Biology subjects

Jacobson, M.

Publications and source records attributed to Jacobson, M..

10 recordsLinked to original sources

bioRxiv2022

A scalable screening platform for phenotypic subtyping of ALS patient-derived fibroblasts

A major challenge for understanding and treating Amyotrophic Lateral Sclerosis (ALS) is that most patients have no known genetic cause. Even within defined genetic subtypes, patients display considerable clinical heterogeneity. It is unclear how to identify subsets of ALS patients that share common molecular dysregulation or could respond similarly to treatment. Here, we developed a scalable microscopy and machine learning platform to phenotypically subtype readily available, primary patient-derived fibroblasts. Application of our platform identified robust signatures for the genetic subtype FUS-ALS, allowing cell lines to be scored along a spectrum from FUS-ALS to non-ALS. Our FUS-ALS phenotypic score negatively correlates with age of diagnosis and provides information that is distinct from transcript profiling. Interestingly, the FUS-ALS phenotypic score can be used to identify sporadic patient fibroblasts that have consistent pathway dysregulation with FUS-ALS. Further, we showcase how the score can be used to evaluate the effects of ASO treatment on patient fibroblasts. Our platform provides an approach to move from genetic to phenotypic subtyping and a first step towards rational selection of patient subpopulations for targeted therapies.

systems biology↗

bioRxiv2022

Signal peptide mimicry primes Sec61 for client-selective inhibition

Preventing the biogenesis of disease-relevant proteins is an attractive therapeutic strategy, but attempts to target essential protein biogenesis factors have been hampered by excessive toxicity. Here, we describe KZR-8445, a cyclic depsipeptide that targets the Sec61 translocon and selectively disrupts secretory and membrane protein biogenesis in a signal peptide-dependent manner. KZR-8445 potently inhibits the secretion of proinflammatory cytokines in primary immune cells and is highly efficacious in a mouse model of rheumatoid arthritis. A cryo-EM structure reveals that KZR-8445 occupies the fully opened Se61 lateral gate and blocks access to the lumenal plug domain. KZR-8445 binding stabilizes the lateral gate helices in a manner that traps select signal peptides in the Sec61 channel and prevents their movement into the lipid bilayer. Our results establish a framework for the structure-guided discovery of novel therapeutics that selectively modulate Sec61-mediated protein biogenesis.

biochemistry↗

bioRxiv2021

Protomer alignment modulates specificity of RNA substrate recognition by Ire1

The unfolded protein response (UPR) maintains protein folding homeostasis in the endoplasmic reticulum (ER). In metazoan cells, the Ire1 branch of the UPR initiates two functional outputs-- non-conventional mRNA splicing and selective mRNA decay (RIDD). By contrast, Ire1 orthologs from Saccharomyces cerevisiae and Schizosaccharomyces pombe are specialized for only splicing or RIDD, respectively. The functional specialization lies in Ire1s RNase activity, which is either stringently splice-site specific (as in S. cerevisiae) or promiscuous (as in S. pombe). Here, we developed an assay that reports on Ire1s RNase promiscuity. We found that conversion of two amino acids within the RNase domain of S. cerevisiae Ire1 to their S. pombe counterparts rendered it promiscuous. Using biochemical assays and computational modeling, we show that the mutations rewired a pair of salt bridges at Ire1 RNase domains dimer interface, changing its protomer alignment. Thus, Ire1 protomer alignment affects its substrates specificity.

biochemistry↗

bioRxiv2020

Curation of over 10,000 transcriptomic studies to enable data reuse

Vast amounts of transcriptomic data reside in public repositories, but effective reuse remains challenging. Issues include unstructured dataset metadata, inconsistent data processing and quality control, and inconsistent probe-gene mappings across microarray technologies. Thus, extensive curation and data reprocessing is necessary prior to any reuse. The Gemma bioinformatics system was created to help address these issues. Gemma consists of a database of curated transcriptomic datasets, analytical software, a web interface, and web services. Here we present an update on Gemmas holdings, data processing and analysis pipelines, our curation guidelines, and software features. As of June 2020, Gemma contains 10,811 manually curated datasets (primarily human, mouse, and rat), over 395,000 samples and hundreds of curated transcriptomic platforms (both microarray and RNA-sequencing). Dataset topics were represented with 10,215 distinct terms from 12 ontologies, for a total of 54,316 topic annotations (mean topics/dataset = 5.2). While Gemma has broad coverage of conditions and tissues, it captures a large majority of available brain-related datasets, accounting for 34% of its holdings. Users can access the curated data and differential expression analyses through the Gemma website, RESTful service, and an R package. Database URL: https://gemma.msl.ubc.ca/home.html

bioinformatics↗

bioRxiv2019

VariCarta: a comprehensive database of harmonized genomic variants found in ASD sequencing studies

BackgroundRecent years has seen a boom in the application of the next-generation sequencing technology to the study of human diseases, including Autism Spectrum Disorder (ASD), where the focus has been on identifying rare, possibly causative genomic variants in ASD individuals. Because of the high genetic heterogeneity of ASD, a large number of subjects is needed to establish evidence for a variant or gene ASD-association, thus aggregating data across cohorts and studies is necessary. However, methodological inconsistencies and subject overlap across studies complicate data aggregation.\n\nDescriptionHere we present VariCarta, a web-based database developed to address these challenges by collecting, reconciling and consistently cataloguing literature-derived genomic variants found in ASD subjects using ongoing semi-manual curation. The careful manual curation combined with a robust data import pipeline rectifies errors, converts variants into a standardized format, identifies and harmonizes cohort overlaps and documents data provenance. The harmonization aspect is especially important since it prevents the potential double-counting of variants which can lead to inflation of gene-based evidence for ASD-association.\n\nConclusionVariCarta is the largest collection of systematically curated, harmonized and comprehensively annotated literature-derived ASD-associated variants. The database currently contains 35,615 variant events from 8,044 subjects, collected across 50 publications, and reconciles 6,057 variants that have been reported in literature multiple times. VariCarta is freely accessible at http://varicarta.msl.ubc.ca.

genomics↗

bioRxiv2018

C. elegans granulins promote an age-associated decline in protein homeostasis via lysosomal protease inhibition

The progressive failure of protein homeostasis is a hallmark of aging and a common feature in neurodegenerative disease. As the enzymes executing the final stages of autophagy, lysosomal proteases (or cathepsins) are key contributors to maintenance of protein homeostasis with age. Here, we identify the cysteine-rich granulin peptides as a new class of regulators of lysosomal aspartyl protease activity. Granulins are produced in an age and stress-dependent manner through cleavage of the neurodegenerative disease protein, progranulin. Once liberated, granulins selectively interact with the aspartyl protease ASP-3/cathepsin D to impair enzymatic activity. Consequently, protein homeostasis and lysosome function is disrupted, prompting cells to activate a compensatory transcriptional program. Our results support a model in which granulin production modulates a critical transition between the normal, physiological regulation of protease activity and the impairment of lysosomal function that can occur with age and disease.

neuroscience↗

bioRxiv2018

Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins

Post-translational modifications of the RNA polymerase II C-terminal domain (CTD) coordinate the transcription cycle. Crosstalk between different modifications is poorly understood. Here, we show how acetylation of lysine residues at position 7 of characteristic heptad repeats (K7ac)--only found in higher eukaryotes--regulates phosphorylation of serines at position 5 (S5p), a conserved mark of polymerases initiating transcription. We identified the regulator of pre-mRNA domain-containing (RPRD) proteins as reader proteins of K7ac. K7ac enhanced CTD peptide binding to the CTD-interacting domain (CID) of RPRD1A and RPRD1B proteins in isothermal calorimetry and molecular modeling experiments. Deacetylase inhibitors increased K7ac- and decreased S5-phosphorylated polymerases, consistent with acetylation-dependent S5 dephosphorylation by an RPRD-associated S5 phosphatase. Consistent with this model, RPRD1B knockdown increased S5p, but enhanced K7ac, indicating RPRD proteins recruit K7 deacetylases, including HDAC1. We also report auto-regulatory crosstalk between K7ac and S5p via RPRD proteins and their interactions with acetyl- and phospho-eraser proteins.

molecular biology↗

bioRxiv2018

Identification of novel inhibitors of DLK palmitoylation by High Content Screening

After axonal insult and injury, Dual leucine-zipper kinase (DLK) conveys retrograde pro-degenerative signals to neuronal cell bodies via its downstream target c-Jun N-terminal kinase (JNK). We recently reported that such signals critically require modification of DLK by the fatty acid palmitate, via a process called palmitoylation. Compounds that inhibit DLK palmitoylation could thus reduce neurodegeneration, but identifying such inhibitors requires a suitable assay. Here we report that DLK subcellular localization in non-neuronal cells is highly palmitoylation-dependent and can be used as a proxy readout to identify inhibitors of DLK palmitoylation by High Content Screening (HCS). We exploited this highly specific localization of DLK-GFP as the basis for a screen of the Prestwick Compound Library. We found that ketoconazole, a Prestwick Library compound that most dramatically affected DLK subcellular localization in our primary screen, inhibited DLK palmitoylation in a dose-dependent manner in follow-up biochemical assays. Moeroever, ketoconazole significantly blunted phosphorylation of c-Jun in primary sensory neurons subjected to Trophic Deprivation, a well known model of DLK-dependent pro-degenerative signaling. These findings suggest that our HCS platform is capable of identifying novel inhibitors of DLK palmitoylation and signalling that may have considerable therapeutic potential.

neuroscience↗

bioRxiv2018

Monitoring changes in the Gene Ontology and their impact on genomic data analysis

The Gene Ontology (GO) is one of the most widely used resources in molecular and cellular biology, largely through the use of \"enrichment analysis\". To facilitate informed use of GO, we present GOTrack (https://gotrack.msl.ubc.ca), which provides access to historical records and trends in the Gene Ontology and GO annotations (GOA). GOTrack gives users access to gene- and term-level information on annotations for nine model organisms as well as an interactive tool that measures the stability of enrichment results over time for user-provided \"hit lists\" of genes. To document the effects of GO evolution on enrichment, we analyzed over 2500 published hit lists of human genes (most over 9 years old). 53% of hit lists were considered to yield significantly stable enrichment results. Because stability is far from assured for any individual hit list, GOTrack can lead to more informed and cautious application of GO to genomics research.

bioinformatics↗

bioRxiv2017

Evolutionarily Conserved Roles For Blood-Brain Barrier Xenobiotic Transporters In Endogenous Steroid Partitioning And Behavior

Optimal brain function depends upon efficient control over the brain entry of blood components; this is provided by the blood-brain barrier (BBB). Curiously, some brain-impermeable drugs can still cause behavioral side effects.\n\nTo investigate this phenomenon, we asked whether the promiscuous drug efflux transporter Mdr1 has dual functions in transporting drugs and endogenous molecules. If this is true, brain-impermeable drugs may cause behavioral side effects by affecting brain levels of endogenous molecules.\n\nUsing computational, genetic and pharmacologic approaches across diverse organisms we demonstrate that BBB-localized efflux transporters are critical for regulating brain levels of endogenous steroids, and steroid-regulated behaviors (sleep in Drosophila and anxiety in mice). Furthermore, we show that Mdr1-interacting drugs are associated with anxiety-related behaviors in humans.\n\nWe propose a general mechanism for common behavioral side effects of prescription drugs: pharmacologically challenging BBB efflux transporters disrupts brain levels of endogenous substrates, and implicates the BBB in behavioral regulation.\n\nAbbreviations

neuroscience↗