Biology subjects

Roberson, E. D. O.

Publications and source records attributed to Roberson, E. D. O..

8 recordsLinked to original sources

bioRxiv2025

The small genomics lab experience optimizing data cold storage

Translational research is often a collaborative enterprise that involves basic science researchers, clinicians, and experts in genomics and bioinformatics. While there are central university and industry cores to support data generation, long-term storage often falls to the individual investigators. We frequently fulfill the role of long-term FASTQ file storage for our collaborators. To reduce our cold storage space, we tested the space savings for gzip and zstandard algorithms on an old set of FASTQ files. We found that zstandard had a better overall compression ratio than the best gzip algorithm, amounting to more than 20% space savings overall compared to gzip. It may be worth transitioning to zstandard compression for small, collaborative genomics labs to minimize cold storage costs.

bioinformatics↗

bioRxiv2024

Systemic delivery of murine SOD2 mRNA to experimental abdominal aortic aneurysm mitigates expansion and rupture

BackgroundOxidative stress is implicated in the pathogenesis and progression of abdominal aortic aneurysm (AAA). Antioxidant delivery as a therapeutic for AAA is of substantial interest although clinical translation of antioxidant therapy has met with significant challenges due to limitations in achieving sufficient antioxidant levels at the site of AAA. We posit that nanoparticle-based approaches hold promise to overcome challenges associated with systemic administration of antioxidants. MethodsWe employed a peptide-based nanoplatform to overexpress a key modulator of oxidative stress, superoxide dismutase 2 (SOD2). The efficacy of systemic delivery of SOD2 mRNA as a nanotherapeutic agent was studied in two different murine AAA models. Unbiased mass spectrometry-enabled proteomics and high-dimensional bioinformatics were used to examine pathways modulated by SOD2 overexpression. ResultsThe murine SOD2 mRNA sequence was mixed with p5RHH, an amphipathic peptide capable of delivering nucleic acids in vivo to form self-assembled nanoparticles of [~]55 nm in diameter. We further demonstrated that the nanoparticle was stable and functional up to four weeks following self-assembly when coated with hyaluronic acid. Delivery of SOD2 mRNA mitigated the expansion of small AAA and largely prevented rupture. Mitigation of AAA was accompanied by enhanced SOD2 protein expression in aortic wall tissue. Concomitant suppression of nitric oxide, inducible nitric oxide synthase expression, and cell death was observed. Proteomic profiling of AAA tissues suggests that SOD2 overexpression augments levels of microRNAs that regulate vascular inflammation and cell apoptosis, inhibits platelet activation/aggregation, and downregulates mitogen-activated protein kinase signaling. Gene set enrichment analysis shows that SOD2 mRNA delivery is associated with activation of oxidative phosphorylation, lipid metabolism, respiratory electron transportation, and tricarboxylic acid cycle pathways. ConclusionsThese results confirm that SOD2 is key modulator of oxidative stress in AAA. This nanotherapeutic mRNA delivery approach may find translational application in the medical management of small AAA and the prevention of AAA rupture.

cell biology↗

bioRxiv2022

Inhibition of extracellular vesicle-encapsulated miRNA produced by estrogen-mediated upregulation of cellular processing suppresses target organ inflammation in a humanized model of systemic lupus erythematosus

Background/PurposeDistinct, disease-associated intracellular miRNA (miR) expression profiles have been identified from peripheral blood mononuclear cells (PBMCs) of systemic lupus erythematous (SLE) patients. We have previously demonstrated novel estrogenic responses in PBMCs from SLE patients and discovered that estrogen lowers the threshold of immune cell activation to a greater extent in females, including significant upregulation of toll-like receptor (TLR)7 and TLR8 expression. TLR7 and TLR8 bind viral-derived single-stranded RNA to stimulate innate inflammatory responses, but recent studies have shown that miR-21, mir-29a, and miR-29b can also bind and activate these receptors when packaged and secreted in extracellular vesicles (EVs). ObjectiveThe objective of this study was to characterize the estrogen-mediated immunomodulatory effects of distinct EV-encapsulated miR profiles in SLE and evaluate the potential therapeutic approach of miR inhibition in a humanized mouse model. MethodsSLE patients meeting revised ACR guidelines and age/sex-matched healthy controls provided informed consent to participate in this IRB-approved study. Plasma-derived EVs were isolated by differential ultracentrifugation and quantified. PBMCs were isolated from whole blood and cultured in hormone free conditions before stimulation with 17{beta}-estradiol (estrogen; E2). RNA was isolated following E2 stimulation or EV isolation and bulk RNA-sequencing (RNAseq) reads were analyzed. Additionally, PBMCs from active SLE patients were injected into immunodeficient mice to produce chimeras. Prior to transfer, the PBMCs were incubated with liposomal EVs containing complementary locked nucleic acid (LNA) antagonists to miR-21, mir-29a, and miR-29b. After three weeks, blood was collected for both immunophenotyping and cytokine analysis and tissue was harvested for histopathological examination. ResultsEVs were found to be increased in the plasma of SLE patients and differentially expressed EV-derived miR profiles were detected compared to healthy controls, including miR-21, mir-29a, and miR-29b. E2 stimulation of PBMCs identified upregulated pathways involved in miR transcription/processing. Specifically, small RNA binding proteins and synthesis enzymes demonstrated significant signaling pathway association and upregulation with E2 treatment. Human immune cell subtypes were successfully recovered from whole blood of chimeric mice at similar levels with and without miR inhibition, but levels of human IL-6, IL-1{beta}, IL-4, and TNF- were significantly reduced by the LNA antagonists. Moreover, miR antagonists significantly reduced histopathological infiltrates in the small intestine, liver, and kidney, as demonstrated by H&E-stained tissue sections and immunohistochemistry measuring human CD3. ConclusionThese data suggest E2-mediated regulation of miR synthesis and demonstrate distinct EV-derived small RNA signatures representing SLE-associated biomarkers. Targeting upregulated EV-encapsulated miR signaling by antagonizing miRs that may bind to TLR7 and TLR8 reveals a novel therapeutic opportunity to suppress autoimmune-mediated inflammation and pathogenesis in SLE.

immunology↗

bioRxiv2021

RNA-Seq analysis identifies novel roles for the primary cilia gene SPAG17 and the SOX9 locus non-coding RNAs in systemic sclerosis

Systemic sclerosis (SSc) is characterized by immune activation, vasculopathy, and unresolving fibrosis in the skin, lungs, and other organs. We performed RNA-Seq analysis on skin biopsies and peripheral blood mononuclear cells (PBMCs) from SSc patients and controls to better understand SSc pathogenesis. We analyzed these data to 1) test for case-control differences, and 2) identify genes whose expression levels correlate with SSc severity as measured by local skin score, modified Rodnan skin score (MRSS), forced vital capacity (FVC), or diffusion capacity for carbon monoxide (DLCO). We found that PBMCs from SSc patients showed a strong type 1 interferon signature. This signal replicated in the skin, with additional signals for increased extracellular matrix (ECM) genes, classical complement pathway activation, and the presence of B cells. Notably, we observed a marked decrease in the expression of SPAG17, a cilia component, in SSc skin. We identified genes that correlated with MRSS, DLCO, and FVC in SSc PBMCs and skin using weighted gene co-expression analysis (WGCNA). These genes were largely distinct from the case/control differentially expressed genes. In PBMCs, type 1 interferon signatures negatively correlated with DLCO. In SSc skin, ECM gene expression positively correlated with MRSS. Network analysis of SSc skin genes correlated with clinical features identified the non-coding RNAs SOX9-AS1 and ROCR, both near the SOX9 locus, as highly connected, "hub-like" genes in the network. These results identify non-coding RNAs and SPAG17 as novel factors potentially implicated in SSc pathogenesis.

genomics↗

bioRxiv2021

Transcriptomes of peripheral blood mononuclear cells from juvenile dermatomyositis patients show elevated inflammation even when clinically inactive

In juvenile dermatomyositis (JDM), the most common pediatric inflammatory myopathy, weakness is accompanied by a characteristic rash that often becomes chronic, and is associated with vascular damage. We hoped to understand the molecular underpinnings of JDM, particularly in untreated disease, which would facilitate the identification of novel mechanisms and clinical targets that might disrupt disease progression. We studied the RNA-Seq data from untreated JDM peripheral blood mononuclear cells (PBMCs; n=11), PBMCs from a subset of the same patients when clinically inactive (n=8/11), and separate samples of untreated JDM skin and muscle (n=4 each). All JDM samples were compared to non-inflammatory control tissues. The untreated JDM PBMCs showed a strong signature for type1 interferon response, along with IL-1, IL-10, and NF-{kappa}B. Surprisingly, PBMCs from clinically inactive JDM individuals had persistent immune activation that was enriched for IL-1 signaling. JDM skin and muscle both showed evidence for type 1 interferon activation and genes related to antigen presentation, and decreased expression of genes related for cellular respiration. Additionally we found that PBMC gene expression correlates with disease activity scores (DAS; skin, muscle, and total domains) and with nailfold capillary end row loop number (an indicator of microvascular damage). This included otoferlin, which was significantly increased in untreated JDM PBMCs and correlated with all 3 DAS domains. Overall, these data demonstrate that PBMC transcriptomes are informative of molecular disruptions in JDM and provide transcriptional evidence of chronic inflammation despite clinical quiescence.

genomics↗

bioRxiv2019

A catalog of CasX genome editing sites in common model organisms

DpbCasX, also called Cas12e, is an RNA-guided DNA endonuclease isolated from Deltaproteobacteria. In this paper I characterized the CasX-compatible genome editing sites in the reference genomes of yeast (Saccharomyces cerevisiae), flatworms (Caenorhabditis elegans), flies (Drosophila melanogaster), zebrafish (Danio rerio), mouse (Mus musculus), rats (Rattus norvegicus), and humans (Homo sapiens). Across those genomes there were >27,000 CasX sites per megabase on average. More than 90% of genes in each genome had at least one unique site overlapping an exon, with median unique sites per gene of 6 - 45. I also annotated sites in the GRCm38 reference and 15 additional mouse strain genomes. The presence of specific guide sequences varied amongst the strains, with CAST/EiJ and PWK/PhJ showing the greatest divergence from the reference strain. The high density of CasX sites and number of exon overlapping sites suggests that CasX has the potential to be used as a common genome editor.

bioinformatics↗

bioRxiv2018

Nicastrin haploinsufficiency alters expression of type-I interferon-stimulated genes in two immortalized human cell lines

A.BackgroundHidradenitis suppurativa (HS) is a chronic skin disease. The symptoms can be severe, and include intensely painful nodules and abscesses in apocrine-gland rich inverse skin, such as the buttocks, under the arms, and the groin. Autosomal dominant forms of HS exist, but are rare. Some of these kindred have heterozygous loss-of-function rare variants in the {gamma}-secretase complex component nicastrin (NCSTN).\n\nObjectivesWe wanted to know what effect NCSTN haploinsufficiency has on human keratinocytes to assess potential mechanisms for lesion development.\n\nMethodsWe knocked down nicastrin using an shRNA construct in both a keratinocyte cell line (HEK001) and an embryonic kidney cell line (HEK293). We assessed differential gene expression using RNA microarray. We also generated a NCSTN heterozygous deletion in the HEK293 line using CRISPR/Cas9 genome-editing and assessed NFKB activity in this line using a luciferase reporter.\n\nResultsThe keratinocyte NCSTN knockdown cell line demonstrated significantly increased expression of genes related to the type-I interferon response pathway when compared to controls. Both HEK001 and HEK293 knockdowns demonstrated evidence for altered growth. We observed a small, but significant increase in NFKB signaling in response to TNF treatment a HEK293 line genome-edited for reduced NCSTN.\n\nConclusionsOur data suggest a role for increased keratinocyte inflammatory responsiveness in familial HS. Confirming this phenotype, and characterizing additional effects in different cell types, will require study beyond cell lines in primary cells and tissues.

cell biology↗

bioRxiv2018

Motif Scraper: A cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files

SummaryMany genomic features are defined not by exact sequence matches, but by degenerate nucleotide motifs that represent multiple compatible matches. While there are databases cataloging genomic features, such as the location of transcription factor motifs, for commonly used model species, identifying the locations of novel motifs, known motifs in non-model genomes, or known motifs in personal whole-genomes is difficult. I designed motif scraper to overcome this limitation, allowing for efficient, multiprocessor motif searches in any FASTA file.\n\nAvailability and implementationThe motif scraper package is available via PyPI, and the Python source is available on GitHub at https://github.com/RobersonLab/motif_scraper.\n\nContact: eroberson@wustl.edu

bioinformatics↗