Biology subjects

Li, Q.

Publications and source records attributed to Li, Q..

At least 469 records · Page 26Linked to original sources

bioRxiv2022

Effect of Ascosphaera apis infestation on the activities of four antioxidant enzymes in Asian honey bee larval guts

Ascosphaera apis exclusively infects bee larvae and causes chalkbrood, a lethal fungal disease that results in the sharp reduction in adult bees and colony productivity. However, little is known about the effect of A. apis infestation on the activities of antioxidant enzymes in bee larvae. Here, A. apis spores were purified and used to inoculate Asian honey bee (Apis cerana) larvae, followed by detection of the host survival rate and evaluation of the activities of four major antioxidant enzymes. At 6 days post inoculation (dpi) with A. apis spores, white mycelia penetrated the posterior end of the larva, extended to the anterior end, and eventually covered the entire larval body surface, presenting an obvious symptom of chalkbrood disease similar to that occurs in Apis mellifera larvae. Additionally, PCR identification showed that the expected fragment was amplified from the A. apis-inoculated larval guts and the A. apis spores, verifying the A. apis infection of A. cerana larvae. The survival rate of larvae inoculated with A. apis was high at 1-2 dpi, sharply decreased to 4.16% at 4 dpi, and reached 0% at 5 dpi; whereas that of un-inoculated larvae was always high at 1~8 dpi, with an average survival rate of 95.37%, indicating the negative impact of A. apis infection on larval survival. Furthermore, in comparison with those in the corresponding un-inoculated groups, the superoxide dismutase (SOD) and catalase (CAT) activities in the 4-day-old larval gut in the A. apis-inoculated groups were reduced (p > 0.05), while those in the 5- and 6-day-old larval guts were significantly decreased (p < 0.05); the glutathione S-transferase (GST) activity in the 4- and 5-day-old larval guts was significantly increased (p < 0.05), while that in the 6-day-old larval gut was reduced (p > 0.05); the polyphenol oxidase (PPO) activity in 4-day-old larval gut was increased (p > 0.05) and that in the 5-day-old larval gut was significantly increased (p < 0.05), whereas that in the 6-day-old larval gut was significantly reduced (p < 0.01). These results together suggested that the activities of SOD and CAT in the larval guts were suppressed during the process of A. apis infestation, while the GST activity was induced to activation, and the PPO activity was first enhanced and then inhibited. Our findings not only unravel the response of A. cerana larvae to A. apis infestation from a biochemical perspective, but also offer a valuable insight into the interaction between Asian honey bee larvae and A. apis.

molecular biology↗

bioRxiv2022

Structural insights into human ABCC4 mediated transport of platelet agonist and inhibitor

The activation and accumulation of human platelets contributes to hemostasis and thrombosis, the imbalance of which would cause cardiovascular diseases, an increasing threat to the global health. Human ABC transporter ABCC4 that pumps out the platelet agonist and anti-platelet drug such as aspirin, might become a promising target for preventing cardiovascular diseases. Here we solve the structures of human ABCC4 in the apo and two complexed forms, all of which adopt a typical architecture of type-IV ABC transporters in an inward-facing conformation. Structure of ABCC4 complexed with U46619, an analog of the unstable TXA2, provides the first structural evidence that the platelet agonist TXA2 is also exported via ABCC4. The dipyridamole-complexed structure reveals the inhibitory mechanism of dipyridamole against ABCC4. Structural comparisons enabled us to identify a transmembrane pocket in ABCC4 that provides a defined space for the rational design of specific anti-platelet drugs.

biochemistry↗

bioRxiv2022

Nucleic acid sensing by STING induces an interferon-like antiviral response in a marine invertebrate

The cytosolic detection of pathogen derived nucleic acids has evolved as an essential strategy for host innate immune defense in mammals. The stimulator of interferon genes (STING) functions as a crucial signaling adaptor, linking the cytosolic detection of DNA by cyclic GMP-AMP (cGAMP) synthase (cGAS) to the downstream Type I interferon (IFN) signaling axis. However, this process remains elusive in invertebrates. Herein, we demonstrated that a STING ortholog from a marine invertebrate (shrimp) Litopenaeus vannamei can directly sense DNA to activate an interferon-like antiviral response. Unlike STING homologs exclusively functioning as a sensor for cyclic dinucleotides (CDNs) in other eukaryotic organisms, shrimp STING can bind to double-stranded DNA (dsDNA) in addition to CDNs, including 2'3'-cGAMP. In vivo, shrimp STING can directly sense DNA nucleic acids from an infected virus, accelerate IRF dimerization, nuclear translocation and induce the expression of an interferon functional analog protein (Vago4), and finally establish an antiviral state. Surprisingly, the shrimp cGAS-like homolog is not involved in dsDNA-intrigued and STING-dependent IRF-Vago axis activation. Taken together, our results uncovered a novel dsDNA-STING-IKK{varepsilon}-IRF-Vago antiviral axis in an arthropod, and provided some novel insights into the functional origin of a DNA-sensing pathway in evolution.

immunology↗

bioRxiv2022

Causal network inference based on cross-validation predictability

Identifying causal relations or causal networks among molecules/genes, rather than just their correlations, is of great importance but challenging in biology and medical field, which is essential for unravelling molecular mechanisms of disease progression and developing effective therapies for disease treatment. However, there is still a lack of high-quality causal inference algorithms for any observed data in contrast to time series data. In this study, we developed a new causal concept for any observed data and its causal inference algorithm built on cross-validated predictability (CVP) can quantify the causal effects among molecules/genes in the whole system. The causality was extensively validated by combining a large variety of statistical simulation experiments and available benchmark data (simulated data and various real data). Combining the predicted causal network and the real benchmark network, the CVP algorithm demonstrates high accuracy and strong robustness in comparison with the mainstream algorithms. In particular, the CVP algorithm is robust in identifying reliable driver genes and network biomarkers from the perspective of network biology, with the prediction results outperforming the mainstream conventional methods for predicting driver genes. CRISPR-Cas9 knockdown experiments in the liver cancer have validated that the functional driver genes identified by the CVP algorithm effectively inhibit the growth and colony formation of liver cancer cells. By knockdown experiments, we demonstrated the accuracy and significance of the causality predicted by CVP and identified the novel regulatory targets of functional driver genes SNRNP200 and RALGAPB in the liver cancer. These inferred causal networks explain regulatory patterns in different biological contexts in a clear sense and provide biological insights into molecular mechanisms of disease progression from a causality perspective.

systems biology↗

bioRxiv2022

Hypo-responsiveness of human alveolar macrophages to IFN-γ is not due to attenuated STAT1 signaling

Alveolar macrophages (AM) perform a primary defense mechanism in the lung through phagocytosis of inhaled particles and microorganisms. AM are known to be relatively immunosuppressive consistent with the aim to limit alveolar inflammation and maintain effective gas exchange in the face of these constant challenges. How AM respond to T cell derived cytokine signals, which are critical to the defense against inhaled pathogens, is less well understood. For example, successful containment of Mycobacterium tuberculosis (Mtb) in lung macrophages is highly dependent on IFN-{gamma} secreted by Th-1 lymphocytes, however, the proteomic IFN-{gamma} response profile in AM remains mostly unknown. In this study, we measured IFN-{gamma} induced protein abundance changes in human AM and autologous blood monocytes (MN). AM cells were activated by IFN-{gamma} stimulation resulting in STAT1 phosphorylation and production of MIG/CXCL9 chemokine. However, the global proteomic response to IFN-{gamma} in AM was dramatically limited in comparison to that of MN (9 AM vs 89 MN differentially abundant proteins). AM hypo-responsiveness was not explained by reduced JAK-STAT1 signaling nor increased SOCS1 expression. These findings suggest that AM have a tightly regulated response to IFN-{gamma} which may prevent excessive pulmonary inflammation but may also provide a niche for the initial survival and growth of Mtb and other intracellular pathogens in the lung.

immunology↗

bioRxiv2022

Effect of rectified gap junctional electrical coupling and spatial distribution of biologically engineered pacemaking cells on ventricular excitation

AimBiologically engineered pacemaker, or bio-pacemaker, is a promising replacement for electronic pacemakers for treating cardiac dysfunction. Previous animal experimental studies, however, have not been able to accurately demonstrate the stability and efficiency of the bio-pacemaker yet. This study aimed to elucidate the underlying factors that affect bio-pacemakers performance and to discover possible optimising solutions to enable the potential use of bio-pacemaker therapy. Methods and resultsThe human ventricular myocytes model in this study followed the ten Tussuchers model in 2006, and the bio-pacemaker single cell model was modified based on it as what has been expatiated in our previous work. In tissue model, two factors were primarily evaluated for their effects on bio-pacemakers to pace and drive surrounding cardiac tissue: gap junction between bio-pacemaker cells (PMs) and adjacent ventricular myocytes (VMs) and the spatial distribution of bio-pacemakers. A suppressed gap junctional electrical coupling between and heterotypic gap junctions were simulated and a combination of them led to the best performance of the bio-pacemaker. Then, the pacemaking behaviours of three kinds of idealised PM-VM slices were simulated, in which an electrically isolated distribution of bio-pacemaker showed optimal drive capacities. Finally, a real human ventricular slice model was used to verified the conclusions in idealized tissues. ConclusionThis study develops a theory that weak-rectified electrical coupling and electrically isolated distribution can enhance the pacemaking efficiency of bio-pacemakers, which lays the groundwork for future research into therapeutic applications of bio-pacemakers. Author summaryBiologically engineered pacemakers are expected to be a substitute for electronic pacemakers because of their physiological superiority, but how to transform them for practical application remains challenging. In this paper, we presented a theoretical perspective on optimising biological pacemaking capability based on a computational simulation approach. By manipulating the gap junctional electrical coupling among bio-pacemaking cells and between the pacemaker and their surrounding cells, and controlling spatial distribution of bio-pacemaker, we demonstrated that an enhanced capacity of a bio-pacemaker can be achieved. The results of this study may provide a theoretical basis for the further clinical development of bio-pacemakers.

biophysics↗

bioRxiv2022

Transcription factor TFAP2C affects porcine early embryo development via regulating epigenetic modification

Transcription factors (TFs) have the potential function in regulating gene expression. Transcription factor TFAP2C plays important roles in the regulation of post-implantation embryonic development in mice, the reprogramming process, trophectoderm formation and carcinogenesis, but its role in porcine early embryo development remains unclear. This study was conducted to investigate the role of TFAP2C in porcine early embryo development using siRNA cytoplasmic injection. The RNAseq and immunofluorescence staining were performed to detect gene expression, and ChIP and dual luciferase reporter assays were used to elucidate the mechanism. The results showed that the deficiency of TFAP2C could lead to embryonic development disorder. The percentage of the blastocyst in the TFAP2C knockdown (TFAP2C-KD) group (7.76{+/-}1.86%) was significantly decreased compared to the control group (22.92{+/-}1.97%) (P**<0.01). The RNAseq results showed that 1208 genes were downregulated and 792 genes were upregulated after siRNA injection. The expression of epigenetic modification enzymes KDM5B, SETD2 (P**<0.01) etc. were significantly elevated in TFAP2C-KD group. Meanwhile, the modification levels of H3K4me3, H3K4me2 and H3K9me3 (P*<0.05) were significantly decreased, and the modification levels of H3K36me3 (P**<0.01) and DNA methylation (P**<0.01) were significantly increased in TFAP2C-KD group. DNMT1 was mostly expressed in cytoplasm in the control group, while it was mainly expressed in nuclei in the TFAP2C-KD group. In addition, TFAP2C could bind to the promoter region of SETD2, and the mutation of the TFAP2C binding site resulted in increased activity of SETD2 promoter (P**<0.01). The knockdown of TFAP2C affects histone modification and DNA methylation by regulating the expression of SETD2, KDM5B etc. and other genes, thereby inhibiting embryonic development. TFAP2C binds to the promoter region of SETD2 and acts as a hindrance protein. This study fills in the deficiency of TFAP2C in porcine early embryo development and provides theoretical support for animal husbandry production and biomedicine. Author SummaryThe correct activation of embryonic genes is required during early embryonic development, and the activation of these genes is subject to strict epigenetic regulation, such as DNA methylation, histone acetylation and methylation, with abnormalities in either leading to birth defects and developmental defects in individuals. TFs have specific binding motifs that regulate gene expression by binding to them. TFAP2C has been studied in post-implantation embryonic development and trophectoderm generation, however, the effect on early embryo development is unknown. Our findings suggest that TFAP2C deficiency disrupts gene expression patterns and leads to abnormal epigenetic modifications, resulting in abnormal embryo development. Furthermore, we found for the first time that TFAP2C can bind to the promoter region of SETD2, thereby affecting early embryo development in pigs. This indicates the critical role of TFAP2C in early embryo development in pigs on one hand, and also provides theoretical support for livestock production and biomedicine.

developmental biology↗

bioRxiv2022

NR5A2 connects genome activation to the first lineage segregation in early mouse development

After fertilization, zygotic genome activation (ZGA) marks the beginning of the embryonic program for a totipotent embryo, which further gives rise to the pluripotent embryonic lineages and extraembryonic trophectoderm after the first lineage commitment. While much has been learned about pluripotency regulation, how ZGA is connected to the pluripotency commitment in early embryos remains elusive. Here, we investigated the role of nuclear receptor 1 family transcription factors (TFs) in mouse pre-implantation embryos, whose motifs are highly enriched in accessible chromatin at the 2-cell (2C) to 8-cell (8C) stages after ZGA. We found NR5A2, an NR TF highly induced upon ZGA, is required for early development, as both the knockdown and knockout of Nr5a2 from 1C embryos led to morula arrest. While the zygotic genome was largely activated at the 2C stage, 4-8C-specific gene activation (mid-preimplantation activation) was substantially impaired. Genome-wide chromatin binding and RNA-seq analyses showed NR5A2 preferentially regulates its binding targets including a subset of key pluripotency genes (i.e., Nanog, Pou5f1, and Tdgf1). Finally, NR5A2-occupied sites at the 2C and 8C stages predominantly reside in accessible B1 elements where its motif is embedded. Taken together, these data identify NR5A2 as a key regulator that connects ZGA to the first lineage segregation in early mouse development.

developmental biology↗

bioRxiv2022

Functional gradients reveal altered functional segregation in patients with amnestic mild cognitive impairment and Alzheimer' s disease

BackgroundAlzheimers disease (AD) and amnestic mild cognitive impairment (aMCI) are associated with disrupted functional organization in brain networks, yet the finer changes in the topological organization in aMCI and AD remain to be investigated. Connectome gradients are a new tool representing brain functional topological organization in a low-dimensional space to smoothly capture the human macroscale hierarchy. MethodsHere, we examined altered topological organization in aMCI and AD by connectome gradient mapping. We further quantified functional segregation by gradient dispersion. Then, we systematically compared the alterations observed in aMCI and AD patients with those in normal controls (NCs) in a two-dimensional functional gradient space from both the whole-brain level and module level. ResultsCompared with NCs, the first gradient, which described the neocortical hierarchy from unimodal to transmodal regions, showed a distributed and significant suppression in AD patients, while abnormalities were only limited to local regions in aMCI patients. The second gradient showed a decreased pattern in the somatomotor module in both aMCI and AD patients. Furthermore, gradient dispersion showed significant decreases in AD patients at both the global level and module level, whereas this alteration was limited only to limbic areas in aMCI. Notably, we demonstrated that suppressed gradient dispersion in aMCI and AD patients was associated with cognitive scores. ConclusionsChanges in functional gradients could reflect different degrees of altered brain network segregation in aMCI and AD. These findings provide new evidence for altered brain hierarchy in aMCI and AD, which strengthens our understanding of the progressive mechanism of cognitive decline.

neuroscience↗

bioRxiv2022

ame-miR-34 modulates the larval body weight and immune response of Apis mellifera workers to Ascosphara apis invasion

MiRNAs are critical regulators of numerous physiological and pathological processes. Ascosphaera apis exclusively infects bee larvae and causes chalkbrood disease. However, the function and mechanism of miRNAs in the bee larval response to A. apis infection is poorly understood. Here, ame-miR-34, a previously predicted miRNA involved in the response of Apis mellifera ligustica larvae to A. apis invasion, was subjected to molecular validation, and overexpression and knockdown were then conducted to explore the regulatory functions of ame-miR-34 in larval body weight and immune response. Stem-loop RT-PCR and Sanger sequencing confirmed the authenticity of ame-miR-34 in the larval gut of A. m. ligustica. RT-qPCR results demonstrated that compared with that in the uninfected larval guts, the expression level of ame-miR-34 was significantly downregulated (P < 0.001) in the guts of A. apis-infected 4-, 5-, and 6-day-old larvae, indicative of the remarkable suppression of host ame-miR-34 due to A. apis infection. In comparison with the corresponding negative control (NC) groups, the expression level of ame-miR-34 in the larval guts in the mimic-miR-34 group was significantly upregulated (P < 0.001), while that in the inhibi- tor-miR-34 group was significantly downregulated (P < 0.01). Similarly, effective overexpression and knockdown of ame-miR-34 were achieved. In addition, the body weights of 5- and 6-day-old larvae were significantly increased compared with those in the mimic-NC group; the weights of 5-day-old larvae in the inhibitor-miR-34 group were significantly decreased in comparison with those in the inhibitor-NC group, while the weights of 4- and 6-day-old larvae in the inhibi- tor-miR-34 group were significantly increased, indicating the involvement of ame-miR-34 in modulating larval body weight. Furthermore, the expression levels of both hsp and abct in the guts of A. apis-infected 4-, 5- and 6-day-old larvae were significantly upregulated after ame-miR-34 overexpression. In contrast, after ame-miR-34 knockdown, the expression levels of the aforementioned two key genes in the A. apis-infected 4-, 5- and 6-day-old larval guts were significantly downregu- lated. Together, the results demonstrated that effective overexpression and knockdown of ame-miR-34 in both noninfected and A. apis-infected A. m. ligustica larval guts could be achieved by the feeding method, and ame-miR-34 exerted a regulatory function in the host immune response to A. apis invasion through positive regulation of the expression of hsp and abct. Our findings not only provide a valuable reference for the functional investigation of bee larval miRNAs but also reveal the regulatory role of ame-miR-34 in A. mellifera larval weight and immune response. Additionally, the results of this study may provide a promising molecular target for the treatment of chalkbrood disease.

molecular biology↗

bioRxiv2022

DIFFERENTIAL MEMORY IMPAIRMENT ACROSS RELATIONAL DOMAINS IN TEMPORAL LOBE EPILEPSY

BO_SCPLOWACKGROUNDC_SCPLOWTemporal lobe epilepsy (TLE) is typically associated with pathology of the hippocampus, a key structure involved in relational memory processes, including episodic, semantic, and spatial memory. While it is widely accepted that TLE-associated hippocampal alterations may underlie global deficits in memory, it remains poorly understood whether TLE may present with shared or unique impairment across distinct relational memory domains. MO_SCPLOWETHODSC_SCPLOWWe administered a recently validated behavioral paradigm to evaluate episodic, semantic, and spatial memory in 20 pharmacoresistant TLE patients and 53 age- and sex-matched healthy controls. We implemented linear mixed effects models to identify memory deficits in individuals with TLE relative to controls, and used partial least squares analysis to identify factors contributing to overall variations in relational memory performance across both cohorts. RO_SCPLOWESULTSC_SCPLOWTLE patients showed marked impairment in episodic memory compared to controls, while spatial and semantic memory remained relatively intact. Findings were robust, with slight decreases in effect sizes after controlling for performance on executive function tests. Via partial least squares analysis, we identified group, age, and bilateral hippocampal volumes as important variables relating to relational memory impairment. CO_SCPLOWONCLUSIONC_SCPLOWOur behavioral framework provides a granular approach for assessing relational memory deficits in people with TLE and may inform future prognostic strategies in patients with hippocampal pathology. Our work warrants further investigations into the underlying neural substrates of relational memory.

neuroscience↗

bioRxiv2022

(Z, Z, Z)-3,6,9-nonadecadiene, a potential inhibitor of sex pheromone of Ectropis grisescens Warren (Lepidoptera: Geometridae): electroantennogram test, wind tunnel, and in silico study

Application of sex pheromone is the most environmental-friendly technique to control pests. Moreover, it has been discovered that pheromone analogs can disturb or inhibit mating communication in some species of moths. Ectropis grisescens Warren (Lepidoptera: Geometridae), is the most severe tea defoliator in China. Thus, in our study, an analog of the pest sex pheromone component, (Z, Z, Z)-3,6,9-nonadecadiene (Z3Z6Z9-19:Hy), was selected to determine its potential activity in controlling the pest. Electroantennogram (EAG), Y-tube olfactometer, and wind tunnel experiments separately showed potential inhibition of Z3Z6Z9-19:Hy. The response elicited by Z3Z6Z9-19:Hy displayed a dose-dependent way in EAG test. Furthermore, in Y-tube olfactometer, percentage of positive response of E. grisescens males was significantly (P<0.01) reduced by Z3Z6Z9-19:Hy up to 70%. In wind tunnel, all types of behavioral response were significantly (P<0.01) inhibited by Z3Z6Z9-19:Hy, percentage of contacting source was utterly inhibited at the lowest dose tested. Based on these results, the combination of the analog and SNMP1 protein was also studied. Our study revealed the potential of Z3Z6Z9-19:Hy as a sex pheromone inhibitor, which would provide new perspectives in monitoring and mating disruption of E. grisescens in pest-control strategies.

ecology↗

bioRxiv2022

How do Vampires Suck Blood?

Lampreys are blood-sucking vampires in the marine. From a survival perspective, it is expected that lamprey buccal gland exhibits a repository of pharmacologically active components to modulate the hosts homeostasis, inflammatory and immune responses. Several proteins have been found to function as anticoagulants, ion channel blockers, and immune suppressors in lampreys, while small metabolites have never been explored in detail. In this study, by analyzing the metabolic profiles of 14 different lamprey tissues, we have identified two groups of blood-sucking-associated metabolites, i.e., kynurenine pathway metabolites and prostaglandins, in the buccal gland and they can be injected into the host fish to ensure a steady and sustained blood flow to the feeding site. These findings demonstrate the complex nature of lamprey buccal gland and highlight the diversity in the mechanisms utilized for blood-sucking in lampreys. In addition, a lamprey spatial metabolomics database (https://www.lampreydb.com) was constructed to assist studies using lampreys as model animal. The database contains detailed qualitative, quantitative, and spatial distribution information of each detected metabolite, and users can easily query and check their metabolites of interest, and/or identify unknown peaks using the database. Significance StatementLampreys are one of the two surviving jawless vertebrate groups that hold the key to our understanding of the early vertebrate evolution, adaptive immune origin, and developmental neurobiology. Here, we applied a spatial metabolomics approach to study the lamprey-host interaction. Two groups of metabolites, i.e., kynurenine pathway metabolites and prostaglandins, were found in the lamprey buccal gland, which modulate the hosts homeostasis, inflammatory and immune responses. The establishment of the first tissue-wide spatial lamprey metabolomics database in this study facilitate future studies in biochemistry, clinical chemistry, natural product discovery, medicine, and metabolomics using lampreys as a model animal.

biochemistry↗

bioRxiv2022

An armored marine reptile from the Early Triassic of South China

Sauropterygia was a taxonomically and ecomorphologically diverse clade of Mesozoic marine reptiles spanning the Early Triassic to the Late Cretaceous. Sauropterygians are traditionally divided into two groups representing two markedly different body plans - the short-necked, durophagous Placodontia and the long-necked Eosauropterygia - whereas Saurosphargidae, a small clade of marine reptiles possessing a dorsal rib-basket, is considered as the sauropterygian sister-group. However, the early evolutionary history of sauropterygians and their phylogenetic relationships with other groups within Diapsida are still incompletely understood. Here, we report a new saurosphargid from the Early Triassic of South China - Prosaurosphargis yingzishanensis gen. et sp. nov. - representing the earliest known occurrence of the clade. An updated phylogenetic analysis focussing on the interrelationships within diapsid reptiles recovers saurosphargids as nested within sauropterygians, forming a clade with eosauropterygians to the exclusion of placodonts. Furthermore, a clade comprising Eusaurosphargis and Palatodonta is recovered as the sauropterygian sister-group within Sauropterygomorpha tax. nov. The phylogenetic position of several Early and Middle Triassic sauropterygians of previously uncertain phylogenetic affinity, such as Atopodentatus, Hanosaurus, Majiashanosaurus and Corosaurus, is also clarified, elucidating the early evolutionary assembly of the sauropterygian body plan. Finally, our phylogenetic analysis recovers Testudinata and Archosauromorpha within Archelosauria, a result strongly supported by molecular data, but until now not recovered by any phylogenetic analysis using a morphology-only data set. Our study provides evidence for the rapid diversification of sauropterygians in the aftermath of the Permo-Triassic mass extinction event and emphasises the importance of broad taxonomic sampling in reconstructing phylogenetic relationships among extinct taxa.

paleontology↗

bioRxiv2022

Genetic Dissection of Mutual Interference between Two Consecutively Learned Tasks in Drosophila

Animals can continuously learn different tasks to adapt to changing environments and therefore have strategies to effectively cope with inter-task interference, including both proactive interference (Pro-I) and retroactive interference (Retro-I). Many biological mechanisms are known to contribute to learning, memory, and forgetting for a single task, however, mechanisms involved only when learning sequential different tasks are relatively poorly understood. Here, we dissect the respective molecular mechanisms of Pro-I and Retro-I between two consecutive associative learning tasks in Drosophila. Pro-I is more sensitive to inter-task interval (ITI) than Retro-I. They occur together at short ITI (<20 min), while only Retro-I remains significant at ITI beyond 20 min. Acutely overexpressing Corkscrew (CSW), an evolutionarily conserved protein tyrosine phosphatase SHP2, in mushroom body (MB) neurons reduces Pro-I, whereas acute knockdown of CSW exacerbates Pro-I. Such function of CSW is further found to rely on the {gamma} subset of MB neurons and the downstream Raf/MAPK pathway. In contrast, manipulating CSW does not affect Retro-I as well as a single learning task. Interestingly, manipulation of Rac1, a molecule that regulates Retro-I, does not affect Pro-I. Thus, our findings suggest that learning different tasks consecutively triggers distinct molecular mechanisms to tune proactive and retroactive interference.

animal behavior and cognition↗

bioRxiv2022

Development of an affinity-enhanced clinical candidate TCR targeting NY-ESO-1 with optimal potency and high specificity

The clinical success of T-cell receptor (TCR)-based immunotherapy depends on the efficacy and specificity of TCRs. Naturally occurring TCRs have limited anti-tumor potency due to their low affinity for tumor antigens. Affinity enhancement is a promising strategy to generate highly potent TCRs. However, it is concerned that affinity-enhanced TCRs are prone to lose specificity. We isolated low affinity TCRs specific for NY-ESO-1157-165/HLA-A*02:01 from peripheral blood mononuclear cells of healthy donors. An affinity-enhanced TCR candidate with optimal affinity and specificity was generated using phage display and an extensive set of in vitro and in vivo assays. Alanine scanning mutagenesis showed that the TCR candidate retained specificity by making extensive contacts to the side chains of NY-ESO-1157-165 peptide. Adoptive transfer of T cells engineered with this candidate (termed TAEST16001) significantly inhibited tumor growth in subcutaneous, metastatic, and patient-derived xenograft (PDX) mouse tumor models. This study demonstrates that sophisticated engineering and screening techniques can be utilized to generate a clinical candidate TCR with potent anti-tumor activity without losing specificity. TAEST16001 was approved by the Center for Drug Evaluation (CDE) as the first TCR-based immunotherapy clinical trial in China (ClinicalTrials.gov Identifier: NCT03159585).

immunology↗

bioRxiv2022

Resting-State Electroencephalography for Continuous, Passive Prediction of Coma Recovery After Acute Brain Injury

Accurately predicting emergence from disorders of consciousness (DoC) after acute brain injury can profoundly influence mortality, acute management, and rehabilitation planning. While recent advances in functional neuroimaging and stimulus-based EEG offer the potential to enrich shared decision-making, their procedural sophistication and expense limit widespread availability or repeated performance. We investigated continuous EEG (cEEG) within a passive, "resting-state" framework to provide continuously updated predictions of DoC recovery at 24-, 48-, and 72-hour prediction horizons. To develop robust, continuous prediction models from a large population of patients with acute brain injury (ABI), we leveraged a recently described pragmatic approach transforming Glasgow Coma Scale assessment sub-score combinations into frequently assessed DoC diagnoses: coma, vegetative state, minimally conscious state with or without language, and post-injury confusional or recovered states. We retrospectively identified consecutive patients undergoing cEEG following acute traumatic brain injury (TBI), subarachnoid hemorrhage (SAH), or intracerebral hemorrhage (ICH). Models continuously predicting DoC diagnosis for multiple prediction horizons were evaluated utilizing recent clinical assessments with or without cEEG information, which comprised a comprehensive EEG feature set of 288 time, frequency, and time-frequency characteristics computed from consecutive 5-minute EEG epochs, with 6 additional features capturing each EEG features temporal dynamics. Features were fed into a predictive model developed with cross-validation; the ordinal DoC diagnosis was discriminated using an ensemble of XGBoost binary classifiers. For 201 ABI patients (46 TBI, 140 SAH, 15 ICH patients comprising 27,280 cEEG-hours with concomitant clinical assessments), cEEG-augmented models accurately predicted the future DoC diagnosis at 24 hours (one-vs-rest AU-ROC, 92.4%; weighted-F1 84.1%), 48 hours (one-vs-rest AU-ROC=88%, weighted-F1=80%) and 72 hours (one-vs-rest AU-ROC=86.3%, weighted-F1=76.6%). Models were robust to utilizing different ordinal cut-points for the DoC prediction target and evaluating additional models derived from specific sub-populations using a confound-isolating cross-validation framework. The most robust features across evaluation configurations included Petrosian fractal dimension, relative power of high to low (gamma-beta to delta-alpha) EEG frequency spectra, energy within the 12-35 Hz frequency band in the short-time Fourier transform domain, and wavelet entropy. The cEEG-augmented model exceeded the performance of models using preceding clinical assessments, continuously predicting future DoC diagnosis with one-vs-rest AU-ROC in the range of 84.3-92.4% while utilizing approaches to limit overfitting. The proposed continuous, resting-state cEEG prediction method represents a promising tool to predict DoC emergence in ABI patients. Enabling these methods prospectively would represent a new paradigm of continuous prognostic monitoring for predicting coma recovery and assessing treatment response.

neuroscience↗

bioRxiv2022

Differential requirement for BRCA1-BARD1 E3 ubiquitin ligase activity in DNA damage repair and meiosis in the Caenorhabditis elegans germ line

The tumor suppressor BRCA1-BARD1 complex functions in many cellular processes; of critical importance to its tumor suppressor function is its role in genome integrity. Although RING E3 ubiquitin ligase activity is the only known enzymatic activity of the complex, the in vivo requirement for BRCA1-BARD1 E3 ubiquitin ligase activity has been controversial. Here we probe the role of BRCA1-BARD1 E3 ubiquitin ligase activity in vivo using C. elegans. Genetic, cell biological, and biochemical analyses of mutants defective for E3 ligase activity reveal both E3 ligase-dependent and independent functions of the complex in the context of DNA damage repair and meiosis. We show that E3 ligase activity is essential for BRCA1-BARD1 to concentrate at both DNA damage and recombination sites in meiotic germ cells, but not at DNA damage sites in proliferating germ cells. While BRCA1 alone is capable of monoubiquitylation, BARD1 is required with BRCA1 to promote polyubiquitylation. We find that the requirement for E3 ligase activity and BARD1 in DNA damage signaling and repair can be partially alleviated by driving the nuclear accumulation and self-association of BRCA1. Our data suggest that in addition to E3 ligase activity, BRC-1 serves a structural role for DNA damage signaling and repair while BRD-1 plays an accessory role to enhance BRC-1 function. Author SummaryBRCA1-BARD1 is a E3 ubiquitin ligase, which modifies proteins by the addition of the small protein ubiquitin. While mutations that disrupt E3 ligase activity and stability of the BRCA1-BARD1 complex lead to a predisposition for breast and ovarian cancer, the specific requirement for E3 ligase activity in tumor suppression is not known. Here we probe the function of E3 ligase activity and BARD1 in the maintenance of genome integrity by engineering point mutations that disrupt E3 ligase activity in C. elegans BRCA1 as well as a null mutation in BARD1. We find that while E3 ligase activity is important for genome integrity, the complex plays additional roles besides ubiquitylating proteins. Further, our data suggest that BRCA1 is the key functional unit of the complex while BARD1 is an accessory partner that enhances BRCA1s function. These findings may help explain why there is a higher prevalence of cancer-causing mutations in BRCA1 compared to BARD1.

genetics↗