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Wilson, E.

Publications and source records attributed to Wilson, E..

At least 19 recordsLinked to original sources

Oncostatin M-driven leak in human endothelial cells with preserved tight junctions

Blood vessels must preserve blood volume while permitting exchange of nutrients. Endothelial cells line the lumen of all blood vessels and form the intercellular junctions that govern vascular permeability. In acute critical illness the barrier fails, fluid escapes into tissues, and the resulting loss of volume and impaired nutrient exchange cause organ failure. Several inflammatory cytokines are known to disrupt junctions in cultured cells, yet therapies targeting these models have failed. How blood vessels respond to critical illness has remained largely elusive because endothelial cells are generally inaccessible. Here we profile endothelial cells recovered directly from critically ill children to show that oncostatin M drives a previously unrecognized mode of vascular leak. Oncostatin M increases permeability by forming narrow, nanoscale channels within the overlapping borders of adjacent cells, around intact tight junctions. These channels permit passage of small and intermediate sized solutes. Their formation depends on non-canonical signaling in which the kinase JAK1 activates two required parallel pathways (via ERK1 and AKT1) that converge on the transcription factor c-Fos. Inhibiting JAK1, either parallel pathway or depleting c-Fos, prevents oncostatin M-induced loss of barrier function. These results identify a permeability mechanism distinct from the junction disassembly driven by the cytokines that have dominated this field and implicate kinases already targeted by approved drugs as potential points of intervention. More broadly, vascular barriers are transiently loosened during immune-cell trafficking and metastasis, raising the possibility that diverse forms of vascular permeability arise through regulated nanoscale remodeling rather than junctional breakdown.

cell biology↗

Profilin-1 Deficiency Activates STING to Drive T Cell-Mediated Anti-Tumor Immunity in Breast Cancer

Dysregulation of actin-binding protein Profilin1 (Pfn1) in tumor cells has prominent impacts on the tumor-intrinsic aspects of tumor progression. However, whether and how modulation of Pfn1 expression in tumor cells influences immune surveillance in cancer is not known. We utilized an inducible CRISPR/Cas9 knockout (KO) model to first demonstrate that triggering Pfn1 depletion in breast cancer cells leads to features of genomic instability (polyploidy, micronuclei, and DNA damage) and intrinsic defects in both homologous-recombination- and non-homologous end-joining-mediated double-stranded DNA repair. Pfn1-deficient breast cancer cells exhibit nuclear envelope abnormality and the accumulation of cytosolic DNA. This leads to activation of the nucleic acid-sensing cGAS-STING pathway and the type-I interferon (IFN) response including STING-mediated upregulation of pro-inflammatory chemokines. In an immunocompetent mouse model of breast cancer, triggering Pfn1 loss selectively in tumor cells promotes an immunogenic tumor microenvironment marked by a striking increase in intratumoral presence of CD8 T cells, leading to a robust tumor regression. Pfn1 knockout-induced tumor regression requires an intact immune system and can also be reversed by CD8+ T cell depletion. Based on these findings, we conclude that Pfn1 loss in tumor cells leverages a type I IFN response to drive a T-cell-mediated anti-tumor response in breast cancer. These findings for the first time reveal promising therapeutic opportunities in targeting Pfn1-driven pathways to enhance immunotherapeutic outcomes in breast cancer. Significance StatementExpression of actin-binding protein Profilin-1 is frequently altered in cancer; yet how these changes impact the immune response against tumors is unclear. Here we show that triggering Profilin-1 depletion in breast cancer cells promotes features of genomic instability, defects in DNA repair, and cytosolic release of DNA. This activates the cGAS-STING pathway, triggering a type I interferon response and immune-cell-attracting signals that drive a CD8+ T cell-mediated anti-tumor immune response and tumor regression in vivo. Therefore, Profilin-1 could be a novel actionable target for achieving immunological benefit in breast cancer. On a broader level, our studies establish a conceptual framework of how dysregulation of actin cytoskeletal proteins can harness nuclear damage-sensing signaling to augment anti-tumor immune response in cancer.

cancer biology↗

Genetic basis of glycine and L-serine toxicity in Staphylococcus aureus and the case for glycine as an antibiotic adjuvant

The toxicity of the amino acids glycine and L-serine at high concentrations in bacteria was discovered decades ago. In this work, we used deep transposon insertion sequencing (Tn-seq) experiments to determine the genes necessary to tolerate excess L-serine, diglycine or glycine in the human pathogen Staphylococcus aureus. Our results indicate that intracellular accumulation of specific counterbalancing amino acids--such as alanine in excess glycine--is the primary mechanism of resistance to amino acid toxicity. Consistent with this model, specific amino acid and peptide uptake transporters were required for fitness in each treatment; the peptide transporter DtpT was crucial for fitness in excess L-serine or glycine, and the alanine transporter AapA was essential in diglycine. Tn-seq results also identified the cystine/cysteine uptake transporter TcyABC as necessary in excess L-serine, suggesting that both peptide and cysteine uptake contribute to L-serine tolerance. In addition to uptake mechanisms, glycine and diglycine toxicity is neutralized by D-alanine aminotransferase (Dat), which is required for D-alanine synthesis. The requirement for Dat and DtpT function--but not AapA--in excess glycine is explained by excess glycine inhibiting alanine uptake. Building on this finding, we found that combined treatment with glycine and the alanine analog antibiotic D-cycloserine was strongly synergistic in inhibiting S. aureus growth. Overall, our findings identify targetable mechanisms underlying excess amino acid tolerance in S. aureus, with implications for developing novel combination treatments using the accessible and biocompatible amino acids glycine and L-serine. IMPORTANCEGrowing evidence supports the beneficial effects of glycine and L-serine supplementation in combating bacterial infections. Previous researchers have found that combining antibiotic treatment with high glycine concentrations has additive effects with many antibiotics, even reversing resistance to antibiotics in some bacteria. In vivo, activating glycine and L-serine metabolism heightens the sensitivity of bacterial pathogens to the host complement system, and studies of glycine or L-serine treatments show low toxicity and reduced inflammation in mouse and human subjects. This study reveals that glycine may be an effective antibiotic adjuvant with D-cycloserine, and treatment with glycine or L-serine could potentiate other drugs that target alanine or cysteine metabolism, respectively.

microbiology↗

Primary cilia promote cardiac fibrosis and limit heart function after myocardial infarction

Cardiomyocytes die and do not regenerate after an injury such as a myocardial infarction (MI), a leading cause of mortality worldwide. Following MI, cardiac fibroblasts (CFs) proliferate and differentiate into myofibroblasts, which then produce increased collagen and extracellular matrix (ECM) leading to fibrosis. Fibrosis can weaken cardiac output via excessive stiffening and interference with electric signal transmission, but can also prevent wall rupture under load (reviewed in (1)). Thus, dampening fibrosis has been investigated as a potential therapeutic intervention. Most mammalian cells possess a single primary cilium involved in intercellular communication. We investigated the role of CF primary cilia in sensing injury signals and initiating fibrotic remodeling. We found that deleting CF cilia reduced fibrosis and improved cardiac output after MI, demonstrating that cilia act as a signaling hub that amplifies the fibrotic response in the injured heart.

physiology↗

Cancer Cell Line Encyclopedia Data Suggest that Ligands for ERBB Family Receptors May Drive BRAF-WT Melanomas

I.Cutaneous skin melanomas with wild-type BRAF alleles ("BRAF-WT melanomas") remain relatively difficult to treat, even though they typically possess driver mutations in a RAS gene or NF1. For example, these tumors respond relatively poorly to combinations of MEK and BRAF inhibitors, and their response to ICIs is muted compared to the response of BRAF-mutant melanomas. ERBB2 and ERBB4, which encode receptor tyrosine kinase genes, are necessary and sufficient for the proliferation of multiple BRAF-WT melanoma cell lines. Consequently, we have postulated that ERBB4-ERBB2 heterodimerization drives BRAF-WT melanomas. This mechanism is consistent with the observation that elevated ERBB4 transcription or ERBB4 mutations are found in a significant fraction of BRAF-WT melanoma tumor samples. Moreover, a subset of ERBB4 mutations found in BRAF-WT melanoma samples increases proliferation in a BRAF-WT melanoma cell line. Because the elevated ERBB4 transcription observed in BRAF- WT melanomas is typically insufficient to cause ligand-independent ERBB4 signaling, we have postulated that ligands for ERBB family receptors drive the elevated ERBB4-ERBB2 heterodimerization responsible for the proliferation of BRAF-WT melanoma cell lines. We have explored this hypothesis by analyzing data found in the Broad Institutes Cancer Cell Line Encyclopedia. These data suggest that some EGF family hormones are required for the proliferation of BRAF-WT melanoma cell lines. Likewise, the G11/Gq pathway, which can stimulate cleavage and maturation of EGF family hormones, is also required for the proliferation of BRAF-WT melanoma cell lines. Thus, these data suggest additional therapeutic targets in BRAF-WT melanomas. Moreover, because many uveal (ocular) melanomas possess elevated G11/Gq signaling, these data suggest that ligand stimulation of ERBB receptor signaling may contribute to uveal melanomagenesis or progression.

cancer biology↗

Genetic control of Group 3 (K96) capsule synthesis and complement resistance in an extraintestinal pathogenic Escherichia coli ST69 strain

Extraintestinal pathogenic Escherichia coli (ExPEC) often produce capsules belonging to Groups 2 or 3, which contribute to invasive disease in humans and other animals. Group 3 capsule loci contain conserved kps genes flanking serotype-specific glycosyltransferase and nucleotide-sugar biosynthesis genes, but little is known about genetic factors that control synthesis, or the specific roles that K96 capsules play in virulence. Previously, we identified a Group 3 serotype K96 capsule in a mastitis-associated strain M12 that is critical for its survival in some host tissues. In this study, we show that the K96 capsule of strain M12 confers resistance to human serum complement. We conducted genetic screens to determine how K96 capsule expression is controlled, which led to two principal findings. First, Group 3 capsule synthesis is unstable. Sequencing of spontaneously appearing mutants revealed potential phase-variable control of capsule expression. Some mutants harbored reversible frameshift mutations in a homopolymeric site within kpsC, which were also identified in other K96-encoding ExPEC isolates. Second, a transposon mutagenesis screen revealed that capsule synthesis requires proteins encoded outside of the kps locus, including the RfaH antiterminator and OxyR transcriptional regulator, which control activation of an unusually distant promoter. An {Delta}oxyR mutant of strain M12 failed to produce capsule, was extremely sensitive to complement-mediated killing, and avirulent in Galleria mellonella. ImportanceGroup 2 capsules are established extraintestinal pathogenic Escherichia coli (ExPEC) virulence factors and are the type most often associated with human isolates. Group 3 capsules have previously been considered a sub-type of Group 2, although nothing was known about factors controlling their expression. Capsule serotype K96-encoding ExPEC strains are increasingly isolated from human infections and inhabit numerous other hosts. It is critical to understand the factors that enable their pathogenic versatility and survival in specific environments. Our study shows that K96 capsule of strain M12 is required for human complement resistance. Additionally, we have identified genetic factors that control Group 3 capsule synthesis, including a potential phase-variable mechanism as well as transcriptional control by OxyR. Co-regulation of Group 3 capsule synthesis genes with genes necessary for oxidative stress resistance may increase the virulence of some versatile ExPEC strains.

microbiology↗

Optimal TELSAM-Target Protein Linker Character is TargetProtein-Dependent

Fusing a variant of the sterile alpha motif domain of the human translocation ETS leukaemia protein (TELSAM) to a protein of interest has been shown to significantly enhance crystallization propensity. TELSAM is a pH-dependent, polymer-forming protein crystallization chaperone which, when covalently fused to a protein of interest, forms a stable, well-ordered crystal lattice. However, despite its success, a challenge persists in that crystal quality and diffraction limits appear to be heavily dependent on the choice of linker between TELSAM and the protein of interest, with identification of a functional linker relying on trial-and-error methods. Likewise, previous studies revealed that the 10xHis tag at the TELSAM N-terminus can either facilitate or hinder the ordered crystallization of target proteins attached via flexible or semi-flexible linkers. To address these challenges, we designed multiple constructs with several types of linkers--rigid (helical fusion), semi-flexible (Pro-Alan), and flexible (poly-Gly)--of varying lengths to fuse a designed ankyrin repeat protein (DARPin) to the TELSAM C-terminus. Semi-flexible and flexible linker constructs were made with and without the 10xHis tag. Our findings indicate that short semi-flexible and rigid linkers consistently yield large crystals within 24 hours with a DARPin target protein, but that flexible linkers perform best with a TNK1 UBA domain target protein. Removing the 10xHis tag enhanced crystallization rates, improved crystal morphology, and increased the crystallization propensity of semi-flexible and flexible linker constructs. While removing the His tag did not have a significant effect on crystal size, it improved the diffraction limits and crystal quality of the 1TEL-PA-DARPin construct. These results suggest that the ideal linker selection primarily depends on the properties of the target protein. Our data support the recommendation to use a short yet flexible or semi-flexible linker between TELSAM and the target protein to facilitate protein crystallization and high-resolution structure determination. SynopsisIn this study, we examine the effect of short to medium-length flexible, semi-flexible, and rigid linkers on the crystallization of a DARPin fused to the 1TEL protein crystallization chaperone, demonstrating that while rigid linkers impair crystallization and reduce diffraction quality, the ideal linker character remain target-protein dependent. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/672704v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@b90d1org.highwire.dtl.DTLVardef@1508e7dorg.highwire.dtl.DTLVardef@1baf0d1org.highwire.dtl.DTLVardef@1843df_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

Opposing roles for iron transport systems in gallium tolerance in extraintestinal pathogenic Escherichia coli

Gallium is a promising antibacterial candidate because it displaces iron atoms inside bacterial cells but does not undergo redox cycling. It inhibits growth by disrupting essential iron-dependent processes. However, Escherichia coli are naturally less sensitive to gallium than many other bacteria, and the mechanisms that control gallium tolerance are not completely understood. We performed a genome-wide transposon sequencing (TnSeq) screen to identify genes important for the survival of an extraintestinal pathogenic E. coli isolate (M12) in gallium nitrate. The TnSeq results indicated that inactivation of enterobactin siderophore-related genes (entS, fepD, fes, fepB) enhances bacterial survival in gallium, while disrupting the ferric dicitrate transport system increases susceptibility. We validated these findings through targeted gene knockouts and gallium sensitivity experiments. Our findings suggest that enterobactin can complex with gallium for cellular uptake, but that the ferric citrate receptor FecA can discriminate between gallium citrate and iron citrate. Expression of fecA increased with gallium exposure, showing that gallium induces FecA-mediated iron uptake. Gallium also increased intracellular levels of manganese in the {Delta}fecA strain. Supplementation with iron or manganese restored growth of M12 {Delta}fecA in gallium, suggesting that gallium sensitivity is linked to both iron starvation and oxidative stress. As the ferric dicitrate transport system is an important virulence factor in several extraintestinal infection sites, our results suggest that targeting FecA may increase E. coli susceptibility to gallium while also suppressing virulence. ImportanceEscherichia coli extraintestinal infections that are resistant to traditional antibiotics are associated with more deaths than any other species. Gallium-based therapies may represent a non-antibiotic approach to treating extraintestinal pathogenic E. coli strains that affect both humans and animals. Our results are significant as they show that the enterobactin siderophore and the ferric dicitrate iron transport systems expressed by these bacteria have opposing roles in E. coli gallium sensitivity. These findings could be leveraged to enhance the efficacy of gallium therapeutics.

microbiology↗

Differential control of growth and identity by HNF4α isoforms in pancreatic ductal adenocarcinoma

BackgroundAlthough transcriptomic studies have stratified pancreatic ductal adenocarcinoma (PDAC) into clinically relevant subtypes, classical or basal-like, further research is needed to identify the transcriptional regulators of each subtype. Previous studies identified HNF4 as a key regulator of the classical subtype, but the distinct contributions of its isoforms (P1 and P2), which display dichotomous functions in normal development and gastrointestinal malignancies, remain unexplored. ObjectiveThe objective of this study is to investigate the role of HNF4 P1 and P2 isoforms in regulating growth and differentiation. DesignWe performed functional, transcriptomic, and epigenetic analysis after exogenous expression in HNF4-negative models or CRISPRi-mediated knockdown of endogenous isoforms. ResultsWe characterized the variable expression of P1 isoforms in HNF4-positive tumors. We demonstrate that P1 isoforms are less compatible with growth than P2 isoforms. Despite sharing a common DNA binding domain, we show that P1 isoforms are stronger transcriptional regulators. ConclusionsOur study characterizes the functional roles of HNF4 P1 and P2 isoforms in PDAC and highlights the necessity of considering different isoforms when studying molecular regulators.

cancer biology↗

Pooled CAR-T screening in nonhuman primates identifies designs with enhanced proliferation, trafficking, and persistence

Chimeric antigen receptor T (CAR-T) cell therapy has revolutionized treatment for B-cell malignancies, yet over 60% of patients relapse within one year, often due to insufficient CAR-T persistence. While mouse and primary cell models have been instrumental in advancing CAR-T therapy, they frequently fail to predict clinical outcomes, underscoring the need for more translationally relevant models. To address this limitation, we conducted the first systematic evaluation of CAR structure-function relationships in an immunocompetent nonhuman primate (NHP) model. We engineered an array of 20 CD20-targeted CARs with distinct combinations of hinge, transmembrane, and costimulatory domains. Following ex vivo characterization, we administered pooled autologous CAR-T arrays to three NHPs and tracked CAR abundance longitudinally using a novel digital droplet PCR assay. Ex vivo, CAR-T cells incorporating the MyD88-CD40 costimulatory domain exhibited markedly distinct functional profiles, including increased activation, unique cytokine secretion, tonic signaling, and resistance to exhaustion. In vivo, MyD88-CD40 CARs expanded dramatically, comprising up to 100% of peripheral T cells and significantly outperforming canonical CD28- and 4-1BB-based CARs. This expansion was associated with robust B-cell depletion across all animals. MyD88-CD40 CARs, particularly those with a CD28 hinge and transmembrane domain, demonstrated superior trafficking to secondary lymphoid tissues and persistence through study endpoint, unlike other CARs which waned by day 28. Our findings highlight the value of NHP models for screening CAR designs and identify MyD88-CD40 CARs as candidates with unmatched potency. The unique functional attributes conferred by this domain may provide key insights into features that drive enhanced CAR-T cell activity. Key pointsO_LIWe developed the first pooled CAR-T screening platform in an immunocompetent nonhuman primate model to directly compare CAR designs. C_LIO_LIWe identified MyD88-CD40 costimulatory domain as vastly superior to conventional domains in proliferation, trafficking and persistence. C_LI

immunology↗

Spatial profiling of longitudinal glioblastoma reveals consistent changes in cellular architecture, post-treatment

Glioblastoma (GBM), the most aggressive adult brain cancer, comprises a complex tumour microenvironment (TME) with diverse cellular interactions driving progression and pathobiology. How these spatial patterns and interactions evolve with treatment remains unclear. Here, we apply imaging mass cytometry to analyse protein-level changes in paired pre- and post-treatment GBM samples from five patients. We find a significant post-treatment increase in normal brain cells alongside a reduction in vascular cells. Moreover, despite minimal overall change in cellular diversity, interactions among astrocytes, oligodendrocytes, and vascular cells increase post-treatment, suggesting reorganisation of the TME. The GBM TME cells form spatially organized layers driven by hypoxia pre-treatment, but this influence diminishes post-treatment, giving way to less organised layers with organisation driven by reactive astrocytes and lymphocytes. These findings provide insight into treatment-induced shifts in GBMs cellular landscape, highlighting aspects of the evolving TME that appear to facilitate recurrence and are, therefore, potential therapeutic targets. Key pointsO_LISpatial organisation in primary GBM consist of layers driven by the presence of hypoxia C_LIO_LIThe layers in recurrent GBM appear are driven more by the presence of reactive astrocytes C_LIO_LIIncreased cellular cross-talk in recurrent GBM presents novel therapeutic targets C_LI

cancer biology↗

GCN5a is a telomeric lysine acetyltransferase whose loss primes Toxoplasma gondii for latency

Toxoplasma gondii is a protozoan parasite that causes persistent infection in warm-blooded vertebrates by undergoing differentiation from a replicative stage (tachyzoites) to a latent encysted stage (bradyzoites). Stage differentiation is critical for transmission and pathogenesis and relies on gene regulation driven by a network of transcription and epigenetic factors. We previously found in non-cystogenic type I RH strain parasites that the lysine acetyltransferase (KAT), GCN5a, is dispensable in tachyzoites but required to upregulate stress-response genes, suggesting a link with bradyzoite conversion. To address this possibility, we generated endogenously tagged GCN5a parasites and a genetic knockout in cystogenic type II Pru strain. We show that GCN5a protein, but not mRNA, increases during differentiation and complexes with unique protein partners, most of which contain AP2 domains. Pru strain tachyzoites lacking GCN5a augment bradyzoite-specific gene expression in the absence of stress. Loss of GCN5a slowed tachyzoite replication and heightened sensitivity to bradyzoite conversion but resulted in smaller cyst sizes compared to wildtype. Using CUT&Tag, we delineated the chromosomal occupancy of GCN5a relative to the essential KAT, GCN5b. While GCN5b localizes to coding regions, GCN5a surprisingly localizes exclusively to telomeres. These findings suggest that the loss of GCN5a leads to telomere dysfunction, which slows replication and promotes the transition to latency. IMPORTANCEToxoplasma gondii is a single-celled parasite that persists in warm-blooded hosts, including humans, because it converts into latent tissue cysts. Switching from its replicating form into dormant cysts is a tightly regulated process that involves epigenetic factors such as lysine acetyltransferases GCN5a and GCN5b. This study is the first to examine the role of GCN5a in a cyst-forming Toxoplasma strain. We found that GCN5a protein, but not mRNA, increases during cyst development. Additionally, parasites lacking GCN5a replicate more slowly and are quicker to form cysts when stressed. We show that GCN5a and GCN5b work in different multi-protein complexes and localize to different areas of the genome; while GCN5b targets promoters of gene coding regions, GCN5a is exclusively found at telomeric regions. Our findings suggest a novel role for GCN5a in telomere biology that, when depleted, produces a fitness defect that favors development of latent stages.

microbiology↗

Predictive Coding of Reward in the Hippocampus

A fundamental objective of the brain is to anticipate future outcomes1-7. This process requires learning the states of the world as well as the transitional relationships between those states. The hippocampal cognitive map is believed to be one such internal model8. However, evidence for predictive coding9-12 and reward sensitivity13-19 in the hippocampal neuronal representation suggests that its role extends beyond purely spatial representation. In fact, it raises the question of what kind of spatial representation is most useful for learning and maximizing future rewards? Here, we track the evolution of reward representation over weeks as mice learn to solve a cognitively demanding reward-based task. Our findings reveal a highly organized restructuring of hippocampal reward representations during the learning process. Specifically, we found multiple lines of evidence, both at the population and single-cell levels, that hippocampal representation becomes predictive of reward over weeks. Namely, both population-level information about reward and the percentage of reward-tuned neurons decrease over time. At the same time, the representation of the animals choice and reward approach period (the period between choice and reward) increased over time. By tracking individual reward cells across sessions, we found that neurons initially tuned for reward shifted their tuning towards choice and reward approach periods, indicating that reward cells backpropagate their tuning to anticipate reward with experience. These findings underscore the dynamic nature of hippocampal representations, highlighting their critical role in learning through the prediction of future outcomes.

neuroscience↗

Human melanoma cell lines that possess wild-type BRAF alleles but are dependent on ERBB4 and ERBB2

Metastatic skin cutaneous melanomas that contain wild-type BRAF alleles typically possess an activating mutation in a RAS allele or a loss-of-function mutation in an NF1 allele ("BRAF-WT&RAS/NF1-mutant melanomas"). Nonetheless, these tumors remain a significant clinical challenge; they are resistant to MEK and BRAF inhibitors, their response to immune checkpoint inhibitors is less robust than the response of BRAF mutant melanomas to these agents, and additional validated targets for therapeutic intervention have yet to be identified. Previous work from our laboratory has demonstrated that ERBB4 is required for the proliferation of the IPC-298, MEL-JUSO, MeWo, and SK-MEL-2 BRAF-WT&RAS/NF1-mutant melanoma cell lines. Surprisingly, the synthetic constitutively dimerized and active Q646C ERBB4 mutant allele appears to strongly inhibits the proliferation of BRAF-WT&RAS/NF1- mutant melanoma cell lines. Given that we have also previously demonstrated that ERBB4-ERBB2 and ERBB4-EGFR heterodimers are more potent drivers of proliferation than are ERBB4 homodimers, here we begin to test the hypothesis that ERBB4 heterodimers drive the proliferation of BRAF-WT&RAS/NF1-mutant melanoma cell lines. Here we demonstrate that the kinase-deficient (dominant-negative) ERBB2 K753A mutant allele inhibits the clonogenic proliferation of the IPC-298, MEL-JUSO, and MeWo ERBB4-dependent, BRAF-WT&RAS/NF1-mutant melanoma cell lines. Moreover, the kinase-deficient (dominant-negative) EGFR K721A mutant allele inhibits the clonogenic proliferation of the MeWo cell line, but not the IPC-298 or MEL-JUSO cell lines. Finally, the clonogenic proliferation of the SK-MEL-2 ERBB4-dependent, BRAF-WT&RAS/NF1-mutant melanoma cell line is unaffected by the ERBB2 K753A or EGFR K721A dominant-negative mutant alleles. We discuss these findings in the context of our hypothesis that ERBB4 heterodimers drive the proliferation of BRAF-WT&RAS/NF1-mutant melanoma cell lines.

cancer biology↗

Progressive multi-stage extrapolation of predictable motion in human visual cortex

Neural processing of sensory information takes time. Consequently, to estimate the current state of the world, the brain must rely on predictive processes - for example, extrapolating the motion of a ball to determine its probable present position. Some evidence implicates early (pre-cortical) processing in extrapolation, but it remains unclear whether extrapolation continues during later-stage (cortical) processing, where further delays accumulate. Moreover, the majority of such evidence relies on invasive neurophysiological techniques in animals, with accurate characterisation of extrapolation effects in the human brain currently lacking. Here, we address these issues by demonstrating how precise probabilistic maps can be constructed from human EEG recordings. Participants (N = 18, 2 sessions) viewed a stimulus moving along a circular trajectory while EEG was recorded. Using LDA classification, we extracted maps of stimulus location over time and found evidence of a forwards temporal shift occurring across temporally distinct processing stages. This accelerated emergence of position representations indicates extrapolation occurring at multiple stages of processing, with representations progressively shifted closer to real-time. We further show evidence of representational overshoot during early-stage processing following unexpected changes to an objects trajectory, and demonstrate that the observed dynamics can emerge without supervision in a simulated neural network via spike-timing-dependent plasticity.

neuroscience↗

FoxA1/2-dependent epigenomic reprogramming drives lineage switching in lung adenocarcinoma

The ability of cancer cells to alter their identity is essential for tumor survival and progression. Loss of the pulmonary lineage specifier NKX2-1 within KRAS-driven lung adenocarcinoma (LUAD) enhances tumor progression and results in a pulmonary-to-gastric lineage switch that is dependent upon the activity of pioneer factors FoxA1 and FoxA2; however, the underlying mechanism remains largely unknown. Here, we show that FoxA1/2 reprogram the epigenetic landscape of NKX2-1-negative LUAD to facilitate a gastric identity. After Nkx2-1 deletion, FoxA1/2 mediate demethylation of gastric-defining genes through recruitment of TET3, an enzyme that induces DNA demethylation. H3K27ac ChIP-seq and HiChIP show that FoxA1/2 also control the activity of regulatory elements and their 3D interactions at gastric loci. Furthermore, oncogenic KRAS is required for the FoxA1/2-dependent epigenetic reprogramming. This work demonstrates the role of FoxA1/2 in rewiring the methylation and histone landscape and cis-regulatory dynamics of NKX2-1-negative LUAD to drive cancer cell lineage switching.

cancer biology↗

Genes associated with fitness and disease severity in the pan-genome of mastitis-associated Escherichia coli

Bovine mastitis caused by Escherichia coli may manifest as subclinical through severe acute disease and can be transient or persistent in nature. Little is known about bacterial factors that impact clinical outcomes or allow some strains to outcompete others in the mammary gland (MG) environment. Mastitis-associated E. coli (MAEC) may have distinctive characteristics which may contribute to the varied nature of the disease. In this study, we sequenced the genomes of 96 MAEC strains isolated from cattle with clinical mastitis (CM). We utilized clinical severity data to perform genome-wide association studies to identify accessory genes associated with strains isolated from mild or severe CM, or with high or low competitive fitness during in vivo competition assays. Genes associated with pathogenic or commensal strains isolated from bovine and avian sources were also identified. A type-2 secretion system (T2SS) and a chitinase (ChiA) exported by this system were strongly associated with pathogenic isolates compared with commensal strains. Strains carrying these genes also had higher competitive fitness during experimental intramammary infections. Deletion of chiA from MAEC isolates decreased their adherence to cultured bovine mammary epithelial cells, suggesting that the increased fitness associated with strains possessing this gene may be due to better attachment in the MG. ImportanceBovine mastitis caused by MAEC compromises animal health and inflicts substantial product losses in dairy farming. Given their high levels of intraspecies genetic variability, virulence factors of commonly used MAEC model strains may not be relevant to all members of this group. Here we analyzed clinical data as well as fitness (quantified in a mouse MG model) of diverse MAEC isolates to identify accessory genes that contribute to infection. We demonstrated a novel role for chitinase in promoting attachment to mammary epithelial cells. Reverse genetic approaches can be applied to the collection of strains and their complete genome sequences that we have presented here. Overall, these results provide a much richer understanding of MAEC and suggest bacterial processes that may underlie the clinical diversity associated with mastitis and their adaptation to this unique environment.

microbiology↗

Decreasing the flexibility of the TELSAM-target protein linker and omitting the cleavable fusion tag improves crystal order and diffraction limits

TELSAM crystallization promises to become a revolutionary tool for the facile crystallization of proteins. TELSAM can increase the rate of crystallization and form crystals at low protein concentrations without direct contact between TELSAM polymers and, in some cases, with very minimal crystal contacts overall (Nawarathnage et al., 2022). To further understand and characterize TELSAM-mediated crystallization, we sought to understand the requirements for the composition of the linker between TELSAM and the fused target protein. We evaluated four different linkers Ala-Ala, Ala-Val, Thr-Val, and Thr-Thr, between 1TEL and the human CMG2 vWa domain. We compared the number of successful crystallization conditions, the number of crystals, the average and best diffraction resolution, and the refinement parameters for the above constructs. We also tested the effect of the fusion protein SUMO on crystallization. We discovered that rigidification of the linker improved diffraction resolution, likely by decreasing the number of possible orientations of the vWa domains in the crystal, and that omitting the SUMO domain from the construct also improved the diffraction resolution. SynopsisWe demonstrate that the TELSAM protein crystallization chaperone can enable facile protein crystallization and high-resolution structure determination. We provide evidence to support the use of short but flexible linkers between TELSAM and the protein of interest and to support the avoidance of cleavable purification tags in TELSAM-fusion constructs.

biochemistry↗