scholarly journals The tongue biofilm metatranscriptome identifies metabolic pathways associated with halitosis and its prevention

2021 ◽  
Author(s):  
Miguel Carda-Dieguez ◽  
Bob T. Rosier ◽  
Sandra Lloret ◽  
Carmen Llena ◽  
Alex Mira
Keyword(s):  
Gene Expression ◽  
Hydrogen Sulfide ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Fusobacterium Nucleatum ◽  
Sulfide Concentration ◽  
Methyl Mercaptan ◽  
Over Expression ◽  
Expression Of Genes ◽  
Taxonomic Studies

Halitosis is an oral condition caused by an increase in the concentration of volatile sulfur compounds (VSCs), such as methyl mercaptan and hydrogen sulfide, generated as a consequence of bacterial metabolism on the tongue biofilm. Microbial communities on the tongue of halitosis patients have been studied by bacterial culture, 16S rRNA taxonomic studies and metagenomics. However, there are currently no reports on the microbial gene-expression profiles. In this study, we performed RNAseq of tongue coating samples from control individuals and halitosis patients with different levels and composition of VSCs, as determined by gas chromatography. In this metatranscriptomic study, the activity of Streptococcus, Veillonella and Rothia species was associated with halitosis-free individuals while Prevotella, Fusobacterium and Leptotrichia species were associated with halitosis. Although methyl mercaptan is considered an indicator of halitosis, the metatranscriptome of patients in which only this VSC was present in elevated levels was similar to that of halitosis-free individuals. Veillonella dispar, Streptococcus parasanguinis and Rothia mucilaginosa were over-represented in halitosis-free communities in comparison to the rest of the groups, suggesting that these species could be used as a halitosis-free biomarkers. In contrast, the abundance of Prevotella shahi and Fusobacterium nucleatum were significantly higher when hydrogen sulfide concentration was over the established halitosis-threshold, making these species putative halitosis biomarkers. Finally, gene expression profiles showed a significant over-expression of genes involved in L-cysteine and L-homocysteine synthesis in halitosis-free individuals and an over-expression of genes responsible for cysteine degradation into hydrogen sulfide in halitosis patients. In addition, nitrate reduction into nitrite was also over-expressed in halitosis-free patients. In conclusion, halitosis was associated with communities that degrade amino acids and reduce sulfide, whereas tongue communities that produce L-cysteine from hydrogen sulfide and that reduce nitrate were associated with the absence of halitosis. The latter could provide new strategies to treat this condition.

Monitoring expression of genes involved in drug metabolism and toxicology using DNA microarrays

2001 ◽  
Vol 5 (4) ◽  
pp. 161-170 ◽  
Author(s):  
DAVID GERHOLD ◽  
MEIQING LU ◽  
JIAN XU ◽  
CHRISTOPHER AUSTIN ◽  
C. THOMAS CASKEY ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drug Metabolism ◽  
Stress Responses ◽  
Dna Microarrays ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Metabolic Effects ◽  
Microarray Technology ◽  
Drug Candidates ◽  
Expression Of Genes

Oligonucleotide DNA microarrays were investigated for utility in measuring global expression profiles of drug metabolism genes. This study was performed to investigate the feasibility of using microarray technology to minimize the long, expensive process of testing drug candidates for safety in animals. In an evaluation of hybridization specificity, microarray technology from Affymetrix distinguished genes up to a threshold of ∼90% DNA identity. Oligonucleotides representing human cytochrome P-450 gene CYP3A5 showed heterologous hybridization to CYP3A4 and CYP3A7 RNAs. These genes could be clearly distinguished by selecting a subset of oligonucleotides that hybridized selectively to CYP3A5. Further validation of the technology was performed by measuring gene expression profiles in livers of rats treated with vehicle, 3-methylcholanthrene (3MC), phenobarbital, dexamethasone, or clofibrate and by confirming data for six genes using quantitative RT-PCR. Responses of drug metabolism genes, including CYPs, epoxide hydrolases ( EHs), UDP-glucuronosyl transferases ( UGTs), glutathione sulfotransferases ( GSTs), sulfotransferases ( STs), drug transporter genes, and peroxisomal genes, to these well-studied compounds agreed well with, and extended, published observations. Additional gene regulatory responses were noted that characterize metabolic effects or stress responses to these compounds. Thus microarray technology can provide a facile overview of gene expression responses relevant to drug metabolism and toxicology.

Immune- and tumor-intrinsic gene expression profiles of response or resistance to tislelizumab as monotherapy or in combination with chemotherapy in non-small cell lung cancer (NSCLC).

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e15258-e15258
Author(s):  
Jayesh Desai ◽  
Jie Wang ◽  
Qing Zhou ◽  
Jun Zhao ◽  
Sanjeev Deva ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Repair ◽  
Clinical Benefit ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Rank Test ◽  
M2 Macrophage ◽  
Intrinsic Factors ◽  
Expression Of Genes ◽  
Intrinsic Gene

e15258 Background: Tislelizumab, an anti-PD-1 monoclonal antibody, showed clinical benefit for patients (pts) with NSCLC alone (NCT02407990, CTR20160872) and in combination with chemotherapy (NCT03432598). Gene expression profiles (GEP) associated with response and resistance to tislelizumab in these studies were assessed. Methods: The GEP of baseline tumor samples from 59 nonsquamous (NSQ) and 42 squamous (SQ) NSCLC pts treated with tislelizumab monotherapy (mono) as ≥1L treatment, and 16 NSQ and 21 SQ pts treated with tislelizumab plus chemotherapy (combo) as 1L treatment were assessed using the 1392-gene HTG GEP EdgeSeq panel. NSQ and SQ cohorts were analyzed separately due to distinct GEP features shown by PCA and t-SNE clustering. Results: Tislelizumab mono and combo showed antitumor activity in NSCLC (Table). In 80 biomarker-evaluable samples, inflamed tumor signatures (inflammatory GEP; antigen presentation GEP) were associated with longer overall survival (log-rank test, NSQ mono: P=0.04, 0.003; NSQ combo: P=0.05, 0.02; SQ combo: P=0.06, 0.06). Monotherapy non-responders (NRs) were clustered into 2 subgroups (NR1, NR2) with distinct GEPs. Compared with responders, NR1 had proliferation signatures (elevated cell cycle [CC] and DNA repair) in both NSQ ( P=0.2, 0.02) and SQ ( P=0.03, 0.4) cohorts, trending toward low inflamed tumor signatures. In NR pts receiving combo, CC and DNA repair signatures were not enriched, and high CC and DNA repair scores were observed in some SQ combo responders versus NRs ( P=0.2, 0.02). NR2 had higher M2 macrophage and Treg cell signatures versus responders in both NSQ and SQ mono, despite high inflamed tumor and low proliferation signatures. NR2 also had increased expression of genes related to immune regulation and angiogenesis, including PIK3CD, CCR2, CD244, IRAK3, and MAP4K1 ( P<0.05) in NSQ, and PIK3CD, CCR2, CD40, CD163, MMP12, VEGFC, and TEK ( P<0.05) in SQ. Conclusions: Clinical benefit in pts with NSCLC receiving tislelizumab (mono or combo) was associated with high inflamed tumor signatures, while elevated immune suppressive cell signatures may indicate resistance. High proliferation signatures were associated with resistance to monotherapy, but not to combination therapy. Both immune- and tumor-intrinsic factors may be considered for validation in future clinical trials. [Table: see text]

scholarly journals Dynamic Clustering of Gene Expression

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Lingling An ◽  
R. W. Doerge
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Optimal Number ◽  
Sequential Data ◽  
Dynamic Clustering ◽  
Biological Processes ◽  
Time Frequency ◽  
Expression Of Genes

It is well accepted that genes are simultaneously involved in multiple biological processes and that genes are coordinated over the duration of such events. Unfortunately, clustering methodologies that group genes for the purpose of novel gene discovery fail to acknowledge the dynamic nature of biological processes and provide static clusters, even when the expression of genes is assessed across time or developmental stages. By taking advantage of techniques and theories from time frequency analysis, periodic gene expression profiles are dynamically clustered based on the assumption that different spectral frequencies characterize different biological processes. A two-step cluster validation approach is proposed to statistically estimate both the optimal number of clusters and to distinguish significant clusters from noise. The resulting clusters reveal coordinated coexpressed genes. This novel dynamic clustering approach has broad applicability to a vast range of sequential data scenarios where the order of the series is of interest.

scholarly journals Over-expression of the kayopherin 𝛂2 gene (KPNA2) in high-grade serous ovarian cancers.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Gene Expression ◽  
Ovarian Cancer ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Global Gene Expression ◽  
High Grade ◽  
Over Expression ◽  
Ovarian Cancers ◽  
Microarray Datasets

Ovarian cancer is the most lethal gynecologic malignancy and 70-80% of ovarian cancers are of the high-grade serous type (1-3). To identify the most significant changes in gene expression in high-grade serous ovarian cancer (HGSC), we compared global gene expression profiles of tumors from patients with HGSC to that of normal ovary using published microarray datasets (4, 5). We found that the nuclear import receptor karyopherin 𝛂2 (KPNA2) (6) was among the genes whose expression changed most significantly when comparing HSGC tumors to the ovary. Karyopherin 𝛂2 may be relevant to the biology of high-grade serous ovarian tumors.

The changes of gene expression profiles in hydatidiform mole and choriocarcinoma with hyperplasia of trophoblasts

2004 ◽  
Vol 14 (5) ◽  
pp. 984-997 ◽  
Author(s):  
J. Q. Cui ◽  
Y. F. Shi ◽  
H. J. Zhou ◽  
J. Q. Li
Keyword(s):  
Gene Expression ◽  
Cell Proliferation ◽  
Cdna Microarray ◽  
Expression Profiles ◽  
Hydatidiform Mole ◽  
Gene Expression Profiles ◽  
Small Subunit ◽  
Altered Expression ◽  
Expression Of Genes ◽  
Hydatidiform Moles

The purpose of this study is to investigate changes of gene expression profiles in hydatidiform moles (HM) and choriocarcinoma and to explore causes of trophoblastic hyperplasia. Using cDNA microarray, 4096 genes were analyzed in two pairs of the tissues of HM versus normal villi and in two pairs of normal primary culture trophoblasts versus JAR cell line of choriocarcinoma. The expressions of two genes in normal villi and HM, as well as in JAR and JEG-3, were examined with the help of immunohistochemistry, immunoblot, and reverse transcriptase-polymerase chain reaction in order to confirm the findings of cDNA microarray. Twenty-four genes were upregulated and 65 genes were downregulated in all HM. Four hundred thirty-three genes were upregulated and 380 genes were downregulated in JAR. Forty-six genes were upregulated in both HM and choriocarcinoma, whereas 13 genes were downregulated. Genes associated with the inhibition of cell proliferation were significantly downregulated, whereas genes associated with cell proliferation, malignant transformation, metastasis, and drug resistance were upregulated. Thymidine kinase-1 (TK-1) and small subunit ribonucleotide reductase (RRM-2) were overexpressed in HM, JAR, and JEG-3. The expressions of TK-1 and RRM-2 in moles were positively correlated with proliferative index of trophoblasts. Our results suggest that altered expression of genes exist in HM and choriocarcinoma. Trophoblastic hyperplasia may be involved in the overexpression of DNA synthetic enzymes.

Comparing Initial Wound Healing and Osteogenesis of Porous Tantalum Trabecular Metal and Titanium Alloy Materials

2019 ◽  
Vol 45 (3) ◽  
pp. 173-180 ◽  
Author(s):  
Sompop Bencharit ◽  
Thiago Morelli ◽  
Silvana Barros ◽  
Jackson T. Seagroves ◽  
Steven Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Wound Healing ◽  
Titanium Alloy ◽  
Dental Implants ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Trabecular Metal ◽  
Porous Tantalum ◽  
Expression Of Genes ◽  
Conventional Titanium Alloy

Porous tantalum trabecular metal (PTTM) has long been used in orthopedics to enhance neovascularization, wound healing, and osteogenesis; recently, it has been incorporated into titanium alloy dental implants. However, little is known about the biological responses to PTTM in the human oral cavity. We have hypothesized that, compared with conventional titanium alloy, PTTM has a greater expression of genes specific to neovascularization, wound healing, and osteogenesis during the initial healing period. Twelve subjects requiring at least 4 implants in the mandible were enrolled. Four 3 × 5mm devices, including 2 titanium alloy tapered screws and 2 PTTM cylinders, were placed in the edentulous mandibular areas using a split-mouth design. One device in each group was trephined for analysis at 2 and 4 weeks after placement. RNA microarray analysis and ingenuity pathway analysis were used to analyze osteogenesis gene expression and relevant signaling pathways. Compared to titanium alloy, PTTM samples exhibited significantly higher expressions of genes specific to cell neovascularization, wound healing, and osteogenesis. Several genes—including bone morphogenic proteins, collagens, and growth factors—were upregulated in the PTTM group compared to the titanium alloy control. PTTM materials may enhance the initial healing of dental implants by modifying gene expression profiles.

scholarly journals Fatty Acid and Transcript Profiling in Developing Seeds of Three Brassica napus Cultivars

2015 ◽  
Vol 72 (1) ◽  
pp. 3-32
Author(s):  
Mariana Petkova ◽  
Wun S. Chao ◽  
Leonard Cook ◽  
Mark West ◽  
Mukhlesur Rahman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fatty Acid ◽  
Brassica Napus ◽  
Erucic Acid ◽  
Seed Development ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Eicosenoic Acid ◽  
Expression Of Genes ◽  
Spring Canola

Abstract Fatty acid levels and gene expression profiles for selected genes associated with the synthesis of fatty acids (FA), triacylglycerol, and oil body proteins were examined in three oilseed rape (Brassica napus) cultivars that have utility for cultivar development in our spring canola breeding program. The seed oil content of Bronowski, Q2, and Westar was 39.0, 40.1, and 40.6%, respectively at 40 days after flowering (DAF). During the 20 to 40 day period of seed development, cultivars had varying levels of palmitic, stearic, oleic, linoleic, α-linolenic, eicosenoic, and erucic acid. In general, the percentage of each FA was similar among the cultivars during seed development. However, the level of oleic acid was lower and the levels of eicosenoic acid and erucic acid were higher in Bronowski than in Q2 and Westar seeds; linoleic acid also tended to be lower in Bronowski. Gene expression among the cultivars was similar from 10 to 40 DAF. The few exceptions were that expression of KAS1 and SAD were higher in Westar and Q2 than in Bronowski at 25 DAF, SAD was highest in Q2, intermediate in Westar, and lowest in Bronowski at 35 DAF, FAD2 was higher in Q2 than in Bronowski at 35 DAF, FAD3 was higher in Q2 than in Bronowski at 15 DAF and Q2 and Westar at 25 and 30 DAF, and FAE1 was higher in Westar and Q2 than in Bronowski at 30 DAF. Correlation analysis for gene expression against DAF for each genotype supported a common trend in gene expression among the three cultivars with gene expression tending to decrease over time; except for LPAAT, which tended to increase. The correlation between the level of FAs and expression of genes by genotype indicated no general trend; rather correlations seem to depend on the genotype.

scholarly journals Over-expression of the retinoid-inducible nuclear factor, RINF (CXXC5) in high-grade serous ovarian cancers.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Gene Expression ◽  
Ovarian Cancer ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Global Gene Expression ◽  
Nuclear Factor ◽  
High Grade ◽  
Gene Encoding ◽  
Over Expression ◽  
Ovarian Cancers

Ovarian cancer is the most lethal gynecologic malignancy and 70-80% of ovarian cancers are of the high-grade serous type1-3. To identify the most significant changes in gene expression in high-grade serous ovarian cancer (HGSC), we compared global gene expression profiles of tumors from patients with HGSC to that of normal ovary using published microarray datasets4,5. We found that gene encoding the retinoid-inducible nuclear factor, RINF (also known as CXXC finger protein 5, CXXC5)6 was among the genes whose expression changed most significantly when comparing HSGC tumors to the ovary. RINF/CXXC5 may be relevant to the biology of high-grade serous ovarian tumors.

scholarly journals Tensor Decomposition of Stimulated Monocyte and Macrophage Gene Expression Profiles Identifies Neurodegenerative Disease-specific Trans-eQTLs

2018 ◽  
Author(s):  
Satesh Ramdhani ◽  
Elisa Navarro ◽  
Evan Udine ◽  
Brian M. Schilder ◽  
Madison Parks ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Variants ◽  
Gene Networks ◽  
Disease Risk ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Tensor Decomposition ◽  
Innate Immune ◽  
Primary Role ◽  
Expression Of Genes

AbstractRecent human genetic studies suggest that cells of the innate immune system have a primary role in the pathogenesis of neurodegenerative diseases. However, the results from these studies often do not elucidate how the genetic variants affect the biology of these cells to modulate disease risk. Here, we applied a tensor decomposition method to uncover disease-associated gene networks linked to distal genetic variation in stimulated human monocytes and macrophages gene expression profiles. We report robust evidence that some disease-associated genetic variants affect the expression of multiple genes in trans. These include a Parkinson’s disease locus influencing the expression of genes mediated by a protease that controls lysosomal function, and Alzheimer’s disease loci influencing the expression of genes involved in type 1 interferon signaling, myeloid phagocytosis, and complement cascade pathways. Overall, we uncover gene networks in induced innate immune cells linked to disease-associated genetic variants, which may help elucidate the underlying biology of disease.

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