Biology subjects

Foster, C.

Publications and source records attributed to Foster, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Proteolytic control of the SARS-CoV-2 furin cleavage site defines the phenotypic evolution from the pandemic to endemic state

The successive emergence of SARS-CoV-2 variants with altered tissue tropism has progressively decoupled transmissibility from lower respiratory tract pathogenicity. Omicron lineages transmit exceptionally well whilst limiting severe lung disease. Here, we demonstrate that this phenotype has evolved through two temporally distinct tissue-specific proteolytic controls at the Spike (S) furin cleavage site (FCS). At the virion level, cell-type-dependent furin-mediated FCS hyper-cleavage depletes S in lung but not nasal epithelial cells. At the infected cell membrane during cell-cell spread, TMPRSS2 mediates S FCS cleavage but is negatively regulated in the presence of ACE2. Tissue-specific solute carriers SLC6A19 and SLC6A20 sequester ACE2, thereby relieving inhibition of TMPRSS2 and enabling S FCS cleavage during cell-cell spread. Critically, whilst all SARS-CoV-2 lineages benefit from this latter pathway, Omicron variants have evolved exclusive dependence on it, a strategic consolidation that focuses S proteolytic activation to TMPRSS2 alone. The combined outcomes of S protein regulation across viral and cell membranes reveal how tissue-specific proteolytic optimisation drives Omicron's transmission fitness advantage in the upper respiratory tract but at the cost of heavy attenuation in the lower respiratory tract.

microbiology↗

bioRxiv2026

Novel Methylation Markers in a Prostate Cancer Cohort are Associated with Disease Development and Relapse

Prostate cancer remains one of the most common cancers among men globally. While significant strides have been made in diagnosis and treatment, understanding the complex genetic and epigenetic underpinnings of the disease remains crucial for guiding intervention and developing more personalized and effective therapies. The importance of DNA methylation in prostate cancer has been known for some time, but important facets of the modulation of the epigenome during carcinogenesis remain obscure, partly because the bulk of cancer methylation data have been produced using microarray technologies. Here we utilise the TruSeq methyl capture method (EPICseq) to profile the, previously defined, UK Prostate ICGC cohort of well-annotated primary prostate cancers. To this we add methylation sequencing of benign tissue from the same men. These data allow us to identify differentially methylated regions distinguishing cancerous and non-cancerous prostate tissue, while identifying numerous genes whose methylation profiles can perform that task as well as distinguishing between classes of prostate cancer. We describe a describe a methylation-based control mechanism for prostate-cancer-associated SNPs, and show that this seems a likely mechanism of action for a SNP near the MMP7 gene. We describe three novel molecular signatures that arise from different aspects of the biology of prostate cancer revealed by sequencing. Each is shown to be an independent classifier of cancers into groups with different expected times to relapse. These consist of patterns in driver gene methylation, strand-specific methylation, and signal arising in mitochondrial reads. We show that these signatures, combined with existing molecular tools, provide a powerful predictor of time to recurrence. By substantially enhancing understanding of prostate cancer risk, detection, and prognosis, we pave the way for the development of clinical practices that will benefit patients and improve outcomes.

cancer biology↗

bioRxiv2026

Spatial localisation of touch on a robotic limb in the absence of direct haptic feedback

Artificial limbs typically lack somatosensory receptors, limiting users access to haptic feedback about movement outcomes. However, indirect tactile signals generated during object interaction are transmitted to the body-limb interface and may serve as a haptic feedback source. This study investigates whether such indirect tactile signals convey distinct information that can support localisation of touch on an artificial body part. Using an additional robotic thumb (The Third Thumb, Dani Clode Design), we measured tactile signals at the interface between the Third Thumb and the hand following stimulation from four vibration motors positioned along the Thumb. We then assessed whether participants could discriminate these signals and integrate them with different Thumb postures to spatially localise touch. Measurements showed that each stimulation site produced distinct tactile signatures at the interface. Behaviourally, participants localised touch at above-chance levels. Representational similarity analyses further revealed that performance was best explained by the spatial positions of stimuli, rather than by limb-based coordinates or indirect signal patterns alone, indicating flexible mapping of indirect touch signals onto the Third Thumb posture. Together, these findings demonstrate that indirect tactile signals transmitted through an artificial limb can be discriminated and flexibly remapped to support spatial localisation of touch.

neuroscience↗

bioRxiv2026

Chemogenetic Pericyte Activation Reveals Broad Contractile Ability and Limbic Vulnerability to Capillary Flow Deficits

Capillary pericytes contact most of the brains microvasculature. Yet, their influence on blood flow remains incompletely understood both locally in capillary networks and across brain regions. Here, we sparsely expressed the chemogenetic actuator Gq-DREADD in mouse brain pericytes to stochastically probe their contractility and influence on tissue perfusion and oxygenation. Chemogenetic stimulation induced robust contraction of pericytes over minutes, including those with thin processes on capillary segments proximal to venules, indicating control of vascular tone across the entire capillary bed. Pericyte contraction combined circumferential compression with longitudinal tension applied through thin processes, resulting in vasoconstriction and hypoperfusion. Histology revealed hypoxic microdomains induced by sparse pericyte contraction across the brain, and enriched hypoxia in limbic structures including the amygdala and hippocampus. These microscale perfusion deficits were undetectable by arterial spin labeling MRI. Our findings reveal the in vivo mechanics of pericyte contraction and identify limbic system vulnerability to capillary flow impairment.

neuroscience↗

bioRxiv2025

A genome-wide approach uncovers the suite of genes important for swarming motility in the biocontrol bacteria Pseudomonas protegens Pf-5

Motility is a crucial bacterial trait, important for competitive success in many contexts. Plant growth promoting rhizobacteria, such as Pseudomonas protegens Pf-5, can protect agricultural crops against disease, relying on motility to access and colonize the plant rhizosphere. Swarming motility is the multicellular movement of bacteria powered by rotating flagella across a semi-solid surface which allows bacteria to move rapidly, search for and acquire food, avoid toxic substances, and colonize new niches. Here we performed genome-wide investigations, using transposon-directed insertion site sequencing (TraDIS) to identify 136 genes involved in P. protegens Pf-5 swarming motility. This method identified flagella biosynthesis, assembly, structure and regulatory genes, as expected. We also identified an additional suite of genes important for swarming, including chemotaxis, c-di-GMP turnover, cell division, peptidoglycan turnover, lipopolysaccharide biosynthesis, metabolism of thiamine (vitamin B1) and transport of pyoverdine. Overall, this study increases our understanding of pseudomonad motility and expands the breadth of lifestyles and habitats examined in relation to swarming motility. Understanding the genetic basis of swarming motility in biocontrol bacteria is important for successful application of these important plant growth promoting microbes in agricultural settings.

genomics↗

bioRxiv2025

Novel Lipophagy Inducers as Potential Therapeutics for Lipid Metabolism Disorders

Dysregulation of lipid homeostasis is associated with a wide range of pathologies encompassing neurological, metabolic, cardiovascular, oncological, and renal disorders. We previously showed that lipid droplet (LD) accumulation in podocytes contributes to the progression of diabetic kidney disease (DKD) and reducing LDs preserves podocyte function and prevents albuminuria. Here, we sought to identify compounds that treat pathological LD accumulation. We developed a phenotypic assay using human podocytes and deployed it to screen a combinatorial library comprising over 45 million unique small molecules. This led to the identification of a compound series that effectively reduce LD accumulation in stressed podocytes. Mechanistic studies revealed that these compounds activate lipophagy, reduce LD accumulation, and rescue podocytes from cell death. In contrast, compounds known to induce general autophagy failed to mimic these effects, indicating a novel lipophagy-specific mechanism of action (MoA), which was confirmed with unbiased phenotypic profiling. An advantage of this therapeutic strategy is its potential to not only halt the progression of pathological lipid accumulation but also reverse it. These compounds will serve as tools for uncovering novel drug targets and therapeutic MoAs for treating DKD and other diseases with similar etiologies. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=39 SRC="FIGDIR/small/642628v1_ufig1.gif" ALT="Figure 1"> View larger version (12K): org.highwire.dtl.DTLVardef@16039e2org.highwire.dtl.DTLVardef@7865c3org.highwire.dtl.DTLVardef@60e886org.highwire.dtl.DTLVardef@41db90_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

The First Comprehensive Description of the Platelet Single Cell Transcriptome

Platelets are derived from megakaryocytes, either in peripheral or pulmonic circulation. The transcriptome of megakaryocytes has been studied, while the platelet transcriptome is thought to be a reflection of their parent cells; it has not yet been investigated. Although platelets lack nuclei, they inherit RNA from their parent megakaryocytes, while only about 10% of them are believed to contain enough RNA for meaningful analysis. This study explores the potential of single-cell RNA sequencing to analyze the platelet transcriptome, aiming to expand our understanding of platelets beyond their traditional role in coagulation. Using acridine orange staining and antibody-based sequencing, we successfully sequenced RNA from seven healthy donors. Results revealed significant heterogeneity in gene expression, with common platelet markers, such as ITGA2B and GP1B, being less abundant than expected. Interestingly, immune markers associated with lung megakaryocytes were not strongly represented in peripheral platelets. Comparison with current algorithms for cell identification suggests that platelets are often misclassified as other blood cell types, highlighting limitations of existing pipelines in platelet annotation. This misclassification may have led to misrepresentation of platelet transcriptomics in previous studies. These findings underscore the need for tailored sequencing methods to accurately profile platelets and set the foundation for further exploration of platelet biology and immune function, potentially opening avenues for therapeutic interventions in immune modulation, drug delivery, and the use of platelets as disease biomarkers in cancer and other conditions. Key PointsPlatelet single cell sequencing can be implemented with appropriate technical refinements to ensure optimal isolation without exogenous activation. In comparison to bulk sequencing techniques, single cell analysis affords the ability to exclude contaminating cells enabling examination of the authentic platelet transcriptome. This is critically important as contaminating cells contain far more RNA ultimately skewing results of transcriptomic analysis. Most platelets do not contain significant levels of commonly expected transcripts such as ITGA2B, GP1B, TREML1. In the context of recent data, our single cell transcriptomic data supports the intradividual and interindividual heterogeneity of the platelet transcriptome. The lung megakaryocyte signature is not disguisable in peripheral platelets. Further studies are needed to understand sources of RNA within platelets and the impact of the platelet microenvironment. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/618506v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@556339org.highwire.dtl.DTLVardef@1e543c4org.highwire.dtl.DTLVardef@c41cb5org.highwire.dtl.DTLVardef@138d779_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOVisual abstractC_FLOATNO C_FIG

bioinformatics↗

bioRxiv2023

Identifying the suite of genes central to swimming in the biocontrol bacteria Pseudomonas protegens Pf-5

Swimming motility is a key bacterial trait, important to success in many niches, including assisting in colonization of host surfaces. Biocontrol bacteria, such as Pseudomonas protegens Pf-5 are increasingly being used as an agricultural tool to control crop diseases, where motility is a factor in successful colonization of the plant rhizosphere. Swimming motility has been studied in a range of bacteria and typically involves a suite of flagella and chemotaxis genes, however the specific gene set employed for both regulation and biogenesis can differ substantially between organisms. Here we used transposon directed insertion site sequencing (TraDIS), a genome-wide approach, to identify 249 genes involved in P. protegens Pf-5 swimming motility. As expected, flagella and chemotaxis genes comprised a large proportion of these genes. However we also identified a suite of additional genes important for swimming, including genes related to peptidoglycan turnover, O-antigen biosynthesis, cell division, signal transduction, c-di-GMP turnover and phosphate transport, along with 27 conserved hypothetical proteins. Experimental gene knockout mutants and TraDIS data together suggest that defects in the Pst phosphate transporter lead to enhanced swimming motility. Overall, this study expands our knowledge of pseudomonad motility and highlights the utility of a TraDIS-based approach for systematically analyzing the functions of thousands of genes. This work sets a foundation for understanding how swimming motility may be related to the inconsistency in biocontrol bacteria effectiveness and reliability in the field. ImportanceBiocontrol bacteria, such as Pseudomonas protegens Pf-5 are increasingly being used as an agricultural tool to control crop diseases, and motility is a key factor in their successful colonization of plant surfaces. Here we use a high-throughput approach to identify the suite of genes important for swimming motility in P. protegens Pf-5. These included flagella and chemotaxis genes, as well as a variety of cell surface, cell division and signalling genes. We also show that defects in the Pst phosphate transporter lead to enhanced swimming motility, a hitherto unreported link between phosphate transport and swimming motility. Understanding the genetic basis of swimming motility enhances our knowledge of key processes in biocontrol bacteria that are needed to ensure their competitive success. This will contribute to developing strategies to increase the utility of biocontrol bacteria in agricultural settings to prevent crop losses.

genomics↗

bioRxiv2022

Dynamic spatial coding in parietal cortex mediates hand movement planning towards touch

Movements towards touch on the body require integrating tactile location and body posture information. Tactile processing and movement planning both rely on posterior parietal cortex (PPC) but their interplay is not understood. Here, human participants received tactile stimuli on their crossed and uncrossed feet, dissociating stimulus location relative to anatomy versus external space. Participants pointed to the touch or the equivalent location on the other foot, which dissociates sensory and motor locations. Multi-voxel pattern analysis of concurrently recorded fMRI signals revealed that tactile location was coded anatomically in anterior PPC but spatially in posterior PPC during sensory processing. After movement instructions were specified, PPC exclusively represented the movement goal in space, in regions associated with visuo-motor planning and with regional overlap for sensory, rule-related, and movement coding. Thus, PPC flexibly updates its spatial codes to accommodate rule-based transformation of sensory input to generate movement to environment and own body alike.

neuroscience↗

bioRxiv2022

The influence of familiarity on the neural coding of face sex

In behaviour, humans have been shown to represent the sex of faces categorically when the faces are familiar to them. This leads to them judging faces crossing the category boundary (i.e. from male to female) as more different than faces that are within the same category. In this study, we investigated how faces of different sexes are encoded in the brain, and how familiarity changes the neural coding of sex. We recorded participants brain activity using fMRI while they viewed both familiar and unfamiliar faces that were morphed in their sex characteristics (i.e. between male and female). Participants viewed pairs of faces that were either identical, or differed in their sex morph level, with or without a categorical change in perceived sex (i.e. crossing the perceived male/female category boundary). This allowed us to disentangle physical and categorical neural coding of face sex, and to investigate if neural coding of face categories was enhanced by face familiarity. Our results show that the sex of familiar, but not unfamiliar, faces was encoded categorically in the medial prefrontal and orbitofrontal cortex as well as in the right intraparietal sulcus. In contrast, the fusiform face area showed a sensitivity to the physical changes in the sex of faces that was unaffected by face familiarity. The occipital face area showed its highest responses to faces towards the ends of the sex morph continuum (i.e. the most male or most female faces), and these responses were also unaffected by face familiarity. These results suggest that there is a dissociation between the brain regions encoding physical and categorical representations of face sex, with occipital and fusiform face regions encoding physical face sex properties and frontal and parietal regions encoding high-level categorical face sex representations that are linked to face identity.

neuroscience↗

bioRxiv2022

Spatial and temporal origin of the third SARS-CoV-2 Outbreak in Taiwan

Since the first report of SARS-CoV-2 in December 2019, Taiwan has gone through three local outbreaks. Unlike the first two outbreaks, the spatial and temporal origin of the third outbreak (April 20 to November 5, 2021) is still unclear. We assembled and analyzed a data set of more than 6,000 SARS-CoV-2 genomes, including 300 from Taiwan and 5812 related sequences downloaded from GISAID as of 2021/12/08. We found that the third outbreak in Taiwan was caused by a single virus lineage belonging to Alpha (B.1.1.7) strain. This lineage, T-III (the third outbreak in Taiwan), carries a distinct genetic fingerprint, consisting of spike M1237I (S-M1237I) and three silent mutations, C5812T, C15895T, and T27869C. The T-III is closest to the sequences derived from Turkey on February 8, 2021. The estimated age of the most recent common ancestor (TMRCA) of T-III is March 23, 2021 (95% highest posterior density [HPD] February 24 - April 13, 2021), almost one month before the first three confirmed cases on April 20, 2021. The effective population size of the T-III showed approximately 20-fold increase after the onset of the outbreak and reached a plateau in early June 2021. Our results reconcile several unresolved observations, including the occurrence of two infection clusters at the same time without traceable connection and several airline pilots who were PCR negative but serum IgM-/IgG+ for SARS-CoV-2 in late April. Therefore, in contrast to the general notion that the third SARS-CoV-2 outbreak in Taiwan was sparked by two imported cases from USA on April 20, 2021, which, in turn, was caused by the partial relaxation of entry quarantine measures in early April 2021, our comprehensive analyses demonstrated that the outbreak was most likely originated from Europe in February 2021.

evolutionary biology↗

bioRxiv2021

Determinants of precocious B-cell aging in European adolescences living with perinatally acquired HIV-1 after over 10 years of suppressive therapy

HIV infection results in a state of chronic immune activation leading to premature immune aging, B-cells dysfunction, that persists despite prolonged virological suppression. In this scenario, adolescence living with perinatally acquired HIV (PHIV), deserve a peculiar attention since potentially exposed for their entire life to chronic immune activation. Here we identified determinants of precocious aging B cells in 40 PHIV undergoing suppressive antiretroviral therapy (ART) for median 13.5 years. All individuals started ART by 2nd year of life and achieved virus suppression within the 1st year of ART, with majority of patient maintaining suppression until analysis and 5/40 experiencing viral Spike (transient elevation of HIV-1 VL, 50-999 copies/ml). We employed a multiomics approach including deep immunological B and T cell phenotype in PBMC, with aging B cells defined by the expression of T-bet and CD11c; plasma proteomics analysis by mass spectrometry and serum level of anti-measles antibodies as correlates of humoral response. We found that individuals with expansion of aging B cell, defined by the expression of T-bet+CD11c+, were those starting treatment later, presenting detectable levels of cell-associated HIV-1 RNA, history of Spikes, and a higher frequency of exhausted T-cells, including those expressing PD-1, LAG3, TIGIT. Accordingly, the proteomic analysis revealed that subjects with expansion of aging B cells and exhausted T cells had enrichment of proteins involved in immune inflammation and complement activation pathways, such as CLU and APCS which are also involved in tumor progression. Signs of precocious aging were associated with a reduced capacity to maintain virological memory against measles vaccination. To our knowledge, this is the first study focusing on precocious B-cell aging and dysfunctionality in PHIV with long-term virological suppression. Our experimental strategy enabled identification of clinical, viral, cellular and plasma soluble markers associated with B-cells aging. Our results pave the way to further define risk of disease progression or lymphoproliferative disorders in PHIV. Author summaryDespite a successful antiretroviral therapy (ART), adolescence living with perinatally acquired HIV (PHIV) experience B-cells dysfunction, including loss of vaccine-induced immunological memory and higher risk of developing B-cells associated tumors. It is thus paramount to define novel and precise correlates of precious aging B cell for the definition of novel therapeutic strategies. Here, we studied 40 PHIV who started treatment by 2nd year of life and maintain virological suppression for 13.5 years, with 5/40 patients experiencing transient elevation of the HIV-1 load in the plasma (Spike). We applied a multi-omics approach including immunological B and T cell phenotype, plasma proteomics analysis and serum level of anti-measles antibodies as functional correlates of vaccine-induced immunity. We found that levels of aging B cells were positively associated with age at ART start, cell associated HIV-1 RNA (caHIV-1 RNA) and the presence of Spikes. Individuals with increased proportions of aging B cells had concomitant expansion of exhausted T cells and were unable to maintain vaccine-induced immunity over time. B-cell aging, and T-cell exhaustion were also associated with proteins involved in immune inflammation. The factors found here to be associated with aging B-cell could inform further therapeutic studies.

immunology↗

bioRxiv2021

Separated and overlapping neural coding of face and body identity

Recognising a persons identity often relies on face and body information, and is tolerant to changes in low-level visual input (e.g. viewpoint changes). Previous studies have suggested that face identity is disentangled from low-level visual input in the anterior face-responsive regions. It remains unclear which regions disentangle body identity from variations in viewpoint, and whether face and body identity are encoded separately or combined into a coherent person identity representation. We trained participants to recognize three identities, and then recorded their brain activity using fMRI while they viewed face and body images of the three identities from different viewpoints. Participants task was to respond to either the stimulus identity or viewpoint. We found consistent decoding of body identity across viewpoint in the fusiform body area, right anterior temporal cortex, middle frontal gyrus and right insula. This finding demonstrates a similar function of fusiform and anterior temporal cortex for bodies as has previously been shown for faces, suggesting these regions may play a general role in extracting high-level identity information. Moreover, we could decode identity across neural activity evoked by faces and bodies in the early visual cortex, right inferior occipital cortex, right parahippocampal cortex and right superior parietal cortex, revealing a distributed network that encodes person identity abstractly. Lastly, identity decoding was consistently better when participants attended to identity, indicating that attention to identity enhances its neural representation. These results offer new insights into how the brain develops an abstract neural coding of person identity, shared by faces and bodies.

neuroscience↗

bioRxiv2021

Using dual-calibrated functional MRI to map brain oxygen supply and consumption in multiple sclerosis

Evidence suggests that cerebrovascular function and oxygen consumption are altered in multiple sclerosis (MS). Here, we quantified the vascular and oxygen metabolic MRI burden in patients with MS (PwMS) and assessed the relationship between these MRI measures of and metrics of damage and disability. In PwMS and in matched healthy volunteers, we applied a newly developed dual-calibrated fMRI method of acquisition and analysis to map grey matter (GM) cerebral blood flow (CBF), oxygen extraction fraction (OEF), cerebral metabolic rate of oxygen consumption (CMRO2) and effective oxygen diffusivity of the capillary network (DC). We also quantified physical and cognitive function in PwMS and controls. There was no significant difference in GM volume between 22 PwMS and 20 healthy controls (p=0.302). Significant differences in CBF (PwMS vs. controls: 44.91 {+/-} 6.10 vs. 48.90 {+/-} 5.87 ml/100g/min, p=0.010), CMRO2 (117.69 {+/-} 17.31 vs. 136.49 {+/-} 14.48 mol/100g/min p<0.001) and DC (2.70 {+/-} 0.51 vs. 3.18 {+/-} 0.41 mol/100g/mmHg/min, p=0.002) were observed in the PwMS. No significant between-group differences were observed for OEF (PwMS vs. controls: 0.38 {+/-} 0.09 vs. 0.39 {+/-} 0.02, p=0.358). Regional analysis showed widespread reductions in CMRO2 and DC for PwMS compared to healthy volunteers. There was a significant correlation between physiological measures and T2 lesion volume, but no association with current clinical disability. Our findings demonstrate concurrent reductions in oxygen supply and consumption in the absence of an alteration in oxygen extraction that may be indicative of a reduced demand for oxygen (O2), an impaired transfer of O2 from capillaries to mitochondria, and/or a reduced ability to utilise O2 that is available at the mitochondria. With no between-group differences in GM volume, our results suggest that changes in brain physiology may precede MRI-detectable GM loss and thus may be one of the pathological drivers of neurodegeneration and disease progression.

neuroscience↗

bioRxiv2020

Elucidating essential genes in plant-associated Pseudomonas protegens Pf-5 using transposon insertion sequencing

Gene essentiality studies have been performed on numerous bacterial pathogens, but essential gene sets have been determined for only a few plant-associated bacteria. Pseudomonas protegens Pf-5 is a plant-commensal, biocontrol bacteria that can control disease-causing pathogens on a wide range of crops. Work on Pf-5 has mostly focused on secondary metabolism and biocontrol genes, but genome-wide approaches such as high-throughput transposon mutagenesis have not yet been used in this species. Here we generated a dense P. protegens Pf-5 transposon mutant library and used transposon-directed insertion site sequencing (TraDIS) to identify 446 genes essential for growth on rich media. Genes required for fundamental cellular machinery were enriched in the essential gene set, while genes related to nutrient biosynthesis, stress responses and transport were under-represented. Comparison of the essential gene sets of Pf-5 and P. aeruginosa PA14, an opportunistic human pathogen, provides insight into the biological processes important for their different lifestyles. Key differences include cytochrome c biogenesis, formation of periplasmic disulfide bonds, lipid biosynthesis, ribonuclease activity, lipopolysaccharides and cell surface structures. Comparison of the Pf-5 in silico predicted and in vitro determined essential gene sets highlighted the essential cellular functions that are over- and underestimated by each method. Expanding essentiality studies into bacteria with a range of lifestyles can improve our understanding of the biological processes important for survival and growth in different environmental niches. ImportanceEssential genes are those crucial for survival or normal growth rates in an organism. Essential gene sets have been identified in numerous bacterial pathogens, but only a few plant-associated bacteria. Employing genome-wide approaches, such as transposon insertion sequencing, allows for the concurrent analysis of all genes of a bacterial species and rapid determination of essential gene sets. We have used transposon insertion sequencing to systematically analyze thousands of Pseudomonas protegens Pf-5 genes and gain insights into gene functions and interactions that are not readily available using traditional methods. Comparing Pf-5 essential genes with those of P. aeruginosa PA14, an opportunistic human pathogen, provides insight into differences in gene essentiality which may be linked to their different lifestyles.

genomics↗

bioRxiv2020

SHP2 Inhibition Abrogates Adaptive Resistance to KRASG12C-Inhibition and Remodels the Tumor Microenvironment of KRAS-Mutant Tumors

KRAS is the most frequently mutated oncogene in human cancer, and KRAS inhibition has been a longtime therapeutic goal. Recently, inhibitors (G12C-Is) that bind KRASG12C-GDP and react with Cys-12 were developed. Using new affinity reagents to monitor KRASG12C activation and inhibitor engagement, we found that, reflecting its action upstream of SOS1/2, SHP2 inhibitors (SHP2-Is) increased KRAS-GDP occupancy, enhancing G12C-I efficacy. SHP2-Is abrogated feedback signaling by multiple RTKs and blocked adaptive resistance to G12C-Is in vitro, in xenografts, and in syngeneic KRASG12C-mutant pancreatic ductal adenocarcinoma (PDAC) and non-small cell lung cancer (NSCLC) models. Biochemical analysis revealed enhanced suppression of ERK-, MYC-, anti-apoptotic-, and cell-cycle genes, and increased pro-apoptotic gene expression in tumors from combination-treated mice. SHP2-I/G12C-I also evoked favorable changes in the immune microenvironment, decreasing myeloid suppressor cells, increasing CD8+ T cells, and sensitizing tumors to PD-1 blockade. Experiments using cells expressing inhibitor-resistant SHP2 showed that SHP2 inhibition in PDAC cells is required for tumor regression and remodeling of the immune microenvironment, but also revealed direct inhibitory effects on angiogenesis resulting in decreased tumor vascularity. Our results demonstrate that SHP2-I/G12C-I combinations confer a substantial survival benefit in PDAC and NSCLC and identify additional combination strategies for enhancing the efficacy of G12C-Is.

cancer biology↗

bioRxiv2020

Genetically Defined, Syngeneic Organoid Platform for Developing Combination Therapies for Ovarian Cancer

The paucity of genetically informed, immune-competent tumor models impedes evaluation of conventional, targeted, and immune therapies. By engineering mouse fallopian tube (FT) organoids using lentiviral gene transduction and/or CRISPR/Cas9 mutagenesis, we generated multiple high grade serous ovarian carcinoma (HGSOC) models exhibiting mutational combinations seen in patients. Detailed analysis of homologous recombination (HR)-proficient (Tp53-/-;Ccne1OE;Akt2OE; KrasOE), HR-deficient (Tp53-/-;Brca1-/-;MycOE) and unclassified (Tp53-/-;Pten-/-;Nf1-/-) organoids revealed differences in in vitro properties and tumorigenicity. Tumorigenic organoids had variable sensitivity to HGSOC chemotherapeutics and evoked distinct immune microenvironments. These findings enabled development of a chemotherapy/immunotherapy regimen that yielded durable, T-cell dependent responses in Tp53-/-;Ccne1OE;Akt2OE;Kras HGSOC; by contrast, Tp53-/-;Pten-/-;Nf1-/- tumors failed to respond. Genotype-informed, syngeneic organoid models could provide an improved platform for rapid evaluation of tumor biology and therapeutics. HIGHLIGHTSO_LIOrthotopic injection of genetically defined fallopian tube organoids yield HGSOC. C_LIO_LIOvarian tumors with different genotypes evoke distinct immune microenvironments C_LIO_LICombining Gemcitabine, anti-PD-L1, and anti-CTLA-4 result in complete responses in Tp53-/-;Ccne1OE;Akt2OE;KrasOE organoid-derived HGSOC C_LIO_LITherapeutic response is tumor genotype-specific C_LI

cancer biology↗

bioRxiv2019

Assessment of the effects of aerobic fitness on cerebrovascular function in young adults using multiple inversion time arterial spin labelling MRI

The cross-sectional study investigated the effects of aerobic fitness on cerebrovascular function in the healthy brain. We quantified grey matter (GM) cerebral blood flow (CBF) and cerebrovascular reactivity (CVR), in a sample of young adults within a normal fitness range. Based on existing TCD and fMRI evidence, we predicted a positive relationship between fitness and resting GM CBF, and CVR. Exploratory hypotheses that higher [Formula] peak would be associated with higher GM volume and cognitive performance were also investigated. 20 adults underwent a [Formula] peak test and a battery of cognitive tests. All subjects underwent an MRI scan where multiple inversion time (MTI) pulsed arterial spin labelling (PASL) was used to quantify resting CBF and CVR to 5% CO2. ROI analysis showed a non-significant negative correlation between whole-brain GM CBF and [Formula] peak; r=-0.4, p=0.08, corrected p (p) =0.16 and a significant positive correlation between [Formula] peak and voxelwise whole-brain GM CVR; r=0.62, p=0.003, p =0.006. Voxelwise analysis revealed a significant inverse association between [Formula] peak and resting CBF in the left and right thalamus, brainstem, right lateral occipital cortex, left intracalcarine cortex and cerebellum. The results of this study suggest that aerobic fitness is associated with lower CBF and greater CVR in young adults.

neuroscience↗