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PubMed1995

Thirteen loci physically assigned to sheep chromosome 2 by cell hybrid analysis and in situ hybridization.

Sheep x hamster cell hybrids containing sheep metacentric Chromosome (Chr) 2 were produced by fusing blood leukocytes from normal sheep with hamster auxotrophic Ade F-minus mutants. Cell clones that were isocitrate dehydrogenase 1 (IDH1) positive were cytogenetically characterized, confirming that they contained sheep Chr 2. The following loci were newly assigned by Southern hybridization to sheep Chr 2: lipoprotein lipase (LPL), glycoprotein-4-beta galactosyltransferase 2 (GGTB2), neurofilament light polypeptide (68 kDa; NEFL), surfactant-associated protein 2 (SFTP2), lymphocyte-specific protein tyrosine kinase (LCK), and nebulin (NEB). These new assignments and the in situ localization of gelsolin (GSN) to sheep Chr 2pter-p24 are consistent with the predicted homology of cattle Chr 8 (U18) with sheep Chr 2p, and of cattle Chr 2 (U17) with sheep 2q. In addition, the assignment by cell hybrid analysis of loci previously mapped to Chr 2 in sheep, viz., cholinergic receptor, nicotinic, delta polypeptide (CHRND), collagen type III alpha 1 (COL3A1), fibronectin 1 (FN1), isocitrate dehydrogenase (IDH1), and villin 1 (VIL1), confirmed the localization of sheep syntenic group U11 to this chromosome. By nutritional selection and complementation of the hamster auxotrophic Ade F mutation, the multifunctional enzyme locus phosphoribosylaminoimidazolecarboxamide formyltransferase (AICAR transformylase)/IMP cyclohydrolase (inosinicase) (provisionally given the symbol PRACFT) has also been newly assigned to sheep Chr 2. This report significantly extends the number of loci physically mapped to sheep Chr 2 and confirms its close homology with cattle Chrs 2 and 8.

Animals↗

PubMed2026

Unravelling the biological nexus of smoking and postpartum depression: a meta-analysis and functional genomics approach.

PURPOSE: Postpartum depression (PPD) is a prevalent psychological condition among birthing women. While several psycho-socio-economic and neurobiological factors influence its development, its relationship with smoking behavior and nicotine addiction remains largely inconclusive. METHODS: In this combinatorial study, we first evaluate the relationship between smoking and depressive behaviors in postpartum women using data extracted from pertinent primary epidemiological studies. Additionally, to discern the molecular and cellular mechanisms underlying this association, we identified common genetic elements and evaluated their functional attributes using in silico analyses. RESULTS: Meta-analytical assessment of systematically collected data from 38 studies indicated that smoking women are twice as likely to develop PPD, compared to their non-smoking counterparts. While geocultural attributes did not affect this relationship, timing of smoking was a significant moderator, with current and gestational smoking statuses being more strongly linked with PPD outcome, compared to the past smoking habit. Further, depression scores in smoking postpartum women were higher than those in non-smoking controls. Analysis of the common protein-encoding genes underlying the pathophysiology of nicotine addiction and PPD revealed several critical hub proteins (viz., AKT1, JUN, CTNNB1, PTEN, EGFR, ESR1, SRC, STAT3, FN1, IL1B, IL6, TNF, TP53, GAPDH, INS, MYC, and ALB) which were predicted to alter multiple pathophysiological pathways associated with transcriptional expression, intra- and intercellular signaling transduction, metabolism, and immune functions. CONCLUSION: Our results indicate that smoking is strongly associated with depressive behavior in postpartum women, although this association involve mediation of additional environmental and psychosocial elements. Moreover, network analysis of common genetic elements identified several potentially disrupted neurophysiological pathways in postpartum women with smoking and depressive behaviors which may aid in characterizing the underlying relationship between the two conditions.

Humans↗

PubMed2005

Characterization of gene expression in major types of salivary gland carcinomas with epithelial differentiation.

Gene expression profiles were studied in 13 cases of salivary gland carcinoma including mucoepidermoid carcinoma (MEC), acinic cell carcinoma (ACC), and salivary duct carcinoma (SDC) using a cDNA array. A total of 162 genes were deregulated. Only 5 genes were overexpressed in all carcinomas including fibronectin 1 (FN1), tissue metalloproteinase inhibitor 1 (TIMP1), biglycan (BGN), tenascin-C (HXB), and insulin-like growth factor binding protein 5 (IGFBP5), whereas 16 genes were underexpressed. The small number of similarly deregulated genes in these carcinoma entities suggests an extensive genetic variation between them. This result agrees with the great histopathological diversity of different entities of salivary gland carcinoma. Furthermore, diversity in gene expression between the carcinoma types was identified also by hierarchical clustering. Each carcinoma entity was clustered together but MEC, SDC, and ACC were separated from each other. Significance analysis of microarrays identified 27 genes expressed differently between the groups. In MEC, overexpressed genes included those of cell proliferation (IL-6 and SFN) and cell adhesion (SEMA3F and COL6A3), whereas many underexpressed genes were related to DNA modification (NTHL1 and RBBP4). Apoptosis-related genes CASP10 and MMP11 were overexpressed in SDC, in accordance with the typical tumor necrosis seen in this entity. An intermediate filament protein of basal epithelial cells, cytokeratin 14 (KRT14) was clearly differently expressed between the 3 types of carcinoma, and can be used as an aid in their differential diagnosis. The array results were validated by RT-PCR and immunohistochemistry.

Adolescent↗

PubMed2004

Perinatal changes of brain-derived neurotrophic factor in pre- and fullterm neonates.

BACKGROUND: Brain-derived neurotrophic factor (BDNF) is abundant in brain and peripheral nerves, affects normal development, growth and survival and is implicated in immune response. AIM: To determine in single preterm (P) and fullterm (F) neonates, circulating intra- and extrauterine levels of BDNF, supposingly reflecting their neuronal and immune maturity. STUDY DESIGN: Prospective study. SUBJECTS: Thirty healthy, appropriate for gestational age (AGA) F (mean gestational age 39.2+/-1.4 weeks), 15 healthy AGA P (29.4+/-1.3 weeks), and their mothers. OUTCOME MEASURES: BDNF was measured by enzyme immunoassay methods in the serum of: mothers at the first stage of labor (MS), the umbilical cord (UC) and the neonates on days 1 (N1) and 4 (N4) postpartum. RESULTS: Levels of BDNF in (a). FMS did not differ from PMS, but both were significantly higher than respective (F or P) UC, N1 and N4 (p ranging from <0.01 to <0.001), (b). FUC, FN1 and FN4 were significantly higher than PUC (p<0.001), PN1 (p<0.03) and PN4 (p<0.02), respectively, (c). PN1 increased significantly as compared to PUC (p<0.05). CONCLUSIONS: Higher BDNF MS levels may reflect the mature nervous and immune systems of mothers. Higher BDNF levels in F than P may also be due to advanced maturity in the former. Increased BDNF levels in PN1 as compared to PUC may indicate stimulation of immune response with exposure to antigenic stimuli from the extrauterine environment. Nevertheless, this stimulation is insufficient in P, who by decreasing N4 levels are by far less protected than F.

Adult↗

PubMed2006

Identification of cis and trans-acting transcriptional regulators in chondroinduced fibroblasts from the pre-phenotypic gene expression profile.

Cell differentiation is regulated via expression of successive sets of genes. In an in vitro model of chondrocyte differentiation, human dermal fibroblasts (hDFs) cultured in collagen sponges are induced to express cartilage matrix genes after 7 days' culture with demineralized bone powder (DBP). A shift in expression of many other genes occurs within 3 days, before chondroblast phenotypic genes are detectable. In this study, the pre-chondrogenic gene expression profile was used as a starting point to derive information on transcriptional regulation of chondrocyte differentiation induced by DBP. Putative cis regulatory elements were identified by comparing promoter regions from three genes that are highly upregulated in chondroinduced hDFs (BIGH3, COL1A2, and FN1) [Zhou, S., Glowacki, J., Yates, K.E, 2004. Comparison of TGF-beta/BMP pathways signaled by demineralized bone powder and BMP-2 in human dermal fibroblasts. J. Bone Min. Res. 19, 1732-1741] and whose products are known to interact in the matrix [Kim, J.E., et al., 2002. Molecular properties of wild-type and mutant betaIG-H3 proteins. Investig. Ophthalmol. Vis. Sci. 43, 656-661]. The effect of DBP on nuclear protein binding to cis elements was measured with an array-based assay. Nuclear extracts from hDFs cultured in DBP/collagen sponges for 3 days showed increased binding to several cis elements belonging to the families that were identified by promoter analysis. Of note, those elements represented targets of both signal-activated and developmentally regulated transcription factors. Direct measurement of mRNAs showed increased gene expression of both types of transcription factors in chondroinduced hDFs, including NFKB2 (290% of control), RELA (160%), and GATA2 (190%). Moreover, DBP increased gene expression of chondrogenic transcription factors SOX9 (160% of control) and RUNX2 (180%). Immunoblot analysis showed that DBP increased both expression (200% of control) and phosphorylation (300%) of the Creb protein, a transcription factor that is downstream of several signal transduction pathways. Inhibition of protein kinase A, protein kinase C, or MAP kinase in hDFs cultured in DBP/collagen sponges reduced induction of BIGH3 to approximately 50% of control. These results suggest that both signal-activated and developmentally controlled transcriptional mechanisms contribute to chondroinduction of hDFs by DBP.

Binding Sites↗

PubMed2024

High yield of monogenic short stature in children from Kurdistan, Iraq: A genetic testing algorithm for consanguineous families.

PURPOSE: Genetic testing in consanguineous families advances the general comprehension of pathophysiological pathways. However, short stature (SS) genetics remain unexplored in a defined consanguineous cohort. This study examines a unique pediatric cohort from Sulaimani, Iraq, aiming to inspire a genetic testing algorithm for similar populations. METHODS: Among 280 SS referrals from 2018-2020, 64 children met inclusion criteria (from consanguineous families; height ≤ -2.25 SD), 51 provided informed consent (30 females; 31 syndromic SS) and underwent investigation, primarily via exome sequencing. Prioritized variants were evaluated by the American College of Medical Genetics and Genomics standards. A comparative analysis was conducted by juxtaposing our findings against published gene panels for SS. RESULTS: A genetic cause of SS was elucidated in 31 of 51 (61%) participants. Pathogenic variants were found in genes involved in the GH-IGF-1 axis (GHR and SOX3), thyroid axis (TSHR), growth plate (CTSK, COL1A2, COL10A1, DYM, FN1, LTBP3, MMP13, NPR2, and SHOX), signal transduction (PTPN11), DNA/RNA replication (DNAJC21, GZF1, and LIG4), cytoskeletal structure (CCDC8, FLNA, and PCNT), transmembrane transport (SLC34A3 and SLC7A7), enzyme coding (CYP27B1, GALNS, and GNPTG), and ciliogenesis (CFAP410). Two additional participants had Silver-Russell syndrome and 1 had del22q.11.21. Syndromic SS was predictive in identifying a monogenic condition. Using a gene panel would yield positive results in only 10% to 33% of cases. CONCLUSION: A tailored testing strategy is essential to increase diagnostic yield in children with SS from consanguineous populations.

Humans↗

PubMed2026

Mapping articular cartilage maturation across postnatal development by proteomics.

OBJECTIVE: Articular cartilage has a specialised extracellular matrix that provides tensile strength and resistance to compression, but repair capacity is limited. Matrix remodelling during growth is essential for long-term tissue function, yet the underlying protein-level adaptations remain poorly characterised in large-animal models relevant to human joint biology. DESIGN: Using non-targeted, label-free mass spectrometry-based proteomics, we profiled full-thickness articular cartilage from goats across seven postnatal ages from neonatal to adult (n = 3 per age). Cartilage proteins were extracted using guanidine-based solubilisation and analysed by mass spectrometry. Selected proteins were further examined by immunohistochemistry. RESULTS: We identified 799 proteins across the seven ages, of which 157 matrisome components grouped into six categories. Development was associated with increased abundance of proteins involved in matrix organisation and stabilisation, including COL6A1, LOX, TIMP3 and CILP. Enrichment analysis revealed a shift from collagen biosynthesis and fibrillogenesis in early postnatal cartilage to elastic fibre organisation, integrin-matrix interactions and glycosaminoglycan metabolism in mature tissue, consistent with transition from matrix assembly to maintenance. Lysozyme increased with age, suggesting a structural role that warrants further study. Several proteins enriched in mature cartilage, including CILP, HTRA1, FN1 and SPP1, have also been implicated in osteoarthritis, suggesting that some molecular features of mature ECM maintenance are shared with diseased tissue. Immunohistochemistry confirmed stable COL2 localisation, loss of deep-zone COL10 staining with maturation and emergence of superficial PRG4 expression in adult cartilage. CONCLUSIONS: Our findings define the proteomic trajectory of cartilage maturation and provide a molecular reference for joint development and matrix ageing.

Animals↗

PubMed2006

Production and purification of functional truncated soluble forms of human recombinant L1 cell adhesion glycoprotein from Spodoptera frugiperda Sf9 cells.

L1 is a human cell adhesion glycoprotein involved in the development of the central nervous system that comprises six immunoglobulin-like domains (Ig1-Ig6), five fibronectin-type III (FN1-FN5) domains, a single transmembrane region and a cytoplasmic domain. It contains 20 potential N-glycosylation sites and is heavily glycosylated in a variety of cell types. In this work, seven truncated soluble forms including L1 ectodomain (L1/ECD) and Ig domains 5-6 (L1/Ig5-6) have been constructed by PCR and have been cloned, as well as the full-length form (L1), in the stable expression vector for insect cells pMIB/V5-His-TOPO. Spodoptera frugiperda Sf9 cell lines expressing the truncated forms have been obtained, and all proteins were successfully secreted. L1/ECD and L1/Ig5-6 were produced in shake flasks with productions of 3 and 32 mg/L on the third and fourth day of culture, respectively. When L1/Ig5-6 was produced for four days in 2L bioreactor 200 mg/L protein were recovered from the supernatants on the fourth day of culture. Affinity-purified L1/ECD and L1/Ig5-6 were immobilized on poly-d-lysine coated coverslips, and were shown to be active in inducing neurite outgrowth from human NT2N neurons. Therefore, correctly folded and functional truncated forms of human L1 have been produced in high amounts from insect cells using a stable expression system.

Animals↗

PubMedDate not supplied

Differential display RT-PCR analysis of human choriocarcinoma cell lines and normal term trophoblast cells: identification of new genes expressed in placenta.

In this study, we performed the differential display technique to identify genes specifically expressed in human choriocarcinoma cell lines (JEG-3, JAR and BeWo) and normal placental term cells. Few differences were found among the expression profiles of the three choriocarcinoma cell lines and most of the differentially expressed genes were detected in normal term placenta. A total of 36 cDNA fragments were isolated and analysed. Of these, 19 sequences corresponded to regions in the human genome coding for potential novel genes. We confirmed by RT-PCR, the placental mRNA expression of three selected new human genes, on chromosomes 16q12, 9q32 and 6q22. The other 17 sequences showed high similarity to known human genes (like PSG3, FN1, PAI-2). Interestingly, the functions of five known proteins (from genes IK, TRA-1, HERPUD1, UBA-2, and TRAP240) have not yet been well characterized in placenta tissue. In addition, new alternative spliced mRNAs were detected for IK, TRAP240 and PLAC3 genes. The differential expression of the PAI-2 gene among the choriocarcinoma cell lines was also confirmed. The genes identified in this analysis will be of interest for future studies regarding both a better understanding of the biology of the trophoblast cell and the formation of placental tumors.

Adult↗

PubMed2025

Polygenic enrichment analysis in multi-omics levels identifies cell/tissue specific associations with schizophrenia based on single-cell RNA sequencing data.

OBJECTIVE: Understanding the specific cellular origin and tissue heterogeneity in schizophrenia is critically important for exploring the disease etiology. This study aims to investigate these aspects by performing multiple analyses based on omics data. METHOD: We performed single-cell disease relevance score (scDRS) algorithm to link brain single-cell RNA sequencing (scRNA-seq) with schizophrenia risk across multi-omics scales at single-cell resolution. This approach identified cell types with overexpression of schizophrenia-related genes implicated by multi-omics panels (ATAC-seq, RNA-seq, TWAS, and GWAS). Schizophrenia-related genes from these multi-omics panels were extracted and combined with scRNA-seq data to calculate scDRS. Subsequently, the cell-type vs. disease association and tissue heterogeneity were assessed using scDRS for each omics panel. RESULTS: We identified two novel cell subpopulations in the brain that differentially express SCUBE3 (59 cells, 7.0 %) and FN1 (21 cells, 2.5 %). At the individual cell level, schizophrenia-associated cell subpopulations included microglial cell associated with ATAC-seq panel (Passociation = 0.002, Pheterogeneity = 0.009) and deep layer neuron suggestively associated with GWAS panel (Passociation = 0.033, Pheterogeneity = 0.017). At the brain tissue level, microglial cell was significantly associated with cortical plate in ATAC-seq panel (Passociation = 0.002, Pheterogeneity = 0.011). Gene level analysis identified several genes associated with schizophrenia across multi-omics panels. CONCLUSIONS: Our study outlines the signature of cell subpopulations, brain regions, and disease risk genes in schizophrenia at single-cell resolution across multi-omics scales. These findings provide a reference for future precision medicine approaches targeting specific cell types and brain regions in schizophrenia.

Schizophrenia↗

PubMed2026

CRISPR activation reveals SOX5/6/9 as key transcriptional regulators directing iPSC-derived cells toward a notochordal lineage.

Intervertebral disc (IVD) degeneration, a leading cause of chronic lower back pain, is associated with loss of vacuolated notochordal cells (NCs) and fibrotic remodeling of the nucleus pulposus. Emerging therapies increasingly focus on NCs, which are rare but therapeutically relevant cells for regenerating degenerated IVDs. In this study, we used CRISPR-based transactivation (CRISPRa) to direct the differentiation of human induced pluripotent stem cells (iPSCs) into the NC lineage. We tested CRISPRa-mediated activation of NOTO, TBXT, FOXA2, SOX5, SOX6, and SOX9, coupled with single-cell sequencing of Aggrecan-2A-mScarlet reporter iPSCs. This approach identified the SOX5/6/9 combination (SOX-trio) as critical for promoting NC lineage commitment. The SOX-trio yielded the largest cell population expressing a range of genes previously associated with NC identity, including SHH, FOXA1, FOXA2, FOXJ1, FN1, ALCAM, KRT8, and KRT18. Our study demonstrates the integration of CRISPRa with single-cell technologies as a powerful platform for investigating and enriching iPSC-derived NCs, supporting future regenerative strategies across various fields.

Humans↗

PubMed2006

Mouse model of paraquat-poisoned lungs and its gene expression profile.

Paraquat (PQ)-induced pulmonary toxicity is characterized by initial development of pulmonary edema, infiltration of inflammatory cells, and damage to the alveolar epithelium, which may progress to severe fibrosis. However, the exact role of PQ in the progression of the pathogenesis has not been clearly established. To understand the mechanism of PQ in pulmonary toxicity, we developed an animal model of PQ-induced lung injury by intranasal instillation of PQ solution using C57Black/6J mice. Twenty microliters of PQ solution (0.01, 0.01, and 0.04 mg/mouse) was applied through the nares, and the same amount of vehicle was applied in control mice. The pathological progression of lung pathology in our mouse model was very similar to that of patients suffering from PQ poisoning. The lungs of some animals exposed to PQ showed acute fulmination, resulting in death from 5 days post-exposure, but others showed a more protracted injury, resulting in typical pulmonary fibrosis at 3 weeks. Using this PQ-poisoned mouse model, we examined the gene expression at the initial destructive phase (within 5 days) that fibrosis has not completely developed. We prepared RNAs after 6h, 24h, and 5 days and examined the changes of the expression levels for 45 selected genes. The genes showing >2-fold increase at 6h or a time-dependent decrease during this experimental period may be the early markers for the destructive phase. These genes are Mt1, Mt2, Hmox1, Gcl, GR, IL-6, IL-13, Txn1, Fas, FasL, Lpin2, Mmp1a, Mmp12, Sfp-B, Sfp-D, CAT, EC-SOD, GST, and Pltp. On the other hand, the genes involved in the development of fibrosis, such as procollagen, Fn1, Eln, SMA, and Mmp9, Timp1 were significantly increased on day 5, not at 6h nor at 24h, after PQ treatment (the late marker). The genes showing a significant increase (Mmp3 and Mmp8) or decrease (VEGFA) at 24h and 5 days and not at 6h may be also the late markers. These changes in gene expression, which are equalled to functional activities of proteins, will be the targets for future studies focused on the development on PQ-induced pulmonary damage.

Administration, Intranasal↗

PubMed2006

Gene expression array analyses predict increased proto-oncogene expression in MMTV induced mammary tumors.

Exogenous infection by milk-borne mouse mammary tumor viruses (MMTV) typically induce mouse mammary tumors in genetically susceptible mice at a rate of 90-95% by 1 year of age. In contrast to other transforming retroviruses, MMTV acts as an insertional mutagen and under the influence of steroid hormones induces oncogenic transformation after insertion into the host genome. As these events correspond with increases in adjacent proto-oncogene transcription, we used expression array profiling to determine which commonly associated MMTV insertion site proto-oncogenes were transcriptionally active in MMTV induced mouse mammary tumors. To verify our gene expression array results we developed real-time quantitative RT-PCR assays for the common MMTV insertion site genes found in RIII/Sa mice (int-1/wnt-1, int-2/fgf-3, int-3/Notch 4, and fgf8/AIGF) as well as two genes that were consistently up regulated (CCND1, and MAT-8) and two genes that were consistently down regulated (FN1 and MAT-8) in the MMTV induced tumors as compared to normal mammary gland. Finally, each tumor was also examined histopathologically. Our expression array findings support a model whereby just one or a few common MMTV insertions into the host genome sets up a dominant cascade of events that leave a characteristic molecular signature.

Animals↗

PubMed2004

Elementary swelling and gelling theories.

It has been experimentally illustrated that it is possible to form an n-phase thermodynamic system where n> or =2 and has a value which is limited by the properties of the system. For example, to attain limited chemical reversibility of a mineral matrix such as vermiculite using specific butyl ammonium vermiculite, it is necessary to reform chemical bonds using an additive and a particular ion. In other words, to obtain a similar thin film using exfoliated vermiculite as that obtained with natural vermiculite, hydrophobic or binding electrostatic bonds must be formed or reformed. It has also been observed that complementary structural compounds can be formed from other silicates, such as glycerine/sodium silicate. These compounds can also encase the vermiculite matrices. (Film Formation) is proportional to (A/Temp). (Pressure).(Ionic Content). Hence F=L(A/T)PE, where F=film formation, L=functional constant for the matrix compound, T=temperature, A=temperature constant, P=pressure, E=electrostatic force and P=force/area. Thus, F=LTE2 for unit area. SigmaF=pfL. TE2/SigmaPefl=F1, where P=the probability for film formation and SigmaPef(L) is the partition function for the film formation. This concept can be extended to a response geometric algorithm. This means that for every mineral matrix there is an algorithm to describe its formation or its response to an applied field. Thus deltasec2(E)tan(E1) is the response for (F1). V---, V1...Vn, F1...Fn1, ..., Fp, ...Fnp.

Aluminum Silicates↗

PubMed2006

A proteomic study of serum from children with autism showing differential expression of apolipoproteins and complement proteins.

Modern methods that use systematic, quantitative and unbiased approaches are making it possible to discover proteins altered by a disease. To identify proteins that might be differentially expressed in autism, serum proteins from blood were subjected to trypsin digestion followed by liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) on time-of-flight (TOF) instruments to identify differentially expressed peptides. Children with autism 4-6 years of age (n=69) were compared to typically developing children (n=35) with similar age and gender distributions. A total of 6348 peptide components were quantified. Of these, five peptide components corresponding to four known proteins had an effect size >0.99 with a P<0.05 and a Mascot identification score of 30 or greater for autism compared to controls. The four proteins were: Apolipoprotein (apo) B-100, Complement Factor H Related Protein (FHR1), Complement C1q and Fibronectin 1 (FN1). In addition, apo B-100 and apo A-IV were higher in children with high compared to low functioning autism. Apos are involved in the transport of lipids, cholesterol and vitamin E. The complement system is involved in the lysis and removal of infectious organisms in blood, and may be involved in cellular apoptosis in brain. Despite limitations of the study, including the low fold changes and variable detection rates for the peptide components, the data support possible differences of circulating proteins in autism, and should help stimulate the continued search for causes and treatments of autism by examining peripheral blood.

Apolipoproteins↗

PubMed2003

cDNA microarray analysis of genes associated with ERBB2 (HER2/neu) overexpression in human mammary luminal epithelial cells.

To investigate changes in gene expression associated with ERBB2, expression profiling of immortalized human mammary luminal epithelial cells and variants expressing a moderate and high level of ERBB2 has been carried out using cDNA microarrays corresponding to approximately 6000 unique genes/ESTs. A total of 61 significantly up- or downregulated (2.0-fold) genes were identified and further validated by RT-PCR analysis as well as microarray comparisons with a spontaneously ERBB2- overexpressing breast cancer cell line and ERBB2-positive primary breast tumors. The expression and clinical relevance of proteins predicted to be associated with ERBB2 overexpression in breast cancers were analysed together with their clinical relevance by antibody screening using a tissue array. Differentially regulated genes include those involved in cell-matrix interactions including proline 4-hydroxylase (P4HA2), galectin 1 (LGALS1) and galectin 3 (LGALS3), fibronectin 1 (FN1) and p-cadherin (CDH3), and cell proliferation (CRIP1, IGFBP3) and transformation (S100P, S100A4). A number of genes associated with MYC signalling were also differentially expressed, including NDRG1, USF2 and the epithelial membrane proteins 1 and 3 (EMP1, EMP3). These data represent profiles of the transcriptional changes associated with ERBB2-related pathways in the breast, and identify novel and potentially useful targets for prognosis and therapy.

Breast↗

PubMed2006

Specific gene expression profiles distinguish among functional allelic variants of the mouse Pthlh gene in transfected human cancer cells.

The mouse parathyroid hormone-like hormone (Pthlh) gene encodes three allelic variants characterized by amino acid substitutions that are associated with susceptibility (Pthlh(Pro)) or resistance (Pthlh(Thr) and Pthlh(SerAspTyr)) to two-stage skin carcinogenesis and to modulation of cell migration in vitro in transfected human cancer cells. cDNA microarray hybridization analysis of 8473 transcript clones revealed a similar gene expression profile for the Pthlh(Thr) and Pthlh(SerAspTyr) alleles but a distinct pattern for the Pthlh(Pro) allele, suggesting an association between a specific gene expression profile and biological function of the Pthlh alleles. Some of the genes modulated by the Pthlh alleles, e.g., ANXA1, CCL2, FN1 and TFF3, play a role in cell migration and may represent candidate targets for this Pthlh function. Our study demonstrates the potential usefulness of gene expression profiling of genetic variants for the functional characterization of candidate cancer modifier genes.

Alleles↗

PubMed2004

Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes.

BACKGROUND: Several gene-expression signatures can be used to predict the prognosis in diffuse large-B-cell lymphoma, but the lack of practical tests for a genome-scale analysis has restricted the use of this method. METHODS: We studied 36 genes whose expression had been reported to predict survival in diffuse large-B-cell lymphoma. We measured the expression of each of these genes in independent samples of lymphoma from 66 patients by quantitative real-time polymerase-chain-reaction analyses and related the results to overall survival. RESULTS: In a univariate analysis, genes were ranked on the basis of their ability to predict survival. The genes that were the strongest predictors were LMO2, BCL6, FN1, CCND2, SCYA3, and BCL2. We developed a multivariate model that was based on the expression of these six genes, and we validated the model in two independent microarray data sets. The model was independent of the International Prognostic Index and added to its predictive power. CONCLUSIONS: Measurement of the expression of six genes is sufficient to predict overall survival in diffuse large-B-cell lymphoma.

Adolescent↗