Biology subjects
Publications and source records attributed to Warren, J..
Formalin-fixed paraffin-embedded (FFPE) samples are valuable but underutilized in single-cell omics research due to their low DNA and RNA quality. In this study, leveraging recent single-cell genomic technology advances, we introduce a versatile method to derive high-quality single-nucleus transcriptomic data from FFPE samples.
Hippocampus is critical for memory, imagination and constructive reasoning. However, recent models have suggested that its neuronal responses can be well explained by graphs, or state-spaces, that model the transitions between experiences. Here we use simulations and hippocampal recordings to reconcile these views. We show that if state-spaces are constructed compositionally from existing building blocks, or primitives, hippocampal responses can be interpreted as compositional memories, binding these primitives together. Critically, this enables agents to behave optimally in novel environments with no new learning, inferring behaviour directly from the composition. We predict a role for hippocampal replay in building and consolidating these compositional memories. Importantly, due to their compositional nature, replay can construct states the agent has never experienced - effectively building memories of the future. We test these predictions in two datasets by showing that replay events from newly discovered landmarks induce and strengthen new remote firing fields. These memories, built in replay, are compositional. When the landmark is moved, replay builds a new firing field at the same vector to the new location. Together, these findings provide a framework for reasoning about compositional memories, and demonstrate that such memories are formed in hippocampal replay.
Monogenic diseases can often manifest diverse clinical phenotypes and cause diagnostic dilemmas. While monoallelic loss-of-function variants in TNFAIP3 (Haploinsufficiency of A20; HA20) cause a highly penetrant autoinflammatory disease, the variable expressivity suggest a role for additional genetic and environmental disease modifiers. Here, we identify critically ill children who inherited a family-specific TNFAIP3 deletion from one of their otherwise healthy parents. Each of the probands also inherited in trans a subtle loss-of-function I207L TNFAIP3 variant that is common in Oceania, originally introgressed from Denisovans. Modelling this compound heterozgous state in mice under specific pathogen free conditions demonstrated a reduced threshold to break immune tolerance. Exaggerated immune responses were precipitated by inheriting the two genetic hits on the TNFAIP3 checkpoint coupled with increasing the microbial challenge to immune tolerance, either by co-housing with pet store mice carrying a wild microbial burden or by transient dietary exposure to a chemical that diminishes the intestinal mucin barrier separating gut microbes from immune sensing systems. These data illuminate second-hit genetic and environmental modifiers contributing to complex inflammatory and autoimmune disease. Increased mechanistic understanding of the presence and contribution of disease modifiers will aid diagnostic and prognostic patient stratification and potentially reveal novel therapeutic opportunities.
BackgroundHemorrhagic stroke is associated with loss of middle cerebral artery (MCA) autoregulation in the stroke-prone spontaneously hypertensive rat (SHRsp). The signaling mechanism associated with the functional loss has yet to be defined. We hypothesize that physiological alterations coincide with changes to cerebrovascular inflammatory and contractile signaling and altered calcium signaling. METHODS: SHRsp rats were fed a high salt (4% NaCl) diet and sacrificed at 9 weeks of age for pre-stroke and after evidence of stroke for post-stroke samples. The MCAs were isolated for measuring protein levels using immunofluorescence (IF) & western blot (WB) for inflammatory signaling and contractile proteins. Tissues surrounding the MCA were analyzed for neuro-inflammation, neuronal damage, total and activated inflammatory proteins (ERK1/2 and p38MAPK), cerebrovascular contraction (PKC and MLC), and transient receptor potential V4 (TRPV4) expression. RESULTS: Our data show increase in activated inflammatory proteins after stroke with an associated decrease in expression of activated contractile proteins and TRPV4 channel expression compared to pre-stroke MCA. The post-stroke samples also show significant increase in neuro-inflammation and neuronal damage compared to pre-stroke samples. CONCLUSIONAn increase in activated/total (p38 MAPK &ERK1/2) is accompanied by a decrease in activated/total PKC & TRPV4 channel expression in post-stroke SHRsps. The decrease in vessel structural integrity and altered vascular tone of the MCAs may affect its ability to contract in response to pressure. Significant neuro-inflammation and neuronal damage in the brain tissues surrounding the MCA in post-stroke samples suggest MCA dysfunction is accompanied with neuronal and neural damage during stroke.
We investigated auditory processing in a young patient who experienced a single embolus causing an infarct in the right middle cerebral artery territory. This lead to damage to auditory cortex including planum temporale that spared medial Heschls gyrus, and included damage to the posterior insula and inferior parietal lobule. She first reported difficulty hearing all sounds, which fully recovered within days, but she subsequently reported chronic difficulties with segregating speech from noise and segregating elements of music. Clinical tests showed no evidence for abnormal cochlear function. Follow-up tests confirmed difficulties with auditory segregation in her left ear that spanned multiple domains, including speech-in-noise and music streaming. Testing with a stochastic figure-ground task--a way of estimating generic acoustic foreground and background segregation--demonstrated that this was also abnormal. This is the first demonstration of an acquired deficit in the segregation of complex acoustic patterns due to cortical damage, which we argue is a causal explanation for the symptomatic deficits in the segregation of speech and music. These symptoms are analogous to the visual symptom of simultaneous agnosia. Consistent with functional imaging studies on normal listeners, the work implicates non-primary auditory cortex. Further, the work demonstrates a (partial) lateralisation of the necessary anatomical substrate for segregation that has not been previously highlighted. HighlightsO_LIRare case of auditory agnosia in a young patient with a right-hemisphere infarct C_LIO_LIDamage affecting non-primary auditory cortex, but sparing primary auditory cortex C_LIO_LIGeneralised auditory segregation deficit, revealed by auditory figure-ground task C_LIO_LIThis explains segregation deficits for speech-in-noise and music streaming C_LIO_LIThe deficit affects stimuli presented on the left C_LI
Germline loss-of-function variation in TNFAIP3, encoding A20, has been implicated in a wide variety of autoinflammatory and autoimmune conditions, with acquired somatic missense mutations linked to cancer progression. Furthermore, human sequence data reveals that the A20 locus contains ~400 non-synonymous coding variants which are largely uncharacterised. The growing number of A20 coding variants with unknown function, but potential clinical impact, poses a challenge to traditional mouse-based approaches. Here we report the development of a novel functional genomics approach that utilises the new A20-deficient zebrafish (Danio rerio) model to investigate the impact of TNFAIP3 genetic variants in vivo. Similar to A20-deficient mice, A20-deficient zebrafish are hyper-responsive to inflammatory triggers and exhibit spontaneous early lethality. While ectopic addition of human A20 rescued A20-null zebrafish from lethality, missense mutations at two conserved A20 residues, S381A and C243Y reversed this protective effect. Ser381 represents a phosphorylation site important for enhancing A20 activity that is abrogated by its mutation to alanine, or by a C243Y mutation that associates with human autoimmune disease. These data reveal an evolutionarily conserved role for A20, but also demonstrate how a zebrafish functional genomics pipeline can be utilized to investigate the in vivo significance of medically relevant TNFAIP3 gene variants. This approach could be utilised to investigate genetic variation for other conserved genes.
Listeria monocytogenes is an important foodborne pathogen in human and veterinary health, causing significant morbidity and mortality including abortion. It has a particular tropism for the gravid uterus, however, the route of infection in reproductive tissues of ruminants (i.e. placentome), is much less clear. In this study, we aimed to investigate a bovine caruncular epithelial cell (BCEC) line as a model for L. monocytogenes infection of the bovine reproductive tract. The BCEC infection model was used to assess the ability of 14 different L. monocytogenes isolates to infect these cells. Lysozyme sensitivity and bacterial survival in 580 {micro}g lysozyme/ml correlated with attenuated ability to proliferate in BCEC (p=0.004 and p=0.02, respectively). Four isolates were significantly attenuated compared to the control strain 10403S. One of these strains (AR008) showed evidence of compromised cell wall leading to increased sensitivity to {beta}-lactam antibiotics, and another (7644) had compromised cell membrane integrity leading to increased sensitivity to cationic peptides. Whole genome sequencing followed by Multi Locus Sequence Type analysis identified that five invasive isolates had the same sequence type, ST59, despite originating from three different clinical conditions. Virulence gene analysis showed that the attenuated isolate LM4 was lacking two virulence genes (uhpT, virR) known to be involved in intracellular growth and virulence. In conclusion, the BCEC model was able to differentiate between the infective potential of different isolates. Moreover, resistance to lysozyme correlated with the ability to invade and replicate within BCEC, suggesting co-selection for surviving challenging environments as the abomasum.
By developing a high-density murine immunophenotyping platform compatible with high-throughput genetic screening, we have established profound contributions of genetics and structure to immune variation. Specifically, high-throughput phenotyping of 530 knockout mouse lines identified 140 monogenic \"hits\" (>25%), most of which had never hitherto been implicated in immunology. Furthermore, they were conspicuously enriched in genes for which humans show poor tolerance to loss-of-function. The immunophenotyping platform also exposed dense correlation networks linking immune parameters with one another and with specific physiologic traits. By limiting the freedom of individual immune parameters, such linkages impose genetically regulated \"immunological structures\", whose integrity was found to be associated with immunocompetence. Hence, our findings provide an expanded genetic resource and structural perspective for understanding and monitoring immune variation in health and disease.
Resisting or tolerating microbes are alternative strategies to survive infection, but little is known about the evolutionary mechanisms controlling this balance. Here, genomic analyses of anatomically modern humans, extinct Denisovan hominins, and mice revealed a series of missense variants in the immune response inhibitor A20 (encoded by TNFAIP3), substituting non-catalytic residues of the ubiquitin protease domain to diminish I{kappa}B-dependent phosphorylation and activation of A20. Two A20 variants with partial phosphorylation deficits appeared beneficial: one originating in Denisovans and introgressed in modern humans throughout Oceania, and another in a mouse strain resistant to Coxsackievirus. By contrast, a variant with 95% loss of phosphorylation caused spontaneous inflammatory disease in humans and mice. Analysis of the partial phosphorylation variant in mice revealed diminished tolerance of bacterial lipopolysaccharide or to poxvirus inoculation as trade-offs for enhanced immunity.\n\nOne Sentence SummaryModern and ancient variants reveal a genetically tunable element for balancing immunity and microbial tolerance.
Stringent regulation of cellular levels of evolutionarily conserved centromeric histone H3 variant (CENP-A in humans, CID in flies, Cse4 in yeast) prevents its mislocalization to non-centromeric chromatin. Overexpression and mislocalization of CENP-A has been observed in cancers and leads to aneuploidy in yeast, flies, and human cells. Ubiquitin-mediated proteolysis of Cse4 by E3 ligases such as Psh1 and Sumo-Targeted Ubiquitin Ligase (STUbL) Slx5 prevent mislocalization of Cse4. Previously, we identified Siz1 and Siz2 as the major E3 ligases for sumoylation of Cse4. In this study, we identify lysine 65 (K65) in Cse4 as a SUMO site and show that sumoylation of Cse4 K65 regulates its ubiquitin-mediated proteolysis by Slx5. Strains expressing cse4 K65R exhibit reduced levels of sumoylated and ubiquitinated Cse4 in vivo. Furthermore, co-immunoprecipitation experiments reveal reduced interaction of cse4 K65R with Slx5. Defects in sumoylation of cse4 K65R contribute to increased stability and mislocalization of cse4 K65R under normal physiological conditions. Based on the increased stability of cse4 K65R in psh1{triangleup} strains but not in slx5{triangleup} strains, we conclude that Slx5 targets sumoylated Cse4 K65 for ubiquitination-mediated proteolysis independent of Psh1. In summary, we have identified and characterized the physiological role of Cse4 sumoylation and determined that sumoylation of Cse4 K65 regulates ubiquitin-mediated proteolysis and prevents mislocalization of Cse4 which is required for genome stability.