scholarly journals Transcriptomic-based clustering of advanced atherosclerotic plaques identifies subgroups of plaques with differential underlying biology that associate with clinical presentation

2021 ◽  
Author(s):  
Michal Mokry ◽  
Arjan Boltjes ◽  
Kai Cui ◽  
Lotte Slenders ◽  
Joost M. Mekke ◽  
...  
Keyword(s):  
Gene Expression ◽  
Clinical Presentation ◽  
Clinical Symptoms ◽  
Expression Profiles ◽  
Thrombotic Event ◽  
Gene Expression Profiles ◽  
Molecular Signature ◽  
Expression Of Genes ◽  
Neutrophil Degranulation ◽  
Histopathological Studies

Histopathological studies have revealed key processes of atherosclerotic plaque thrombosis. However, the diversity and complexity of lesion types highlight the need for improved sub-phenotyping. We hypothesized that unbiased clustering of plaques based on gene expression results in an alternative categorization of late-stage atherosclerotic lesions. We analyzed the gene expression profiles of 654 advanced human carotid plaques. The unsupervised, transcriptome-driven clustering revealed five dominant plaque types. These novel plaque phenotypes associated with clinical presentation (p<0.001) and showed differences in cellular compositions. Validation in coronary segments showed that the molecular signature of these plaques was linked to coronary ischemia. One of the plaque types with most severe clinical symptoms pointed to both inflammatory and fibrotic cell lineages. This highlighted plaque phenotype showed high expression of genes involved in active inflammatory processes, neutrophil degranulation, matrix turnover, and metabolism. For clinical translation, we did a first promising attempt to identify circulating biomarkers that mark these newly identified plaque phenotypes. In conclusion, the definition of the plaque at risk for a thrombotic event can be fine-tuned by in-depth transcriptomic based phenotyping. These differential plaque phenotypes prove clinically relevant for both carotid and coronary artery plaques and point to differential underlying biology of symptomatic lesions.

scholarly journals Transcriptional profiling enables molecular classification of adrenocortical tumours

2009 ◽  
Vol 161 (1) ◽  
pp. 141-152 ◽  
Author(s):  
Cecilia Laurell ◽  
David Velázquez-Fernández ◽  
Kristina Lindsten ◽  
Christofer Juhlin ◽  
Ulla Enberg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Clinical Symptoms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Molecular Signature ◽  
Survival Prediction ◽  
Cdna Clones ◽  
Hormonal Activity ◽  
Adrenocortical Tumours

ObjectiveTumours in the adrenocortex are common human tumours. Malignancy is however, rare, the yearly incidence being 0.5–2 per million inhabitants, but associated with a very aggressive behaviour. Adrenocortical tumours are often associated with altered hormone production with a variety of clinical symptoms. The aggressiveness of carcinomas together with the high frequency of adenomas calls for a deeper understanding of the underlying biological mechanisms and an improvement of the diagnostic possibilities.MethodsMicroarray gene expression analysis was performed in tumours of adrenocortex with emphasis on malignancy as well as hormonal activity. The sample set consisted of 17 adenomas, 11 carcinomas and 4 histological normal adrenocortexes. RNA from these was hybridised according to a reference design on microarrays harbouring 29 760 human cDNA clones. Confirmation was performed with quantitative real time-PCR and western blot analysis.ResultsUnsupervised clustering to reveal relationships between samples based on the entire gene expression profile resulted in two subclusters; carcinomas and non-cancer specimens. A large number of genes were accordingly found to be differentially expressed comparing carcinomas to adenomas. Among these were IGF2, FGFR1 and FGFR4 in growth factor signalling the most predominant and also the USP4, UBE2C and UFD1L in the ubiquitin-proteasome pathway. Moreover, two subgroups of carcinomas were identified with different survival outcome, suggesting that survival prediction can be made on the basis of gene expression profiles. Regarding adenomas with aldosterone overproduction, OSBP and VEGFB were among the most up-regulated genes compared with the other samples.ConclusionsAdrenocortical carcinomas are associated with a distinct molecular signature apparent in their gene expression profiles. Differentially expressed genes were identified associated with malignancy, survival as well as hormonal activity providing a resource of candidate genes for an exploration of possible drug targets and diagnostic and prognostic markers.

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.

Gene Expression Profiles in Acute Myeloid Leukemia (AML): From Diagnosis to Prognosis.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2996-2996
Author(s):  
Sanggyu Lee ◽  
Jianjun Chen ◽  
Goulin Zhou ◽  
Run Shi ◽  
Masha Kocherginsky ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Major Change ◽  
Molecular Signature ◽  
Human Leukemia ◽  
Prognostic Information ◽  
Myeloid Progenitor Cells ◽  
Novel Transcripts

Abstract Chromosome translocations are among the most common genetic abnormalities in human leukemia. The abnormally expressed genes from each translocation can be used to identify specific markers for clinical diagnosis of each translocation. Microarrays have identified genes differentially expressed in different translocations but the results between laboratories are not always compatible. We used SAGE to quantitate gene expression in bone marrow(BM) samples from 22 patients with four types of AML, [de novo AML M2 with t(8;21), AML M3 or M3V with t(15;17), AML M4Eo with inv(16), AML M5 with t(9;11) or secondary t(9;11)].We made SAGE libraries from CD15+ leukemic myeloid progenitor cells, collecting over 106 SAGE tags, of which 209,486 were unique tags; 136,010 were known genes and ESTs, and 73,476 were novel transcripts. SAGE tags for further analysis were selected based on a 5-fold difference between patient’s samples and normal CD15+ BM; they were also statistically significantly different at the 5% level. Using these strict criteria, we identified 2,381 unique tags, of which 2,053 were known genes and ESTs, and 328 were novel transcripts that were either specific for each translocation or were common(55) SAGE tags for all 4 translocations. The major change in all translocations was a decrease in expression in leukemia cells compared with normal cells; the decrease was least in the t(8;21) cells. Changes in expression of these known genes, which fall into different gene ontology functional categories, varied by translocation. Those associated with macromolecular biosynthesis, transport and transcription were most altered in the t(8;21); those related to defense response and apoptosis were altered in the t(15;17); cell proliferation genes were most affected by the t(9;11). From this analysis, we identified the functional molecular signature of each translocation. We designed a custom microarray to validate our SAGE data analysis. Our initial microarray contained 349 probes including 212 known genes, 61 ESTs, 28 novel sequences based on our data and 48 genes reported by others. We have now included 65 additional probes that appeared to be correlated with survival. Using 63 samples with the four translocations [16 inv(16), 4 t(9;11), 20 t(15;17), 4 t(8;21) and 19 other translocations], we are validating which genes provide a robust, reproducible “fingerprint” for each translocation, for all translocations, and which ones provide reliable information related to prognosis and survival. Our results will provide new insights into genes that collaborate with each translocation to lead to a fully leukemic phenotype as well as which genes appear to provide valid prognostic information.

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 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.

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.

302. FIBROID ASSOCIATED HEAVY MENSTRUAL BLEEDING: CORRELATION OF CLINICAL SYMPTOMS, DOPPLER ULTRASOUND ASSESSMENT OF VASCULATURE AND TISSUE GENE EXPRESSION PROFILES

2010 ◽  
Vol 22 (9) ◽  
pp. 102
Author(s):  
S. Tsiligiannis ◽  
M. Zaitseva ◽  
P. Coombs ◽  
P. Shekleton ◽  
B. Vollenhoven ◽  
...  
Keyword(s):  
Gene Expression ◽  
Doppler Ultrasound ◽  
Clinical Symptoms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Heavy Menstrual Bleeding ◽  
Spectral Doppler ◽  
Ultrasound Assessment ◽  
Angiogenic Gene ◽  
Tissue Gene Expression

Understanding of the mechanisms that cause fibroid associated heavy menstrual bleeding (HMB) is limited. Despite many fibroids having a highly vascular peri-fibroid myometrial (PFM) zone, angiogenic gene expression in this area has never been investigated. The aim of this study was to correlate clinical symptoms, ultrasound appearances and tissue gene expression profiles in women scheduled for hysterectomy due to symptomatic fibroids. We hypothesised that fibroid heterogeneity, colour flow and spectral Doppler resistive indices would correlate with differences in gene expression profiles. It was thought and that increased peri-fibroid gene expression of key angiogenic genes would correlate with increased peri-fibroid vascularity. N = 6 patients underwent B-mode, colour and spectral Doppler ultrasound assessment. Following hysterectomy tissue samples collected from three areas – fibroid, PFM and distant myometrium (DM) were analysed using quantitative RT-PCR and a customised angiogenesis PCR array. A higher mean peak systolic velocity (PSV) in the PFM region when compared to mean PSV within the fibroid (P < 0.001) was seen. Differences in angiogenic gene expression were consistent with the heterogeneity of the clinical data collected. One fibroid sample showed dissimilar gene expression to all other fibroids; at ultrasound and sample collection significant degenerative features were observed. Fibroid heterogeneity within a single uterus was also demonstrated, with two fibroids from the one uterus having significantly dissimilar gene profiles and ultrasound appearances. No differences in gene expression were found between PFM and DM. Despite this, gene interaction maps showed different interaction of genes between fibroid and PFM regions compared to genes between the fibroid and the DM. These are the first molecular data demonstrating that the PFM region may be functionally distinct from distant myometrium.

scholarly journals Differential gene expression profiles of invasive and non-invasive non-functioning pituitary adenomas based on microarray analysis

2010 ◽  
Vol 17 (2) ◽  
pp. 361-371 ◽  
Author(s):  
Françoise Galland ◽  
Ludovic Lacroix ◽  
Patrick Saulnier ◽  
Philippe Dessen ◽  
Geri Meduri ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pituitary Adenomas ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Molecular Signature ◽  
Specific Gene ◽  
Tumor Invasiveness ◽  
Non Invasive ◽  
Qrt Pcr ◽  
Non Functioning Pituitary Adenomas

Non-functioning pituitary adenomas (NFPAs) may be locally invasive. Markers of invasiveness are needed to guide patient management and particularly the use of adjuvant radiotherapy. To examine whether invasive NFPAs display a specific gene expression profile relative to non-invasive tumors, we selected 40 NFPAs (38 of the gonadotroph type) and classified them as invasive (n=22) or non-invasive (n=18) on the basis of magnetic resonance imaging and surgical findings. We then performed pangenomic analysis with the 44k Agilent human whole genome expression oligonucleotide microarray in order to identify genes with differential expression between invasive and non-invasive NFPAs. Candidate genes were then tested in qRT-PCR. Prediction class analysis showed that the expression of 346 genes differed between invasive and non-invasive NFPAs (P<0.001), of which 233 genes were up-regulated and 113 genes were down-regulated in invasive tumors. On the basis of Ingenuity networks and the degree of up- or down-regulation in invasive versus non-invasive tumors, 35 genes were selected for expression quantification by qRT-PCR. Overexpression of only four genes was confirmed, namely IGFBP5 (P=0.02), MYO5A (P=0.04), FLT3 (P=0.01), and NFE2L1 (P=0.02). At the protein level, only myosin 5A (MYO5A) immunostaining was stronger in invasive than in non-invasive NFPAs. Molecular signature allows to differentiate ‘grossly’ invasive from non-invasive NFPAs. The product of one of these genes, MYO5A, may be a useful marker of tumor invasiveness.

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