Investigation Of Gene Expression Profiles Research Articles

#163 Multiome-seq and spatial transcriptomics of refractory PLA2RAb(+) membranous nephropathy reveals importance of immunomodulatory function of B cells

Abstract Background and Aims PLA2RAb-associated membranous nephropathy (MN) is a glomerulonephritis that may require immunosuppression to achieve proteinuria remission. However, the disease course is heterogeneous, and some patients exhibit refractory or relapsing nephrotic-range proteinuria. Additional biomarker studies are necessary to dissect the molecular profiles that reflect substantial differences in treatment response and clinical courses. Multiome-seq includes the investigation of gene expression profiles and ATAC-sequencing for open-chromatin regions, which may reveal pathophysiologic gene expression biomarkers and pathways. Method We performed multiome-sequencing of peripheral blood mononuclear cells (PBMCs) from 6 refractory or relapsing primary PLA2RAb-associated MN cases, 7 PLA2RAb-associated MN cases that reached complete remission, and disease controls including 6 minimal change disease and 6 diabetic kidney disease cases. We also collected PBMCs from 7 healthy controls. Cell type clustering, comparison of cell type proportions, and differential gene expression analysis were performed. Additionally, we conducted ATAC-sequencing analysis and identified open-chromatin profiles specific to the refractory or relapsing MN group. Lastly, we investigated the glomerular spatial transcriptome using GeoMx digital spatial profiling to determine whether transcriptomic profiles differ based on the disease courses of MN in the initial kidney tissue. Results We successfully identified diverse PBMCs in the multiome-seq data. In the DEG analysis, we identified a number of cell-type-specific DEGs in the refractory or relapsing MN cases. Of these, CD83 was the top gene that was lowly expressed in the B cells of refractory/relapsing MN compared to the remission cases. In the ATAC data, among the number of differentially expressed peaks, NFKB2 was the region that consistently showed a low open chromatin profile in the B cells of CD83. When comparing the cell subtype proportions, refractory or relapsing MN cases showed low regulatory T cells in the peripheral blood. Lastly, in the kidney tissue spatial transcriptomic profiling, there were no significant DEGs between the refractory/relapsing MN and MN with remission in the glomerulus. Conclusion The clinical course or risk of remission of PLA2RAb-associated MN was more likely a result of differences in systemic immunity rather than differences in the glomerular transcriptome at the initial diagnosis. Both CD83 and NFκB2 are well-known biomarkers of activated B cells that may have immunomodulatory roles leading to the enrichment of regulatory T cells. Such a deficient immunomodulatory status in refractory/relapsing PLA2RAb-associated MN may explain the disease course.

Growth increase and gonadal dysfunction of the lined seahorse triggered by zinc exposure

Seahorses are characterized by unique characteristics such as a male pregnancy reproductive strategy and grasping preferences, which make these species vulnerable to various environmental risks. Zinc (Zn) is one of the most frequently occurring toxic elements in coastal waters; however, little is known about the effect of Zn exposure on seahorses. In the present study, line seahorses (Hippocampus erectus) were exposed to waterborne Zn (0.2 and 1.0 mg/L) and the impact on growth and gonadal development was investigated. Zn exposure induced growth improvement, but also led to gonadal dysfunction in the lined seahorse. Female seahorses exhibited high testosterone levels, immature follicles, and weight increase after Zn exposure, which is the typical characteristics of a polycystic ovary syndrome (PCOS)-like phenotype. Transcriptomic data suggested that the Zn-induced growth promotion resulted from the dysregulated expression of fat accumulation genes. Further investigation of gene expression profiles in the brain, ovaries, and testes indicated that Zn affected the expression of genes involved in growth, immunity, tissue remodeling, and gonadal development by regulating serum steroid hormone levels and androgen receptor expression. This study not only clarifies the complex impact of Zn on seahorses using physiological, histological, and molecular evidence but can also provide new insights into the mechanism underlying PCOS in reproductive-aged women. Moreover, this work demonstrates the risk of the common practice of Zn supplementation in the aquaculture industry as the consequent growth yield may not represent a healthy condition.

Protective effects of EVs/exosomes derived from permanently growing human MSC on primary murine ALS motor neurons

In recent years, the neuroprotective potential of mesenchymal stroma-/stem-like cells (MSC) as well as of MSC-derived extracellular vesicles (EVs) like exosomes has been intensively explored. This included preclinical evaluation regarding treatment of neurodegenerative disorders such as the fatal motor neuron disease amyotrophic Lateral Sclerosis (ALS). Several studies have reported that MSC-derived exosomes can stimulate tissue regeneration and reduce inflammation. MSC release EVs and trophic factors and thereby modify cell-to-cell communication. These cell-free products may protect degenerating motor neurons (MNs) and represent a potential therapeutic approach for ALS. In the present study we investigated the effects of exosomes derived from a permanently growing MSC line on both, wild type and ALS (SOD1G93A transgenic) primary motor neurons. Following application in a normal and stressed environment we could demonstrate beneficial effects of MSC exosomes on neurite growth and morphology indicating the potential for further preclinical evaluation and clinical therapeutic development. Investigation of gene expression profiles detected transcripts of several antioxidant and anti-inflammatory genes in MSC exosomes. Characterization of their microRNA (miRNA) content revealed miRNAs capable of regulating antioxidant and anti-apoptotic pathways.

Assessment of efficacy of carboxytherapy in management of skin aging through evaluation of gene expression profile: a 2-split randomized clinical trial.

Skin aging is a continuous and irreversible process which results in impairment of the skin role as barrier against all aggressive exogenous factors. It mainly manifests by photoaging, laxity, sagging, wrinkling, and xerosis. Carboxytherapy is considered as a safe, minimally invasive modality used for rejuvenation, restoration, and recondition of the skin. In the current study, the efficacy of carboxytherapy in the treatment of skin aging was assessed through investigation of gene expression profile for Coll I, Coll III, Coll IV, elastin, FGF, TGF-β1, and VEGF. Our study is a 2-split clinical trial in which carboxytherapy was performed on one side of the abdomen in 15 cases with intrinsically skin aging manifestations weekly for 10 sessions, while the other side of the abdomen was left without treatment. Two weeks after the last session, skin biopsies were taken from both the treated and control sides of the abdomen in order to assess gene expression profile by qRT-PCR. The analysis of gene expression levels for all of Coll I, Coll III, Coll IV, elastin, TGF-β1, FGF and VEGF genes showed a statistically significant difference between the interventional and control groups. The findings for all of these seven genes showed increase in the interventional group, among which Coll IV, VEGF, FGF, and elastin showed the higher mean changes. Our study confirmed the effectiveness of carboxytherapy in treating and reversing the intrinsically aging skin.Clinical Trial Registration Code and Date of Registration: ChiCTR2200055185; 2022/1/2.

Abstract 1406: Long non-coding RNA DUXAP10 is a putative determinant of anaplastic thyroid cancer

Abstract Anaplastic Thyroid Cancer (ATC) is one of the most aggressive forms of cancer, with only a 4% survival rate with metastatic disease. ATC is highly refractory and resistant to both traditional therapeutic modalities and recently discovered small molecule inhibitors. The elucidation of molecular mechanisms that contribute to ATC’s metastatic propensity, and the identification of molecular biomarkers for early diagnosis, prognosis, and therapeutic intervention are critical unmet clinical needs-highlighting the importance of novel avenues of intervention. Recently, long non-coding RNAs (lncRNA) have been described as regulators of gene expression and cancer cell phenotypes, exhibiting the importance of identifying non-coding profiles that potentially impact ATC behavior. Publicly available datasets provided by Gene Expression Omnibus (GSE33630, GSE85457) enabled investigation of gene expression profiles of ATC vs. normal thyroid patient tissue. Bioinformatic analyses with the GEO2R program identified the lncRNA, Double Homeobox A Pseudogene 10 (DUXAP10), to be highly upregulated in ATC patient-derived tissue samples when compared to normal thyroid tissue by about 5logFC. Analysis using Gene Expression Profiling Interactive Analysis shows that high DUXAP10 expression is correlated with decreased survival in thyroid cancer patients. To recapitulate this patient data in an in vitro model, we found that the expression of DUXAP10 is also upregulated in the ATC cell line, T238, in comparison to Nthy-ori-3-1, an immortalized “normal” thyroid cell line. To understand the consequences of DUXAP10 overexpression in ATC, we used CRISPRi technology to determine the phenotypic and genotypic effects of DUXAP10 downregulation. CRISPRi knockdown of DUXAP10 significantly reduces the migratory capabilities of T238 by 50%, invasiveness by 37%, clonogenicity by 70%, cell size by 34%, and proliferation by 28%, 45%, and 36% at 24, 48, and 72 hours, respectively. This provides evidence that elevated DUXAP10 expression may increase the probability and negative consequences of metastases. Thus, targeting DUXAP10 expression may have beneficial clinical outcomes. Identification of the molecular innervations of DUXAP10 that orchestrate these pro-metastatic phenotypic changes are currently in progress. Immediate next steps are aimed toward determining if DUXAP10 can be utilized as a potential biomarker for ATC diagnosis and prognosis, as well as elucidating the full range of interactions that DUXAP10 has in shaping the ATC phenotype. Citation Format: Nicole R. DeSouza, Michelle Carnazza, Danielle Quaranto, Tara Jarboe, Kaci Kopec, Sarnath Singh, Augustine Moscatello, Jan Geliebter, Raj K. Tiwari. Long non-coding RNA DUXAP10 is a putative determinant of anaplastic thyroid cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1406.

Evaluation of Quantitative Real-Time Pcr Reference Genes for the Investigation of Gene Expression Profiles in Honeybee Developmental Stages

In addition to its role as an essential pollinator, the Western honeybee, Apis mellifera, is regarded as a good model insect due to its highly evolved sociality, labor division, and flexibility of colony management. Therefore, to identify the molecular mechanisms involved in various colony compositions and flexibility of worker division, it is essential to investigate the gene expression in various developmental stages of the honeybee. For target gene quantification, quantitative real-time PCR (qRT-PCR) has been widely used. However, a reliable reference gene stably expressing across different samples should be selected. Thus, to identify credible reference genes in honeybee colonies, we evaluated five candidate genes (RPS5, RPS18, GAPDH, ARF1, and RAD1a) in samples collected from seven developmental stages (egg, 1<SUP>st</SUP> instar larvae, 3<SUP>rd</SUP> instar larvae, 5<SUP>th</SUP> instar larvae, pupa, nurse, and forager) using three analysis programs algorithms (geNorm, NormFinder, and BestKeeper). Although the reference gene ranked slightly different in analysis algorithms, our study suggests that RAD1a is the most suitable reference gene for accurate normalization of target gene expression at the developmental stage of the honeybee.

Modulation of cell cycle progression and chromatin dynamic as tolerance mechanisms to salinity and drought stress in maize.

Salinity and drought are the major abiotic stresses that disturb several aspects of maize plants growth at the cellular level, one of these aspects is cell cycle machinery. In our study, we dissected the molecular alterations and downstream effectors of salinity and drought stress on cell cycle regulation and chromatin remodeling. Effects of salinity and drought stress were determined on maize seedlings using 200 mM NaCl (induced salinity stress), and 250 mM mannitol (induced drought stress) treatments, then cell cycle progression and chromatin remodeling dynamics were investigated. Seedlings displayed severe growth defects, including inhibition of root growth. Interestingly, stress treatments induced cell cycle arrest in S-phase with extensive depletion of cyclins B1 and A1. Further investigation of gene expression profiles of cell cycle regulators showed the downregulation of the CDKA, CDKB, CYCA, and CYCB. These results reveal the direct link between salinity and drought stress and cell cycle deregulation leading to a low cell proliferation rate. Moreover, abiotic stress alters chromatin remodeling dynamic in a way that directs the cell cycle arrest. We observed low DNA methylation patterns accompanied by dynamic histone modifications that favor chromatin decondensation. Also, the high expression of DNA topoisomerase 2, 6 family was detected as consequence of DNA damage. In conclusion, in response to salinity and drought stress, maize seedlings exhibit modulation of cell cycle progression, resulting in the cell cycle arrest through chromatin remodeling.

Identification of Target Genes Mediated by Two-Component Regulators of Staphylococcus aureus Using RNA-seq Technology.

Transcriptomics enables us to elucidate comprehensive gene expression profiles in given experimental conditions. Global regulators, which include transcriptional regulators and two-component regulatory systems, have evolved in a variety of bacterial systems. They play important roles in bacterial fitness and pathogenesis by regulating target gene expression. Advanced next-generation RNA sequencing technology (RNA-seq) provides a powerful and effective tool to analyze the transcriptome of bacterial cells. In this chapter, we provide a detailed procedure for the investigation of gene expression profiles and identification of target genes, regulons, and/or pathways that are mediated by a regulator. This procedure is done using RNA-seq analysis, which involves RNA purification, mRNA enrichment, decontamination, RNA-seq data analysis, and quantitative real-time reverse transcription PCR.

Investigation of gene expression profiles in a rat adjuvant arthritis model suggests an effective role of triptolide via PI3K-AKT signaling.

Rheumatoid arthritis (RA) is a common systemic autoimmune disease mainly involving the formation of a synovial pannus, for which no effective treatment is available. In order to study the molecular biological mechanisms underlying the inhibition of RA synovial pannus by triptolide, differentially expressed genes in synovial tissues from an adjuvant arthritis (AA) rat model with and without triptolide treatment were detected in an mRNA microarray profile produced by Agilent Technologies and verified by reverse transcription-quantitative polymerase chain reaction analysis (RT-qPCR). An AA model was established by subcutaneously injecting 0.1 ml Freund's complete adjuvant daily for 18 days and scored by arthritis index assessment. Subsequently, triptolide (0.4 mg/kg) or an equivalent amount of saline was administered daily for 14 days. At the end of the experiment, synovial tissues were obtained from the ankle joints of the rats' hind legs. Total RNA was extracted and purified, and microarray hybridization was used to obtain the gene expression profile for RA with and without triptolide treatment. A total of 48 genes were identified to be differentially expressed between the treatment and model groups, including 32 upregulated and 16 downregulated genes. The possible signaling pathways associated with the effect of triptolide were investigated by Gene Ontology and pathway analysis, revealing that the phosphoinositide-3 kinase (PI3K)/AKT signaling pathway has a key role in the proliferation and apoptosis of synovial cells in RA joints. Reverse transcription-quantitative polymerase chain reaction analysis was applied to confirm the aberrant expression of key mRNAs and revealed that vascular endothelial growth factor (VEGF) A and C1q and tumor necrosis factor related protein 3 (C1QTNF3) were downregulated in the treatment group compared with the model group (P<0.05). In conclusion, triptolide may exert its effects against RA via the PI3K/AKT pathway and has an inhibitory effect on the expression of VEGFA and C1QTNF3, thus are potentially associated with the occurrence and development of RA.

Bicoid signal extraction: Another powerful approach

This belief has been widely accepted that Bicoid (Bcd) protein distributes in a concentration gradient that organizes the anterior/posterior axis of the Drosophila embryo. Segment polarity protein provides positional cues for the development of head and thoracic segments. Therefore As a result of its essential role, modeling the Bicoid gradient has been welcomed by many researchers in various scientific fields. In this paper, We present investigation of gene expression profiles by means of Singular Spectrum Decomposition (SSD), an optimizing version of Singular Spectrum Analysis for filtering and extracting the bicoid gene expression signal. The results with strong evidence suggest that the proposed technique is capable of eliminating noise and can be considered as an acceptable method for filtering gene expression.

Mummy Prevents IL-1β-Induced Inflammatory Responses and Cartilage Matrix Degradation via Inhibition of NF-қB Subunits Gene Expression in Pellet Culture System.

Purpose: In Persian traditional medicine, application of Mummy material has been advised since hundred years ago for treatment of different diseases as bone fracture, cutaneous wounds and joint inflammation. Regarding to the claim of indigenous people for application of this material in the treatment of joint inflammation, the present study was designed to evaluate whether Mummy can revoke the inflammatory responses in chondrocytes stimulated with interleukin 1-β (IL-1β).Methods: Isolated chondrocytes at the second passage were plated in 50 ml conical tubes at density of 1x106 for pellet culture or were plated in T75 culture flasks as monolayer. Cells in both groups were treated as control (receiving serum free culture medium), negative control (receiving IL-1β (10ng/ml for 24 hr)) and IL-1β pre-stimulated cells which treated with Mummy at concentrations of 500 and 1000µg/ml for 72hrs. After 72 hrs, to evaluate whether Mummy can revoke the inflammatory response in chondrocytes, cell in different groups were prepared for investigation of gene expression profile of collagen II, Cox-2, MMP-13, C-Rel and P65 using real-time RT-PCR.Results: Treatment of chondrocytes with IL-1β (10ng/ml) resulted in a significant increase in expression level of Cox-2, MMP-13, C-Rel and P65 in pellet culture system, while treatment of IL-1β-stimulated choncrocytes with Mummy at both concentrations of 500 and 1000µg/ml inhibited the expression level of above mentioned genes. Compared to the pellet culture, Mummy did not affect expression level of genes in monolayer condition.Conclusion: The obtained data from this investigation revealed that Mummy can be used as a potent factor for inhibiting the inflammatory responses induced by IL-1β in chondrocytes probably through inhibition of NF-қB subunits activation.

Healthy glucocorticoid receptor N363S carriers dysregulate gene expression associated with metabolic syndrome

The glucocorticoid receptor single-nucleotide polymorphism (SNP) N363S has been reported to be associated with metabolic syndrome, type 2 diabetes, and cardiovascular disease. Our aim was to determine how the N363S SNP modifies glucocorticoid receptor signaling in a healthy population of individuals prior to the onset of disease. We examined the function of the N363S SNP in a cohort of subjects from the general population of North Carolina. Eighteen N363S heterozygous carriers and 36 noncarrier, control subjects were examined for clinical and biochemical parameters followed by a low-dose dexamethasone suppression test to evaluate glucocorticoid responsiveness. Serum insulin measurements revealed that N363S carriers have higher levels of insulin, although not statistically significant, compared with controls. Glucocorticoid receptor protein levels evaluated in peripheral blood mononuclear cells from each clinical subject showed no difference between N363S and control. However, investigation of gene expression profiles in macrophages isolated from controls and N363S carriers using microarray, quantitative RT-PCR, and NanoString analyses revealed that the N363S SNP had an altered profile compared with control. These changes in gene expression occurred in both the absence and the presence of glucocorticoids. Thus, our observed difference in gene regulation between normal N363S SNP carriers and noncarrier controls may underlie the emergence of metabolic syndrome, type 2 diabetes, and cardiovascular disease associated with the N363S polymorphism.

Investigation of Gene Expression Profile of A549 Cells after Overexpression of GPC5 by High Throughput Transcriptome Sequencing

背景与目的磷脂酰肌醇蛋白聚糖-5(glypican-5, GPC5)是一个重要的抑癌基因, 然而GPC5对肺腺癌细胞增殖能力和基因表达的影响目前研究甚少。本研究拟在肺腺癌A549细胞中过表达GPC5以研究细胞增殖能力和基因表达变化情况。方法通过慢病毒载体构建稳定过表达GPC5的A549细胞株, 通过Cell Counter Kit 8 (CCK8)、平板克隆和EdU实验检测细胞增殖能力; 通过高通量转录组测序研究基因表达变化。结果相对于空白载体组, CCK8实验发现过表达GPC5可以明显抑制A549细胞的增殖速率; 平板克隆实验结果显示, 过表达GPC5之后A549细胞克隆形成能力下降(181±17 vs 278±23);EdU染色结果显示过表达GPC5后阳性染色细胞比例下降。转录组测序结果提示过表达GPC5之后, 2, 108个基因表达发生明显变化, 其中具有正性调节细胞增殖作用的基因明显下调。结论过表达GPC5可以明显抑制肺腺癌细A549的增殖能力, 而且过表达GPC5后具有正性调节细胞增殖作用的基因表达下调。

A Modified ABCDE Model of Flowering in Orchids Based on Gene Expression Profiling Studies of the Moth Orchid Phalaenopsis aphrodite

Previously we developed genomic resources for orchids, including transcriptomic analyses using next-generation sequencing techniques and construction of a web-based orchid genomic database. Here, we report a modified molecular model of flower development in the Orchidaceae based on functional analysis of gene expression profiles in Phalaenopsis aphrodite (a moth orchid) that revealed novel roles for the transcription factors involved in floral organ pattern formation. Phalaenopsis orchid floral organ-specific genes were identified by microarray analysis. Several critical transcription factors including AP3, PI, AP1 and AGL6, displayed distinct spatial distribution patterns. Phylogenetic analysis of orchid MADS box genes was conducted to infer the evolutionary relationship among floral organ-specific genes. The results suggest that gene duplication MADS box genes in orchid may have resulted in their gaining novel functions during evolution. Based on these analyses, a modified model of orchid flowering was proposed. Comparison of the expression profiles of flowers of a peloric mutant and wild-type Phalaenopsis orchid further identified genes associated with lip morphology and peloric effects. Large scale investigation of gene expression profiles revealed that homeotic genes from the ABCDE model of flower development classes A and B in the Phalaenopsis orchid have novel functions due to evolutionary diversification, and display differential expression patterns.

Investigation of gene expression profiles before and after embryonic genome activation and assessment of functional pathways at the human metaphase II oocyte and blastocyst stage

To compare the oocyte versus the blastocyst transcriptome and provide data on molecular pathways before and after embryonic genome activation. Prospective laboratory research study. An IVF clinic and a specialist preimplantation genetics laboratory. Couples undergoing or having completed IVF treatment donating surplus oocytes or cryopreserved blastocysts after patient consent. Sets of pooled metaphase II (MII) oocytes or blastocysts were processed for RNA extraction, RNA amplification, and analysis with the use of the Human Genome Survey Microarrays v2.0 (Applied Biosystems). Association of cell type and gene expression profile. Totals of 1,909 and 3,122 genes were uniquely expressed in human MII oocytes and human blastocysts respectively, and 4,910 genes were differentially expressed between the two sample types. Expression levels of 560 housekeeping genes, genes involved in the microRNA processing pathway, as well as hormones and hormone receptors were also investigated. The lists of genes identified may be of use for understanding the processes involved in early embryo development and blastocyst implantation, and for identifying any dysregulation leading to infertility.

Genes regulated in metastatic osteosarcoma: evaluation by microarray analysis in four human and two mouse cell line systems.

Osteosarcoma (OS) is a rare bone neoplasm that affects mainly adolescents. It is associated with poor prognosis in case of metastases formation. The search for metastasis predicting markers is therefore imperative to optimize treatment strategies for patients at risk and important for the search of new drugs for the treatment of this devastating disease. Here, we have analyzed by microarray the differential gene expression in four human and two mouse OS cell line systems consisting of parental cell lines with low metastatic potential and derivatives thereof with increased metastatic potential. Using two osteoblastic cell line systems, the most common OS phenotype, we have identified forty-eight common genes that are differentially expressed in metastatic cell lines compared to parental cells. The identified subset of metastasis relevant genes in osteoblastic OS overlapped only minimally with differentially expressed genes in the other four preosteoblast or nonosteoblastic cell line systems. The results imply an OS phenotype specific expression pattern of metastasis regulating proteins and form a basis for further investigation of gene expression profiles in patients' samples combined with survival analysis with the aim to optimize treatment strategies to develop new drugs and to consequently improve the survival of patients with the most common form of osteoblastic OS.

Gene expression profiling in whole blood identifies distinct biological pathways associated with obesity

BackgroundObesity is reaching epidemic proportions and represents a significant risk factor for cardiovascular disease, diabetes, and cancer.MethodsTo explore the relationship between increased body mass and gene expression in blood, we conducted whole-genome expression profiling of whole blood from seventeen obese and seventeen well matched lean subjects. Gene expression data was analyzed at the individual gene and pathway level and a preliminary assessment of the predictive value of blood gene expression profiles in obesity was carried out.ResultsPrincipal components analysis of whole-blood gene expression data from obese and lean subjects led to efficient separation of the two cohorts. Pathway analysis by gene-set enrichment demonstrated increased transcript levels for genes belonging to the "ribosome", "apoptosis" and "oxidative phosphorylation" pathways in the obese cohort, consistent with an altered metabolic state including increased protein synthesis, enhanced cell death from proinflammatory or lipotoxic stimuli, and increased energy demands. A subset of pathway-specific genes acted as efficient predictors of obese or lean class membership when used in Naive Bayes or logistic regression based classifiers.ConclusionThis study provides a comprehensive characterization of the whole blood transcriptome in obesity and demonstrates that the investigation of gene expression profiles from whole blood can inform and illustrate the biological processes related to regulation of body mass. Additionally, the ability of pathway-related gene expression to predict class membership suggests the feasibility of a similar approach for identifying clinically useful blood-based predictors of weight loss success following dietary or surgical interventions.

Investigation of gene expression profiles in coronary heart disease and functional analysis of target gene

The research outlined here includes constitution of the differential gene expression profile by means of oligonucleotide gene microarray and functional analysis of the target gene for coronary heart disease (CHD). In a microarray screening experiment, the predominance of inflammation- and immune-related genes is presented in the expression profile of 107 differential genes based on the analysis of gene ontology and gene pathway. IL-8, an inflammatory factor, is identified as one of the genes that were markedly up-regulated in CHD. The plasma level of IL-8 is significantly raised in patients with CHD (n = 30) compared with healthy controls (n = 40), which underscores the clinical relevance of the in vitro finding. The further functional analysis shows that IL-8 affects platelet aggregation percentage, expression of CD62p and platelet aggregation morphology in 12 healthy volunteers to some extent. These findings suggest the relevance of inflammation and immune responses to CHD at the DNA level. Moreover, IL-8 may be involved in the pathogenesis of CHD through the pathway of platelet activation.

Investigation of gene expression profiles in patients with blood stasis syndrome

To investigate the differential gene expression profiles in patients with blood stasis syndrome by oligonucleotide microarray technique. Sixteen patients with blood stasis syndrome were divided into patients with coronary heart disease (CAD) (n=8) and non-CAD patients (n=8) by using coronary angiography. The sex- and age-matched eight healthy persons were enrolled as control group. Venous bloods were collected for extracting RNA. Test-3 chip was first employed to examine the quality of samples. Then the samples were hybridized with Affymetrix U133 Plus 2.0 array to compare the gene expression profiles among the three groups. Gene-array scanner and gene chip operating software were applied to screen hybridization signals and analyze gene expression respectively. Based on the comparison of the three groups of samples, the differential genes related with blood stasis syndrome were analyzed by Gene Ontology (GO) and pathway, and confirmed by real-time reverse transcription polymerase chain reaction (RT-PCR). Forty-eight differential genes were found being associated with blood stasis syndrome, including 26 up-regulated genes and 22 down-regulated genes. Five of the forty-eight genes (10.4%) were related to inflammatory reaction and immune response through the GO analysis. In the pathway analysis, five of ten significant pathways were referred to inflammation and immune response. The results of real-time RT-PCR proved the accuracy of the gene chip. Inflammatory- and immune-related genes have a remarkable predominance in blood stasis syndrome gene expression profiles, which may explain the function of inflammation and immune response in the occurrence and development of blood stasis syndrome.

Singular Spectrum Analysis of Gene Expression Profiles of Early Drosophila embryo: Exponential‐in‐Distance Patterns

We present investigation of gene expression profiles by means of singular spectrum analysis (SSA). The biological problem under investigation is the decomposition of bicoid protein profiles of Drosophila melanogaster into the sum of a signal and noise, where the former consists of an exponential-in-distance pattern and is close to constant nonspecific component, or "background." The signal processing problems addressed are (i) trend extraction from a noisy signal, (ii) batch processing of similar data, and (iii) analytical approximation of the signal components by the sum of exponential and constant-like functions. The proposed methods are evaluated on the given 17 series.