Biology subjects

Jackson, M.

Publications and source records attributed to Jackson, M..

45 records · Page 3Linked to original sources

bioRxiv2020

RNF5 Regulation of RBBP4 Defines Acute Myeloid Leukemia Growth and Susceptibility to Histone Deacetylase Inhibitors

Acute myeloid leukemia (AML) remains incurable, largely due to its resistance to conventional treatments. Here, we found that increased expression and abundance of the ubiquitin ligase RNF5 contributes to AML development and survival. High RNF5 expression in AML patients correlated with poor prognosis. RNF5 inhibition decreased AML cell growth in culture and in vivo, and blocked development of MLL-AF9-driven leukemogenesis in mice, prolonging their survival. RNF5 inhibition led to transcriptional changes that overlapped with those seen upon HDAC1 inhibition. RNF5 induced the formation of K29 ubiquitin chains on the histone-binding protein RBBP4, promoting its recruitment and subsequent epigenetic regulation of genes involved in AML development and maintenance. Correspondingly, RNF5 or RBBP4 knockdown enhanced the sensitivity of AML cells to histone deacetylase (HDAC) inhibitors. Notably, low expression of RNF5 and HDAC coincided with a favorable prognosis. Our studies identified ERAD-independent role for RNF5, demonstrating that its control of RBBP4 constitutes an epigenetic pathway that drives AML while highlighting RNF5/RBBP4 as markers to stratify patients for treatment with HDAC inhibitors.

cancer biology↗

bioRxiv2020

Pathway dynamics can delineate the sources of transcriptional noise in gene expression

Single-cell expression profiling has opened up new vistas on cellular processes. Among other important results, one stand-out observation has been the confirmation of extensive cell-to-cell variability at the transcriptomic and proteomic level. Because most experimental analyses are destructive we only have access to snapshot data of cellular states. This loss of temporal information presents significant challenges in inferring dynamics, as well as causes of cell-to-cell variability. In particular, we are typically unable to separate dynamic variability from within individual systems ("intrinsic noise") from variability across the population ("extrinsic noise"). Here we mathematically formalise this non-identifiability; but we also use this to identify how new experimental set-ups coupled to statistical noise decomposition can resolve this non-identifiability. For single-cell transcriptomic data we find that systems subject to population variation invariably inflate the apparent degree of burstiness of the underlying process. Such identifiability problems can, in principle, be remedied by dual-reporter assays, which separates total gene expression noise into intrinsic and extrinsic contributions; unfortunately, however, this requires pairs of strictly independent and identical gene reporters to be integrated into the same cell, which is difficult to implement experimentally in most systems. Here we demonstrate mathematically that, in some cases decomposition of transcriptional noise is possible with non-identical and not-necessarily independent reporters. We use our result to show that generic reporters lying in the same biochemical pathways (e.g. mRNA and protein) can replace dual reporters, enabling the noise decomposition to be obtained from only a single gene. Stochastic simulations are used to support our theory, and show that our "pathway-reporter" method compares favourably to the dual-reporter method.

biophysics↗

bioRxiv2020

ASO-based PKM Splice-switching Therapy Inhibits Hepatocellular Carcinoma Cell Growth

The M2 pyruvate kinase (PKM2) isoform is upregulated in most cancers and plays a crucial role in the Warburg effect, which is characterized by the preference for aerobic glycolysis for energy metabolism. PKM2 is an alternative-splice isoform of the PKM gene and is a potential therapeutic target. Previously, we developed antisense oligonucleotides (ASOs) that switch PKM splicing from the cancer-associated PKM2 to the PKM1 isoform and induce apoptosis in cultured glioblastoma cells. Here, we explore the potential of ASO-based PKM splice-switching as a targeted therapy for liver cancer. We utilize a more potent lead cEt/DNA ASO and demonstrate that it induces PKM splice-switching and inhibits the growth of cultured hepatocellular-carcinoma (HCC) cells. This PKM isoform switch increases pyruvate-kinase activity and alters glucose metabolism. The lead ASO and a second ASO targeting a non-overlapping site inhibit tumorigenesis in an orthotopic-xenograft HCC mouse model. Finally, a surrogate mouse-specific ASO induces Pkm splice-switching and inhibits HCC growth, without observable toxicity, in a genetic HCC mouse model. These results lay the groundwork for a potential ASO therapy for HCC. Statement of significanceAntisense oligonucleotides are used to force a change in PKM isoform usage in HCC, reversing the Warburg effect and inhibiting tumorigenesis.

cancer biology↗

bioRxiv2020

Using rapid prototyping to choose a bioinformatics workflow management system

Workflow management systems represent, manage, and execute multi-step computational analyses and offer many benefits to bioinformaticians. They provide a common language for describing analysis workflows, contributing to reproducibility and to building libraries of reusable components. They can support both incremental build and re-entrancy - the ability to selectively re-execute parts of a workflow in the presence of additional inputs or changes in configuration and to resume execution from where a workflow previously stopped. Many workflow management systems enhance portability by supporting the use of containers, high-performance computing systems and clouds. Most importantly, workflow management systems allow bioinformaticians to delegate how their workflows are run to the workflow management system and its developers. This frees the bioinformaticians to focus on the content of these workflows, their data analyses, and their science. RiboViz is a package to extract biological insight from ribosome profiling data to help advance understanding of protein synthesis. At the heart of RiboViz is an analysis workflow, implemented in a Python script. To conform to best practices for scientific computing which recommend the use of build tools to automate workflows and to re-use code instead of rewriting it, the authors reimplemented this workflow within a workflow management system. To select a workflow management system, a rapid survey of available systems was undertaken, and candidates were shortlisted: Snakemake, cwltool and Toil (implementations of the Common Workflow Language) and Nextflow. An evaluation of each candidate, via rapid prototyping of a subset of the RiboViz workflow, was performed and Nextflow was chosen. The selection process took 10 person-days, a small cost for the assurance that Nextflow best satisfied the authors requirements. This use of rapid prototyping can offer a low-cost way of making a more informed selection of software to use within projects, rather than relying solely upon reviews and recommendations by others. Author summaryData analysis involves many steps, as data are wrangled, processed, and analysed using a succession of unrelated software packages. Running all the right steps, in the right order, with the right outputs in the right places is a major source of frustration. Workflow management systems require that each data analysis step be "wrapped" in a structured way, describing its inputs, parameters, and outputs. By writing these wrappers the scientist can focus on the meaning of each step, which is the interesting part. The system uses these wrappers to decide what steps to run and how to run these, and takes charge of running the steps, including reporting on errors. This makes it much easier to repeatedly run the analysis and to run it transparently upon different computers. To select a workflow management system, we surveyed available tools and selected three for "rapid prototype" implementations to evaluate their suitability for our project. We advocate this rapid prototyping as a low-cost (both time and effort) way of making an informed selection of a system for use within a project. We conclude that many similar multi-step data analysis workflows can be rewritten in a workflow management system.

bioinformatics↗

bioRxiv2020

Modulation of Aplnr signaling is required during the development and maintenance of the hematopoietic system

Apelin receptor (Aplnr/Agtrl1/Apj) marks a transient cell population during the differentiation of hematopoietic progenitor cells (HPCs) from pluripotent stem cells but the function of this signalling pathway during hematopoietic development both in vitro and in vitro is poorly understood. We generated an Aplnr-null mouse embryonic stem cell (mESC) line and demonstrated that they are significantly impaired in the production of HPCs indicating that the Aplnr pathway is required for their formation. Using Aplnr-tdTomato reporter mESCs we demonstrated that is expressed in a population of differentiating mesodermal cells committed to a hematopoietic and endothelial fate. Activation of this signaling pathway by the addition of the Apelin ligand to differentiating ESCs has no effect on the production of HPCs but the addition to ex vivo AGM cultures impaired the generation of long term reconstituting hematopoietic stem cells and appeared to drive myeloid differentiation. Taken together, our data suggest that the Aplnr pathway is required for the generation of cells that give rise to HSCs during development but its subsequent down regulation is required for their maintenance. HIGHLIGHTSO_LIHematopoietic differentiation is impaired in Aplnr-null ESCs C_LIO_LIAplnr-tdTomato reporter marks a subpopulation of ESC-derived mesoderm. C_LIO_LIAplnr signaling drives the maturation of lineage-committed myeloid progenitors C_LIO_LIIn AGM explant cultures HSC activity is reduced in the presence of Aplnr ligands. C_LI

developmental biology↗

bioRxiv2019

Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification

Translational frameshift errors are often deleterious to the synthesis of functional proteins as they lead to the production of truncated or inactive proteins. TrmD (tRNA-(N(1)G37) methyltransferase) is an essential tRNA modification enzyme in bacteria that prevents +1 errors in the reading frame during protein translation and has been identified as a therapeutic target for several bacterial infections. Here we validate TrmD as a target in Mycobacterium abscessus and describe the application of a structure-guided fragment-based drug discovery approach for the design of a new class of inhibitors against this enzyme. A fragment library screening followed by structure-guided chemical elaboration of hits led to the development of compounds with potent in vitro TrmD inhibitory activity. Several of these compounds exhibit activity against planktonic M. abscessus and Mycobacterium tuberculosis. The compounds were further active in macrophage infection models against Mycobacterium leprae and M. abscessus suggesting the potential for novel broad-spectrum mycobacterial drugs.

biochemistry↗

bioRxiv2018

MTSS1/Src family kinase Dysregulation Underlies Multiple Inherited Ataxias

The genetically heterogeneous Spinocerebellar ataxias (SCAs) are caused by Purkinje neuron dysfunction and degeneration, but their underlying pathological mechanisms remain elusive. The Src family of non-receptor tyrosine kinases (SFK) are essential for nervous system homeostasis and are increasingly implicated in degenerative disease. Here we reveal that the SFK suppressor Missing-in-Metastasis (MTSS1) is a novel ataxia locus that links multiple SCAs. MTSS1 loss results in increased SFK activity, reduced Purkinje neuron arborization, and low basal firing rates, followed by cell death. Surprisingly, mouse models for SCA1, SCA2, and SCA5 show elevated SFK activity, with SCA1 and SCA2 displaying dramatically reduced MTSS1 protein levels through reduced gene expression and protein translation, respectively. Treatment of each SCA model with a clinically-approved Src inhibitor corrects Purkinje basal firing, and delays ataxia progression in MTSS1 mutants. Our results identify a common SCA therapeutic target and demonstrate a key role for MTSS1/SFK in Purkinje neuron survival and ataxia progression.\n\nSignificance StatementThe Src family of non-receptor tyrosine kinases (SFK) are essential for nervous system function, and may contribute to neurodegeneration. Spinocerebellar ataxias (SCAs) are neurodegenerative diseases where Purkinje neurons fire irregularly and degenerate leading to motor problems. We show that the SFK suppressor Missing-in-Metastasis (MTSS1) is a novel ataxia gene that links multiple SCAs. MTSS1 loss results in increased SFK activity, degenerating Purkinje neurons with low basal firing rates, and cell death. Surprisingly, mouse models for three different SCAs show elevated SFK activity, with SCA1 and SCA2 models displaying dramatically reduced MTSS1 protein levels. Treatment of each SCA model with SFK inhibitor corrects Purkinje basal firing, and delays ataxia progression in MTSS1 mutants. Our results identify a common link among disparate neurodegenerative diseases.

neuroscience↗

bioRxiv2018

Anti-aging food that improves markers of health in senior dogs by modulating gut microbiota and metabolite profiles

Dysbiosis is one of the major changes in aging that leads to an accumulation of toxic microbial metabolites. The aim of this study was to evaluate the effect of a test food containing components of citrus, carrot, spinach and tomato on gut microbiota and age-related metabolites in senior dogs. The study was conducted on 36 dogs between 8 and 13 years of age. All dogs were maintained on a control food (control 1), which used corn as major source of fiber. After 30 days, the dogs were divided into two groups of 18 dogs. One of the groups received the test food for 30 days while the other group received the control 2 food, containing multiple whole grains as the test food but without the above added sources of fiber present in the test food. After a washout period on the control 1 food for 30 days, a cross-over was performed so that the test or the control 2 food was fed for 30 days to those dogs which had not yet been fed that food. Samples from feces and blood were collected after each 30 days period to analyze changes in gut microbial composition and metabolites. The consumption of the test food led to increased proportions of Adlercreutzia, Oscillospira, Phascolarcobacteria, Faecalibacterium and Ruminococcus, Christensenellaceae, Ruminococcaceae, Cyanobacteria and Acidobacteria and decreased proportions of Megamonas, Salmonella, Enterobacteriaceae and Fusobacterium. Pets had higher levels of glycerol and fatty acids and lower levels of pyrraline and mucin amino acids in feces. The test food also reduced circulating levels of pyrraline, symmetric dimethylarginine and phenolic uremic toxins, including the microbial brain toxin, 4-ethylphenyl sulfate. Christensenellaceae abundance was strongly associated with the observed health benefits. Fermentable fibers from fruits and vegetables enhance health in senior dogs by modulating the gut bacteria and metabolites involved in aging, kidney, brain and gut health.

microbiology↗

bioRxiv2017

Cytokinin signaling alters acid-fast staining of Mycobacterium tuberculosis

It was reported the human-exclusive pathogen Mycobacterium (M.) tuberculosis secretes cytokinins, which previously had only been known as plant hormones. Cytokinins are adenine-based signaling molecules in plants that have never been shown to participate in signal transduction in other kingdoms of life. Here, we show that cytokinins induce the strong expression of the M. tuberculosis gene, Rv0077c. We found that a TetR-like transcriptional regulator, Rv0078, directly repressed expression of the Rv0077c gene. Strikingly, cytokinin-induced expression of Rv0077c resulted in a loss of acid-fast staining of M. tuberculosis. Although acid-fast staining is thought to be associated with changes in the bacterial cell envelope and virulence, Rv0077c-induced loss of acid-fastness did not affect antibiotic susceptibility or attenuate bacterial growth in mice. Collectively, these findings show cytokinins signal transcriptional changes that affect the M. tuberculosis cell envelope, and that cytokinin signaling is no longer limited to the kingdom plantae.

microbiology↗