the predictive value of p53, COX2, EGFR, nm23 in the post-operative patients with colorectal carcinoma

The aim of this study was to evaluate the correlations between p53, COX2, EGFR, nm23 expression and the progression free survival (PFS) of post-operative patients with colorectal carcinoma. Immunohistochemistry was used to detect the expression of p53, COX2, EGFR and nm23 in 459 specimens from colorectal carcinoma patients. Kaplan-Meier estimates, Cox proportional hazard regression analyses and hierarchical analyses were performed on the collected data. Kaplan-Meier estimates analysis suggested that EGFR expression was as a negative predictor, the median PFS of patients with EGFR high expression was 21.73 months, and the median PFS of patients with low EGFR expression was 57.83 months (χ²=20.880, P<0.001); nm23 expression was positive predictive factor for the prognosis of patients with colorectal carcinoma, the median PFS of patients with high nm23 expression was 37.77 months, and the median PFS was 21.47 months in the patients with low nm23 expression (χ²=7.364, P=0.007). Cox regression analysis revealed that comparing with the patients with low expression of EGFR, the patients with high EGFR expression were at higher risk of tumor progression (HR=1.667, P=0.004); Comparing with the patients with high nm23 expression, the patients with nm23 low expression had a higher risk of tumor progression (HR=0.412, P<0.001); and the risk of tumor progression was higher in the patients with high EGFR expression and low nm23 expression (HR=0.245, P<0.001). Hierarchical analysis showed that EGFR expression mainly correlates with the PFS of TNM stage I-II colorectal cancer patients, the median PFS was 33.53 months in the TNM stage I-II colorectal cancer patients with high EGFR expression patients; The median PFS of the TNM stage I-II colorectal cancer patients with low EGFR expression was 70.43 months (χ²=9.530, P=0.002); The median PFS was 19.2 months in the TNM stage III-IV colorectal cancer patients with high expression EGFR, the PFS of the TNM stage III-IV colorectal cancer patients with low EGFR expression was 37.87 months (χ²=7.97, P=0.005). nm23 expression mainly correlates with the PFS of TNM stage III-IV colorecatal cancer patients. The median PFS was 47.27 months in TNM stage I-II colorectal cancer patients with nm23 high expression, the median PFS was 48.85 months in TNM stage I-II colorectal cancer patients with low nm23 expression (χ²=0.101, P=0.750); The median PFS was 28.8 months in TNM stage III-IV colorectal cancer patients with nm23 high expression, the median PFS was 14.7 months in TNM stage III-IV colorectal cancer patients with low nm23 expression (χ²=13.213, P<0.001). EGFR is mainly a predictive factor for the prognosis of post-operative patients with TNM stage I-II colorectal cancer, and nm23 is important for predicting the prognosis of patients with stage III-IV, and EGFR and nm23 could be as predictor of combination.

Biosensors for spatiotemporal detection of reactive oxygen species in cells and tissues

Redox biology has become a major issue in numerous areas of physiology. Reactive oxygen species (ROS) have a broad range of roles from signal transduction to growth control and cell death. To understand the nature of these roles, accurate measurement of the reactive compounds is required. An increasing number of tools for ROS detection is available; however, the specificity and sensitivity of these tools are often insufficient. Furthermore, their specificity has been rarely evaluated in complex physiological conditions. Many ROS probes are sensitive to environmental conditions in particular pH, which may interfere with ROS detection and cause misleading results. Accurate detection of ROS in physiology and pathophysiology faces additional challenges concerning the precise localization of the ROS and the timing of their production and disappearance. Certain ROS are membrane permeable, and certain ROS probes move across cells and organelles. Targetable ROS probes such as fluorescent protein-based biosensors are required for accurate localization. Here we analyze these challenges in more detail, provide indications on the strength and weakness of current tools for ROS detection, and point out developments that will provide improved ROS detection methods in the future. There is no universal method that fits all situations in physiology and cell biology. A detailed knowledge of the ROS probes is required to choose the appropriate method for a given biological problem. The knowledge of the shortcomings of these probes should also guide the development of new sensors.

A novel antibody against cancer stem cell biomarker, DCLK1-S, is potentially useful for assessing colon cancer risk after screening colonoscopy

DCLK1 expression is critically required for maintaining growth of human colon cancer cells (hCCCs). Human colorectal tumors (CRCs) and hCCCs express a novel short isoform of DCLK1 (DCLK1-S; isoform 2) from β-promoter of hDCLK1 gene, while normal colons express long isoform (DCLK1-L; isoform 1) from 5'(α)-promoter, suggesting that DCLK1-S, and not DCLK1-L, marks cancer stem cells (CSCs). Even though DCLK1-S differs from DCLK1-L by only six amino acids, we succeeded in generating a monospecific DCLK1-S-Antibody (PS41014), which does not cross-react with DCLK1-L, and specifically detects CSCs. Subcellular localization of S/L-isoforms was examined by immune-electron-microscopy (IEM). Surprisingly, besides plasma membrane and cytosolic fractions, S/L also localized to nuclear/mitochondrial fractions, with pronounced localization of S-isoform in the nuclei and mitochondria. Sporadic CRCs develop from adenomas. Screening colonoscopy is used for detection/resection of growths, and morphological/pathological criteria are used for risk assessment and recommendations for follow-up colonoscopy. But, these features are not precise and majority of the patients will never develop cancer. We hypothesized that antibody-based assay(s), which identify CSCs, will significantly improve prognostic value of morphological/pathological criteria. We conducted a pilot retrospective study with PS41014-Ab, by staining archived adenoma specimens from patients who developed (high-risk), or did not develop (low-risk) adenocarcinomas within 10-15 years. PS41014-Ab stained adenomas from initial and follow-up colonoscopies of high-risk patients, at significantly higher levels (three to fivefold) than adenomas from low-risk patients, suggesting that PS41014-Ab could be used as an additional tool for assessing CRC risk. CRC patients, with high DCLK1-S-expressing tumors (by qRT-PCR), were reported to have worse overall survival than low expressers. We now report that DCLK1-S-specific Ab may help to identify high-risk patients at the time of index/screening colonoscopy.

FOXD3 Regulates CSC Marker, DCLK1-S, and Invasive Potential: Prognostic Implications in Colon Cancer

The 5' (α)-promoter of the human doublecortin-like kinase 1 (DCLK1) gene becomes epigenetically silenced during colon carcinogenesis, resulting in loss of expression of the canonical long(L)-isoform1 (DCLK1-L) in human colon adenocarcinomas (hCRCs). Instead, hCRCs express a short(S)-isoform2 (DCLK1-S) from an alternate (β)-promoter of DCLK1. The current study, examined if the transcriptional activity of the (β)-promoter is suppressed in normal versus cancerous cells. On the basis of in silico and molecular approaches, it was discovered that FOXD3 potently inhibits the transcriptional activity of the (β)-promoter. FOXD3 becomes methylated in human colon cancer cells (hCCC), with loss of FOXD3 expression, allowing expression of the DCLK1(S) variant in hCCCs/hCRCs. Relative levels of FOXD3/DCLK1(S/L) were measured in a cohort of CRC patient specimens (n = 92), in relation to overall survival (OS). Patients expressing high DCLK1(S), with or without low FOXD3, had significantly worse OS compared with patients expressing low DCLK1(S). The relative levels of DCLK1-L did not correlate with OS. In a pilot retrospective study, colon adenomas from high-risk patients (who developed CRCs in <15 years) demonstrated significantly higher staining for DCLK1(S) + significantly lower staining for FOXD3, compared with adenomas from low-risk patients (who remained free of CRCs). Latter results strongly suggest a prognostic value of measuring DCLK1(S)/FOXD3 in adenomas. Overexpression of DCLK1(S), but not DCLK1(L), caused a significant increase in the invasive potential of hCCCs, which may explain worse outcomes for patients with high DCLK1-S-expressing tumors. On the basis of these data, FOXD3 is a potent repressor of DCLK1-S expression in normal cells; loss of FOXD3 in hCCCs/hCRCs allows upregulation of DCLK1-S, imparting a potent invasive potential to the cells. Mol Cancer Res; 15(12); 1678-91. ©2017 AACR.

Aberrant methylation patterns in colorectal cancer: a meta-analysis

Colorectal cancer is among the leading causes of cancer death worldwide. Despite numerous molecular characterizations of the phenomenon, the exact dynamics of its onset and progression remain elusive. Colorectal cancer onset has been characterized by changes in DNA methylation profiles, that, owing to the stability of their patterns, are promising candidates to shed light on the molecular events laying at the base of this phenomenon.To exploit this stability and reinforce it, we conducted a meta-analysis on publicly available DNA methylation datasets generated on: normal colorectal, adenoma (ADE) and adenocarcinoma (CRC) samples using the Illumina 450k array, in the systems medicine frame, searching for tumor gene episignatures, to produce a carefully selected list of potential drivers, markers and targets of the disease. The analysis proceeds from a differential meta-analysis of the methylation profiles using an analytical pipeline recently developed by our group [1], through network reconstruction, topological and functional analyses, to finally highlight relevant epigenomic features. Our results show that genes already highlighted for their genetic or transcriptional alteration in colorectal cancer are also differentially methylated, reinforcing -regardless of the level of cellular control- their role in the complex of alterations involved in tumorigenesis.These findings were finally validated in an independent cohort from The Cancer Genome Atlas (TCGA).

A plausible role for actin gamma smooth muscle 2 (ACTG2) in small intestinal neuroendocrine tumorigenesis

BACKGROUND

Small intestinal neuroendocrine tumors (SI-NETs) originate from the enterochromaffin cells in the ileum and jejunum. The knowledge about genetic and epigenetic abnormalities is limited. Low mRNA expression levels of actin gamma smooth muscle 2 (ACTG2) have been demonstrated in metastases relative to primary SI-NETs. ACTG2 and microRNA-145 (miR-145) are aberrantly expressed in other cancers and ACTG2 can be induced by miR-145. The aim of this study was to investigate the role of ACTG2 in small intestinal neuroendocrine tumorigenesis.

METHODS

Protein expression was analyzed in SI-NETs (n = 24) and in enterochromaffin cells by immunohistochemistry. The cell line CNDT2.5 was treated with the histone methyltransferase inhibitor 3-deazaneplanocin A (DZNep), the selective EZH2 inhibitor EPZ-6438, or 5-aza-2'-deoxycytidine, a DNA hypomethylating agent. Cells were transfected with ACTG2 expression plasmid or miR-145. Western blotting analysis, quantitative RT-PCR, colony formation- and viability assays were performed. miR-145 expression levels were measured in tumors.

RESULTS

Eight primary tumors and two lymph node metastases displayed variable levels of positive staining. Fourteen SI-NETs and normal enterochromaffin cells stained negatively. Overexpression of ACTG2 significantly inhibited CNDT2.5 cell growth. Treatment with DZNep or transfection with miR-145 induced ACTG2 expression (>10-fold), but no effects were detected after treatment with EPZ-6438 or 5-aza-2'-deoxycytidine. DZNep also induced miR-145 expression. SI-NETs expressed relatively low levels of miR-145, with reduced expression in metastases compared to primary tumors.

CONCLUSIONS

ACTG2 is expressed in a fraction of SI-NETs, can inhibit cell growth in vitro, and is positively regulated by miR-145. Theoretical therapeutic strategies based on these results are discussed.

Molecular Profiling of Multiplexed Gene Markers to Assess Viability of Ex Vivo Human Colon Explant Cultures

Human colon tissue explant culture provides a physiologically relevant model system to study human gut biology. However, the small (20–30 mg) and complex tissue samples used present challenges for monitoring tissue stability, viability, and provision of sufficient tissue for analyses. Combining molecular profiling with explant culture has potential to overcome such limitations, permitting interrogation of complex gene regulation required to maintain gut mucosa in culture, monitor responses to culture environments and interventions. Human ex vivo colon explant gene expression profiles were assayed using an in-house custom-designed hCellMarkerPlex assay at culture time points 0, 1, 2, 4, and 14 h. Characteristic profiles of epithelial cell markers linked to differentiation, cellular polarization, and apoptosis were correlated with visible histochemical changes in explant epithelium during culture and tissue donors. The GenomeLab System provides effective assay of multiple targets not possible from small tissue samples with conventional gene expression technology platforms. This is advantageous to increase the utility of the ex vivo human colon model in applications to interrogate this complex and dynamic tissue environment for use in analytical testing.

Proteins and Carbohydrates from Red Seaweeds: Evidence for Beneficial Effects on Gut Function and Microbiota

Based on their composition, marine algae, and namely red seaweeds, are good potential functional foods. Intestinal mucosal barrier function refers to the capacity of the intestine to provide adequate containment of luminal microorganisms and molecules. Here, we will first outline the component of seaweeds and will summarize the effects of these on the regulation of mucosal barrier function. Special attention will be paid to unique components of red seaweeds: proteins and derived peptides (e.g., phycobiliproteins, glycoproteins that contain “cellulose binding domains”, phycolectins and the related mycosporine-like amino acids) together with polysaccharides (e.g., floridean starch and sulfated galactans, such as carrageenans, agarans and “dl-hybrid”) and minerals. These compounds have been shown to exert prebiotic effects, to regulate intestinal epithelial cell, macrophage and lymphocyte proliferation and differentiation and to modulate the immune response. Molecular mechanisms of action of peptides and polysaccharides are starting to be elucidated, and evidence indicating the involvement of epidermal growth factor receptor (EGFR), insulin-like growth factor receptor (IGFR), Toll-like receptors (TLR) and signal transduction pathways mediated by protein kinase B (PKB or AKT), nuclear factor-κB (NF-κB) and mitogen activated protein kinases (MAPK) will also be summarized. The need for further research is clear, but in vivo experiments point to an overall antiinflammatory effect of these algae, indicating that they can reinforce membrane barrier function.