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At least 865 records · Page 48Linked to original sources
PubMed2025

Identification of potential biomarkers and mechanisms for keloid disorder based on comprehensive bioinformatics analysis and machine learning algorithms.

BACKGROUND: Keloid disorder (KD) encompasses a spectrum of fibroproliferative dermal conditions, the pathogenesis remains complex and incompletely understood. This study sought to identify biomarkers and potential therapeutic targets for KD through an integrative bioinformatics approach and machine learning analysis of RNA sequencing data. METHODS: RNA sequencing was performed on skin tissue samples from 13 patients with KD and 14 healthy controls. Using weighted gene co-expression network analysis and differential expression analysis revealed differentially expressed key module genes, and the CytoHubba plugin identified candidate genes. Subsequently analyzed using least absolute shrinkage and selection operator (LASSO) and support vector machine recursive feature elimination (SVM-RFE) methods to pinpoint feature genes associated with KD. Following this, biomarkers were determined through expression level validation, enrichment analysis, and immune infiltration analysis. RESULTS: A total of 420 differentially expressed key module genes were identified, and the top 10 genes with DMNC values were selected as candidate genes. Five feature genes were selected through LASSO and SVM-RFE, with NID2, MFAP2, COL8A1, and P4HA3 showing significant expression differences between KD and control samples, along with consistent expression patterns across datasets, identified as potential biomarkers. These four biomarkers were proved to possess high diagnostic potential, and they were found to exhibit significant positive correlations with one another. Functional enrichment analysis indicated that the primary KEGG pathways associated with these biomarkers included "steroid hormone biosynthesis" and "cytokine-cytokine receptor interaction." Moreover, immune infiltration analysis revealed that the four biomarkers were negatively correlated with type 17 T helper cells and positively correlated with 15 immune cell types, including activated B cells and central memory CD4 T cells. CONCLUSION: In conclusion, NID2, MFAP2, COL8A1, and P4HA3 were identified as key biomarkers for KD, offering new avenues for more targeted and effective diagnostic and therapeutic strategies for managing this condition.

Humans↗
PubMed1989

[Preliminary molecular phylogeny of the fishes based on sequence analysis of 28S ribosomal RNA].

"Fish" phylogeny has been studied using partial 28 S ribosomal RNA sequences of 14 species among which 12 are "fish" ranging from lamprey to perciforms. Our results are in good agreement with generally accepted cladograms based on anatomical and paleontological data. Two interesting conclusions emerged: a) Polypterus is the sister-group of all other actinopterygians; b) the divergences of the Clasdistia, Tetrapoda and Chondrichthyes seem to have occurred during a relatively short period of time.

Animals↗
PubMed2026

Reporting and representation of population descriptors in public RNA-seq databases.

Diverse and globally representative datasets are essential to genomic science and medicine. Here, we analyzed population descriptor metadata from RNA sequencing (RNA-seq) studies in two major public repositories: the Sequence Read Archive (SRA) and the Database of Genotypes and Phenotypes. We examined geographic and economic characteristics of institutions depositing the data and compared SRA-deposited descriptors to empirical estimates of genetic ancestry and to those reported in publications, analyzing trends over time. We found that 55% of RNA-seq samples were deposited by United States (US) institutions and 90% by institutions in high-income countries. Only 3% of SRA samples were associated with population descriptors, and among those with US Census terms, 69% were labeled as White. Among samples with continental descriptors, 56% were labeled as European. Our analyses emphasize widespread bias in the composition of public RNA-seq datasets and, more generally, a lack of consistent and careful reporting of population descriptors needing urgent improvement.

Humans↗
PubMed1996

Investigating and improving the specificity of ribozymes directed against the bcr-abl translocation.

Chronic myelogenous leukaemia (CML) is associated with a translocation between the ABL and BCR genes on chromosomes 9 and 22, t(9;22). The resulting transcription and translation products, bcr-abl mRNA and p210bcr-abl, are unique to the malignant cells and as such are ideal targets for specific chemicals or drugs. We have designed hammerhead ribozymes to cleave the two predominant forms of bcr-abl mRNA, b2a2 and b3a2. Synthetic bcr-abl RNA substrates were cleaved by the ribozymes in vitro, but so was a wild-type abl RNA sequence. bcr RNA was not cleaved in vitro and mutant ribozymes showed no cleavage activity. Ribozymes designed to cleave 9 nucleotides (nt) from either of the fusion points were non-specific for the bcr-abl substrate, but a ribozyme designed to cleave 3 nt upstream of the b3a2 fusion point was specific for b3a2 RNA. However, this ribozyme was less efficient than the others. The shortening of one of the ribozymes arms from 10 nt to 4 nt resulted in a ribozyme that was more specific without losing any efficiency. We conclude that it is possible to specifically cleave bcr-abl RNA in vitro by using hammerhead ribozymes.

Base Sequence↗
PubMed1979

Comparison of poly(A)-containing RNAs in different cell types of the lower eukaryote Schizophyllum commune.

Poly(A)-containing RNAs were isolated from morphologically different cells of the fungus Schizophyllum commune. Using mRNA markers the number-average length of poly(A)-containing RNA in total RNA and in purified poly(A)-containing RNA was estimated as 1100 nucleotides. Number-average length of poly(A)-tracts was 33 nucleotides. 2.5% of total RNA is poly(A)-containing RNA and probably up to 7.5% are non-polyadenylated polydisperse RNA sequences. Saturation hybridization of poly(A)-containing RNA to gap-translated [3H]DNA resulted in 16% of the reactive single-copy DNA to become S1 nuclease resistant. It was found that purified poly(A)-containing RNA represented the entire RNA complexity, i.e. 10 000 different RNA sequences in S. commune. RNA sequences isolated from morphologically different mycelia and from fruiting and non-fruiting mycelia were identical for at least 90%.

Agaricales↗
PubMed1983

Secondary structure of the Tetrahymena ribosomal RNA intervening sequence: structural homology with fungal mitochondrial intervening sequences.

Splicing of the ribosomal RNA precursor of Tetrahymena is an autocatalytic reaction, requiring no enzyme or other protein in vitro. The structure of the intervening sequence (IVS) appears to direct the cleavage/ligation reactions involved in pre-rRNA splicing and IVS cyclization. We have probed this structure by treating the linear excised IVS RNA under nondenaturing conditions with various single- and double-strand-specific nucleases and then mapping the cleavage sites by using sequencing gel electrophoresis. A computer program was then used to predict the lowest-free-energy secondary structure consistent with the nuclease cleavage data. The resulting structure is appealing in that the ends of the IVS are in proximity; thus, the IVS can help align the adjacent coding regions (exons) for ligation, and IVS cyclization can occur. The Tetrahymena IVS has several sequences in common with those of fungal mitochondrial mRNA and rRNA IVSs, sequences that by genetic analysis are known to be important cis-acting elements for splicing of the mitochondrial RNAs. In the predicted structure of the Tetrahymena IVS, these sequences interact in a pairwise manner similar to that postulated for the mitochondrial IVSs. These findings suggest a common origin of some nuclear and mitochondrial introns and common elements in the mechanism of their splicing.

Base Sequence↗
PubMed1992

Quantitation of radioactively labeled RNA by hybrid selection using biotinylated oligonucleotides.

We describe a procedure to quantify specific, radioactively labeled RNA sequences. This procedure combines hybrid selection of an RNA using biotinylated oligonucleotides with gel electrophoretic analysis of the selected RNA. We show that the hybrid selection procedure is specific and quantitative. It enriches a specific RNA sequence at least 600-fold. Specificity and sensitivity are increased to at least 10,000-fold enrichment by a combination of RNase T1 digestion of the RNA:oligonucleotide hybrid prior to selection, followed by gel electrophoretic fractionation of the selected RNA fragment. Furthermore, this modification allows one to quantify specific regions of an RNA transcript, as well as to monitor several different RNA sequences in one experiment. It is estimated that the sensitivity of this procedure is high enough to detect specific RNA sequences present at 1 part in 100,000.

Base Sequence↗
PubMed1981

Immunoglobulin mu- and gamma-ribonucleic acid sequences in thymocytes and splenocytes from normal and hyperimmune mice.

The immunoglobulin heavy-chain ribonucleic acid (RNA) repertoire of mouse thymocytes was examined. Previously, this laboratory reported immunoglobulin alpha-chain RNA sequences in mouse thymocytes [Near, R. I., & Storb, U. (1979 Biochemistry, 18, 964]. We have extended these studies to encompass mu, gamma 2b, and gamma 1 heavy-chain RNA sequences, mu-, gamma 2b-, and gamma 1-messenger RNAs (mRNAs) were purified from myelomas to 45, 22, and 54% purity, respectively. Each of these mRNAs faithfully translated into the appropriate immunoprecipitable protein in a reticulocyte lysate translation system. The gamma 1-mRNA translated into two major immunoprecipitable products of about 52 500 and 51 000 daltons while mu- and gamma 2b-mRNAs yielded only a single major protein. Complementary deoxyribonucleic acids (cDNAs) prepared from the mRNAs were used as hybridization probes and revealed the presence of about 70 mu-RNA sequences per average thymocyte as determined by hybridization kinetics, while gamma 1 and gamma 2b sequences were at the limits of detection. The mu-RNA sequences are present in the cytoplasm and are greater than 50% polyadenylated. Upon hyperimmunization of mice with sheep red blood cells, gamma 1-RNA in splenocytes increased by about 100-fold while only slightly increasing in thymocytes. mu and gamma 2b increased 2-3-fold in splenocytes and only slightly in thymocytes. The results argue against RNA sequences appearing in thymocytes due to contamination with peripheral confirmed with cloned cDNA probes. Thymocyte RNA analyzed by Northern blots displayed bands of the same size as those in splenocyte RNA or in purified mRNA when hybridized to mu, gamma 2b and alpha cloned probes. Also, K light-chain RNAs of the same size were found in spleen and thymus by using a cloned K-DNA probe. The results are consistent with the thymus containing mu-, alpha-, and K- and small amounts of gamma 1- or gamma 2b-RNAs coding for heavy- and light-chain-like proteins which may play a role in T-cell function.

Animals↗
PubMed1998

Transcriptional sequencing: A method for DNA sequencing using RNA polymerase.

We have developed a sequencing method based on the RNA polymerase chain termination reaction with rhodamine dye attached to 3'-deoxynucleoside triphosphate (3'-dNTP). This method enables us to conduct a rapid isothermal sequencing reaction in <30 min, to reduce the amount of template required, and to do PCR direct sequencing without the elimination of primers and 2'-dNTP, which disturbs the Sanger sequencing reaction. An accurate and longer read length was made possible by newly designed four-color dye-3'-dNTPs and mutated RNA polymerase with an improved incorporation rate of 3'-dNTP. This method should be useful for large-scale sequencing in genome projects and clinical diagnosis.

DNA↗
PubMed1995

Isolation of virus-neutralizing RNAs from a large pool of random sequences.

RNA and ribonuclease-resistant RNA analogs that bound and neutralized Rous sarcoma virus (RSV) were isolated from a large pool of random sequences by multiple cycles of in vitro selection using infectious viral particles. The selected RNA pool of RSV-binding sequences at a concentration of 0.16 microM completely neutralized the virus. Of 19 sequences cloned from the selected pool, 5 inhibited RSV infection. The selected RNA and RNA analogs were shown to neutralize RSV by interacting with the virus, rather than by adversely affecting the host cells. The selection of the anti-RSV RNA and RNA analogs by intact virions immediately suggests the potential application of this approach to develop RNA and RNA analogs as inhibitors of other viruses such as human immunodeficiency virus.

Antiviral Agents↗
PubMed2001

Characterization of culture-derived spiral bacteria by 16S ribosomal RNA gene sequence analysis.

Broad range amplification and sequence analysis of the 16S ribosomal RNA gene was used to identify three spiral-form organisms. The agents were identified as Campylobacter fetus, "Flexispira rappini", and Borrelia burgdorferi, respectively, using either proprietary or public sequence databases. In each case, the rDNA sequence showed 99-100% homology with known sequence data. Sequence-based analysis for each isolate required only 2-3 days, whereas traditional means of identification took 8-12 days to complete. The identification of spirochetes and vibrio-like agents from human clinical samples is often time consuming and results may be difficult to interpret, sometimes due to atypical phenotypic characteristics. Analysis of 16S rDNA or other molecular targets may provide a way to accurately and rapidly characterize isolates that are recalcitrant to speciation.

Adult↗
PubMed1984

3'-Terminal sequences of influenza C virion RNA. Brief report.

The 3'-terminal nucleotides of the genome segments of influenza C/Taylor/47. C/Bavaria/79 and C/Johannesburg/1/66 were identified by two RNA sequencing techniques. These comprised 11 nucleotides (3' UCGUCUUCGUC) which were found to be conserved among the genome segments of each virus.

Base Sequence↗
PubMed2001

Identification of Sam68 arginine glycine-rich sequences capable of conferring nonspecific RNA binding to the GSG domain.

Sam68 is an RNA-binding protein that contains a heterogeneous nuclear ribonucleoprotein K homology domain embedded in a larger RNA binding domain called the GSG (GRP33, Sam68, GLD-1) domain. This family of proteins is often referred to as the STAR (signal transduction and activators of RNA metabolism) proteins. It is not known whether Sam68 is a general nonspecific RNA-binding protein or whether it recognizes specific response elements in mRNAs with high affinity. Sam68 has been shown to bind homopolymeric RNA and a synthetic RNA sequence called G8-5 that has a core UAAA motif. Here we performed a structure function analysis of Sam68 and identified two arginine glycine (RG)-rich regions that confer nonspecific RNA binding to the Sam68 GSG domain. In addition, by using chimeric proteins between Sam68 and QKI-7, we demonstrated that one of the Sam68 RG-rich sequences of 26 amino acids was sufficient to confer homopolymeric RNA binding to the GSG domain of QKI-7, another STAR protein. Furthermore, that minimal sequence can also give QKI-7 the ability (as Sam68) to functionally substitute for HIV-1 REV to facilitate the nuclear export of RNAs. Our studies suggest that neighboring RG-rich sequences may impose nonspecific RNA binding to GSG domains. Because the Sam68 RNA binding activity is negatively regulated by tyrosine phosphorylation, our data lead us to propose that Sam68 might be a specific RNA-binding protein when tyrosine phosphorylated.

Amino Acid Sequence↗
PubMed1998

Application of the ribonuclease P (RNase P) RNA gene sequence for phylogenetic analysis of the genus Saccharomonospora.

Sequences of the RNase P RNA gene were investigated for the phylogenetic analysis of the genus Saccharomonospora. Aligned nucleotide sequences, determined from the PCR-amplified RNase P RNA gene of representative strains of the genus Saccharomonospora, displayed 94.2 +/- 1.3% interspecific variances. The intraspecific similarity value was 99.7-100% in all species tested. Saccharomonospora azurea K161T and 'Saccharomonospora caesia' K76T displayed identical RNase P RNA gene sequences in the region that was determined and Saccharomonospora sp. K180 showed sequences distinct from validly described species with a similarity value of 94.6 +/- 1.0%. The phylogenetic trees constructed by aligning the sequences either within the genus Saccharomonospora or with other Gram-positive bacteria were similar to the ones derived using sequences of the 16S rDNA gene. Advantageous features of this gene for application as a molecular phyletic marker are discussed.

Actinomycetales↗
PubMed1996

The KRAB zinc finger gene ZNF74 encodes an RNA-binding protein tightly associated with the nuclear matrix.

We previously cloned ZNF74, a developmentally expressed zinc finger gene commonly deleted in DiGeorge syndrome. Here, the intron/exon organization of the human gene and the functional properties of the expressed protein are presented. This zinc finger gene from the transcription factor IIIA/Kruppel family contains three exons. A truncated Kruppel-associated box (KRAB) located at the N terminus of the predicted 64-kDa zinc finger protein is encoded by exon 2. The remainder of the protein including the zinc finger domain as well as the 3'-untranslated region (UTR) is encoded by exon 3. Both 5'-UTR (exon 1) and 3'-UTR contain repetitive Alu elements. In vitro translation of a cDNA encoding the entire ZNF74 coding region produced a 63-kDa protein as determined on sodium dodecyl sulfate-polyacrylamide gel. A bacterially expressed fusion protein shown to bind tightly to 65zinc was used to test the nucleic acid binding properties of ZNF74. By RNA binding assays, ZNF74 was found to bind specifically to poly(U) and poly(G) RNA homopolymers. The restricted binding to these homopolymers and not to poly(A) and poly(C) suggested that ZNF74 displays RNA sequence preferences. RNA binding was mediated by the zinc finger domain. Immunofluorescence studies on transfected cells revealed ZNF74 nuclear localization. The labeling pattern observed in the nuclei clearly excluded the nucleoli. The zinc finger region lacks a classical nuclear localization signal but was found to be responsible for nuclear targeting. Subcellular and in situ sequential fractionations further showed that ZNF74 is associated with the nuclear matrix. The RNA binding properties of this protein and its tight association with the nuclear matrix, a subnuclear compartment involved in DNA replication as well as RNA synthesis and processing, suggest a role for ZNF74 in RNA metabolism.

Amino Acid Sequence↗
PubMed2005

Comparison of genome sequences of single-stranded RNA viruses infecting the bivalve-killing dinoflagellate Heterocapsa circularisquama.

Heterocapsa circularisquama RNA virus (HcRNAV) has at least two ecotypes (types UA and CY) that have intraspecies host specificities which are complementary to each other. We determined the complete genomic RNA sequence of two typical HcRNAV strains, HcRNAV34 and HcRNAV109, one of each ecotype. The nucleotide sequences of the viruses were 97.0% similar, and each had two open reading frames (ORFs), ORF-1 coding for a putative polyprotein having protease and RNA-dependent RNA polymerase (RdRp) domains and ORF-2 encoding a single major capsid protein. Phylogenetic analysis of the RdRp amino acid sequence suggested that HcRNAV belongs to a new previously unrecognized virus group. Four regions in ORF-2 had amino acid substitutions when HcRNAV34 was compared to HcRNAV109. We used a reverse transcription-nested PCR system to amplify the corresponding regions and also examined RNAs purified from six other HcRNAV strains with known host ranges. We also looked at natural marine sediment samples. Phylogenetic dendrograms for the amplicons correlated with the intraspecies host specificities of the test virus strains. The cloned sequences found in sediment also exhibited considerable similarities to either the UA-type or CY-type sequence. The tertiary structure of the capsid proteins predicted using computer modeling indicated that many of the amino acid substitutions were located in regions on the outside of the viral capsid proteins. This strongly suggests that the intraspecies host specificity of HcRNAV is determined by nanostructures on the virus surface that may affect binding to suitable host cells. Our study shows that capsid alterations can change the phytoplankton-virus (host-parasite) interactions in marine systems.

Amino Acid Sequence↗
PubMed2005

Detection of specific sequences in RNA using differential adsorption of single-stranded oligonucleotides on gold nanoparticles.

We have used the disparity in adsorption rates for single- and double-stranded RNA on ionically coated gold nanoparticles suspended in a colloid to design a rapid sequence identification assay. Unlabeled target RNA and a probe sequence are mixed prior to exposure to the gold nanoparticles to enable efficient hybridization. We have designed assays based on either color changes or fluorescence that are sensitive to a few picomoles of target. Single-base mutations on RNA sequences can be detected even in complex oligonucleotide mixtures. The assay requires less than 10 min so that RNA degradation problems are avoided.

Adsorption↗
PubMed2026

Molecular and Immune Landscape of Recurrent and/or Distant Metastatic Squamous Cell Carcinoma of the Head and Neck: An EORTC/IMMUCAN Project.

PURPOSE: Recurrent and/or metastatic (R/M) squamous cell carcinoma of the head and neck (SCCHN) is a heterogeneous clinical entity with a poor prognosis. The molecular and immune landscape of R/M SCCHN is underexplored. To offer a comprehensive view of the tumor microenvironment and molecular profile of R/M SCCHN, we performed an in-depth molecular and immune characterization, evaluating the impact of human papillomavirus (HPV) status, tobacco and alcohol history, primary tumor site, relapse pattern, and treatment history at the genomic, transcriptomic, and immune levels. EXPERIMENTAL DESIGN: We analyzed 253 R/M SCCHN fresh tumor biopsies from the IMMUcan project using RNA sequencing (RNA-seq), whole-exome sequencing, and multiplex immunofluorescence (mIF). RESULTS: The primary clinical factor affecting the immune microenvironment was the number of treatment lines, with significant declines in T cells and B cells observed via mIF and RNA-seq as the number of R/M treatment lines progressed. IL6, IL13, IL15, and NRF2 pathways were enriched in HPV-negative R/M SCCHN compared with HPV-positive tumors, whereas no immune differences were detected between these two clinical groups. Specific genomic alterations were observed in laryngeal cancer (DDR2, FOXP1, KLF5, and ROBO2), whereas nonsmokers/nondrinkers exhibited alterations in SPEN, PBRM1, and CYLD. 11q13.3 amplification was linked to HPV-negative metastatic tumors and hypopharyngeal cancer. HPV-negative SCCHN with locoregional recurrence showed elevated EGFR and CXCL12 pathway activity. Partial epithelial-mesenchymal transition transcriptomic signatures correlated with poor survival, whereas lymphocyte infiltration, especially in the context of tertiary lymphoid structures, was associated with improved survival. CONCLUSIONS: Our study highlights key molecular and immune differences across R/M SCCHN subgroups, identifies potential biomarkers, and suggests biological rationales for tailored therapeutic strategies.

Humans↗