Biology subjects

Reid, L.

Publications and source records attributed to Reid, L..

6 recordsLinked to original sources

bioRxiv2026

HDAC11 Regulates RNA Splicing via De-Fatty Acylation of SF3B2

Histone deacetylase 11 (HDAC11) is a lysine de-fatty acylase whose cellular substrates and mechanisms remain incompletely defined. Here, using metabolic labeling, mass spectrometry, click chemistry, and standard molecular biology, we show that SF3B2 is modified by lysine myristoylation at K10 and that HDAC11 efficiently removes this modification in cells, establishing SF3B2 as a direct enzymatic substrate. A de-myristoylation mimetic mutant (SF3B2 K10R) exhibits altered pre-mRNA binding activity in a context-dependent manner. In HCC cells, loss of SF3B2 lysine myristoylation enhances SF3B2 association with androgen receptor (AR) splice variant loci and promotes alternative splicing towards the AR-v7 variant. Consistently, HDAC11 overexpression increases, and HDAC11 knockdown decreases, the AR-v7/AR-FL splice isoform ratio in HCC cells in a manner requiring HDAC11 catalytic activity and recapitulated by SF3B2 K10R. In contrast, modulation of HDAC11 does not alter AR splicing in prostate cancer cells, indicating cell type specific regulation. Together, these findings establish lysine myristoylation as a reversible regulatory modification on a spliceosomal component and reveal HDAC11-catalyzed de-myristoylation of SF3B2 as a mechanism that can tune alternative splicing in liver cancer cells. In BriefClements et al. utilize metabolic labelling, mass spectrometry, click chemistry, and protein and RNA biochemistry to establish that a histone deacetylase enzyme, HDAC11, can influence RNA splicing through de-fatty acylation of the RNA splicing factor SF3B2. De-fatty acylation of SF3B2 at K10 by HDAC11 modulates SF3B2s pre-mRNA binding to AR splice variant loci, thereby driving alternative splicing of the AR-v7 variant in a cell type dependent manner. This work provides direct mechanistic evidence linking an HDAC to RNA splicing, identifies a reversible lipid modification on SF3B2, and expands current understanding of post-translational regulation of spliceosomal proteins and HDAC11 de-fatty acylation substrates. HighlightsO_LIHDAC11 de-fatty-acylates SF3B2 at K10, revealing a previously unrecognized modification on SF3B2. C_LIO_LISF3B2 de-fatty acylation enhances alternative splice-site binding in liver cancer cells. C_LIO_LIHDAC11 regulates RNA splicing through enzymatic de-fatty acylation of a spliceosomal protein. C_LI

molecular biology↗

bioRxiv2024

A rational approach for the targeted discovery and characterisation of microbiome-derived therapeutics

The human gut microbiome is intrinsically involved in health and disease, representing a wealth of untapped therapeutic potential. Here, we demonstrate the utility and potential of a metagenome guided, large cohort-based approach for the rational selection of live biotherapeutics from the human gut. We applied this approach to Inflammatory Bowel Disease (IBD), identifying several lead candidates that were significantly depleted in individuals with IBD compared to healthy controls. Their therapeutic potential was assessed in preclinical models of IBD where they improved markers of disease pathology by reducing inflammation and promoting mucosal healing and wound repair. All leads had excellent safety profiles in silico and in vitro, and several additionally presented favourable manufacturing properties, supporting their progression into clinical trials. We believe that this rational approach will be generalisable to any disease state with underlying microbiome aetiology and will expedite the development of novel microbiome-derived therapeutics to improve human health.

microbiology↗

bioRxiv2024

Therapeutic DBS for OCD Suppresses the Default Mode Network

BackgroundDeep brain stimulation (DBS) of the anterior limb of the internal capsule (ALIC) is an emerging treatment for severe, refractory obsessive-compulsive disorder (OCD). The therapeutic effects of DBS are hypothesized to be mediated by direct modulation of a distributed cortico-striato-thalmo-cortical network underlying OCD symptoms. However, the exact underlying mechanism by which DBS exerts its therapeutic effects still remains unclear. MethodIn five participants receiving DBS for severe, refractory OCD (3 responders, 2 non-responders), we conducted a DBS On/Off cycling paradigm during the acquisition of functional MRI to determine the network effects of stimulation across a variety of bipolar configurations. We also performed tractography using diffusion-weighted imaging (DWI) to relate the functional impact of DBS to the underlying structural connectivity between active stimulation contacts and functional brain networks. ResultsWe found that therapeutic DBS had a distributed effect, suppressing BOLD activity within regions such as the orbitofrontal cortex, dorsomedial prefrontal cortex, and subthalamic nuclei compared to non-therapeutic configurations. Many of the regions suppressed by therapeutic DBS were components of the default mode network (DMN). Moreover, the estimated stimulation field from the therapeutic configurations exhibited significant structural connectivity to core nodes of the DMN. ConclusionsTherapeutic DBS for OCD suppresses BOLD activity within a distributed set of regions within the DMN relative to non-therapeutic configurations. We propose that these effects may be mediated by interruption of communication through structural white matter connections surrounding the DBS active contacts.

neuroscience↗

bioRxiv2021

Chemical, molecular, and single cell analysis reveal chondroitin sulfate proteoglycan aberrancy in fibrolamellar carcinoma

Fibrolamellar carcinoma (FLC) is an aggressive liver cancer with no effective therapeutic options. The extracellular environment of FLC tumors is poorly characterized and may contribute to cancer growth and/or metastasis. To bridge this knowledge gap, we assessed pathways relevant to proteoglycans, a major component of the extracellular matrix. We first analyzed gene expression data from FLC and non-malignant liver tissue (n=27) to identify changes in glycosaminoglycan (GAG) biosynthesis pathways and found that genes associated with production of chondroitin sulfate, but not other GAGs, are significantly increased by 8-fold. We then implemented a novel LC-MS/MS based method to quantify the abundance of different types of GAGs in patient tumors (n=16) and found that chondroitin sulfate is significantly more abundant in FLC tumors by 6-fold. Upon further analysis of GAG-associated proteins we found that versican (VCAN) expression is significantly up-regulated at the mRNA and protein levels, the latter of which was validated by immunohistochemistry. Finally, we performed single-cell assay for transposon-accessible chromatin-sequencing on FLC tumors (n=3), which revealed for the first time the different cell types in FLC tumors and also showed that VCAN is likely produced not only from FLC tumor epithelial cells but also activated stellate cells. Our results reveal a pathologic aberrancy in chondroitin (but not heparan) sulfate proteoglycans in FLC and highlight a potential role for activated stellate cells. SignificanceThis study leverages a multi-disciplinary approach, including state-of-the-art chemical analyses and cutting-edge single-cell genomic technologies, to identify for the first time a marked chondroitin sulfate aberrancy in fibrolamellar carcinoma (FLC) that could open novel therapeutic avenues in the future.

cancer biology↗

bioRxiv2019

Host defense responses of CO441 and CL30 maize lines to Fusarium graminearum analyzed by comparative label-free quantitative proteomics

Gibberella ear rot is a disease of maize associated with low yields and the production of harmful mycotoxins therein. The disease is caused by the infection of host Zea mays with fungal pathogen Fusarium graminearum. Resistant (CO441) and susceptible (CL30) inbred maize line kernels were inoculated with conidial suspensions of F. graminearum or water (controls). Ears of maize (cobs) from each line were harvested upon maturation and proteins were extracted from the embryo tissue of the kernels to study tissue-specific response of the host. Embryo proteins from both CO441 and CL30 lines were sequenced using mass spectrometry (LC-MS/MS) and quantified using Label Free Quantification (LFQ). Following filtering, 509 proteins were identified. These proteins were grouped into nine functional categories: Fusarium-derived, late embryogenesis abundant, oil-body, metabolism, stress, cellular, protein storage, metabolism, and defense. Defense proteins were up-regulated in response to infection in both CO441 and CL30 lines. Furthermore, F. graminearum derived proteins were only found in CL30 infected kernels suggesting that resistance may be attributed in part to the inability of Fusarium to establish itself in the embryo. To our knowledge this is the first successful application of LFQ mass spectrometry to the study of host-pathogen response to F. graminearum.\n\nBiological significanceFungal pathogen Fusarium graminearum is responsible for billion dollar losses in crops and contamination of global grains with harmful mycotoxins. By studying host-pathogen interactions of Fusarium and maize on a proteomic level with resistant and susceptible genotypes, the biological interactions occurring during infection of the maturing seed were characterized. Mature kernels of the F. graminearum susceptible maize line CL30 and resistant CO441 line were dissected to permit a proteomic survey of the new sporophytic generation, the embryo. Detailed knowledge of this Host-pathogen interactome will assist development of new cereal lines resistant to the rot diseases caused by Fusarium graminearum.\n\nHighlightsSusceptible (CL30) and Resistant (CO441) lines were injected with water mock or F. graminearum LC-MS/MS of maize embryo protein extracts followed by Label Free Quantification (LFQ) permitted identification, quantification and comparison of proteomes between maize genotypes and treatments Fusarium-derived proteins were abundant only in the susceptible infected embryo Defense proteomes were up-regulated in both lines following infection nsLTP and Protease Inhibitor were significantly over-expressed in the Susceptible line after infection; chitinase and WIP1 were significantly over-expressed in the Resistant line after infection

plant biology↗

bioRxiv2019

Early-Stage Ocular Hypertension Alters Retinal Ganglion Cell Synaptic Transmission in the Visual Thalamus

Axonopathy is a hallmark of many neurodegenerative diseases including glaucoma, where elevated intraocular pressure (ocular hypertension, OHT) stresses retinal ganglion cell (RGC) axons as they exit the eye and form the optic nerve. OHT causes early changes in the optic nerve such as axon atrophy, transport inhibition, and gliosis. Importantly, many of these changes appear to occur prior to irreversible neuronal loss, making them promising points for early diagnosis of glaucoma. It is unknown whether OHT has similarly early effects on the function of RGC output to the brain. To test this possibility, we elevated eye pressure in mice by anterior chamber injection of polystyrene microbeads. 5 weeks post-injection, bead-injected eyes showed a modest RGC loss in the peripheral retina, as evidenced by RBPMS antibody staining. Additionally, we observed reduced dendritic complexity and lower spontaneous spike rate of On-RGCs, targeted for patch clamp recording and dye filling using a Opn4-cre reporter mouse line. To determine the influence of OHT on retinal projections to the brain, we expressed Channelrhodopsin-2 (ChR2) in melanopsin-expressing retinal ganglion cells by crossing the Opn4-cre mouse line with a ChR2-reporter mouse line and recorded post-synaptic responses in thalamocortical relay neurons in the dorsal lateral geniculate nucleus (dLGN) of the thalamus evoked by stimulation with 460 nm light. The use of a Opn4-cre reporter system allowed for expression of ChR2 in a narrow subset of RGCs responsible for image-forming vision in mice. Five weeks following OHT induction, paired pulse and high-frequency stimulus train experiments revealed that presynaptic vesicle release probability at retinogeniculate synapses was elevated. Additionally, miniature synaptic current frequency was slightly reduced in brain slices from OHT mice and proximal dendrites of post-synaptic dLGN relay neurons, assessed using a Sholl analysis, showed a reduced complexity. Strikingly, these changes occurred prior to major loss of RGCs labeled with the Opn4-Cre mouse, as indicated by immunofluorescence staining of ChR2-expressing retinal neurons. Thus, OHT leads to pre- and post-synaptic functional and structural changes at retinogeniculate synapses. Along with RGC dendritic remodeling and optic nerve transport changes, these retinogeniculate synaptic changes are among the earliest signs of glaucoma.

neuroscience↗