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An RNA biomarker panel for the diagnosis of Alzheimer's disease from whole blood.

BACKGROUND: Alzheimer’s Disease (AD) diagnosis remains primarily clinical, relying on patient history, cognitive tests, and sometimes brain imaging. Emerging approaches include advanced neuroimaging techniques and the use of protein biomarkers in cerebrospinal fluid and plasma. However, these methods have limitations such as high costs and the need for specialized infrastructures. In contrast, analysis of RNA expression in blood samples could be achieved with a high degree of sensitivity and accuracy in point of care settings, providing an ideal platform for a timely and accurate AD diagnosis.

Characterizing the circular RNA landscape in phloem sap of Brassica napus.

In plants, long-distance transport and phloem-mediated signal distribution play crucial roles in regulating stress adaptation and development. Phloem sap contains various types of RNAs, including small RNAs (sRNAs), messenger RNAs (mRNAs), and long noncoding RNAs (lncRNAs). Recently, endogenous circular RNAs have been identified in phloem sap of apple trees. Some phloem RNAs have been shown to have long-distance signaling functions, but for most, no functions have yet been determined. Due to their stability, circRNAs are interesting candidates with potential functions in long-distance signalin

A Lynch syndrome patient with multiple cancers who was found to have a novel pathogenic variant generating aberrant splicing of MLH1.

Lynch syndrome is an autosomal dominant cancer predisposition syndrome caused by inactivating germline variants in DNA mismatch repair genes. Here, we describe a woman who developed colorectal, gastric, and endometrial cancers and was found to have a rare missense variant, MLH1:c.545G > T/p.Arg182Met. The variant, which was located at the last nucleotide of MLH1exon 6, was initially reported by a clinical testing laboratory as being a variant of uncertain significance. In silico analyses predicted that it would cause splicing aberration, and reverse-transcription polymerase chain reaction anal

Transcriptomic profiling of severe and critical COVID-19 patients reveals alterations in expression, splicing and polyadenylation.

Coronavirus disease 2019 (COVID-19) is a multi-systemic illness that became a pandemic in March 2020. Although environmental factors and comorbidities can influence disease progression, there is a lack of prognostic markers to predict the severity of COVID-19 illness. Identifying these markers is crucial for improving patient outcomes and appropriately allocating scarce resources. Here, an RNA-sequencing study was conducted on blood samples from unvaccinated, hospitalized patients divided by disease severity; 367 moderate, 173 severe, and 199 critical. Using a bioinformatics approach, we ident

Alternative Splicing: A Critical Regulator in Human Bone Biology and Tumor Progression.

Alternative splicing (AS) is the central mechanism of transcriptional regulation and generates diverse splice variants that influence protein structure, function, and intracellular activity. AS plays critical roles in tissue differentiation, organ development, and disease progression. This review focuses on the pivotal roles of AS in bone biology, highlighting its regulatory effects on osteoblasts, osteoclasts, chondrocytes, bone matrix remodeling, and bone remodeling, as well as the involvement of AS-related RNA-binding proteins in these processes. We also emphasize bone-specific AS events an

Совпадение в полном тексте источника
… Generally, RNA splicing can be categorized into 4 categories: group I self-splicing, group II self-splicing, nuclear mRNA spliceosomal splicing, and nuclear transfer RNA (tRNA) enzymatic splicing [ 3 – 5 ]. …

Synergistic Effect of an Antisense Oligonucleotide and Small Molecule on Splicing Correction of the Spinal Muscular Atrophy Gene.

Spinal muscular atrophy (SMA) is treated by increasing the level of Survival Motor Neuron (SMN) protein through correction of SMN2 exon 7 skipping or exogenous expression of SMN through gene therapy. Currently available therapies have multiple shortcomings, including poor body-wide distribution, invasive delivery, and potential negative consequences due to high doses needed for clinical efficacy. Here we test the effects of a combination treatment of a splice-correcting antisense oligonucleotide (ASO) Anti-N1 with the small compounds risdiplam and branaplam. We show that a low-dose treatment o

Identification and characterization of Varicella Zoster Virus circular RNA in lytic infection.

This study investigates the role of circular RNAs (circRNAs) in the context of Varicella-Zoster Virus (VZV) lytic infection. We employ two sequencing technologies, short-read sequencing and long-read sequencing, following RNase R treatment on VZV-infected neuroblastoma cells to identify and characterize both cellular and viral circRNAs. Our large scanning analysis identifies and subsequent experiments confirm 200 VZV circRNAs. Moreover, we discover numerous VZV latency-associated transcripts (VLTs)-like circRNAs (circVLTslytic), which contain multiple exons and different isoforms within the sa

Homozygous splice variant (c.1741-6G>A) of the COL6A1 gene in three patients with Ullrich congenital muscular dystrophy.

The three major collagen VI genes: COL6A1, COL6A2, and COL6A3 encode microfibrillar components of extracellular matrices in multiple tissues including muscles and tendons. Pathogenic variants in the collagen VI genes cause collagen VI-related dystrophies representing a continuum of conditions from Bethlem myopathy at the milder end to Ullrich congenital muscular dystrophy at the more severe end. Here we describe a pathogenic variant in the COL6A1 gene (NM_001848.3; c.1741-6G>A) found in homozygosity in three patients with Ullrich congenital muscular dystrophy. The patients suffered from severe

HIV-1 Rev-RRE functional activity in primary isolates is highly dependent on minimal context-dependent changes in Rev.

During HIV infection, intron-containing viral mRNAs are exported from the cell nucleus to the cytoplasm to complete the replication cycle. Cellular restrictions on the export of incompletely spliced transcripts are overcome by a viral protein, Rev, and an RNA structure found in all unspliced and incompletely spliced viral mRNAs, the Rev Response Element (RRE). Primary HIV isolates display substantial variation in the sequence and functional activity of Rev proteins. We analyzed Rev from two primary isolates with disparate activity that resulted in differences in in vitro fitness of replication

The human tryptophan hydroxylase gene. An unusual splicing complexity in the 5'-untranslated region.

We report the isolation and the organization of the gene encoding human tryptophan hydroxylase (TPH) and an analysis of the corresponding mRNAs. The gene spans a region of 29 kilobases, which contains at least 11 exons and a variably spliced 5'-untranslated region (5'-UTR). The sequence of the coding region and the majority of the positions of the intron-exon boundaries of human TPH gene are very similar to those encoding human tyrosine hydroxylase and phenylalanine hydroxylase, the other members of the aromatic amino acid hydroxylase family. Phylogenetic analysis evidences the early divergenc

ZBP1 in Neuroinflammation and Neurodegeneration: Z-Nucleic-Acid Sensing, RHIM Signalling and Therapeutic Targeting.

In contrast to foreign nucleic acids, some of our own endogenously synthesized nucleic acids may become immunologically active without being considered "foreign". For example, abnormalities in chromatin organization, transcription termination, ribonucleic acid (RNA) splicing, and RNA editing, together with damage to mitochondrial integrity, may render normally functional deoxyribonucleic acid (DNA) and RNA persistently available and aberrantly structured ligands for innate immunity. Z-DNA-binding protein 1 (ZBP1), recently identified as an important component of this innate immune system, reco

hnRNPs in immunity: from nucleic acid sensing to lymphocyte fate determination.

Heterogeneous nuclear ribonucleoproteins (hnRNPs) constitute a family of RNA-binding proteins long recognized for their roles in pre-mRNA processing. However, accumulating evidence has established hnRNPs as central and versatile regulators of immunity. In innate immunity, some hnRNP family members recognize nucleic acids and metabolites to either promote or constrain inflammatory gene expression in a context-dependent manner. In adaptive immunity, they play essential roles in B cell activation and germinal center (GC) responses, as well as T cell activation, survival, and differentiation, prim

[Advances in molecular genetic research on Myelodysplastic syndrome].

Myelodysplastic syndrome (MDS) is a chronic hematologic disorder characterized by ineffective hematopoiesis, dysplasia of one or more cell lines with or without definite genetic changes. Its diagnosis requires a comprehensive analysis combining morphology, immunology, cytogenetics, and molecular biology findings. In recent years, the development of second-generation sequencing (NGS) has provided great assistance in exploring the molecular pathogenesis of hematological malignancies and guidance for clinical practice. Mutations of a series of gene involved in RNA splicing, DNA methylation, trans…

Discontinuous genomic coding and paradigm shifts in molecular biology and immunology: revolutions via "normal science".

The past 60 years have seen explosive changes in the fields of molecular biology and immunology which now affect clinical medicine as well as our knowledge of living systems. The succession of new discoveries and their transforming effects on intellectual paradigms in biology represent an interesting case to compare with Kuhn's dichotomy between "normal science" and "revolutionary science". Here, three conceptually disruptive discoveries are discussed: (1) the discovery and significance of messenger RNA (mRNA) splicing; (2) the discovery and significance of immunoglobulin gene somatic rearrang

Validation of the protein kinase PfCLK3 as a multistage cross-species malarial drug target.

The requirement for next-generation antimalarials to be both curative and transmission-blocking necessitates the identification of previously undiscovered druggable molecular pathways. We identified a selective inhibitor of the Plasmodium falciparum protein kinase PfCLK3, which we used in combination with chemogenetics to validate PfCLK3 as a drug target acting at multiple parasite life stages. Consistent with a role for PfCLK3 in RNA splicing, inhibition resulted in the down-regulation of more than 400 essential parasite genes. Inhibition of PfCLK3 mediated rapid killing of asexual liver- and…

Transgenerational transmission of systemic mast cell activation disease-genetic and epigenetic features.

Systemic mast cell activation disease (MCAD) comprises disorders characterized by an enhanced release of mast cell mediators accompanied by a varying accumulation of dysfunctional mast cells. Within the last years, evidence has been presented that MCAD is a multifactorial polygenic determined disease with the KIT(D816V) mutation and its induced functional consequences considered as special case. The respective genes encode proteins for various signaling pathways, epigenetic regulators, the RNA splicing machinery, and transcription factors. Transgenerational transmission of MCAD appears to be q…

Selective inhibition of MBNL1-CCUG interaction by small molecules toward potential therapeutic agents for myotonic dystrophy type 2 (DM2).

Myotonic dystrophy type 2 (DM2) is an incurable neuromuscular disease caused by expanded CCUG repeats that may exhibit toxicity by sequestering the splicing regulator MBNL1. A series of triaminotriazine- and triaminopyrimidine-based small molecules (ligands 1-3) were designed, synthesized and tested as inhibitors of the MBNL1-CCUG interaction. Despite the structural similarities of the triaminotriazine and triaminopyrimidine units, the triaminopyrimidine-based ligands bind with low micromolar affinity to CCUG repeats (K(d) ∼ 0.1-3.6 µM) whereas the triaminotriazine ligands do not bind CCUG rep

Identification of mutations leading to the Lesch-Nyhan syndrome by automated direct DNA sequencing of in vitro amplified cDNA.

The Lesch-Nyhan (LN) syndrome is a severe X chromosome-linked disease that results from a deficiency of the purine salvage enzyme hypoxanthi … ons include DNA base substitutions, small DNA deletions, a single DNA base insertion, and errors in RNA splicing. The application of these procedures allows DNA diagnosis and carrier identification by the direct detection of the mutant alleles within individual families affected by LN.

Genome-wide analysis of abnormal splicing regulators and alternative splicing involved in immune regulation in systemic lupus erythematosus.

Systemic lupus erythematosus (SLE) is an autoimmune disease with complex clinical manifestations and no current cure. Alternative splicing (AS) plays a key role in SLE by regulating immune-related genes, but its genome-wide regulatory mechanisms remain unclear. To investigate the involvement of abnormal splicing regulators and AS events in the immune regulation of SLE. Transcriptome data from the SLE dataset GSE162828 were analyzed for differential gene expression and AS events using bioinformatics tools. Immune infiltration analysis was conducted with CIBERSORT, and co-expression of key splic

A Novel SLC27A4 Splice Acceptor Site Mutation in Great Danes with Ichthyosis.

Ichthyoses are a group of various different types of hereditary disorders affecting skin cornification. They are characterized by hyperkeratoses of different severity levels and are associated with a dry and scaling skin. Genome-wide association analysis of nine affected and 13 unaffected Great Danes revealed a genome-wide significant peak on chromosome 9 at 57-58 Mb in the region of SLC27A4. Sequence analysis of genomic DNA of SLC27A4 revealed the non-synonymous SNV SLC27A4:g.8684G>A in perfect association with ichthyosis-affection in Great Danes. The mutant transcript of SLC27A4 showed an in