Biology subjects

Gill, S.

Publications and source records attributed to Gill, S..

31 records · Page 2Linked to original sources

bioRxiv2020

DNA methylation and survival differences associated with the type of IDH mutation in 1p/19q non-codeleted astrocytomas

Somatic mutations in the isocitrate dehydrogenase genes IDH1 and IDH2 occur at high frequency in several tumour types. Even though these mutations are confined to distinct hotspots, we show that gliomas are the only tumour type with an exceptionally high percentage of IDH1R132H mutations. This high prevalence is important as IDH1R132H is presumed to be relatively poor at producing D-2-hydroxyglutarate (D-2HG) whereas high concentrations of this oncometabolite are required to inhibit TET2 DNA demethylating enzymes. Indeed, patients harbouring IDH1R132H mutated tumours have lower levels of genome-wide DNA-methylation, and an associated increased gene expression, compared to tumours with other IDH1/2 mutations ("non-R132H mutations"). This reduced methylation is seen in multiple tumour types and thus appears independent of site of origin. For 1p/19q non-codeleted glioma patients, we show that this difference is clinically relevant: in samples of the randomised phase III CATNON trial, patients harbouring non-R132H mutated tumours have better outcome (HR 0.41, 95% CI [0.24, 0.71], p=0.0013). Non-R132H mutated tumours also had a significantly lower proportion of tumours assigned to prognostically poor DNA-methylation classes (p<0.001). IDH mutation-type was independent in a multivariable model containing known clinical and molecular prognostic factors. To confirm these observations, we validated the prognostic effect of IDH mutation type on a large independent dataset. The observation that non-R132H mutated 1p/19q non-codeleted gliomas have a more favourable prognosis than their IDH1R132H mutated counterpart is clinically relevant and should be taken into account for patient prognostication. Single sentence summaryAstrocytoma patients with tumours harbouring IDH mutations other than p.R132H have increased DNA methylation levels and longer survival

cancer biology↗

bioRxiv2020

Validation and Long-Term Follow Up of CD33 Off-Targets Predicted In Vitro and In Silico Using Error-Corrected Sequencing in Rhesus Macaques

ABSTRACTThe programmable nuclease technology CRISPR/Cas9 has revolutionized gene editing in the last decade. Due to the risk of off-target editing, accurate and sensitive methods for off-target characterization are crucial prior to applying CRISPR/Cas9 therapeutically. Here, we utilized a rhesus macaque model to ask whether CIRCLE-Seq (CS), an in vitro off-target prediction method, more accurately identifies off-targets compared to in silico prediction (ISP) based solely on genomic sequence comparisons. We use AmpliSeq HD error-corrected sequencing to validate off-target sites predicted by CIRCLE-Seq and ISP for guide RNAs designed against TET2 and CD33 genes. A gRNA targeting TET2 designed using modern algorithms and predicted to have low off-target risk by both ISP and CIRCLE-Seq created no detectable mutations at off-target sites in hematopoietic cells following transplantation, even when applying highly sensitive error-corrected sequencing. In contrast, a CD33 gRNA designed using less robust algorithms with over 10-fold more off-targets sites predicted by both ISP and CIRCLE-Seq, however there was poor correlation between the sites predicted by the two methods. When almost 500 sites identified by each method were searched for in hematopoietic cells following transplantation, 19 detectable mutations in off-target sites were detected via error-corrected sequencing. Of these 19 sites, 8 sites were predicted in the top 500 sites by both methods, 8 by CIRCLE-Seq only, and 3 by ISP only. Cells with off-target editing exhibited no expansion or abnormal behavior in vivo in animals followed for up to 2 years. In conclusion, neither methodology predicted all sites, and a combination of careful gRNA design, followed by screening for predicted off-target sites in target cells by multiple methods may be required for optimizing safety of clinical development.Competing Interest StatementThe authors have declared no competing interest.View Full Text

molecular biology↗

bioRxiv2020

Characterization of chondroitinase-induced lumbar intervertebral disc degeneration in a sheep model intended for assessing biomaterials

Intervertebral disc (IVD) degeneration (IVDD) leads to structural and functional changes. Biomaterials for restoring IVD function and promoting regeneration are currently being investigated; however, such approaches require validation using animal models that recapitulate clinical, biochemical, and biomechanical hallmarks of the human pathology. Herein, we comprehensively characterized a sheep model of chondroitinase-ABC (C-ABC) induced IVDD. Briefly, C-ABC (1U) was injected into the L1/2, L2/3, and L3/4 IVDs. Degeneration was assessed via longitudinal magnetic resonance (MR) and radiographic imaging. Additionally, kinematic, biochemical, and histological analyses were performed on explanted functional spinal units (FSUs). At 17-weeks, C-ABC treated IVDs demonstrated significant reductions in MR index (p=0.030) and disc height (p=0.009) compared to pre-operative values. Additionally, C-ABC treated IVDs exhibited significantly increased creep displacement (p=0.004) and axial range of motion (p=0.007) concomitant with significant decreases in tensile (p=0.034) and torsional (p=0.021) stiffnesses and long-term viscoelastic properties (p=0.016). C-ABC treated IVDs also exhibited a significant decrease in NP glycosaminoglycan: hydroxyproline ratio (p=0.002) and changes in microarchitecture, particularly in the NP and endplates, compared to uninjured IVDs. Taken together, this study demonstrated that intradiscal injection of C-ABC induces significant degeneration in sheep lumbar IVDs and its potential for use in evaluating biomaterials for IVD repair. Statement of SignificanceSelecting the appropriate model for assessing biomaterials to repair and/or support regeneration of the intervertebral disc (IVD) has been controversial, leading to the use of many methods of simulating IVD degeneration (IVDD) in multiple species. Many of these models lack thorough characterization of their fidelity to human IVDD, which could hinder the translation of novel biomaterials and therapies due to unknown confounding factors. Herein, further investigation of one such model was performed using the matrix-degrading enzyme chondroitinase-ABC to induce degeneration in sheep lumbar IVDs. Degenerative changes were quantified using outcome measures relevant to human IVDD, and this dosage and method induces an aggressive degeneration environment that could be used to assess biomaterials that mimic the structure and function of the entire composite IVD. These findings may aid investigators in their selection of an appropriate animal model for preclinical testing of biomaterials and other therapeutics.

bioengineering↗

bioRxiv2020

Long-term associations and insights on social structure of the Humpback whales in Prince William Sound, Alaska

Humpback whale (Megaptera novaeangliae) social structure is more complex than previously thought. Because of the fluid "fission-fusion" nature of their relationships: individuals foraging, traveling, and socializing with a number of animals, where associations form and are broken numerous times, little has been confirmed about their long-term associations. Humpback whales of the North Pacific Ocean migrate annually between tropical breeding areas to northern latitudes where they congregate and feed. The purpose of this study was to explore the social and feeding habits of the summer population of humpback whales returning to Prince William Sound (PWS) in the south central coast of Alaska. Fluke photographs of pigmentation patterns were used to document individual whales between the years 1983 and 2009 to determine, population characteristics, reproductive rates, long-term associations, feeding habits and spatial partitioning. During the 27 year study period there were 3,017 encounters with 405 unique whales. Forty of these whales (9.88%) had long sighting histories, showing strong site fidelity. Association indices for all pairs of whales were calculated. Long-lasting associations were found between thirty-two of the forty whales. Two distinct groups were determined by the highest association coefficients. Although the overall ranges of the two groups overlapped, they did not often mingle and offspring did not join their maternal group. All but two females had enduring bonds with at least one male. Associate males were sometimes found at a distance from others of their "clan" and would rejoin periodically. Two whales from one of these clans were found together in Hawaiian waters, a male escorting a female with a newborn calf, suggesting these long lasting associations endure through migration and into the southern breeding areas. Optimal observation conditions of a small population of humpback whales in sheltered waters allowed the discovery of two social groups enduring almost three decades.

animal behavior and cognition↗

bioRxiv2019

Evaluation of deacetylase inhibition in metaplastic breast carcinoma using multiple derivations of preclinical models of a new patient-derived tumor

Metaplastic breast carcinoma (MBC) is a clinically aggressive and rare subtype of breast cancer, with similar features to basal-like breast cancers. Due rapid growth rates and characteristic heterogeneity, MBC is often unresponsive to standard chemotherapies; and novel targeted therapeutic discovery is urgently needed. Histone deacetylase inhibitors (DACi) suppress tumor growth and metastasis through regulation of the epithelial-to-mesenchymal transition axis in various cancers, including basal-like breast cancers. We utilized a new MBC patient-derived xenograft (PDX) to examine the effect of DACi therapy on MBC. Cell morphology, cell cycle-associated gene expressions, transwell migration, and metastasis were evaluated in patient-derived cells and tumors after treatment with romidepsin and panobinostat. Derivations of our PDX model, including cells, spheres, organoids, explants, and in vivo implanted tumors were treated. Finally, we tested the effects of combining DACi with approved chemotherapeutics on relative cell biomass. DACi significantly suppressed the total number of lung metastasis in vivo using our PDX model, suggesting a role for DACi in preventing circulating tumor cells from seeding distal tissue sites. These data were supported by our findings that DACi reduced cell migration, populations, and expression of mesenchymal-associated genes. While DACi treatment did affect cell cycle-regulating genes in vitro, tumor growth was not affected compared to controls. Importantly, gene expression results varied depending on the cellular or tumor system used, emphasizing the importance of using multiple derivations of cancer models in preclinical therapeutic discovery research. Furthermore, DACi sensitized and produced a synergistic effect with approved oncology therapeutics on inherently resistant MBC. This study introduced a role for DACi in suppressing the migratory and mesenchymal phenotype of MBC cells through regulation of the epithelial-mesenchymal transition axis and suppression of the CTC population. Preliminary evidence that DACi treatment in combination with MEK1/2 inhibitors exerts a synergistic effect on MBC cells was also demonstrated.

cancer biology↗

bioRxiv2019

Small-molecule control of super-Mendelian inheritance in gene drives

By surpassing the 50% inheritance limit of Mendels law of independent assortment, CRISPR-based gene drives have the potential to fight vector-borne diseases or suppress crop pests. However, contemporary gene drives could spread unchecked, posing safety concerns that limit their use in both laboratory and field settings. Current technologies also lack chemical control strategies, which could be applied in the field for dose, spatial and temporal control of gene drives. We describe in Drosophila the first gene-drive system controlled by an engineered Cas9 and a synthetic, orally-available small molecule.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=51 SRC=\"FIGDIR/small/665620v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (15K):\norg.highwire.dtl.DTLVardef@1aa8522org.highwire.dtl.DTLVardef@a99c8org.highwire.dtl.DTLVardef@1f63636org.highwire.dtl.DTLVardef@1613408_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

genetics↗

bioRxiv2019

Impaired tumor death receptor signaling drives resistance to CAR T cell therapy

Cellular immunotherapy using T cells engineered to express chimeric antigen receptors targeting CD19 (CART19) leads to long-term remission in patients with B-cell malignancies1-5. Unfortunately, a significant fraction of patients demonstrate primary resistance to CART19 or experience relapse after achieving remission. Beyond loss of target antigen, the molecular pathways governing CART19 failure are unknown. Here we demonstrate that death receptors, cell surface signaling molecules that induce target cell apoptosis, are key mediators of leukemic resistance and CART19 failure. Using a functional CRISPR/Cas9-based genome-wide knockout screen6 in B-cell acute lymphoblastic leukemia (ALL), we identified the death receptor signaling pathway as a central regulator of sensitivity to CART19-induced cell death. In the absence of the pro-apoptotic death receptor signaling molecules BID or FADD, ALL cells were resistant to CART19 cytotoxicity, resulting in rapid disease progression in mice. We found that this initial resistance to cytotoxicity led to persistence of tumor cells, which drove the development of T cell dysfunction that further compromised anti-tumor immunity and permitted tumor outgrowth. We validated these findings using clinical samples collected from patients with ALL treated with CD19-targeted CAR T cells and found that expression of pro-apoptotic death receptor pathway genes in pre-treatment tumor samples correlated with CAR T cell expansion and persistence, as well as patient response and overall survival. Our findings indicate that tumor-intrinsic death receptor signaling directly contributes to CAR T cell failure.

immunology↗

bioRxiv2019

Differential Effector Response of Amnion- and Adipose-Derived Mesenchymal Stem Cells to Inflammation; Implications for Intradiscal Therapy

Intervertebral disc degeneration (IVDD) is a progressive condition marked by inflammation and tissue destruction. The effector functions of mesenchymal stem cells (MSCs) make them an attractive therapy for patients with IVDD. While several sources of MSCs exist, the optimal choice for use in the inflamed IVD remains a significant question. Adipose (AD)- and amnion (AM)-derived MSCs have several advantages compared to other sources, however, no study has directly compared the impact of IVDD inflammation on their effector functions. Human MSCs were cultured in media with or without supplementation of interleukin-1{beta} and tumor necrosis factor- at concentrations produced by IVDD cells. MSC proliferation and production of pro- and anti-inflammatory cytokines were quantified following 24- and 48-hours of culture. Additionally, the osteogenic and chondrogenic potential of AD- and AM-MSCs was characterized via histology and biochemical analysis following 28 days of culture. In inflammatory culture, AM-MSCs produced significantly more anti-inflammatory IL-10 (p=0.004) and larger chondrogenic pellets (p=0.04) with greater percent area staining positively for glycosaminoglycan (p<0.001) compared to AD-MSCs. Conversely, AD-MSCs proliferated more resulting in higher cell numbers (p=0.048) and produced higher concentrations of pro-inflammatory cytokines PGE2 (p=0.030) and IL-1{beta} (p=0.010) compared to AM-MSCs. Additionally, AD-MSCs produced more mineralized matrix (p<0.001) compared to AM-MSCs. These findings begin to inform researchers and clinicians as to which MSC source may be optimal for different IVD therapies including those that may promote regeneration or fusion. Further study is warranted evaluating these cells in systems which recapitulate the nutrient- and oxygen-deprived environment of the degenerate IVD.

bioengineering↗

bioRxiv2018

Pesticide exposure affects flight dynamics and reduces flight endurance in bumblebees

The emergence of agricultural land use change creates a number of challenges that insect pollinators, such as eusocial bees, must overcome. Resultant fragmentation and loss of suitable foraging habitats, combined with pesticide exposure, may increase demands on foraging, specifically the ability to reach resources under such stress. Understanding the effect that pesticides have on flight performance is therefore vital if we are to assess colony success in these changing landscapes. Neonicotinoids are one of the most widely used classes of pesticide across the globe, and exposure to bees has been associated with reduced foraging efficiency and homing ability. One explanation for these effects could be that elements of flight are being affected, but apart from a couple of studies on the honeybee, this has scarcely been tested. Here we used flight mills to investigate how exposure to a field realistic (10ppb) acute dose of imidacloprid affected flight performance of a wild insect pollinator - the bumblebee, Bombus terrestris audax. Intriguingly, intial observations showed exposed workers flew at a significantly higher velocity over the first [3/4] km of flight. This apparent hyperactivity, however, may have a cost as exposed workers showed reduced flight distance and duration to around a third of what control workers were capable of achieving. Given that bumblebees are central place foragers, impairment to flight endurance could translate to a decline in potential forage area, decreasing the abundance, diversity and nutritional quality of available food, whilst potentially diminishing pollination service capabilities.\n\nSummary StatementAcute neonicotinoid exposure impaired flight endurance and affected velocity of Bombus terrestris workers, which may dramatically reduce colony foraging potential and pollination provision in pesticide applied landscapes.

ecology↗

bioRxiv2018

Multi-laminate Annulus Fibrosus Repair Scaffold with an Interlamellar Matrix Enhances Impact Resistance, Prevents Herniation and Assists in Restoring Spinal Kinematics

Focal defects in the annulus fibrosus (AF) of the intervertebral disc (IVD) from herniation or surgical injury have detrimental impacts on IVD mechanical function. Thus, biomaterial-based repair strategies, which can restore the mechanical integrity of the AF and support long-term tissue regeneration are needed. Accordingly, a collagen-based multi-laminate scaffold with an underlying \"angle-ply\" architecture has been previously reported demonstrating similar mechanical properties to native AF tissue. The objectives of this work were to: 1) enhance the biomaterials impact strength, 2) define its contribution to spinal kinematics, and 3) assess its ability to prevent IVD herniation. First, AFRPs were enriched with a glycosaminoglycan-based (GAG) interlamellar matrix (ILM), and then tested for its radially-directed impact resistance under physiological stresses. Subsequent kinematic testing was conducted using a characterized GAG-enriched AFRP as an AF focal defect closure device. In summary, AFRPs demonstrated 1) incorporation of a GAG-based ILM significantly increased radial impact strength, 2) restoration of axial FSU kinematics and 3) ability to prevent herniation of native IVD tissues. Together, these results suggest that the AFRP demonstrates the mechanical robustness and material properties to restore an IVDs physiological mechanical function through the adequate closure of an AF focal defect.

bioengineering↗

bioRxiv2018

A pilot investigation of chemonucleolysis-induced intervertebral disc degeneration in the ovine lumbar spine

Intervertebral disc (IVD) degeneration (IVDD) initiates in the nucleus pulposus (NP) and is marked by elevated levels of pro-inflammatory cytokines and matrix-degrading proteases, leading to structural and functional disruption. IVDD therapeutics are currently being investigated; however, such approaches require validation using large animal models that recapitulate clinical, biochemical, and biomechanical hallmarks of the human pathology. Others have previously utilized intradiscal administration of chondroitinase-ABC (C-ABC) to initiate IVDD in the NP of sheep lumbar IVDs. While these studies examined changes in IVD height, hydration, and tissue micro-architecture, changes in biochemical content and mechanical properties were not assessed. Thus, the objective herein was to comprehensively characterize this ovine model IVDD for salient features reported in human degenerate IVDs by evaluating biochemical, biomechanical, and histological changes. Briefly, C-ABC (1U) was administered via intradiscal injection into the L1/2, L2/3, and L3/4 IVDs, and degeneration was assessed at 6- and 10-weeks via longitudinal magnetic resonance (MR) imaging. After 6 weeks, degenerative samples showed significant reductions in IVD heights (p=0.048) and MR imaging index (p=0.048), which worsened at 10 weeks. Post-mortem degenerate and controls IVDs were evaluated for differences in interleukin-1{beta} concentration, axial and torsional functional spinal unit kinematics, and histological microarchitecture. Degenerate IVDs demonstrated significantly elevated concentrations of interleukin-1{beta} (p=0.002). Additionally, degenerative samples showed increased creep displacement (p=0.022) and compressive stiffnesss (p=0.007) concurrent with decreased long-term elastic (p=0.007) and viscous dampening coefficients (p=0.002). Histological analysis of degenerative IVDs showed changes in microarchitecture, including derangement of the nucleus pulposus and annulus fibrosus tissue as well as cartilaginous end-plate irregularities. This pilot study demonstrated that intradiscal injection of 1U C-ABC induces significant and progressive degeneration of sheep lumbar IVDs over the time course investigated. The changes observed in this pilots study small sample size resemble the hallmarks of moderate to severe IVD degeneration observed in humans. Further study is warranted on a larger sample size to further validate these findings.

bioengineering↗

bioRxiv2017

The crossmodal congruency effect, a tool incorporation metric, suffers from a learning effect with repeated exposures

The incorporation of feedback into a persons body schema is well established. The crossmodal congruency effect (CCE) task is used to objectively quantify incorporation without being susceptible to experimenter biases. This visual-tactile interference task is used to calculate the CCE score as a difference in response time for incongruent and congruent trials. Here we show that this metric is susceptible to a learning effect that causes attenuation of the CCE score due to repeated task exposure sessions. We demonstrate that this learning effect is persistent, even after a 6 month hiatus in testing. Two mitigation strategies are proposed: 1. Only use CCE scores that are taken after learning has stabilized, or 2. Use a modified CCE protocol that decreases the task exposure time. We show that the modified and shortened CCE protocol, which may be required to meet time or logistical constraints in laboratory or clinical settings, reduced the impact of the learning effect on CCE results. Importantly, the CCE scores from the modified protocol were not significantly more variable than results obtained with the original protocol. This study highlights the importance of considering exposure time to the CCE task when designing experiments and suggests two mitigation strategies to improve the utility of this psychophysical assessment.

neuroscience↗

bioRxiv2016

Genome-wide association analyses of sleep disturbance traits identify new loci and highlight shared genetics with neuropsychiatric and metabolic traits

Chronic sleep disturbances, associated with cardio-metabolic diseases, psychiatric disorders and all-cause mortality1,2, affect 25-30% of adults worldwide3. While environmental factors contribute importantly to self-reported habitual sleep duration and disruption, these traits are heritable4-9, and gene identification should improve our understanding of sleep function, mechanisms linking sleep to disease, and development of novel therapies. We report single and multi-trait genome-wide association analyses (GWAS) of self-reported sleep duration, insomnia symptoms including difficulty initiating and/or maintaining sleep, and excessive daytime sleepiness in the UK Biobank (n=112,586), with discovery of loci for insomnia symptoms (near MEIS1, TMEM132E, CYCL1, TGFBI in females and WDR27 in males), excessive daytime sleepiness (near AR/OPHN1) and a composite sleep trait (near INADL and HCRTR2), as well as replication of a locus for sleep duration (at PAX-8). Genetic correlation was observed between longer sleep duration and schizophrenia (rG=0.29, p=1.90x10-13) and between increased excessive daytime sleepiness and increased adiposity traits (BMI rG=0.20, p=3.12x10-09; waist circumference rG=0.20, p=2.12x10-07).

genetics↗