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Biology subjects

Boczkowska, M.

Publications and source records attributed to Boczkowska, M..

7 recordsLinked to original sources

Loss of the Coronary Artery Disease Risk Gene Leiomodin1 in Vascular Smooth Muscle Cells Triggers Rapid Onset Coronary Atherosclerosis

BackgroundAtherosclerosis is the primary underlying cause of coronary artery disease (CAD). Leiomodin1 is a vascular smooth muscle cell (VSMC)-restricted CAD risk gene whose role in coronary artery pathophysiology is unknown. Global loss of Leiomodin1 causes lethal neonatal visceral myopathy, requiring unique approaches for study in VSMCs. MethodsSeveral distinct Leiomodin1 mutant mouse models were generated by clustered regularly interspaced short palindromic repeats (CRISPR). Control (Lmod1WT) and VSMC-restricted Lmod1 knockout (Lmod1SMKO) mice were subjected to various atherogenic regimens. Atherosclerosis and LMOD1 expression in mouse and human coronary arteries were assessed by histopathology and confocal immunofluorescence microscopy. Coronary arteries from Lmod1WT and Lmod1SMKO mice were analyzed with assorted stains and antibodies, immunogold lineage tracing, spatial metabolomics/transcriptomics, and single-cell RNA sequencing (scRNA-seq). Mouse aortic SMCs from Lmod1WT and Lmod1SMKO mice were subjected to lipid loading with lentiviruses expressing wild-type Lmod1, a nucleation deficient Leiomodin1 (Lmod1ND), or a short hairpin RNA (shRNA) targeting Thrombospondin (Thbs1). ResultsUnder atherogenic conditions, Lmod1SMKO mice displayed unremarkable vessels in several organs but developed diffuse and occlusive coronary atherosclerosis. No such disease was observed in Lmod1WT mice. Time-course studies documented lipid insudation and VSMC foam cell formation in the coronary arteries of Lmod1SMKO mice as early as six days post-regimen. Immunogold lineage tracing demonstrated 46% of coronary plaque cells being of VSMC origin, with most showing evidence of lipid uptake. An intronic deletion of Lmod1, containing a conserved region where the single nucleotide variant associated with CAD exists, showed attenuated LMOD1 expression; heterozygous Lmod1SMKO mice, with a similar reduction in LMOD1, showed no CAD. Spatial metabolomics uncovered multiple lipid species within coronary atheromata of Lmod1SMKO mice, and spatial/scRNA-seq of similar coronary lesions disclosed altered lipid pathways with a consistent elevation in Thbs1. In vitro mechanistic studies revealed lipid accumulation in Lmod1SMKO VSMCs that was rescued by Lmod1WT, Lmod1ND, and Thbs1 shRNA. VSMC-restricted expression of Lmod1ND in mice resulted in negligible coronary atherosclerosis. ConclusionsUnder proatherogenic conditions, Lmod1SMKO mice present with rapidly manifesting coronary atherosclerosis that appears to be independent of the actin nucleation function of LMOD1. Targeting Thbs1 represents a viable strategy to mitigate VSMC foam cell formation. Clinical PerspectiveO_ST_ABSWhat is new?C_ST_ABSO_LIVascular smooth muscle cell (VSMC) loss of Leiomodin1 (Lmod1) causes diffuse and occlusive coronary atherosclerosis in mice, with little or no such disease in other vascular beds. C_LIO_LIA novel immunogold lineage tracing assay shows VSMC migration to the intima as early as six days following an atherogenic regimen, and quantitative studies demonstrate that 46% of coronary plaque cells are of SMC origin. C_LIO_LIThe coronary phenotype appears to be independent of LMOD1s actin nucleation activity, but VSMC lipid uptake is thrombospondin-dependent. C_LI What are the clinical implications?O_LILMOD1 is an annotated smooth muscle cell-restricted risk allele for human coronary artery disease (CAD), offering new insight into the role of smooth muscle cells in atherogenesis. C_LIO_LIThe rapidly manifesting CAD phenotype in Lmod1 knockout mice enables expedited testing of novel therapeutics to mitigate disease progression. C_LIO_LINew insight into LMOD1 pathobiology will help inform further SNV interrogation of the LMOD1 locus for CAD risk in patients. C_LI

pathology↗

New molecular players: siRNA expression and gene regulation in Hordeum vulgare ageing seeds after germination

Small interfering RNAs (siRNAs), a subclass of small non-coding RNAs, play crucial roles in regulating seed germination and viability through epigenetic mechanisms like RNA-directed DNA methylation (RdDM). This study presents the first comprehensive investigation of siRNA profiles linked to seed viability and germination in barley (Hordeum vulgare), utilizing a unique set of seeds from a single batch subjected to controlled long-term storage. Some seeds lost viability due to moisture exposure from unsealing, creating a natural experimental model to explore vigor effects. sRNA sequencing revealed 85,728 differentially expressed siRNAs, with distinct patterns between regenerated, high-viability, and low-viability seeds. Notably, trans-acting siRNAs (ta-siRNAs) showed peak abundance at different imbibition times depending on seed quality, suggesting dynamic regulation. Around 46% of siRNAs were 21 nucleotides, and 54% were 22 nucleotides long. Gene Ontology and degradome analyses confirmed siRNA target genes involved in vital biological processes such as cytochrome complex function, root development, cell maturation, and carbohydrate metabolism. Despite RNA degradation in low-viability seeds, siRNAs remained relatively stable, indicating their potential role in maintaining seed metabolic activity during dormancy release and germination initiation. This pioneering research uncovers novel insights into siRNA-mediated control of seed longevity and germination, highlighting the innovative use of stable, well-characterized plant material to disentangle molecular mechanisms underpinning seed vigor and germination success.

plant biology↗

k-mer-based GWAS in a wheat collection reveals novel and diverse sources of powdery mildew resistance

BackgroundWheat landraces and cultivars stored in gene banks worldwide represent a valuable source of genetic diversity for discovering genes critical for agriculture, which is increasingly constrained by climate change and inputs reduction. We assembled and genotyped, using DArTseq technology, a panel of 461 accessions representative of the genetic diversity of Swiss wheat material. The collection was evaluated for powdery mildew resistance under field conditions for two consecutive years and at the seedling stage with 10 different wheat powdery mildew isolates. ResultsTo identify the genetic basis of mildew resistance in wheat, we developed a k-mer-based GWAS approach using multiple fully-assembled genomes including Triticum aestivum as well as four progenitor genomes. Compared to approaches based on single reference genomes, we unambiguously mapped an additional 25% resistance-associated k-mers. Our approach outperformed SNP-based GWAS in terms of number of loci identified and precision of mapping. In total, we detected 34 (Pm) powdery mildew resistance loci, including seven previously-described and more importantly 27 novel loci active at the seedling stage. Furthermore, we identified a region associated with adult plant resistance, which was not detected with SNP-based approaches. ConclusionsThe described non-reference-based approach highlights the potential of integrating multiple wheat reference genomes with k-mer GWAS to harness the untapped genetic diversity present in germplasm collections.

genomics↗

Improved Degradome Sequencing Protocol via Reagent Recycling from sRNAseq Library Preparations

BackgroundOne of the key elements in the analysis of gene expression and its post-translational regulation is miRNAs. Degradome-seq analyses are performed to analyze the cleavage of target RNAs in the transcriptome. In this work, an improved library preparation protocol for degradome sequencing is presented. The developed protocol improves the efficiency of library preparation in degradome-seq analysis used to identify microRNA targets, reduces the time of library preparation and lowers the cost of purchasing reagents.. ResultsThe aim of this study was the development of an efficient protocol for the construction of degradome sequencing libraries using residual reagents from the sRNA-seq library preparation kit. To this end, modified primers and adaptors were designed. The library purification step based on automated electrophoresis and high-resolution agarose was modified and optimized in the presented protocol. Size standards of 60 and 65 bp were developed. They were prepared for precise band excision from the gel. Cloning to plasmid and sequencing of the inserted fragment, i.e., a fragment from the degradome library, verified the correctness of the library preparation using the developed protocol. ConclusionThe developed protocol allowed the construction and sequencing of degradome libraries even from RNA samples with low RIN. It significantly reduces the cost of library construction. This is due to the use of residues from the sRNA-seq library kit. The precision of the excised fragment after electrophoresis performed during the procedure to isolate fragments of the correct length is significantly improved by the use of additional size markers. Compared to previously used methods, optimizing the purification method of degradom-seq libraries allowed to increase the yield of fragments obtained. Notably, the time required for the entire library preparation protocol does not exceed three days, also a significant time savings.

plant biology↗

Aging and Germination of Long-term Stored Seeds: Can MicroRNAs Unlock the Secrets?

BackgroundSmall non-coding RNAs appear to be one of the key components of the germination process. To investigate how small non-coding RNAs correlate with germination of seeds with different levels of viability, miRNA-Seq analyses were performed. ResultsOur analysis sequencing identified 62 known miRNAs from 11 families and 234 new miRNAs after imbibition process. Among the miRNAs with the highest expression levels, we can mention: miR159, miR168 and miR166. The study placed particular emphasis on miRNAs with significant differences in expression levels at different stages of imbibition and among seeds with different viability. DEG analysis identified 28 miRNAs with significant differences in expression levels, their function was assessed by in silico analyses and confirmed by degradome-seq analysis. The expression of miRNAs was verified by qRT-PCR. ConclusionOur data provides a useful source of information on miRNA during germination long term storage seeds with different viability. The studies suggest that miRNAs are involved in the germination process by their regulation DNA and RNA binding, regulation of developmental process and ribosome.

plant biology↗

Myosin-I Synergizes with Arp2/3 Complex to Enhance Pushing Forces of Branched Actin Networks

Myosin-Is colocalize with Arp2/3 complex-nucleated actin networks at sites of membrane protrusion and invagination, but the mechanisms by which myosin-I motor activity coordinates with branched actin assembly to generate force are unknown. We mimicked the interplay of these proteins using the "comet tail" bead motility assay, where branched actin networks are nucleated by Arp2/3 complex on the surface of beads coated with myosin-I and the WCA domain of N-WASP. We observed that myosin-I increased bead movement efficiency by thinning actin networks without affecting growth rates. Remarkably, myosin-I triggered symmetry breaking and comet-tail formation in dense networks resistant to spontaneous fracturing. Even with arrested actin assembly, myosin-I alone could break the network. Computational modeling recapitulated these observations suggesting myosin-I acts as a repulsive force shaping the networks architecture and boosting its force-generating capacity. We propose that myosin-I leverages its power stroke to amplify the forces generated by Arp2/3 complex-nucleated actin networks.

biophysics↗

Molecular mechanism of Arp2/3 complex inhibition by Arpin

Positive feedback loops involving signaling and actin assembly factors mediate the formation and remodeling of branched actin networks in processes ranging from cell and organelle motility to mechanosensation. The Arp2/3 complex inhibitor Arpin controls the directional persistence of cell migration by interrupting a feedback loop involving Rac-WAVE-Arp2/3 complex, but Arpins mechanism of inhibition is unknown. Here, we describe the cryo-EM structure of Arpin bound to Arp2/3 complex at 3.24-[A] resolution. Unexpectedly, Arpin binds Arp2/3 complex similarly to WASP-family nucleation-promoting factors (NPFs) that activate the complex. However, whereas NPFs bind to two sites on Arp2/3 complex, on Arp2-ArpC1 and Arp3, Arpin only binds to the site on Arp3. Like NPFs, Arpin has a C-helix that binds at the barbed end of Arp3. Mutagenesis studies in vitro and in cells reveal how sequence differences within this helix define the molecular basis for inhibition by Arpin vs. activation by NPFs.

biochemistry↗