Miracle-dz/UniFAR-FTUs huggingface dataset:
The functional landscape of patient derived RNF43 mutations predicts Wnt inhibitor sensitivity

A subset of Wnt-addicted cancers are sensitive to targeted therapies that block Wnt secretion or receptor engagement. RNF43 loss-of-function mutations that increase cell surface Wnt receptor abundance cause sensitivity to Wnt inhibitors. However, it is not clear which of the clinically identified RNF43 mutations affect its function in vivo. We assayed 90 missense and 45 truncating RNF43 mutations found in human cancers, using a combination of cell-based reporter assays, genome editing, flow cytometry and immunofluorescence microscopy. Patent-derived xenograft (PDX) models with C-terminal truncating RNF43 mutations were tested for Wnt inhibitor sensitivity. We find that five common germline variants of RNF43 have wild-type activity. The majority of cancer-associated missense mutations in the RING and PA domains are either loss of function or hyperactivating. Hyperactivating mutants appear to function through formation of inactive dimers with endogenous RNF43 and/or ZNRF3. C-terminal truncation mutants including the common G659fs mutant, have discordant behavior in in vitro versus in vivo assays. PDXs and cell lines with C-terminal truncations show increased cell surface FZD, Wnt/β-catenin signaling and are responsive to PORCN inhibition in vivo, providing clear evidence of RNF43 loss of function. In conclusion, RNF43 nonsense and frameshift mutations, including those in the C-terminal domain, and specific missense mutations in RING and PA are loss of function and predict response to upstream Wnt inhibitors in microsatellite stable cancers. This study expands the landscape of actionable RNF43 mutations, potentially extending the benefit of these therapies to additional patients. Statement of Significance Loss of function RNF43 mutations, first described in pancreatic cancers, drive progression of multiple cancers by increasing cellular sensitivity to Wnt ligands. These cancers are therefore uniquely sensitive to agents such as PORCN inhibitors that block Wnt production. As the PORCN inhibitors and other upstream inhibitors advance into clinical trials it is important to identify the right patients to treat with these upstream Wnt inhibitors. Hence a detailed map of mutations that are actionable is required. Here we systematically examined a spectrum of 135 patient-derived RNF43 mutations from multiple cancers. Using cell-based reporter assays, genome editing and patient-derived xenografts, we identify rules to guide patient selection. MSS cancers with either truncating mutations anywhere in the gene, including C-terminal truncations around the G659 position, or point mutations in well-defined functional domains, are likely to have RNF43 loss of function and hence a response to therapy.
Circadian Modulation of Neurons and Astrocytes Controls Synaptic Plasticity in Hippocampal Area CA1

Most animal species operate according to a 24-hour period set by the suprachiasmatic nucleus (SCN) of the hypothalamus. The rhythmic activity of the SCN is known to modulate hippocampal-dependent memory processes, but the molecular and cellular mechanisms that account for this effect remain largely unknown. Here, we show that there are cell-type specific structural and functional changes that occur with circadian rhythmicity in neurons and astrocytes in hippocampal area CA1. Pyramidal neurons change the surface expression of NMDA receptors, whereas astrocytes change their proximity to synapses. Together, these phenomena alter glutamate clearance, receptor activation and integration of temporally clustered excitatory synaptic inputs, ultimately shaping hippocampal-dependent learning in vivo. We identify corticosterone as a key contributor to changes in synaptic strength. These findings identify important mechanisms through which neurons and astrocytes modify the molecular composition and structure of the synaptic environment, contribute to the local storage of information in the hippocampus and alter the temporal dynamics of cognitive processing.
Analyzing and interpreting DNA double-strand break sequencing data

DNA double-strand breaks (DSBs), are a major threat to genomic stability and may lead to cancer. Several technologies to accurately detect DSBs genome-wide have been developed recently, but still lacking publicly available tools for analysis of the resulting data. Here, we present a step-by-step iSeq package (http://breakome.utmb.edu/software.html), custom designed for analysis and interpretation of DSB-sequencing data. iSeq performs barcode trimming and read counting, and identifies DSB-enriched regions by statistical test and annotate them to the desired genomic features. Applying this package, users can identify and annotate DSB-enriched regions from base pair (eg. Cas9 cleavage sites) up to megabase (eg. DNA replication stress-induced) resolution, and if possible quantify DSB frequencies per cell genome-wide by combining with qDSB-Seq. iSeq can be used for any sequencing-based DSB detection techniques. The analysis for Steps 1-19 can be performed within ~4 hours.
Deletion of Autophagy gene ATG1 and F-box motif encoding gene YDR131C together leads to Synthetic Growth Defects and Flocculation behaviour in Saccharomyces cerevisiae

F-box motif encoding YDR131C is functionally uncharacterized gene which forms the complex with the SCF-E3 ligase. The F-box motif containing proteins are involved in substrate recruitment for the ubiquitination and subsequent degradation through 26S proteasome. Autophagy gene, ATG1 (ULK1in human) is a well conserved serine-threonine kinase, required for vesicle formation and cytoplasm to vacuole targeting pathway. Atg1p forms the complex with Atg13p and Atg17p during autophagy. The understanding of crosstalk between ubiquitin and autophagy pathways is crucial for synthetic lethality screen and drug targeting. Here we have conducted the study for genetic interaction between uncharacterized YDR131C and ATG1 gene representing both specific and non-specific protein degradation pathways. The single and double gene knockout strains of YDR131Cand ATG1 genes were constructed in the BY4741 genetic background and analysed for growth fitness. The strains were also evaluated for cellular growth response in presence of hydroxyurea (HU), methyl methane sulfonate (MMS), and hydrogen peroxide (H2O2) stress causing agents by spot assay. The ydr131cΔatg1Δ showed the synthetic growth defect phenotype with floc formation in rich medium which showed floc disruption in presence of EDTA. The ydr131cΔatg1Δ cells showed the sensitivity to stress agents HU, MMS, and H2O2 when compared with ydr131cΔ, atg1Δ, and WT cells. Based on the observations, we report that YDR131C and ATG1 functions in parallel pathways for growth fitness and cellular growth response to stress agents. Interestingly this study also revealed the crosstalk between ubiquitination and autophagy pathways. The defects in both the pathways could lead to synthetic growth defects which may have implication for the precision medicine initiatives.
Mupirocin-associated temporal changes in the nasal microbiota and host’s antimicrobial responses: A pilot study in healthy staphylococcal carriers

Background How mupirocin affects the human nasal microbiota over time remains uncharacterized. Methods We repeatedly sampled the anterior nares of four healthy staphylococcal carriers before and after mupirocin use. By sequencing bacterial 16S ribosomal cDNA, we characterized sequential changes in the carriage status, the nasal microbiota, and the hosts’ antimicrobial peptide expression up to 90 days after decolonization. Results Before mupirocin use, the nasal microbiota differed by the initial, culture-based staphylococcal carriage status, with Firmicutes (54.1%) being the most predominant in carriers and Proteobacteria (75.8%) in the only noncarrier. The nasal microbiota became less diverse (Shannon diversity: 1.33, 95% confidence interval [CI]: 1.06-1.54) immediately after decolonisation than that before decolonisation (1.78, 95%CI: 0.58-1.93). Based on results of differential abundance analysis, Firmicutes were significantly enriched (log2 fold changes ≥ 4, Benjamini-Hochberg adjusted P < .01) while Actinobacteria, particularly Corynbebacterium, were relatively depleted in samples from staphylococcal carriers. Results of nonmetric multidimensional scaling (NMDS) and constrained correspondence analysis (CCA) also suggested that the initial staphylococcal carriage status, human neutrophil peptide 1 levels, and sampling times were major contributors to the between-community dissimilarities (P for marginal permutation test: .014) though the significance attenuated when within-group correlation was considered (P for blocked permutation test: .047). Conclusion These findings suggest that large-scale investigations on antibiotic effects on the human nasal microbiota are warranted.
Presynaptic NMDA receptors cooperate with local action potentials to implement activity-dependent GABA release from the reciprocal olfactory bulb granule cell spine

In the rodent olfactory bulb the smooth dendrites of the principal glutamatergic mitral cells (MCs) form reciprocal dendrodendritic synapses with large spines on GABAergic granule cells (GC), where unitary release of glutamate can trigger postsynaptic local activation of voltage-gated Na+-channels (Navs), i.e. a spine spike. Can such single MC input evoke reciprocal release? We find that unitary-like activation via two-photon uncaging of glutamate causes GC spines to release GABA both synchronously and asynchronously onto MC dendrites. This release indeed requires activation of Navs and high-voltage-activated Ca2+-channels (HVACCs), but also of NMDA receptors (NMDAR). Simulations show temporally overlapping HVACC- and NMDAR-mediated Ca2+-currents during the spine spike, and ultrastructural data prove NMDAR presence within the GABAergic presynapse. This cooperative action of presynaptic NMDARs allows to implement synapse-specific, activity-dependent lateral inhibition and thus could provide an efficient solution to combinatorial percept synthesis in a sensory system with many receptor channels.
Delayed Interval Delivery and Chorionicity

Two multiple pregnancies with delayed delivery after expulsion of the first twin are presented. Case 1: A 37 years old woman with dichorionic diamniotic twin pregnancy and the first foetus was aborted at 16 weeks of gestation. She delivered a healthy male infant at 38 weeks of gestation (22 weeks after the delivery of the first twin). Case 2: A 31 years old monochorionic diamniotic twin pregnancy she aborted the first foetus at 19 weeks of gestation and was managed with cervical cerclage and delivered a healthy male infant at 38 weeks of gestation (19 weeks after the delivery of the first twin). Based on our experience and the review of literature, delayed delivery with careful observation of foetal and maternal condition is recommended for improved survival and decreased morbidity among latter-born siblings.
Evidence for, and Metabolic Consequences of, a Cardiac Mitochondrial KNa1.2 Channel

Controversy surrounds the molecular identity of mitochondrial K+ channels important for protection against cardiac ischemia-reperfusion injury. While KNa1.2 (Kcnt2 gene) is necessary for cardioprotection by volatile anesthetics, electrophysiologic evidence for a mitochondrial KNa1.2 is lacking. The endogenous physiologic role of a potential mito-KNa1.2 is also unclear. Herein, single channel patch-clamp of cardiac mitochondrial inner membranes from wild type (WT) and Kcnt2-/- mice yielded respectively 6/27 and 0/40 channels, matching the known ion-sensitivity, ion-selectivity, pharmacology and conductance properties of KNa 1.2 (WT slope conductance 138±1 pS). The KNa opener bithionol uncoupled respiration in WT but not Kcnt2-/- cardiomyocytes. Furthermore, when oxidizing only fat as substrate, Kcnt2-/- cardiomyocytes and hearts were less responsive to increases in energetic demand. Kcnt2-/- mice had elevated body fat, but no baseline differences in the cardiac metabolome. These data support the existence of a cardiac mitochondrial KNa 1.2 channel with a potential metabolic regulatory role under high energetic demand.
OmicsDB::Pathogens - A database for exploring functional networks of plant pathogens

Plant pathogens are a great threat to food security. To combat them we need an understanding of how they work. Integrating large-scale omics datasets such as genomes and transcriptomes has been shown to provide deeper insights into many aspects of molecular biology. For a better understanding of plant pathogens, we aim to construct a platform for accessing genomic and gene co-expression networks for a range of pathogens and reference species. Currently we have integrated genomic and transcriptomics data from 10 species (Fusarium graminearum, Ustilago maydis, Blumeria graminis, Neurospora crassa, Schizosaccharomyces pombe, Saccharomyces cerevisiae, Escherichia coli, Arabidopsis thaliana, Mus musculus and Homo sapiens). Here we introduce OmicsDB::Pathogens (http://pathogens.omicsdb.org), a publicly available web portal with an underlying database containing genomic, and transcriptomic data and analysis tools. It allows non-bioinformaticians to browse genomic data and inspect and compare biological networks across species. The information is modelled in a graph-based database, enabling flexibility for querying and future extensions. Tools such as BLAST and Cytoscape.js are available together with the option of performing GO enrichment analysis. The database also enables the user to browse information such as Orthologs, Protein domains and publications citing a given gene. Herein we describe how to use this platform for generating hypotheses for the function of a gene. Availability and Implementation Currently, Omicsdb supports networks for 10 organisms and is freely available for public use at http://pathogens.omicsdb. org
Tightly regulated, yet flexible, directional switching mechanism of a rotary motor

Biological switches are wide spread in many biological systems. Among them, the switch of the bacterial flagellar motor has generated much interest because it affects a mechanical process rather than a chemical reaction, it controls the direction of rotation of a rotary motor rather than being an on/off switch, and it is exceptionally ultrasensitive. Yet, the molecular mechanism underlying its function has remained unknown. Here we resolved unique features of this mechanism: On the one hand, it is tightly regulated by multiple means, involving three binding sites and two different covalent modifications, with the binding specificity being dictated by the type of covalent modification and by a strict binding sequence. On the other hand, it endows the motor with flexibility as it involves an intermediate stage of brief switches that provides a “go/no go” situation, in which the motor can either proceed to a stable rotation in the new direction or shift back to the original direction. This intermediate stage appears to be a means of the cell to produce angular deflection of swimming while maintaining directional persistence. Furthermore, we show by mathematical modeling that such a switching mechanism can provide ultrasensitivity. This unique combination of tight regulation, flexibility, and ultrasensitivity makes this switching mechanism of special interest.
Role of the C-terminal tail in regulating Proteinase Activated Receptor 2 (PAR2) signalling

The C-terminal tail of G-protein-coupled receptors contain important regulatory sites that enable interaction with intracellular signalling effectors. Here we examine the relative contribution of the C-tail serine/threonine phosphorylation sites (Ser383-385, Ser387-Thr392) and the helix-8 palmitoylation site (Cys361) in signalling regulation downstream of the proteolytically-activated GPCR, PAR2. We examined Gαq/11-coupled calcium signalling, β-arrestin-1/-2 recruitment, and MAPK activation (p44/42 phosphorylation) by wild-type and mutant receptors expressed in a CRISPR/Cas9 PAR2-knockout HEK-293 cell background. We find that alanine substitution of the membrane proximal serine residues (Ser383-385Ala) had no effect on SLIGRL-NH2- or trypsin-stimulated β-arrestin recruitment. Alanine substitutions in the Ser387-Thr392 cluster resulted in a large (∼50%) decrease in β-arrestin-1/2 recruitment triggered by the activating peptide, SLIGRL-NH2, but was without effect on trypsin-activated β-arrestin-1/-2 recruitment. Additionally, we find that alanine substitution of the helix-8 cysteine residue (Cys361Ala) led to a (∼50%) decrease in β-arrestin-1/-2 recruitment in response to both trypsin and SLIGRL-NH2. We further show that Gαq/11inhibition with YM254890, inhibited ERK phosphorylation by PAR2 agonists, while genetic deletion of β-arrestin-1/-2 by CRISPR/Cas9 enhanced MAPK activation. Knockout of β-arrestins also enhanced Gαq/11-mediated calcium signalling. In line with these findings, C-tail serine/threonine and cysteine residue mutants that have decreased β-arrestin recruitment also showed enhanced ERK activation. Thus, our studies point to multiple mechanisms that regulate β-arrestin interaction with PAR2 to regulate receptor-mediated signalling.
Assortative mate choice and epistatic mating-trait architecture induce complex movement of the crow hybrid zone

Hybrid zones provide a window into the evolutionary processes governing species divergence. While the role of postzygotic isolation has been extensively characterized in the context of hybrid zones, the contribution of prezygotic isolation is less well explored. Here, we investigate the effects of assortative mate choice, the underlying preference function and mating-trait architecture, and the strength of sexual selection on hybrid zone dynamics. We explore this question by means of a mathematical model parameterized with phenotype and genotype data from the hybrid zone between all-black carrion and grey-coated hooded crows. The best-fit model resulted in narrow clines for two mating-trait loci coding for colour phenotype maintained by a moderate degree of assortative mating. Epistasis between the two loci induced hybrid-zone movement in favor of alleles conveying dark plumage followed by a shift in the opposite direction favouring grey-coated phenotypes ∼1,200 generations after secondary contact. Unlinked neutral loci diffused near-unimpeded across the zone. These results were generally robust to the choice of matching rule (self-referencing or parental imprinting) and effects of genetic drift. Overall, this study illustrates under which conditions assortative mating can maintain steep clines in mating-trait loci without generalizing to genome-wide reproductive isolation. It further emphasizes the importance of mating-trait architecture for spatio–temporal hybrid-zone dynamics.
Blood vessel occlusion by Cryptococcus neoformans is a mechanism for haemorrhagic dissemination of infection

Meningitis caused by infectious pathogens are associated with vessel damage and infarct formation, however the physiological cause is unknown. Cryptococcus neoformans, is a human fungal pathogen and causative agent of cryptococcal meningitis, where vascular events are observed in up to 30% of cases, predominantly in severe infection. Therefore, we aimed to investigate how infection may lead to vessel damage and associated pathogen dissemination using a zebrafish model for in vivo live imaging. We find that cryptococcal cells become trapped within the vasculature (dependent on there size) and proliferate there resulting in vasodilation. Localised cryptococcal growth, originating from a single or small number of cryptococcal cells in the vasculature was associated with sites of dissemination and simultaneously with loss of blood vessel integrity. Using a cell-cell junction tension reporter we identified dissemination from intact blood vessels and where vessel rupture occurred. Finally, we manipulated blood vessel stifness via cell junctions and found increased stiffness resulted in increased dissemination. Therefore, global vascular vasodilation occurs following infection, resulting in increased vessel tension which subsequently increases dissemination events, representing a positive feedback loop. Thus, we identify a mechanism for blood vessel damage during cryptococcal infection that may represent a cause of vascular damage and cortical infarction more generally in infective meningitis.
TGF-Β Family Inhibitors Blunt Adipogenesis Via Non-Canonical Regulation Of SMAD Pathways

Adipose tissues (AT) expand in response to energy surplus through adipocyte hypertrophy and hyperplasia (i.e., adipogenesis). The latter is a process by which multipotent precursors differentiate into mature adipocytes. This process is directed by growth factors and cytokines, including members of the TGF-β family, which regulate intracellular signaling pathways that control adipogenic transcriptional programs. As ectopic adipogenesis has been linked with metabolic syndrome and other pathological conditions, we undertook to establish how TGF-β family growth factors and their inhibitors regulate this process in a 3T3-L1 adipogenesis model. We found that intracellular SMAD1/5/8 signaling pathways are activated while SMAD2/3 pathways are suppressed in differentiating cells. Addition of SMAD1/5/8 pathway activating ligands promoted cell proliferation, while SMAD2/3 pathway activating ligands suppressed adipocyte formation. We identified several ligand traps that blunted 3T3-L1 adipogenesis. Strikingly, anti-adipogenic traps and ligands exploited the same mechanism of regulation involving a negative feedback loop that links SMAD2/3 activation with SMAD1/5/8 hyper-phosphorylation, cytoplasmic retention, and reduced signaling. The identified anti-adipogenic traps could be used to control hyperplastic AT expansion and its associated pathological conditions.
Insulin-Like Growth Factor I Modulates Sleep Through Hypothalamic Orexin Neurons

Although metabolic and sleep disturbances are commonly associated, the underlying processes are not yet fully defined. Insulin-like growth factor-I (IGF-I), an anabolic hormone that shows a circadian pattern in the circulation and activity-dependent entrance in the brain, is associated to sleep regulation along evolution. However, its role in this universal homeostatic process remains poorly understood. We now report that the activity of orexin neurons, a discrete cell population in the lateral hypothalamus that is involved in the circadian sleep/wake cycle and arousal, is modulated by circulating IGF-I. Furthermore, mice with blunted IGF-I receptor activity in orexin neurons have lower levels of orexin in the hypothalamus, show altered electrocorticographic patterns with predominant slow wave activity, reduced onset-sleep latency, and less transitions between sleep and awake stages. Collectively, these results extend the role of this pleiotropic growth factor to shaping sleep architecture through regulation of orexin neurons. We speculate that poor sleep quality associated to diverse conditions may be related to disturbed brain IGF-I input to orexin neurons.
Chromosomal resolution reveals symbiotic virus colonization of parasitic wasp genomes

Most endogenous viruses, an important proportion of eukaryote genomes, are doomed to slowly decay. Little is known, however, on how they evolve when they confer a benefit to their host. Bracoviruses are essential for the parasitism success of parasitoid wasps, whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome, for the first time at a chromosomal scale, that symbiotic bracovirus genes spread to and colonized all the chromosomes. Moreover, large viral clusters are stably maintained suggesting strong evolutionary constraints. Genomic comparison with another wasps revealed that this organization was already established ~53 mya. Transcriptomic analyses highlight temporal synchronization of viral gene expression, leading to particle production. Immune genes are not induced, however, indicating the virus is not perceived as foreign by the wasp. This recognition suggests that no conflicts remain between symbiotic partners when benefits to them converge.