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At least 1,225 records · Page 68Linked to original sources
PubMed2005

Discovery of a new biomarker for gastroenterological cancers.

Various genomic technologies have been applied to address crucial problems in cancer biology, because cancer develops through the accumulation of various genetic alterations. Of these, gene expression profiling analysis using microarray technology has been widely applied not only to classify cancers at molecular levels, but also to identify novel molecular targets for therapeutics and/or diagnostics. To gain molecular understanding of gastric carcinogenesis, progression, and diversity, we analyzed primary advanced gastric cancer and noncancerous gastric tissues by high-density oligonucleotide microarray. Genes differentially expressed between cancer and noncancerous tissues were identified. In cancer tissues, genes related to cell cycle, growth factor, cell motility, cell adhesion, and matrix remodeling were highly expressed, whereas those related to gastrointestinal-specific function and immune response were rather downregulated. These results provide not only a new molecular basis for understanding biological properties of gastric cancer but also useful resources for future development of therapeutic and diagnostic biomarkers for gastric cancer. Several microarray studies have been published since and have been compared for validation in meta-analysis. As integration of transcriptome information with other biological data is crucial to interpret gene expression data, we have applied oligonucleotide microarray technology to assess allelic gene dosage at 10000 polymorphic loci, namely with an average interval of 200kb. Using a newly developed algorithm, genome imbalance map, loss of heterozygosity (LOH) status can be determined simultaneously. Besides several loci with genomic amplification, we also identified a homozygously deleted chromosomal region in 7q, where frequent chromosomal instability was observed. Finally, we are currently developing novel biomarkers for gastroenterological cancers. Glypican 3 is detected at high levels in serum of hepatocellular carcinoma patients and could be a potential target for antibody therapy.

Carcinoma, Hepatocellular↗
PubMed2005

[Research strategies towards a holistic characterization of rheumatoid arthritis--a systems biology approach].

Genome-wide screening methods used in functional genomics (genome, transcriptome, proteome and metabolom analysis) have increasingly been conducted in integrative research platforms to enable a comprehensive holistic characterization of multifactorial polygenic diseases. First results of this research strategy demonstrate that extended data sets are compiled whose quality is ensured by the application of standard operating procedures (SOPs) and the integration of specific laboratory information management systems (LIMS). Experimental data derived from this technology and methodology platform are obtained by applying standardized sampling procedures followed by comprehensive experimental validation and bioinformatic comparisons with the world knowledge publicly available. This research strategy should finally lead to a holistic understanding of the pathogenesis presented in rheumatoid arthritis by identifying disease-associated regulatory networks (pathways) and assigning them to cell populations involved in the disease mechanisms. In addition, it has to be investigated to what extent genetic as well as epigenetic factors direct disease initiation and progression in potential conjunction with environmental impacts (infections, smoking, etc.).

Animals↗
PubMed2005

Negative regulation of the expressions of cytokeratins 8 and 19 by SLUG repressor protein in human breast cells.

Invasiveness of tumor cells is often determined by the profile of their expressed genes. To determine the gene expression differences between an invasive and a non-invasive human breast tumor cells, we selected BT-549 (invasive) and MDA-MB-468 (non-invasive) cells, and compared their transcriptomes by cDNA microarray analysis. Among the significant differences in gene expressions, notable are the up-regulation of cytokeratins 8 and 19, and down-regulation of metallothioneins 1G and IL in MDA-MB-468 cells. Since MDA-MB-468 cells do not express SLUG, a member of a small family of E2-box-binding zinc finger silencer proteins, we studied whether the cytokeratin gene overexpressions in these cells are due to the absence of SLUG. Inducible expression of SLUG in MDA-MB-468 cells inhibited the expressions of the cytokeratin 8 and 19 but not others as was revealed by microarray analysis. Similarly, siRNA knock down of SLUG in BT-549 cells increased the expressions of those cytokeratin mRNAs. SLUG levels in the cell regulated the function of cytokeratins 8 and 19 gene promoters. We conclude that the expressions of cytokeratins and metallothioneins may be associated with the differential invasive behaviors of these breast tumor cells and SLUG may have regulatory roles in this process.

Breast Neoplasms↗
PubMed2006

Integrated breast cancer genomics.

Predicting survival and therapy responses of breast cancer patients is a significant challenge. Two studies in this issue of Cancer Cell present a novel integrated analysis of genomic and transcriptomic profiles of 145 primary breast cancers and 51 established cell lines. Data from clinical tumors highlighted mechanisms of disease and facilitated identification of potential therapeutic targets and prognostic biomarkers. An extensive well-characterized cancer cell line resource opens up opportunities to explore the determinants of cellular responses to existing and emerging therapies. Taken together, these studies illustrate how integrated molecular profiling may one day significantly impact diagnosis and therapeutic choice in human breast cancer.

Breast Neoplasms↗
PubMed2004

Analysis of regulatory networks in Pseudomonas aeruginosa by genomewide transcriptional profiling.

Transcriptional profiling using DNA microarrays has proved to be a valuable tool for dissecting bacterial adaptation to various environments, including human hosts. Analysis of genomes and transcriptomes of Pseudomonas aeruginosa shows that this bacterium possesses and expresses a core set of genes, including virulence factors, which allow it to thrive in a range of environments. Transcriptional regulators previously thought to control single virulence traits are now shown to regulate complex global signaling networks. Microarray-based research has led to the discovery of upstream regulators and downstream components of these pathways, as well as probed the response to antibiotics, environmental stresses and other bacteria. Independent studies have highlighted the role of media composition, the makeup of the physical environment and experimental methods in the outcome of microarray analyses. A compilation of all the published data clearly shows transcriptional regulation of genes in all functional classes. Under conditions examined to date, slightly more than a quarter of the genome is regulated, suggesting that P. aeruginosa may use much of its genome for conditions unexplored in the laboratory.

Animals↗
PubMed2000

Analysing uncharted transcriptomes with SAGE.

Methods of comprehensive gene expression analysis have traditionally been limited to analysing bulk tissue or millions of cells. New modifications of serial analysis of gene expression (SAGE) have now permitted the analysis of gene expression in cell subpopulations or microanatomic structures, providing access to unexplored transcriptomes of normal and disease biology.

Animals↗
PubMed2003

Fungal genomics beyond Saccharomyces cerevisiae?

Fungi are used extensively in both fundamental research and industrial applications. Saccharomyces cerevisiae has been the model organism for fungal research for many years, particularly in functional genomics. However, considering the diversity within the fungal kingdom, it is obvious that the application of the existing methods of genome, transcriptome, proteome and metabolome analysis to other fungi has enormous potential, especially for the production of food and food ingredients. The developments in the past year demonstrate that we have only just started to exploit this potential.

Aspergillus↗
PubMed2003

Current and future applications of SAGE to cardiovascular medicine.

The recently sequenced mammalian genomes represent unprecedented resources for advancing our understanding of human diseases. Characterizing gene expression is an important step in translating genomic sequences into clinically useful information. Currently, gene expression studies are revolutionizing the approaches taken to address both basic science and clinical questions. Two major methods have emerged for the global examination of the transcriptome: microarrays and Serial Analysis of Gene Expression (SAGE). The SAGE technique comprehensively maps gene transcription by using the genomic database, yet it remains relatively underutilized for studying cardiovascular biology. This review describes current cardiovascular studies using the SAGE technique and outlines some potential strategies for employing this powerful tool to further our understanding of the cardiovascular system in health and in disease.

Animals↗
PubMed2007

The influence of pharmacogenetics on fatty liver disease in the wistar and kyoto rats: a combined transcriptomic and metabonomic study.

Although fatty liver disease is caused by a number of toxicological insults and the metabolic syndrome, the exact mechanisms by which many of these pathophysiological stimulii induce fatty liver are unknown. The rapid and profound steatosis caused by orotic acid, resulting from an impairment in the production of ApoB, has been investigated in the Wistar strain rat using a combined transcriptomic and metabonomic/metabolomic approach. Analysis of liver tissue from rats exposed to orotic acid for 1, 3, and 14 days was performed by DNA microarrays and high resolution 1H NMR spectroscopy based metabonomics of both tissue extracts and intact tissue (n = 3). Data were analyzed using a combination of ANOVA and principal components analysis, used as a data reduction tool to visualize the most perturbed transcripts and metabolites. Orotic acid produced a profound 8-fold increase in total lipids, and in particular increases in resonances associated with polyunsaturated fats (CH=CH and CH2CH=CH groups). This was accompanied by increases in the concentrations of trimethylamine-oxide (TMAO), betaine, choline, and phosphocholine, as well as a relative decrease in glucose and glycogen. At the transcriptional level, perturbations were detected in both oxidative stress and osmoregulation/pH homeostasis. However, this contrasts with a previous transcriptomic/metabolic study of fatty liver disease in a combined data set of Wistar (out-bred) and Kyoto (in-bred) strains of rats, with only 4 transcripts being found to be in common between the two analyses. This emphasizes the need to understand how strain background interacts with a given toxic lesion or genetic modification.

Animals↗
PubMed2004

Progress in the use of microarray technology to study the neurobiology of disease.

The diverse functions of the brain are mediated by neurons and glia whose phenotype is defined by a dynamically maintained set of gene transcripts, or 'transcriptome'. Large-scale analysis of gene expression in postmortem brain using microarray technology has the potential to elucidate molecular changes that occur in disease states. There are unique challenges associated with studies of postmortem brain, including limited sample sizes and variable clinical phenotypes that are typical of complex disorders. Nevertheless, recent microarray-based studies have implicated both individual dysregulated genes and abnormal patterns of gene expression in brain disorders.

Animals↗
PubMed2024

Heterozygous knockout of Synaptotagmin13 phenocopies ALS features and TP53 activation in human motor neurons.

Spinal motor neurons (MNs) represent a highly vulnerable cellular population, which is affected in fatal neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA). In this study, we show that the heterozygous loss of SYT13 is sufficient to trigger a neurodegenerative phenotype resembling those observed in ALS and SMA. SYT13+/- hiPSC-derived MNs displayed a progressive manifestation of typical neurodegenerative hallmarks such as loss of synaptic contacts and accumulation of aberrant aggregates. Moreover, analysis of the SYT13+/- transcriptome revealed a significant impairment in biological mechanisms involved in motoneuron specification and spinal cord differentiation. This transcriptional portrait also strikingly correlated with ALS signatures, displaying a significant convergence toward the expression of pro-apoptotic and pro-inflammatory genes, which are controlled by the transcription factor TP53. Our data show for the first time that the heterozygous loss of a single member of the synaptotagmin family, SYT13, is sufficient to trigger a series of abnormal alterations leading to MN sufferance, thus revealing novel insights into the selective vulnerability of this cell population.

Humans↗
PubMed2025

The offonome reveals on and off states of gene expression near the detection limit of RNA-seq.

RNA-seq, widely used for gene expression profiling, provides nucleotide level genome coverage and summary gene expression values. Generally, low-expressed genes are ignored due to their unfavorable signal-to-noise ratio, however, these genes may offer crucial information, such as detecting rare cells in bulk tissues. In this study, we applied an approach that transforms the expression levels of low-expressed genes into a robust dichotomized on/off state by leveraging similarities in transcript coverage shape. Applied to three human cancer cohorts from the Cancer Genome Atlas (TCGA), chosen based on tissue morphology and anatomic site, we identified genes, the "offonome" near the detection limit, consistently or occasionally off across samples. Genes in the offonome spectrum proved useful for supervised and unsupervised applications, including characterizing oncogenic pathways, and identifying rare populations of cells in bulk tissue. Interrogating the offonome is relevant to bulk tumor analyses like TCGA, potentially expediting gene investigation in low-input situations like single cell RNA-seq.

Humans↗
PubMed2024

Long noncoding RNA LIRIL2R modulates FOXP3 levels and suppressive function of human CD4+ regulatory T cells by regulating IL2RA.

Regulatory T cells (Tregs) are central in controlling immune responses, and dysregulation of their function can lead to autoimmune disorders or cancer. Despite extensive studies on Tregs, the basis of epigenetic regulation of human Treg development and function is incompletely understood. Long intergenic noncoding RNAs (lincRNA)s are important for shaping and maintaining the epigenetic landscape in different cell types. In this study, we identified a gene on the chromosome 6p25.3 locus, encoding a lincRNA, that was up-regulated during early differentiation of human Tregs. The lincRNA regulated the expression of interleukin-2 receptor alpha (IL2RA), and we named it the lincRNA regulator of IL2RA (LIRIL2R). Through transcriptomics, epigenomics, and proteomics analysis of LIRIL2R-deficient Tregs, coupled with global profiling of LIRIL2R binding sites using chromatin isolation by RNA purification, followed by sequencing, we identified IL2RA as a target of LIRIL2R. This nuclear lincRNA binds upstream of the IL2RA locus and regulates its epigenetic landscape and transcription. CRISPR-mediated deletion of the LIRIL2R-bound region at the IL2RA locus resulted in reduced IL2RA expression. Notably, LIRIL2R deficiency led to reduced expression of Treg-signature genes (e.g., FOXP3, CTLA4, and PDCD1), upregulation of genes associated with effector T cells (e.g., SATB1 and GATA3), and loss of Treg-mediated suppression.

Humans↗
PubMed2003

An ancestral secretory apparatus in the protozoan parasite Giardia intestinalis.

The protozoan parasite Giardia intestinalis belongs to one of the earliest diverged eukaryotic lineages. This is also reflected in a simple intracellular organization, as Giardia lacks common subcellular compartments such as mitochondria, peroxisomes, and apparently also a Golgi apparatus. During encystation, developmentally regulated formation of large secretory compartments containing cyst wall material occurs. Despite the lack of any morphological similarities, these encystation-specific vesicles (ESVs) show several biochemical characteristics of maturing Golgi cisternae. Previous studies suggested that Golgi structure and function are induced only during encystation in Giardia, giving rise to the hypothesis that ESVs, as a Giardia Golgi equivalent, are generated de novo. Alternatively, ESV compartments could be built on the template structure of a cryptic Golgi in trophozoites in response to ER export of cyst wall material during encystation. We addressed this question by defining the molecular framework of the Giardia secretory apparatus using a comparative genomic approach. Analysis of the corresponding transcriptome during growth and encystation revealed surprisingly little stage-specific regulation. A panel of antibodies was generated against selected marker proteins to investigate the developmental dynamics of the endomembrane system. We show evidence that Giardia accommodates the export of large amounts of cyst wall material through re-organization of membrane compartment(s) in trophozoites with biochemical similarities to ESVs. This suggests that ESVs are selectively stabilized Golgi-like compartments in a unique and archetypical secretory system, which arise from a structural template in trophozoites rather than being generated de novo.

Animals↗
PubMed2004

Developing pineapple fruit has a small transcriptome dominated by metallothionein.

In a first step toward understanding the molecular basis of pineapple fruit development, a sequencing project was initiated to survey a range of expressed sequences from green unripe and yellow ripe fruit tissue. A highly abundant metallothionein transcript was identified during library construction, and was estimated to account for up to 50% of all EST library clones. Library clones with metallothionein subtracted were sequenced, and 408 unripe green and 1140 ripe yellow edited EST clone sequences were retrieved. Clone redundancy was high, with the combined 1548 clone sequences clustering into just 634 contigs comprising 191 consensus sequences and 443 singletons. Half of the EST clone sequences clustered within 13.5% and 9.3% of contigs from green unripe and yellow ripe libraries, respectively, indicating that a small subset of genes dominate the majority of the transcriptome. Furthermore, sequence cluster analysis, northern analysis, and functional classification revealed major differences between genes expressed in the unripe green and ripe yellow fruit tissues. Abundant genes identified from the green fruit include a fruit bromelain and a bromelain inhibitor. Abundant genes identified in the yellow fruit library include a MADS box gene, and several genes normally associated with protein synthesis, including homologues of ribosomal L10 and the translation factors SUI1 and eIF5A. Both the green unripe and yellow ripe libraries contained high proportions of clones associated with oxidative stress responses and the detoxification of free radicals.

Ananas↗
PubMed2006

A periodic pattern of mRNA secondary structure created by the genetic code.

Single-stranded mRNA molecules form secondary structures through complementary self-interactions. Several hypotheses have been proposed on the relationship between the nucleotide sequence, encoded amino acid sequence and mRNA secondary structure. We performed the first transcriptome-wide in silico analysis of the human and mouse mRNA foldings and found a pronounced periodic pattern of nucleotide involvement in mRNA secondary structure. We show that this pattern is created by the structure of the genetic code, and the dinucleotide relative abundances are important for the maintenance of mRNA secondary structure. Although synonymous codon usage contributes to this pattern, it is intrinsic to the structure of the genetic code and manifests itself even in the absence of synonymous codon usage bias at the 4-fold degenerate sites. While all codon sites are important for the maintenance of mRNA secondary structure, degeneracy of the code allows regulation of stability and periodicity of mRNA secondary structure. We demonstrate that the third degenerate codon sites contribute most strongly to mRNA stability. These results convincingly support the hypothesis that redundancies in the genetic code allow transcripts to satisfy requirements for both protein structure and RNA structure. Our data show that selection may be operating on synonymous codons to maintain a more stable and ordered mRNA secondary structure, which is likely to be important for transcript stability and translation. We also demonstrate that functional domains of the mRNA [5'-untranslated region (5'-UTR), CDS and 3'-UTR] preferentially fold onto themselves, while the start codon and stop codon regions are characterized by relaxed secondary structures, which may facilitate initiation and termination of translation.

3' Untranslated Regions↗
PubMed2003

Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome.

The chromodomain is 40-50 amino acids in length and is conserved in a wide range of chromatic and regulatory proteins involved in chromatin remodeling. Chromodomain-containing proteins can be classified into families based on their broader characteristics, in particular the presence of other types of domains, and which correlate with different subclasses of the chromodomains themselves. Hidden Markov model (HMM)-generated profiles of different subclasses of chromodomains were used here to identify sequences encoding chromodomain-containing proteins in the mouse transcriptome and genome. A total of 36 different loci encoding proteins containing chromodomains, including 17 novel loci, were identified. Six of these loci (including three apparent pseudogenes, a novel HP1 ortholog, and two novel Msl-3 transcription factor-like proteins) are not present in the human genome, whereas the human genome contains four loci (two CDY orthologs and two apparent CDY pseudogenes) that are not present in mouse. A number of these loci exhibit alternative splicing to produce different isoforms, including 43 novel variants, some of which lack the chromodomain. The likely functions of these proteins are discussed in relation to the known functions of other chromodomain-containing proteins within the same family.

Acetyltransferases↗
PubMed2026

Long-read sequencing reveals widespread novel splicing and neojunction-derived neoantigens in nasopharyngeal carcinoma.

The widespread transcriptomic diversity driven by alternative splicing (AS) contributes to all hallmarks of cancer and represents a critical source of neoantigens for personalized immunotherapy. However, unlike other major malignancies, the full repertoire of AS in nasopharyngeal carcinoma (NPC) remains underexplored. Here, we employ long-read sequencing (LR-seq) to generate a high-resolution, isoform-level transcriptomic atlas from a cohort of 14 NPC tumor samples and four immortalized nasopharyngeal epithelial cell lines. We identify a substantial number of full-length novel transcripts (22,687; ∼44.38%), which reveal diverse splicing patterns and previously unannotated splicing events. By integrating short-read RNA-seq data to quantify isoform expression, we discover a subset of novel transcripts that are differentially expressed between tumor samples and immortalized nasopharyngeal epithelial cell lines. Furthermore, LR-seq enables precise identification of chimeric readthrough fusion transcripts, such as CLDN15-FIS1 and FOXRED2-TXN2 Finally, we develop a computational framework, tumor-specific splicing neoantigen detection (TS-SNAD), to predict neoantigens originating from novel exon-exon junctions (neojunctions) in tumor-specific novel transcripts. Using this framework, we identify neojunction-derived neoantigens and experimentally validate the immunogenicity of selected HLA-B*40:01-restricted neoantigens. These neojunction-derived peptides constitute a new class of noncanonical neoantigens with significant potential for developing personalized cancer vaccines for NPC.

Humans↗