Meta-analysis reveals differential gene expression in tetralogy of Fallot versus controls

OBJECTIVES

Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart defect in the United States. We aimed to identify genetic variations associated with TOF using meta-analysis of publicly available digital samples to spotlight targets for prevention, screening, and treatment strategies.

METHODS

We used the Search Tag Analyze Resource for Gene Expression Omnibus (STARGEO) platform to identify 39 TOF and 19 non-TOF right ventricle tissue samples from microarray data and identified upregulated and downregulated genes. Associated gene expression data were analyzed using ingenuity pathway analysis and restricted to genes with a statistically significant (p < .05) difference and an absolute experimental log ratio >0.1 between disease and control samples.

RESULTS

Our analysis identified 220 genes whose expression profiles were significantly altered in TOF vs. non-TOF samples. The most striking differences identified in gene expression included genes FBXO32, PTGES, MYL12a, and NR2F2. Some top associated canonical pathways included adrenergic signaling, estrogen receptor signaling, and the role of NFAT in cardiac hypertrophy. In general, genes involved in adaptive, defensive, and reparative cardiovascular responses showed altered expression in TOF vs. non-TOF samples.

CONCLUSIONS

We introduced the interpretation of open "big data" using the STARGEO platform to define robust genomic signatures of congenital heart disease pathology of TOF. Overall, our meta-analysis results indicated increased metabolism, inflammation, and altered gene expression in TOF patients. Estrogen receptor signaling and the role of NFAT in cardiac hypertrophy represent unique pathways upregulated in TOF patients and are potential targets for future pharmacologic treatments.

Effects of Sudarshan KriyaYoga and Advanced Meditation Program on Genetic Expression of Pro-inflammatory and Antioxidants Genes

Background Stress leads to immune system dysregulation and dyshomeostasis at the gene level. Mind-body practices are known to influence genomic expression, leading to better health and quality of life. Objective To assess the effect of Advanced Meditation Program (AMP) on the mRNA expression of pro-inflammatory and antioxidative genes among those already practicing Sudarshan Kriya Yoga (SKY). Methods A total of 97 healthy volunteers participated in the study, distributed into two groups. The Group I SKY practitioners attended a four-day AMP (50 participants with an average age of 38.8 ± 11.9 consisting of 37 females and 13 males); they are first-time participants of the AMP. Group II SKY practitioners, on the other hand, consisted of 47 participants with an average age of 36.4 ± 9.3 with 43 females and four males. At day 0, day 5, and day 90, the mRNA expression of pro-inflammatory genes, namely interleukin (IL) 1β, IL6, and the tumor necrosis factor (TNF), and the expression of antioxidative genes, namely superoxide dismutase (SOD), catalase, and glutathione peroxidase (GPx) was observed. The data were analysed in two phases due to the emergence of coronavirus disease 2019 (COVID-19): (i) pre-COVID-19 and (ii) during COVID-19. Results In the pre-COVID-19 data set, IL1β, IL6, and TNF were found to have decreased in both groups. There is a significant increase in the expression of SOD and catalase in Group I and a decrease in Group II by day 90. During COVID-19, pro-inflammatory genes increased in Group I and had no significant change in Group II. All three antioxidant genes had decreased expression by day 90 in Group I; SOD decreased in Group II. Interpretation and conclusions Reduced expression of pro-inflammatory genes and increase in the expression of antioxidative genes during the pre-COVID-19 time suggest that the practice of SKY and added AMP may enhance antioxidative defense and may reduce the chance of getting diseases related to inflammation in the body.

Drought stress-induced the formation of heteromorphic leaves of Populus euphratica Oliv: evidence from gene transcriptome

Populus euphratica Oliv., a dominant species of arid desert community, grows heteromorphic leaves at different crown positions. Whether heteromorphic leaves are a strategy of plant adaptation to drought stress is rarely reported. This study sequenced the transcriptome of three typical heteromorphic leaves (lanceolate, ovate and broad-ovate leaves) of P. euphratica, and measured their drought stress. We wanted to reveal the molecular mechanisms underlying the formation of heteromorphic leaves. Drought stress was increased significantly from lanceolate to ovate to broad-ovate leaves. Gene ontology (GO) and KEGG enrichment analysis showed that the MADs-box gene regulated the expression of peroxidase (POD) in the phenylpropane biosynthetic pathway. The up-regulated expression of the chalcone synthase (CHS) gene in broad-ovate leaves significantly activated the flavonoid biosynthetic pathway. In the process of leaf shape change, the different expressions of homeodomain leucine zipper (HD-ZIP) among the three heteromorphic leaves had potential interactions on the AUX and ABA pathways. The expression of Sucrose phosphate synthase (SPS) and sucrose synthase (SUS) increased from lanceolate to broad-ovate leaves, resulting in a consistent change in starch and sucrose content. We concluded that these resistance-related pathways are expressed in parallel with leaf formation genes, thereby inducing the formation of heteromorphic leaves. Our work provided a new insights for desert plants to adapt to drought stress.

Effects of Soybean Trypsin Inhibitor on Pancreatic Oxidative Damage of Mice at Different Growth Periods

The bioactive components in soybeans have significant physiological functions. However, the intake of soybean trypsin inhibitor (STI) may cause metabolic disorders. To investigate the effect of STI intake on pancreatic injury and its mechanism of action, a five-week animal experiment was conducted, meanwhile, a weekly monitor on the degree of oxidation and antioxidant indexes in the serum and pancreas of the animals was carried out. The results showed that the intake of STI had irreversible damage to the pancreas, according to the analysis of the histological section. Malondialdehyde (MDA) in the pancreatic mitochondria of Group STI increased significantly and reached a maximum (15.7 nmol/mg prot) in the third week. Meanwhile, the antioxidant enzymes superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), trypsin (TPS), and somatostatin (SST) were decreased and reached minimum values (10 U/mg prot, 87 U/mg prot, 2.1 U/mg prot, 10 pg/mg prot) compared with the Group Control. The RT-PCR results of the expression of SOD, GSH-Px, TPS, and SST genes were consistent with the above. This study demonstrates that STI causes oxidative structural damage and pancreatic dysfunction by inducing oxidative stress in the pancreas, which could increase with time.

Variable sensitivity to diethylene glycol poisoning is related to differences in the uptake transporter for the toxic metabolite diglycolic acid

INTRODUCTION/CONTEXT

Poisonings with diethylene glycol are characterized by acute kidney injury and peripheral neuropathy. In animal studies on the toxicities of diethylene glycol and its metabolite diglycolic acid, remarkable differences in susceptibility to acute kidney injury were observed in identically-dosed rats. In those studies, only about 60% showed acute kidney injury, yet all rats with acute kidney injury showed marked diglycolic acid accumulation in tissues, while no diglycolic acid accumulated in rats without injury. Diglycolic acid is taken into renal cells via sodium-dependent dicarboxylate transporters. When sodium-dependent dicarboxylate transporter-1 is inhibited or knocked down in human kidney cells, diglycolic acid uptake and toxicity are reduced. We hypothesize that the variation in sensitivity to tissue diglycolic acid retention and to diethylene glycol/diglycolic acid toxicity is explained by differential expression of sodium-dependent dicarboxylate transporter-1 in rat kidneys.

METHODS

Using kidney tissue from previous studies, we performed rt-PCR analysis of sodium-dependent dicarboxylate transporter-1 mRNA. In those studies, Wistar-Han rats were either gavage with diethylene glycol 6 g/kg every 12 h for 7 days or with single doses of diglycolic acid 300 mg/kg. Kidney tissue was harvested after euthanasia and preserved in formalin. Tissue slices were homogenized and RNA was isolated using an RNAstorm FFPE RNA Isolation Kit. The expression of sodium-dependent dicarboxylate transporter-1 mRNA was compared between groups that showed diglycolic acid accumulation and acute renal injury with those that showed no diglycolic acid accumulation or toxicity.

RESULTS

Significantly higher expression of sodium-dependent dicarboxylate transporter-1 mRNA was present in the kidneys of rats with acute kidney injury and diglycolic acid accumulation compared to those in rats that had no diglycolic acid in their kidneys and no acute kidney injury.

DISCUSSION

The likelihood of acute kidney injury after dosing of rats with diethylene glycol or diglycolic acid is linked with an enhanced ability to take up diglycolic acid into renal cells via the sodium-dependent dicarboxylate transporter-1. The variability in diethylene glycol toxicity in humans, as reported in epidemiological studies, may also be linked with differences in tissue uptake of diglycolic acid.

CONCLUSIONS

Animals with acute kidney injury after exposure to diethylene glycol or diglycolic acid had higher sodium-dependent dicarboxylate transporter-1 expression and greater diglycolic acid accumulation in renal tissues than animals without acute kidney injury.

Transcriptomics Reveals the Mevalonate and Cholesterol Pathways Blocking as Part of the Bacterial Cyclodipeptides Cytotoxic Effects in HeLa Cells of Human Cervix Adenocarcinoma

The incidence of human cervix adenocarcinoma (CC) caused by papillomavirus genome integration into the host chromosome is the third most common cancer among women. Bacterial cyclodipeptides (CDPs) exert cytotoxic effects in human cervical cancer HeLa cells, primarily by blocking the PI3K/Akt/mTOR pathway, but downstream responses comprising gene expression remain unstudied. Seeking to understand the cytotoxic and anti-proliferative effects of CDPs in HeLa cells, a global RNA-Seq analysis was performed. This strategy permitted the identification of 151 differentially expressed genes (DEGs), which were either up- or down-regulated in response to CDPs exposure. Database analysis, including Gene Ontology (COG), and the Kyoto Encyclopedia of Genes and Genomes (KEGG), revealed differential gene expression on cancer transduction signals, and metabolic pathways, for which, expression profiles were modified by the CDPs exposure. Bioinformatics confirmed the impact of CDPs in the differential expression of genes from signal transduction pathways such as PI3K-Akt, mTOR, FoxO, Wnt, MAPK, P53, TGF-β, Notch, apoptosis, EMT, and CSC. Additionally, the CDPs exposure modified the expression of cancer-related transcription factors involved in the regulation of processes such as epigenetics, DNA splicing, and damage response. Interestingly, transcriptomic analysis revealed the participation of genes of the mevalonate and cholesterol biosynthesis pathways; in agreement with this observation, total cholesterol diminished, confirming the blockage of the cholesterol synthesis by the exposure of HeLa cells to CDPs. Interestingly, the expression of some genes of the mevalonate and cholesterol synthesis such as HMGS1, HMGCR, IDI1, SQLE, MSMO1, SREBF1, and SOAT1 was up-regulated by CDPs exposure. Accordingly, metabolites of the mevalonate pathway were accumulated in cultures treated with CDPs. This finding further suggests that the metabolism of cholesterol is crucial for the occurrence of CC, and the blockade of the sterol synthesis as an anti-proliferative mechanism of the bacterial CDPs, represents a reasonable chemotherapeutic drug target to explore. Our transcriptomic study supports the anti-neoplastic effects of bacterial CDPs in HeLa cells shown previously, providing new insights into the transduction signals, transcription factors and metabolic pathways, such as mevalonate and cholesterol that are impacted by the CDPs and highlights its potential as anti-neoplastic drugs.

Egg incubation temperature influences the population-specific outmigration rate of juvenile brown trout Salmo trutta

The present experiment tested if temperature during embryogenesis and parental heritage affected the migratory behaviour of young brown trout Salmo trutta. Two parental forms were used, a freshwater resident form and an anadromous form, both from the same river system but geographically isolated since 1993-95. Four groups of young S. trutta were produced and reared from (a) freshwater resident parents spawning in a tributary to the River Imsa, Norway, (b) anadromous parents spawning in the main stem of the same river system, (c) resident male × anadromous female parents and (d) resident female × anadromous male parents. The eggs were incubated until first exogenous feeding in River Imsa water, either unheated or heated c. 2.7°C above ambient temperature. Thereafter, all fish experienced the same ambient river temperature until release. Groups were released below an impassable waterfall 900 m upstream of the mouth of the River Imsa, either as age-0 in October 2019 or as age-1 in May 2020. About 7.5% of the released fish moved downstream and were captured in a trap at the outlet. For any given body size, the proportion of warm incubated trout that moved downstream was greater than the proportion of cold incubated trout. It was also found that most emigrants of the October-released S. trutta were caught within a month of release. Also, most May-released S. trutta emigrated in October. The offspring of the freshwater resident parents emigrated to a larger extent than offspring of anadromous parents. Thus, the difference in emigration with regard to embryonic temperature was phenotypically plastic and may be associated with an epigenetic effect of the thermal conditions during early development. The effect of parental origin suggests there may be genetic divergence between the geographically isolated populations.

Rare Subtype of Endometrial Cancer: Undifferentiated/Dedifferentiated Endometrial Carcinoma, from Genetic Aspects to Clinical Practice

Endometrial cancer (EC) is one of the most common gynecologic cancers worldwide. There were 417,367 newly diagnosed cases and 97,370 deaths due to this disease worldwide in 2020. The incidence rates have increased over time, especially in countries with rapid socioeconomic transitions, and EC has been the most prevalent gynecologic malignancy in Taiwan since 2012. The new EC molecular classifications of The Cancer Genome Atlas (TCGA) Research Network include clear-cell carcinoma, serous carcinoma, and carcinosarcoma, while undifferentiated/dedifferentiated EC (UDEC) is not mentioned, and most previous clinical trials for EC have not included UDEC. UDEC is rare, has an aggressive growth pattern, tends to be diagnosed at an advanced stage, and is resistant to conventional chemotherapy. In this review, case series or case reports on the clinical features and genomic/epigenetic and expression profiles on UDEC data are summarized in order to identify potential molecular targets for current and future research.

[Research progress on the relationship between lncRNA and the pathogenesis of allergic rhinitis]

Long non-coding RNA（lncRNA） belongs to the category of non-coding RNA, which length exceeds 200 nucleotides and can hardly encode the expression of proteins. Based on the data from several clinical researches, it is considered that lncRNA not only plays the biological role in epigenetics, transcriptional and post-transcriptional levels, but also abnormally expresses in inflammatory response and the related diseases. In recent years, with the intensive study of gene expression regulation of allergic rhinitis（AR）, it has been found that a variety of non-coding RNA, including lncRNA, have close relationship with the occurrence and development of AR. This review mainly summarized the biological function, immunomodulatory effect of lncRNA and the relationship between the lncRNA and the pathogenesis of AR, providing new thoughts and strategies for the further research, prevention as well as the treatment of AR.

[An "a la carte" treatment for patients with pancreatic adenocarcinoma]

Pancreatic adenocarcinoma is a heterogeneous disease. Undeniably, the appearance and accumulation of genetic mutations promote the development of pancreatic adenocarcinoma. However, counterintuitively, genetic analyzes, no matter how precise and in-depth they may be, do not allow stratification of patients to predict their clinical evolution or to select the most effective treatment in each case. This is due to the fact that the clinical evolution and sensitivity to treatments are associated with the tumoral phenotype, which, in turn, is determined by the global expression of genes that is regulated at the transcriptomic level. Therefore, the stratification of these patients must be done by analysis at the transcriptomic level and not by genetic analysis. The data obtained from large cohorts of patients indicate that studying the transcription of a selected set of genes could predict the clinical outcome and can help to decide about the most appropriate treatment. We are moving very rapidly towards a personalized medicine for this disease, which in itself has a poor prognosis, even worse if the therapeutic decision is not the most adapted to each patient. We are convinced that in the near future the treatment of cancers will be preceded by an extensive transcriptomic characterization in order to select the most suitable "a la carte" treatments.

Genetic Polymorphisms of NLRP3 (rs4612666) and CARD8 (rs2043211) in Periodontitis and Cardiovascular Diseases

BACKGROUND

The existing data show that inflammasomes play a role in periodontal disease pathogenesis. However, their role in the pathogenesis of periodontitis and coronary heart disease remains unclear. This study had the objective of assessing NLRP3 (rs4612666) and CARD8 (rs2043211) gene polymorphisms in dental plaque and blood of generalized chronic periodontitis (CP) patients in the presence and absence of coronary heart disease (CHD).

METHODS

A total of 70 subjects were divided into two groups, including CP and CP + CHD subjects. Demographic variables, periodontal, and cardiac parameters were recorded from both groups. Subgingival plaque and blood samples were obtained from both groups and were subjected to further molecular analysis for NLRP3 (rs4612666) and CARD8 (rs2043211) expression and allele change using conventional polymerase chain reaction (PCR) and gene sequencing (Sanger's method).

RESULTS

Amongst the demographic variables, age, and monthly income were statistically significant between the two groups. Plaque index (PI), clinical attachment level (CAL), high-density lipoprotein (HDL), and low density-lipoprotein (LDL) exhibited statistically significant levels between the two groups. NLRP3 (rs4612666) and CARD8 (rs2043211) genes showed a statistically significant association of allele change (frequency) among the groups. In general, when all of the parameters were compared to the allele change of the genes, statistically significant relationships were found between the two groups.

CONCLUSIONS

The present study expressed an allele change of the investigated genes which could profoundly affect the pathobiology of the two diseases under investigation.

Clinical Insights Into Heritable Cardiomyopathies

Cardiomyopathies (CMs) encompass a heterogeneous group of structural and functional abnormalities of the myocardium. The phenotypic characteristics of these myocardial diseases range from silent to symptomatic heart failure, to sudden cardiac death due to malignant tachycardias. These diseases represent a leading cause of cardiovascular morbidity, cardiac transplantation, and death. Since the discovery of the first locus associated with hypertrophic cardiomyopathy 30 years ago, multiple loci and molecular mechanisms have been associated with these cardiomyopathy phenotypes. Conversely, the disparity between the ever-growing landscape of cardiovascular genetics and the lack of awareness in this field noticeably demonstrates the necessity to update training curricula and educational pathways. This review summarizes the current understanding of heritable CMs, including the most common pathogenic gene variants associated with the morpho-functional types of cardiomyopathies: dilated, hypertrophic, arrhythmogenic, non-compaction, and restrictive. Increased understanding of the genetic/phenotypic associations of these heritable diseases would facilitate risk stratification to leveraging appropriate surveillance and management, and it would additionally provide identification of family members at risk of avoidable cardiovascular morbidity and mortality.

Achieving the balance: Biphasic effects of genistein on PC-3 cells

This study examined the response of PC-3 cells to physiological (0.5, 2.5, 5, 10 μM) and pharmacological (50 μM) concentrations of genistein which is a main bioactive compound in soy. Following 48 hr genistein treatment, cell-based assays and genome-wide microarray were performed. It was evidenced that maximal physiologically achievable concentrations of genistein (0.5-10 μM) lead to significant increase in cell viability (p < 0.05) and decrease in migration at 0.5 μM (p = 0.000) and 10 μM (p = 0.001). The highest percentage of apoptotic cells was obtained at 50 μM. Microarray analysis gave the most critical pathways such as cell cycle regulation and proliferation, tumorigenesis, DNA damage and repair, stress response, and apoptosis. Physiological concentrations (≤10 μM) induced activation of CDKs, MAPKs, and RPSKs, while high concentrations of genistein (>10 μM) appeared to have a novel mechanism of action, specifically down-regulating TGF-β by decreasing specifically SMAD 2/3,4 which are in the downstream TGF-β signaling cascade. PRACTICAL APPLICATIONS: This study highlights for the first time that maximal physiologically achievable concentrations of genistein (0.5-10 μM) have proliferative effects evidenced by alterations in global gene expression patterns of PC-3 cells. Our results particularly represent a closer examination of dietary genistein consumption for the prevention and/or treatment of cancer that maximal physiologically achievable concentrations of genistein could have detrimental effects on individuals with prostate cancer. Further studies as in vivo would be necessary to remove shadows on the effect of genistein on prostate cancer progression.

Molecular and Morphological Changes Induced by Leonardite-based Biostimulant in Beta vulgaris L

Humic substances extracted from leonardite are widely considered to be bioactive compounds, influencing the whole-plant physiology and the crop yield. The aim of this work was to evaluate the effect of a new formulate based on leonardite in the early stage of growth of sugar beet (Beta vulgaris L.). A commercial preparation of leonardite (BLACKJAK) was characterized by ionomic analysis, solid-state ¹³C MAS NMR spectroscopy. Seedlings of sugar beet were grown in Hoagland's solution under controlled conditions. After five days of growth, an aliquot of the concentrated BLACKJAK was added to the solution to obtain a final dilution of 1:1000 (0.5 mg C L^-1). The sugar beet response in the early stage of growth was determined by evaluating root morphological traits as well as the changes in the expression of 53 genes related to key morphophysiological processes. Root morphological traits, such as total root length, fine root length (average diameter < 0.5 mm), and number of root tips, were significantly (p < 0.001) increased in plants treated with BLACKJAK, compared to the untreated plants at all sampling times. At the molecular level, BLACKJAK treatment upregulated many of the evaluated genes. Moreover, both Real Time PCR and digital PCR showed that genes involved in hormonal response, such as PIN, ARF3, LOGL 10, GID1, and BRI1, were significantly (p < 0.05) upregulated by treatment with BLACKJAK. Our study provides essential information to understand the effect of a leonardite-based formulate on plant growth hormone metabolism, although the molecular and physiological basis for these complicated regulatory mechanisms deserve further investigations.

Microarray and pathway analysis of two COMMA-Dβ derived clones reveal important differences relevant to their developmental capacity in-vivo

Microarray technologies were used to analyze transcriptomes from Comma-Dβ and clonal derivatives, SP3 (Lobule-competent) and NSP2 (Lobule-incompetent), during different mouse mammary growth phases: in-vitro, in-vivo 5-weeks, and in-vivo 12-weeks. A differentially expressed gene (DEG) algorithm was used to enrich for genes associated with cellular proliferation, differentiation, cell cycle regulation, and carcinogenesis. A pairwise comparison analysis, of SP3 vs. NSP2 in-vitro, revealed a total of 45 DEGs significantly up-regulated in SP3. Of the 45 DEGs, only Ccnd1 (Cyclin D1), Id2 (Inhibitor of DNA binding 2) and Sox9 (SRY Box 9) were identified to be associated with cellular proliferation, regulation of G1/S mitotic cell cycle, mammary gland and alveolar development in SP3. During the regenerative growth phase, in-vivo 5-weeks, we identified a total of 545 DEGs. 308 DEGs, of the 545 DEGs, were significantly up-regulated and 237 DEGs were significantly down-regulated in SP3 vs. NSP2. In addition, we identified 9 DEGs significantly up-regulated, within SP3's cell cycle pathway and a persistent overexpression of Cyclin D1, Id2, and Sox9, consistent with our in-vitro study. During the maintenance phase, in-vivo 12-weeks, we identified 407 DEGs. Of these, 336 DEGs were up-regulated, and 71 were down-regulated in SP3 vs. NSP2. Our data shows 15 DEGs significantly up-regulated, simultaneously, affecting 8 signal transducing carcinogenic pathways. In conclusion, increased expression of Cyclin D1, Id2 and Sox9 appear to be important for lobular genesis in SP3. Also, in-vivo 12 week displays increase expression of genes and pathways, involved in tumorigenesis.

Retinoblastoma treatment: impact of the glycolytic inhibitor 2-deoxy-d-glucose on molecular genomics expression in LH(BETA)T(AG) retinal tumors

PURPOSE

The purpose of this study was to evaluate the effect of 2-deoxy-D-glucose (2-DG) on the spatial distribution of the genetic expression of key elements involved in angiogenesis, hypoxia, cellular metabolism, and apoptosis in LH(BETA)T(AG) retinal tumors.

METHODS

The right eye of each LH(BETA)T(AG) transgenic mouse (n = 24) was treated with either two or six subconjunctival injections of 2-DG (500 mg/kg) or saline control at 16 weeks of age. A gene expression array analysis was performed on five different intratumoral regions (apex, center, base, anterior-lateral, and posterior-lateral) using Affymetrix GeneChip Mouse Gene 1.0 ST arrays. To test for treatment effects of each probe within each region, a two-way analysis of variance was used.

RESULTS

Significant differences between treatment groups (ie, 0, 2, and 6 injections) were found as well as differences among the five retinal tumor regions evaluated (P < 0.01). More than 100 genes were observed to be dysregulated by ≥2-fold difference in expression between the three treatment groups, and their dysregulation varied across the five regions assayed. Several genes involved in pathways important for tumor cell growth (ie, angiogenesis, hypoxia, cellular metabolism, and apoptosis) were identified.

CONCLUSIONS

2-DG was found to significantly alter the gene expression in LH(BETA)T(AG) retinal tumor cells according to their location within the tumor as well as the treatment schedule. 2-DG's effects on genetic expression found here correlate with previous reported results on varied processes involved in its in vitro and in vivo activity in inhibiting tumor cell growth.

Genetic expression profiling of parotid neoplasms by cDNA microarrays

Differentially expressed genes in various benign and malignant salivary gland tumours were identified by use of cDNA microarrays containing 19,000 human expressed sequence tags. Samples were derived from 5 patients with pleomorphic adenoma, 4 with Warthin's tumour, one with clear cell carcinoma, and 2 with mucoepidermoid carcinoma. Tumours were classified by using a subset of 486 genes. Benign Warthin's tumour and pleomorphic adenoma showed very distinctive gene expression patterns. A total of 133 genes differentiated the single malignant clear cell carcinoma from non-tumour salivary glands (p < 0.01), whereas only 16 genes separated it from the highly related benign pleomorphic adenoma (p < 0.01). A total of 57 cDNAs were associated with mucoepidermoid carcinoma (p < 0.01). The results show gene expression alterations common to all tumours and unique to each benign and malignant tumour. The numerous Expressed Sequence Tags of unknown function we identified could also become useful as tumour markers and represent a set of novel tumour-associated genes.

A brain protein unique to the olfactory bulb

Soluble extracts from several regions of the mouse brain manifested regionally specific protein band patterns on polyacrylamide gel electrophoresis. In particular, one protein band appeared to occur uniquely in the olfactory bulb extracts where it was a quantitatively significant constituent of the soluble protein extract. This protein was purified to homogeneity by ammonium sulfate precipitation, DEAE-cellulose column chromatography, and polyacrylamide gel electrophoresis. The purified protein has a minimum molecular weight of about 20,000 by gel electrophoresis in the presence of sodium dodecyl sulfate. Precipitating antiserum prepared against this protein reacted only with the purified protein or with extracts of olfactory bulb, and not with extracts of other mouse tissues or brain regions. Quantitative immunoprecipitation assays indicate that this specific protein represents 1% of the total soluble protein in the mouse olfactory bulb. Soluble extracts of olfactory bulbs from several rodent species gave reactions of identity by agar gel diffusion with the antiserum to the mouse protein. It is suggested that this protein is an example of selective genetic expression within the central nervous system.