Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-Wide Expression Profiling of Human Colonic Epithelial Cell Model Co-challenged with Single, Multi-strain Probiotics and Pro-inflammatory Stimulus, poly (I:C)

ABSTRACT: One of the key impacts of probiotic bacteria is the ability to beneficially modulate innate and adaptive immune responses of various cell types of the gut-associated lymphoid tissue. In this study we used an in vitro intestinal epithelial cell model to investigate the impact of three probiotic bacteria Lactobacillus helveticus R0052, Bifidobacterium longum subsp. infantis R0033 and Bifidobacterium bifidum R0071 individually, in combination (R0033, R0052 and R0071) and of a specific surface-layer protein partially purified from L. helveticus R0052 (R0052-SLP) in response to a known dsRNA pro-inflammatory stimulus, poly (I:C). Genome-wide human expression microarray chips were used to evaluate other cellular pathways and gain a deeper insight into global gene and pathway modulation. Here we report that the challenge by poly (I:C)-only resulted in the differential expression of 863 genes; whereas, the co-challenge with either R0033, R0052, R0071, R0052-SLP and the multi-strain combination (R0052, R0033 and R0071) resulted in differential expression of 467 genes, 369 genes, 293 genes, 219 genes and 132 genes; respectively. The multi-strain combination had a greater impact than each single component strain at reducing the number of genes modulated. Among the major human pathways modulated by probiotics or R0052-SLP in response to poly (I:C) include: immune/virus, cellular/signaling, nervous/endocrine and autoimmune disorder related pathways. Cytokine and chemokine profiling was performed at the protein level based on specific markers from the TNF-α and NF-KB signaling pathways. The results revealed single strain, multi-strain and R0052-SLP specific attenuation for the majority of proteins measured (TNF-α, IL-8, CXCL1, CXCL2, CXCL10 and IL-10) indicating potentially different mechanisms for each strain, multi-strain and protein component and reinforcing the rationale for multi-strain combinations. The overall study design consisted of 8 different treatments/challenges of HT-29. Briefly, HT-29 cells were co-challenge for 3 h with either the single strains (R0033, R0052 or R0071) or probiotic combination (PC) alone or in combination with poly (I:C) at 10 µg/mL. Also, a specific surface layer protein purified from R0052 (R0052-SLP) was also co-challenged with poly (I:C) in HT-29 cells. Treatment/challenges of poly (I:C)-only, surface layer protein-only (R0052-SLP-only) and probiotic combination-only or PC-only were also evaluated. All challenges and co-challenges were compared to unchallenged control HT-29 cells. 4 biological reps were performed for each of the 8 samples/treatments.

ORGANISM(S): Homo sapiens

SUBMITTER: Thomas Tompkins

PROVIDER: E-GEOD-71515 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Genome-wide transcriptional analysis in intestinal epithelial cells (IEC) can aid in elucidating the impact of single versus multi-stain probiotic combinations on immunological and cellular mechanism of action. In this study we used an in vitro intestinal epithelial cell model to investigate the impact of three probiotic bacteria individually or in combination and a surface-layer protein (SLP) partially purified from one of the bacteria on HT-29 cells’ response to a known pro-inflammatory stimulus, polyinosinic:polycytidylic, poly(I:C). Human expression microarray chips were used to evaluate the effect of Lactobacillus helveticus R0052, Bifidobacterium longum subsp. infantis R0033 and Bifidobacterium bifidum R0071 individually, in combination and of a surface-layer protein (SLP) partially purified from R0052 on HT-29 cells’ transcriptional profile to poly(I:C)-induced inflammation. Hierarchical heat map clustering, Set Distiller and String analyses revealed that the effects of R0052 and R0071 diverged from that of R0033 and R0052-SLP. It was evident from the global analyses with respect to the immune, cellular and homeostasis related pathways that the co-challenge with probiotic combination (PC) vastly differed in its effect from the single strains and R0052-SLP treatments. The multi-strain PC resulted in a greater reduction of modulated genes, found through functional connections between immune and cellular pathways. Cytokine and chemokine analyses based on specific outcomes from the TNF-α and NF-κB signaling pathways revealed single, multi-strain and R0052-SLP specific attenuation of the majority of proteins measured (TNF-α, IL-8, CXCL1, CXCL2 and CXCL10), indicating potentially different mechanisms. These findings indicate a synergistic effect of the bacterial combinations relative to the single strain and R0052-SLP treatments in resolving toll-like receptor 3 (TLR3)-induced inflammation in IEC and maintaining cellular homeostasis, reinforcing the rationale for using multi-strain formulations as a probiotic.

Project description:A commercially available product containing three probiotic bacterial strains (Lactobacillus helveticus R0052, Bifidobacterium longum subsp. infantis R0033, and Bifidobacterium bifidum R0071) was previously shown in animal trials to modulate both TH1 and TH2 immune responses. Clinical studies on this combination of bacteria have also shown positive health effects against seasonal winter diseases and rotavirus infection. The goal of this study was to use a well-established in vitro intestinal epithelial (HT-29) cell model that has been shown to constitutively express double-stranded RNA (dsRNA) sensors (Toll-like receptor 3[TLR3], retinoic acid-inducible gene I, melanoma differentiation-associated gene 5, and dsRNA-activated protein kinase). By using the HT-29 cell model, we wanted to evaluate whether or not this combination of three bacteria had the capacity to immune modulate the host cell response to a dsRNA ligand, poly(IM-bM-^@M-"C). Using a custom-designed, two-color expression microarray targeting genes of the human immune system, we investigated the response of HT-29 cells challenged with poly(IM-bM-^@M-"C) both in the presence and in the absence of the three probiotic bacteria. We observed that the combination of the three bacteria had a major impact on attenuating the expression of genes connected to proinflammatory TH1 and antiviral innate immune responses compared to that obtained by the poly(IM-bM-^@M-"C)-only challenge. Major pathways through which the multistrain combination may be eliciting its immune-modulatory effect include the TLR3-TRIF, mitogen-activated protein kinase, and NF-KB signaling pathways.Such a model may be useful for selecting potential biomarkers for the design of future clinical trials The overall design consisted of 3 samples of HT-29 cells treated with poly (I:C)-only, probiotic combination (PC) and poly (I:C) + PC versus unchallenged HT-29 cells. A minimum of four dye-swap hybridizations (4 biological replicates) were performed for each of the 3 samples analyzed. Unchallenged HT-29 cells were controls and challenged HT-29 cells with poly (I:C)-only, PC-only and poly (I:C) + PC were treated samples.

Project description:Metastasis and drug-resistance are major problems in cancer chemotherapy. The purpose of this work was to analyze the molecular mechanisms underlying the invasive potential of drug-resistant colon carcinoma cells. Cellular models included the parental HT-29 cell line and its drug-resistant derivatives selected after chronic treatment with either 5-fluorouracil (5-FU), methotrexate (MTX), doxorubicin (DOX) or oxaliplatin (OXA). Drug-resistant invasive cells were compared to non invasive cells using cDNA microarray, qRT-PCR, flow cytometry, immunoblots and ELISA. Functional and cellular signaling analyses were undertaken using pharmacological inhibitors, function-blocking antibodies, and silencing by retrovirus-mediated RNA interference. 5-FU- and MTX-resistant HT-29 cells expressing an invasive phenotype in collagen type I and a metastatic behaviour in immunodeficient mice exhibited high expression of the chemokine receptor CXCR4. Macrophage migration inhibitory factor (MIF) was identified as the critical autocrine CXCR4 ligand promoting invasion in drug-resistant colon carcinoma HT-29 cells. Silencing of CXCR4 and impairing the MIF-CXCR4 signaling pathways by ISO-1, pAb FL-115, AMD-3100, mAb 12G5, and BIM-46187 abolished this aggressive phenotype. Induction of CXCR4 is associated with up-regulation of two genes encoding transcription factors previously shown to control CXCR4 expression (HIF-2a and ASCL2) and maintenance of intestinal stem cells (ASCL2). Enhanced CXCR4 expression was detected in liver metastases resected from colon cancer patients treated by the standard FOLFOX regimen. Combination therapies targeting the CXCR4-MIF axis can potentially counteract the emergence of the invasive metastatic behaviour in clonal derivatives of drug-resistant colon cancer cells. Samples: HT-29 cell clones were obtained by limiting dilution from HT-29 subpopulations resistant to methothrexate (HT-29 5M21 cell clone) and or to 5-Fluoro-uracil (HT-29 5F7 and HT-29 5F31). Samples were provided by Dr. T Lesuffleur. Xenografts: HT-29 5M21, HT-29 5F7, and HT-29 5F31 xenografts were obtained by a first subcutaneous inoculation of cells in Nude mice and then fragments of subcutaneous tumors were reimplantated in SCID mice. First experiment of microarrays: HT-29 5M21 and HT-29 5F7 cells (that are invasive in in vitro assays on type I collagen) were compared to HT-29 5F31 cells (that are not invasive in vitro on type I collagen). Samples were co-hybridized on Agilent Human 44K GEP arrays (respectively 5F31 vs 5M21, 5F31 vs 5F7, 5M21 vs 5F31 and 5F7 vs 5F31). Second experiment of microarrays: HT-29 5M21 and HT-29 5F7 xenografts (that develop metastases in immuno-deficient mice lungs) were compared to HT-29 5F31 xenografts (that do not develop metastases in immuno-deficient mice lungs). Samples were consequently co-hybridized on human and mouse 4x44K GEP arrays (respectively AG41_5F31-5M21-138869, AG39_5F31-5F7-138867, AG42_5M21-5F31-138870 and AG40_5F7-5F31-138868 for human microarrays; 5M21_5F31_27033_4, 5F31_5M21_27033_3, 5F7_5F31_27033_2 and 5F31_5F7_27033_1_1 for mouse microarrays).

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Genome-Wide Expression Profiling of Human Colonic Epithelial Cell Model Co-challenged with Single, Multi-strain Probiotics and Pro-inflammatory Stimulus, poly (I:C)

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