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PubMed2004

Possibilities and results in the wide-scale genomic analysis of inflammation. Looking for the child among many midwives.

Only recently, available microarray methods have been extended to the investigation of such complex pathophysiological conditions as inflammatory disease. Genome analysis gives the possibility of looking for susceptibility gene loci and their allelic combinations. By the analysis of mRNAs (transcriptome), novel players, functional groups of participants and regulatory pathways involved in the inflammation can be revealed. The possibility of comparing several samples is ideal to increase our knowledge about the kinetics of inflammation. The effects and post-receptor signalling events of individual pro- or anti-inflammatory mediators can also be tested. The use of human post mortem samples could yield otherwise inaccessible information on molecular mechanisms of chronic inflammatory diseases. However, the analysis and interpretation of a huge amount of data, the selection of appropriate experimental systems and time points may hide some pitfalls, which emphasize the need to confirm results with independent methods such as e.g. semi-quantitative Northern, real time PCR, RNA-ase protection assay as well as functional studies.

Acute-Phase Reaction↗
PubMed1995

Comparison of the non-structural protein, NS1, of tick-borne and insect-borne orbiviruses.

The nucleotide sequence of RNA segment 6 of Broadhaven virus (BRDV), a tick-borne orbivirus, was determined principally from two overlapping cDNA clones and RNA end sequence analysis. The genome segment is 1714 base pairs in length and has a coding capacity for a protein of 537 amino acids, having a net charge of +4.0 at neutral pH. Comparison of the predicted amino acid sequence of BRDV RNA segment 6 with the NS1 sequence of insect-borne orbiviruses, bluetongue virus (BTV), African horse sickness virus (AHSV) and epizootic haemorrhagic disease virus (EHDV) of deer, revealed amino acid identities of 21, 22 and 21%, respectively. This compares with amino acid identities of 31 to 50% between the NS1 proteins of these gnat-transmitted orbiviruses. A recombinant baculovirus was produced containing a full-length clone of BRDV segment 6, which expressed a protein of 61 kD in infected Spodoptera frugiperda cells. Like other orbivirus NS1 proteins the expressed protein formed tubules similar to those produced in BRDV-infected BHK21 cells.

Amino Acid Sequence↗
PubMed2005

DNA microarrays and data mining to study hepatic fibrosis.

The pathogenesis of liver fibrosis has evolved dramatically in recent years. Hepatic stellate cells (HSCs) have been recognized as the main fibrogenic cells in the injured liver, and key fibrogenic cytokines have been identified. We propose the use of DNA microarrays to study changes in gene expression in activated HSCs and in fibrotic livers in order to identify key genes involved in liver fibrosis. For this purpose, RNA can be extracted from both cultured cells and liver tissue. The target RNA is hybridized to probes, which are gene-specific sequences immobilized on chips. The hybridization signal is assessed using a confocal laser scanner. Comparison of hybridization signals and patterns allows the identification of mRNAs that are differentially expressed. Statistical analysis enables classification and clustering of genes according to their up- or downregulation. By using this powerful technique, we have identified genes that are differentially regulated in both HSCs and the fibrotic human liver.

Computational Biology↗
PubMed2004

DNA chip technology in brain banks: confronting a degrading world.

DNA microarray technology is based on the principle of hybridization between 2 complementary strands of nucleic acids, one being fixed into a solid membrane, the other being the sample to analyze. This has resulted in a very powerful method to examine differential gene expression between samples, and has been widely used in the study of tumors. The application of DNA microarray technology to the study of the nervous system has to consider several properties of the nervous tissue: composition of various neuronal types, as well as astrocytes, oligodendrocytes, and microglia; regional and area differences; developmental and age-dependent variations; and functional and pathological status. Moreover, human samples are usually obtained postmortem following variable agonal periods and postmortem delays between death and tissue preservation, which are accompanied by variable RNA degradation. Yet human postmortem nervous tissue stored in brain banks offers a unique opportunity to facilitate material for the study of diseases of the nervous system and to gain direct understanding on the mechanisms of disease. This review analyzes the application of DNA microarray technology to current practice using brain-banked tissues in order to recognize and minimize sub-optimal processing of brain samples and to correct pitfalls due to inadequate procedures. Also discussed are RNA preservation and RNA degradation effects on expression pattern assessments, analysis of individual versus pooled samples, array normalization, types of DNA chip platforms, whole genomic analysis versus specialized chips, and microgenomics. Minimizing RNA degradation and improving detection of resistant RNA in postmortem brain has been considered in detail in order to improve the efficiency and reliability of DNA microarray technology employed in the study of human postmortem nervous tissue.

Animals↗
PubMed2006

Singular value decomposition of genome-scale mRNA lengths distribution reveals asymmetry in RNA gel electrophoresis band broadening.

We describe the singular value decomposition (SVD) of yeast genome-scale mRNA lengths distribution data measured by DNA microarrays. SVD uncovers in the mRNA abundance levels data matrix of genes x arrays, i.e., electrophoretic gel migration lengths or mRNA lengths, mathematically unique decorrelated and decoupled "eigengenes." The eigengenes are the eigenvectors of the arrays x arrays correlation matrix, with the corresponding series of eigenvalues proportional to the series of the "fractions of eigen abundance." Each fraction of eigen abundance indicates the significance of the corresponding eigengene relative to all others. We show that the eigengenes fit "asymmetric Hermite functions," a generalization of the eigenfunctions of the quantum harmonic oscillator and the integral transform which kernel is a generalized coherent state. The fractions of eigen abundance fit a geometric series as do the eigenvalues of the integral transform which kernel is a generalized coherent state. The "asymmetric generalized coherent state" models the measured data, where the profiles of mRNA abundance levels of most genes as well as the distribution of the peaks of these profiles fit asymmetric Gaussians. We hypothesize that the asymmetry in the distribution of the peaks of the profiles is due to two competing evolutionary forces. We show that the asymmetry in the profiles of the genes might be due to a previously unknown asymmetry in the gel electrophoresis thermal broadening of a moving, rather than a stationary, band of RNA molecules.

Evolution, Molecular↗
PubMed2005

Gene expression profiling of primary tumor cell populations using laser capture microdissection, RNA transcript amplification, and GeneChip microarrays.

Gene expression profiling from microdissected cell populations is a powerful approach to explore molecular processes involved in development and solid tumor biology. In this chapter, we detail robust and validated methods for tissue preparation and isolation of high-quality RNA from microdissected cell populations. A protocol is also provided for linear transcript amplification using as little as 10 ng of total RNA to produce labeled cRNA targets for hybridization to GeneChip high-density oligonucleotide microarrays. Particular emphasis is placed on troubleshooting each technical step in the protocol and measures of quality assurance for both RNA isolation and resulting microarray data.

Animals↗
PubMed2003

p53-induced gene expression analysis.

Researchers in the p53 field have successfully used many high-throughput screening technologies to analyze and characterize p53-induced gene expression. This chapter will focus on one such technology, the Affymetrix GeneChip. DNA-Chip technology has grown rapidly over the last several years. The ability to hybridize RNA from a sample to thousands to tens of thousands of known and unknown cDNAs spotted on a microarray chip has led to the explosion of information ranging from macro-global expression pattern changes to micro-gene-specific expression changes. The relative ease of making a nonradioactive probe from either total RNA or mRNA to be hybridized to a GeneChip makes microarray technology highly attractive.

Animals↗
PubMed2004

Use of RNA amplification in the optimal characterization of global gene expression using cDNA microarrays.

Microarray analysis of human tissue is frequently hindered by the limited amount of RNA available. Although amplification protocols can be utilized, the relative representation of transcripts present in the starting material must remain unaltered. In this study, 200 ng of total RNA derived from cultured renal epithelial cells from tuberous sclerosis complex (TSC) carriers and control individuals was amplified by in vitro transcription with T7 RNA polymerase. The resulting Cy-labeled cDNAs (from total or amplified RNA (aRNA)) were analyzed as direct replicates and dye-flips on slides containing 10,000 human cDNAs. The Pearson correlation coefficients for the direct replicate experiments were 0.80 (20 microg total RNA), 0.85 (40 microg total RNA), and 0.93 (2 microg of aRNA). Comparisons between the array data revealed that the majority of genes expressed in total RNA (97% for 20 microg and 85% for 40 microg) were also detected in aRNA. The correlation coefficient of the expression ratios for genes detected in both total RNA (40 microg) and aRNA was 0.63. Further, Student's t-test indicated no significant difference (P = 0.83) between these ratios. These results indicate that the number of expressed genes detected with total RNA is proportional to the amount of RNA used and underscore the requirement of large amounts of total RNA for a comprehensive characterization of gene expression profiles. RNA amplification allows the detection of a large number of genes expressed in the starting RNA population without altering their relative intensities significantly. Thus, an RNA amplification step improves the quality of gene expression results obtained by microarray analysis. This study indicates that high quality microarray data can be generated from small amounts of RNA, including those extracted from limiting clinical samples and microdissected histological specimens.

Gene Expression Profiling↗
PubMed2026

Single-cell RNA sequencing reveals disease associated changes in brain endothelial cells in the 5XFAD mouse.

Vascular dysfunction is a key contributor to Alzheimer’s disease (AD) pathology, where changes to the endothelium and its crucial role in maintaining blood-brain barrier (BBB) integrity have been of particular emphasis. The transgenic 5XFAD (5X Familial Alzheimer’s Disease) mouse model, which exhibits AD-related amyloidosis through FAD associated mutations in amyloid precursor protein (APP) and presenilin-1 (PS1), has become a widely adopted preclinical model in AD-related research studies. The need for cross-study standardization, accessibility, and data reproducibility has led to the widespread implementation of the C57BL/6J genetic background for maintaining this model. However, its reliability for studying vascular dysfunction and BBB alterations has been questioned due to conflicting reports in the literature. This variation is often attributed to the previously documented protective nature of the C57BL/6J background and loss of genetic background diversity. Since prior studies have mostly relied on imaging or functional assays, we herein utilized single-cell RNA sequencing (scRNAseq) to investigate AD-related molecular changes to endothelial cell populations in the 5XFAD mouse model. To initially build this resource, we focused on 12-month-old male mice, which revealed differentially expressed genes between 5XFAD and wildtype animals that mapped to signaling pathways involved in DNA damage, immune reactivity, and inflammation, among others. Many of these transcriptomic changes were zonated along the arteriovenous axis and occurred in AD genome-wide association study (GWAS) risk-associated genes. Overall, we anticipate this resource will help clarify the use of the 5XFAD model for studying AD-associated vascular changes and provide the foundation for expanded molecular profiling of brain endothelial cells under AD-associated conditions.

Animals↗
PubMed2026

Precision-Based Filtering Facilitates Cross-Referencing of Conventional and Single-Nucleus Transcriptomes to Identify Time- and Temperature-Sensitive Cell Populations.

Transcriptome analysis via RNA sequencing (RNAseq) has become a ubiquitous method of molecular characterization from whole organisms, dissected tissues, and single cells. These experiments continue to provide an extraordinary volume of data describing molecular states and responses to many conditions. However, standard approaches to RNAseq analysis commonly use expression level filters that eliminate potentially useful data in the service of decreasing noise. Here we describe the implementation of a coefficient of variation-based filter for RNAseq gene expression data. This filter prioritizes consistent data across replicates, allowing lowly-expressed genes with low-variation measurements to be retained for downstream analysis. We show, using two independent Arabidopsis RNAseq datasets, that this filter allows for the inclusion of many more transcription factors than even a low-stringency expression level filter. This effect is independent of sequencing depth. We find that these lowly-expressed genes mark specific cell clusters in our single-nucleus (sn)RNAseq dataset and may facilitate future characterization of currently unknown cell types or states. We further characterize communities of co-expressed genes, sampled across the day at two growth temperatures, in relation to snRNAseq cell clusters, finding evidence for a highly photosynthetic cell population, and a cell state marked by high cell division and translation. These methods can be expanded to RNAseq analysis in many systems, facilitating the construction of more detailed models of tissue-specific gene regulatory networks.

Transcriptome analysis↗
PubMed2002

Identification and characterization of genes involved in the carcinogenesis of human squamous cell cervical carcinoma.

We utilized RT-PCR differential display and cDNA microarrays to identify cellular genes involved in the multi-step carcinogenesis of squamous cell cervical carcinoma. Thirty-eight cervical cancer patients in various stages of the disease and 5 non-cervical cancer patients were studied. Twenty-five cDNA clones were identified and these were subsequently demonstrated to be consistently over-expressed in squamous cell cervical carcinoma biopsies of various FIGO stages. To further evaluate the possible role that these genes may play in the progression of disease, we performed Northern blot analysis and RNA-RNA in situ hybridization studies using cervical cancer biopsies of various FIGO stages. Of particular interest are the 2 clones G32C4B and G30CC that have been identified to be the NADH dehydrogenase 4 gene and the gene that encodes ribosomal protein S12 respectively when compared to sequences available in the GenBank database. Increased expression of these 2 genes were detected in the matched normal tissues collected together with the late FIGO stages of cervical cancer biopsies. In comparison, upregulation of these 2 genes was not detected in cervical squamous epithelium collected from patients admitted for surgery for non-malignant conditions, suggesting that expression of these 2 genes may have altered in the adjacent histopathologically "normal" cervical squamous epithelial tissue from cervical cancer patients. The ribosomal protein S12 and the NADH dehydrogenase 4 genes may therefore be potentially useful as early pre-transformation diagnostic markers for human cervical cancer.

Biomarkers, Tumor↗
PubMed2026

Single-nucleus profiling reveals hepatocyte identity and immune features associated with corticosteroid response in severe alcohol-related hepatitis.

BACKGROUND & AIMS: Severe alcohol-related hepatitis (sAH) is associated with high short-term mortality. However, 30-40% of patients fail to respond to corticosteroids, the only proven pharmacological treatment. The pathophysiological mechanisms underlying sAH and the marked heterogeneity in treatment response remain incompletely understood. We aimed to define cellular changes associated with corticosteroid response in sAH and to identify baseline markers predictive of treatment outcome. METHODS: Single-nucleus RNA sequencing was performed on liver biopsies from patients with biopsy-proven sAH (n = 17), including paired baseline and day 8 biopsies in a subset of patients (n = 8). Patients were classified as corticosteroid responders (sAH-R; Lille score <0.45) or non-responders (sAH-NR; Lille score &#x2265;0.45). Liver biopsies from patients with acute decompensation of alcohol-related cirrhosis (AD; n = 5) and healthy controls (n = 4) were included for comparison. Findings were validated using immunohistochemistry and spatial proteomics in a large multicenter validation cohort (n = 172). RESULTS: At baseline, sAH-R exhibited a significantly higher proportion of liver-infiltrating S100A8+ monocytes compared to sAH-NR, a difference that persisted at day 8. sAH livers showed a marked reduction in mature hepatocytes and an expansion of stressed and intermediate hepatocyte populations, indicating progressive loss of mature hepatocyte identity. This loss was more pronounced in sAH-NR, who also exhibited fewer cycling hepatocytes at day 8, consistent with impaired regenerative capacity. Expression of SULT2A1, a marker of mature hepatocyte identity, was significantly reduced in sAH-NR at baseline. Finally, liver biopsies with &#x2265;50% SULT2A1-positive hepatocytes at baseline were strongly predictive of corticosteroid response. CONCLUSIONS: This study delineates distinct immune and hepatocyte changes associated with corticosteroid response in sAH. Baseline SULT2A1 expression may facilitate stratified treatment approaches in sAH. IMPACT AND IMPLICATIONS: Severe alcohol-related hepatitis (sAH) represents one of the most devastating manifestations of alcohol-related disorders. sAH is characterized by acute hepatic inflammation and high short-term mortality. Clinical management remains challenging, as corticosteroids - the only pharmacological therapy currently applied - are ineffective in a substantial proportion of patients and are associated with significant adverse effects. These limitations highlight the need for a more detailed understanding of sAH pathophysiology and for approaches that enable improved patient stratification and therapeutic decision-making. In this study, we identify distinct pre-treatment differences between corticosteroid responders and non-responders at the level of both hepatocytes and myeloid cells, providing new insight into the cellular mechanisms underlying treatment heterogeneity in sAH. Furthermore, leveraging these findings, we developed a histology-based SULT2A1 scoring system using a commercially available antibody, which predicts corticosteroid response at baseline and may support stratified treatment approaches in clinical practice.

Humans↗
PubMed2002

Yeast tRNA as carrier in the isolation of microscale RNA for global amplification and expression profiling.

The characterization of global gene expression patterns of microscale samples is important in many areas of biological and clinical research. The choice of carrier is critical for the efficient isolation and successful amplification of RNA at the nanogram level. Here we show that recovery of nanograms of RNA is significantly higher when carrier linear polyacrylamide is supplemented with carrier tRNA. Reverse transcription and in vitro transcription reactions remain efficient and specific in the presence of carrier tRNA. Finally, comparison of GeneChip array hybridization patterns demonstrates that the presence of carrier tRNA does not cause detectable distortion in global amplification. Taken together, tRNA is a superior carrier for the isolation and global amplification of microscale RNA.

Cells, Cultured↗
PubMed1979

A mutation which alters initiation of transcription by RNA polymerase III on the Ad5 chromosome.

Mutant dl 309 is a viable Ad5 deletion mutant. Whereas wild-type Ad5-infected HeLa cells contain two VAI RNA species [VAI(A) and VAI(G)] which differ by three nucleotides at their 5' ends, dl 309-infected HeLa cells contain VAI(G) but no VAI(A) RNA. Nucleotide sequence analysis indicates that dl 309 lacks two base pairs which precede the 5' end of VAI(A) by 22 nucleotides. Since the 5' ends of VAI RNAs are not processed, the 309 deletion serves to identify a portion of the sequence required for RNA polymerase III initiation. Since dl 309 grows as well as wild-type Ad5 in HeLa cells, the VAI(A) species is not essential for viral growth in these cells.

Adenoviruses, Human↗
PubMed1987

Adult B-cell repertoire is biased toward two heavy-chain variable-region genes that rearrange frequently in fetal pre-B cells.

Fetal pre-B cells rearrange a very restricted set of immunoglobulin variable genes for the heavy chain (VH). To determine whether the adult B-cell repertoire is similarly skewed, we first identified the genes that rearrange in pre-B cells from BALB/c mice and then determined their frequency of rearrangement in adult B cells. In fetal pre-B cell lines, two genes, VH81X from the 7183 subfamily and VHOx2 from the Q52 subfamily, comprise 75% of the rearranged alleles of an estimated 1000 genes (P less than 0.001). Sequencing analyses revealed that rearrangements involving the two genes were both productive and nonproductive. The biased rearrangement of these two VH genes persists in B-cell hybridomas from adult mice at a frequency of 22%, as determined by Southern gel analysis and RNA sequencing. The sequence of one VHOx2 rearrangement from a hybridoma shows that the rearrangement is productive, suggesting that the gene encodes an antibody that could participate in the immune response. The data indicate that the adult B-cell repertoire is not random concerning usage of individual VH genes, and it may be shaped by the unknown mechanisms that cause preferential rearrangement of certain genes early in ontogeny.

Amino Acid Sequence↗
PubMed2006

Systematic comparison of the T7-IVT and SMART-based RNA preamplification techniques for DNA microarray experiments.

BACKGROUND: Small biological samples obtained from biopsies or laser microdissection often do not yield sufficient RNA for successful microarray hybridization; therefore, RNA amplification is performed before microarray experiments. We compared 2 commonly used techniques for RNA amplification. METHODS: We compared 2 commercially available methods, Arcturus RiboAmp for in vitro transcription (IVT) and Clontech BD SMART for PCR, to preamplify 50 ng of total RNA isolated from mouse livers and kidneys. Amplification factors of 3 sequences were determined by real-time PCR. Differential expression profiles were compared within and between techniques as well as with unamplified samples with 10K 50mer oligomer-spotted microarrays (MWG Biotech). The microarray results were validated on the transcript and protein levels by comparison with public expression databases. RESULTS: Amplification factors for specific sequences were lower after 2 rounds of IVT than after 12 cycles of SMART. Furthermore, IVT showed a clear decrease in amplification with increasing distance of the amplified sequences from the polyA tail, indicating generation of smaller products. In the microarray experiments, reproducibility of the duplicates was highest after SMART. In addition, SMART-processed samples showed higher correlation when compared with unamplified samples as well as with expression databases. CONCLUSIONS: Whenever 1 round of T7-IVT does not yield sufficient product for microarray hybridization, which is usually the case when <200 ng of total RNA is used as starting material, we suggest the use of SMART PCR for preamplification.

3' Untranslated Regions↗
PubMed2002

Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses.

In most microarray assays, labeled cDNA molecules derived from reference and query RNA samples are co-hybridized to probes arrayed on a glass surface. Gene expression profiles are then calculated for each gene based on the relative hybridization intensities measured between the two samples. The most commonly used reference samples are typically isolates from a single representative RNA source (RNA-0) or pooled mixtures of RNA derived from a plurality of sources (RNA-p). Genomic DNA offers an alternative reference nucleic acid with a number of potential advantages, including stability, reproducibility, and a potentially uniform representation of all genes, as each unique gene should have equal representation in a haploid genome. Using hydrogen peroxide-treated Arabidopsis thaliana plants as a model, we evaluated genomic DNA and RNA-p as reference samples and compared expression levels inferred through the reference relative to unexposed plants with expression levels measured directly using an RNA-0 reference. Our analysis demonstrates that while genomic DNA can serve as a reasonable reference source for microarray assays, a much greater correlation with direct measurements can be achieved using an RNA-based reference sample.

Arabidopsis↗