Biology subjects

Zhu, G.

Publications and source records attributed to Zhu, G..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Catalytically inactive SHP1-C453S mutant gain of "robust LLPS" function

SHP1 is a non-receptor protein tyrosine phosphatase extensively expressed in hematopoietic cells, exerting a pivotal role as an immunosuppressive factor. Our previous studies have suggested that SHP1 can undergo liquid-liquid phase separation (LLPS). In this study, the SHP1-C455S mutant, commonly utilized in biochemical assays due to its lack of catalytic phosphatase activity, unexpectedly exhibited a remarkably robust ability for LLPS. Since the C453S mutation has been previously shown to potentially induce a conformational transition of SHP1 from a closed to an open state, we hypothesize that the enhanced LLPS capability of SHP1 may be facilitated by this conformational alteration. The SHP1-C453S mutant exhibited robust LLPS activity, while completely abrogating its phosphatase activity. This allows for effective investigation of the catalytic activity and LLPS capability of SHP1.

molecular biology↗

bioRxiv2024

Heterogeneous hybrid immunity against Omicron variant JN.1 at 11 months following breakthrough infection

A highly transmissible SARS-CoV-2 variant JN.1 is rapidly spreading throughout the nation, becoming the predominant strain in China and worldwide. However, the current immunity against the circulating JN.1 at population level has yet to be fully evaluated. We recruited representative cohorts with stratified age groups and diverse combinations of vaccination and/or infection in recent months, and promptly assessed humoral immunity for these subjects predominantly exhibiting hybrid immunity. We report that at 11 months following BA.5-wave breakthrough infection (BTI), these vaccinated individuals generally showed above-the-threshold yet low level of neutralizing activity against JN.1, with slightly greater potency observed in children and adolescents compared to adults and seniors. Meanwhile, XBB/EG.5-wave reinfection post-BTI significantly boosted the neutralizing antibodies against Omicron variants, including JN.1 in both adults (13.4-fold increase) and seniors (24.9-fold increase). To better understand respiratory mucosal protection against JN.1 over an extended period of months post-BTI, we profiled the humoral immunity in bronchoalveolar lavage samples obtained from vaccinated subjects with or without BTI, and revealed increased potency of neutralizing activity against the BA.5 and JN.1 variants in the respiratory mucosa through natural infection. Notably, at 11 months post-BTI, memory B cell responses against prototype and JN.1 were detectable in both blood and respiratory mucosa, displaying distinct memory features in the circulation and airway compartments. XBB/EG.5-wave reinfection drove the expansion of JN.1-specific B cells, along with the back-boosting of B cells responding to the ancestral viral strain, suggesting the involvement of immune imprinting. Together, this study indicates heterogeneous hybrid immunity over 11 months post-BTI, and underscores the vulnerability of individuals, particularly high-risk seniors, to JN.1 breakthrough infection. An additional booster with XBB-containing vaccine may greatly alleviate the onward transmission of immune-evasive SARS-CoV-2 variants.

immunology↗

bioRxiv2024

Villification of the intestinal epithelium is driven by Foxl1

The primitive gut tube of mammals initially forms as a simple cylinder consisting of the endoderm-derived, pseudostratified epithelium and the mesoderm-derived surrounding mesenchyme. During mid-gestation a dramatic transformation occurs in which the epithelium is both restructured into its final cuboidal form and simultaneously folded and refolded to create intestinal villi and intervillus regions, the incipient crypts. Here we show that the mesenchymal winged helix transcription factor Foxl1, itself induced by epithelial hedgehog signaling, controls villification by activating BMP and PDGFR as well as planar cell polarity genes in epithelial-adjacent telocyte progenitors, both directly and in a feed-forward loop with Foxo3.

developmental biology↗

bioRxiv2024

Cbfβ regulates Wnt/β-catenin, Hippo/Yap, and TGFβ signaling pathways in articular cartilage homeostasis and protects from ACLT surgery-induced osteoarthritis

As the most common degenerative joint disease, osteoarthritis (OA) contributes significantly to pain and disability during aging. Several genes of interest involved in articular cartilage damage in OA have been identified. However, the direct causes of OA are poorly understood. Evaluating the public human RNA-seq dataset showed that Cbf{beta}, (subunit of a heterodimeric Cbf{beta}/Runx1,Runx2, or Runx3 complex) expression is decreased in the cartilage of patients with OA. Here, we found that the chondrocyte-specific deletion of Cbf{beta} in tamoxifen-induced Cbf{beta}f/fCol21-CreERT mice caused a spontaneous OA phenotype, worn articular cartilage, increased inflammation, and osteophytes. RNA-sequencing analysis showed that Cbf{beta} deficiency in articular cartilage resulted in reduced cartilage regeneration, increased canonical Wnt signaling and inflammatory response, and decreased Hippo/YAP signaling and TGF-{beta} signaling. Immunostaining and western blot validated these RNA-seq analysis results. ACLT surgery-induced OA decreased Cbf{beta} and Yap expression and increased active {beta}-catenin expression in articular cartilage, while local AAV-mediated Cbf{beta} overexpression promoted Yap expression and diminished active {beta}-catenin expression in OA lesions. Remarkably, AAV-mediated Cbf{beta} overexpression in knee joints of mice with OA showed the significant protective effect of Cbf{beta} on articular cartilage in the ACLT OA mouse model. Overall, this study, using loss-of-function and gain-of-function approaches, uncovered that low expression of Cbf{beta} may be the cause of OA. Moreover, Local admission of Cbf{beta} may rescue and protect OA through decreasing Wnt/{beta}-catenin signaling, and increasing Hippo/Yap signaling and TGF{beta}/Smad2/3 signaling in OA articular cartilage, indicating that local Cbf{beta} overexpression could be an effective strategy for treatment of OA.

pathology↗

bioRxiv2023

Dopamine and neuromodulation shorten the latency from motor intention to execution in Parkinson's disease

The ability to initiate volitional action is fundamental to human behaviour. Loss of dopaminergic neurons in Parkinsons disease is associated with impaired action initiation, also termed akinesia. Both dopamine and subthalamic deep brain stimulation (DBS) can alleviate akinesia, but the underlying mechanisms are unknown. An important question is whether dopamine and DBS facilitate de novo build-up of neural dynamics for motor execution or accelerate existing cortical movement initiation signals through shared modulatory circuit effects. Answering these questions can provide the foundation for new closed-loop neurotherapies with adaptive DBS, but the objectification of neural processing delays prior to performance of volitional action remains a significant challenge. To overcome this challenge, we studied readiness potentials and trained brain signal decoders on invasive neurophysiology signals in 25 DBS patients (12 female) with Parkinsons disease during performance of self-initiated movements. Combined sensorimotor cortex electrocorticography (ECoG) and subthalamic local field potential (LFP) recordings were performed OFF therapy (N=22), ON dopaminergic medication (N=18) and ON subthalamic deep brain stimulation (N=8). This allowed us to compare their therapeutic effects on neural latencies between the earliest cortical representation of movement intention as decoded by linear discriminant analysis classifiers and onset of muscle activation recorded with electromyography (EMG). In the hypodopaminergic OFF state, we observed long latencies between motor intention and motor execution for readiness potentials and machine learning classifications. Both, dopamine and DBS significantly shortened these latencies, hinting towards a shared therapeutic mechanism for alleviation of akinesia. To investigate this further, we analysed directional cortico-subthalamic oscillatory communication with multivariate granger causality. Strikingly, we found that both therapies independently shifted cortico-subthalamic oscillatory information flow from antikinetic beta (13-35 Hz) to prokinetic theta (4-10 Hz) rhythms, which was correlated with latencies in motor execution. Our study reveals a shared brain network modulation pattern of dopamine and DBS that may underlie the acceleration of neural dynamics for augmentation of movement initiation in Parkinsons disease. Instead of producing or increasing preparatory brain signals, both therapies modulate oscillatory communication. These insights provide a link between the pathophysiology of akinesia and its therapeutic alleviation with oscillatory network changes in other non-motor and motor domains, e.g. related to hyperkinesia or effort and reward perception. In the future, our study may inspire the development of clinical brain computer interfaces based on brain signal decoders to provide temporally precise support for action initiation in patients with brain disorders.

neuroscience↗

bioRxiv2023

Transdifferentiation of fibroblasts into muscle cells to constitute cultured meat with tunable intramuscular fat deposition

Current studies on cultured meat mainly focused on the muscle tissue reconstruction in vitro, but lack the formation of intramuscular fat which is a crucial factor in determining taste, texture and nutritional contents. Therefore, incorporating fat into cultured meat is of superior value. In this study, we employed the myogenic/lipogenic transdifferentiation of chicken fibroblasts in 3D to produce muscle mass and deposit fat into the same cells without the co-culture or mixture of different cells or fat substances. The immortalized chicken embryonic fibroblasts were implanted into the hydrogel scaffold and the cell proliferation and myogenic transdifferentiation were conducted in 3D to produce the whole-cut meat mimics. Compare to 2D, cells grown in 3D matrix showed elevated myogenesis and collagen production. We further induced fat deposition in the transdifferentiated muscle cells and the triglyceride content could be manipulated to match and exceed the levels of chicken meat. The gene expression analysis indicated that both lineage-specific and multi-functional signalings could contribute to the generation of muscle/fat matrix. Overall, we were able to precisely modulate muscle, fat, and extracellular matrix contents according to balanced or specialized meat preferences. These findings provide new avenues for customized cultured meat production with desired intramuscular fat contents that can be tailored to meet the diverse demands of consumers. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/564179v2_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1697f5dorg.highwire.dtl.DTLVardef@128e4a1org.highwire.dtl.DTLVardef@1ba31b4org.highwire.dtl.DTLVardef@11559ba_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

cell biology↗

bioRxiv2023

Landscape of Large-Scale Somatic Genomic Insertions in Non-Small Cell Lung Carcinoma Revealed by Nanopore Sequencing

Previous NSCLC genomic studies were mostly based on the next-generation sequencing of short reads, which is an efficient approach for identifying single nucleotide variants and small indels but ineffective for identifying structural variants, especially large-scale insertions. Here, we studied 151 lung adenocarcinoma (LUAD) and 106 lung squamous cell carcinoma (LUSC) samples and paired blood samples using nanopore sequencing technology. We developed a rigorous computational pipeline and characterized the landscape of large-scale somatic insertions in NSCLC. Combining other omics data, we report three findings: 1. we identified an LUSC-enriched somatic simple repeat expansion shared by approximately 40% of LUSC patients that regulates PTPRZ1 gene expression through distal enhancers; 2. the somatic insertion of transposable elements (TEs) in NSCLC were mostly complex TEs consisting of multiple TE elements; and 3. the insertion of short interspersed nuclear elements, especially from the Alu family in young lineages, is a frequent somatic mutation type that shapes the transcriptome of NSCLC through the expression of these elements.

genomics↗

bioRxiv2023

Requirement of microtubules for secretion of a micronemal protein CpTSP4 in the invasive stage of the apicomplexan Cryptosporidium parvum

The zoonotic Cryptosporidium parvum is a global contributor to infantile diarrheal diseases and opportunistic infections in immunocompromised/weakened individuals. Like other apicomplexans, it possesses several specialized secretory organelles, including micronemes, rhoptry and dense granules. However, the understanding of cryptosporidial micronemal composition and secretory pathway remains limited. Here we report a new micronemal protein in C. parvum, namely thrombospondin repeat domain-containing protein-4 (CpTSP4), providing insights into these ambiguities. Immunostaining and enzyme-linked assays show that CpTSP4 is prestored in the micronemes of unexcysted sporozoites but secreted during sporozoite excystation, gliding and invasion. In excysted sporozoites, CpTSP4 is also distributed on the two central microtubules unique to Cryptosporidium. The secretion and microtubular distribution could be completely blocked by selective kinesin-5 inhibitors, SB-743921 and SB-715992, resulting in the accumulation of CpTSP4 in micronemes. These support the kinesin-dependent microtubular trafficking of CpTSP4 for secretion. We also localize {gamma}-tubulin, consistent with kinesin-dependent anterograde trafficking. Additionally, recombinant CpTSP4 displays nanomolar binding affinity to host cell surface, for which heparin acts as one of the host ligands. A novel heparin-binding motif is identified and biochemically validated for its contribution to the adhesive property of CpTSP4 by peptide competition assays and site-directed mutagenesis. These findings shed light on the mechanisms of intracellular trafficking and secretion of a cryptosporidial micronemal protein and the interaction of a TSP-family protein with host cells. Importance Cryptosporidium parvum is a globally distributed apicomplexan parasite infecting humans and/or animals. Like other apicomplexans, it possesses specialized secretory organelles in the zoites, in which micronemes discharge molecules to facilitate the movement and invasion of zoites. Although past and recent studies have identified several proteins in cryptosporidial micronemes, our understanding on the composition, secretory pathways and domain-ligand interactions of micronemal proteins remains limited. This study identifies a new micronemal protein, namely CpTSP4, that is discharged during excystation, gliding and invasion of C. parvum sporozoites. The CpTSP4 secretion depends on the intracellular trafficking on the two Cryptosporidium-unique microtubes that could be blocked by kinesin-5/Eg5 inhibitors. Additionally, a novel heparin-binding motif is identified and biochemically validated, which contributes to the nanomolar binding affinity of CpTSP4 to host cells. These findings indicate that kinesin-dependent microtubular trafficking is critical to CpTSP4 secretion and heparin/heparan sulfate is one of the ligands for this micronemal protein.

microbiology↗

bioRxiv2023

Decoding the genomic landscape of chromatin-associated biomolecular condensates

Biomolecular condensates play a significant role in chromatin activities, primarily by concentrating and compartmentalizing proteins and/or nucleic acids. However, their genomic landscapes and compositions remain largely unexplored due to a lack of dedicated computational tools for systematic identification in vivo. To address this, we developed CondSigDetector, a computational framework designed to detect condensate-like chromatin-associated protein co-occupancy signatures (CondSigs), to predict genomic loci and component proteins of distinct chromatin-associated biomolecular condensates. Applying this framework to mouse embryonic stem cells (mESC) and human K562 cells enabled us to depict the high-resolution genomic landscape of chromatin-associated biomolecular condensates, and uncover both known and potentially novel biomolecular condensates. Multi-omics analysis and experimental validation further verified the condensation properties of CondSigs. Additionally, our investigation shed light on the impact of chromatin-associated biomolecular condensates on chromatin activities. Collectively, CondSigDetector provides a novel approach to decode the genomic landscape of chromatin-associated condensates, facilitating a deeper understanding of their biological functions and underlying mechanisms in cells.

bioinformatics↗

bioRxiv2023

Quantification of circulating tumor DNA using deep learning

Quantification of circulating tumor DNA (ctDNA) levels in blood enables non-invasive surveillance of cancer progression. Fragle is an ultra-fast deep learning-based method for ctDNA quantification directly from cell-free DNA fragment length profiles. We developed Fragle using low-pass whole genome sequence (lpWGS) data from multiple cancer types and healthy control cohorts, demonstrating high accuracy, and improved lower limit of detection in independent cohorts as compared to existing tumor-naive methods. Uniquely, Fragle is also compatible with targeted sequencing data, exhibiting high accuracy across both research and commercial targeted gene panels. We used this method to study longitudinal plasma samples from colorectal cancer patients, identifying strong concordance of ctDNA dynamics and treatment response. Furthermore, prediction of minimal residual disease in resected lung cancer patients demonstrated significant risk stratification beyond a tumor-naive gene panel. Overall, Fragle is a versatile, fast, and accurate method for ctDNA quantification with potential for broad clinical utility.

bioinformatics↗

bioRxiv2023

Engineering cGAS-agonistic oligonucleotides as therapeutics and vaccine adjuvants for cancer immunotherapy

Current cancer immunotherapy (e.g., immune checkpoint blockade (ICB)) has only benefited a small subset of patients. Cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) activation holds the potential to improve cancer immunotherapy by eliciting type-I interferon (IFN-I) responses in cancer cells and myeloid cells. Yet, current approaches to this end, mostly by targeting STING, have marginal clinical therapeutic efficacy. Here, we report a cGAS-specific agonistic oligonucleotide, Svg3, as a novel approach to cGAS-STING activation for versatile cancer immunotherapy. Featured with a hairpin structure with consecutive guanosines flanking the stem, Svg3 binds to cGAS and enhances cGAS-Svg3 phase separation to form liquid-like droplets. This results in cGAS activation by Svg3 for robust and dose-dependent IFN-I responses, which outperforms several state-of-the-art STING agonists in murine and human immune cells, and human tumor tissues. Nanocarriers efficiently delivers Svg3 to tissues, cells, and cytosol where cGAS is located. Svg3 reduces tumor immunosuppression and potentiates ICB therapeutic efficacy of multiple syngeneic tumors, in wildtype but neither cGas-/- nor goldenticket Sting-/- mice. Further, as an immunostimulant adjuvant, Svg3 enhances the immunogenicity of peptide antigens to elicit potent T cell responses for robust ICB combination immunotherapy of tumors. Overall, cGAS-agonistic Svg3 is promising for versatile cancer combination immunotherapy.

bioengineering↗

bioRxiv2023

Paternal CHH methylation potentiates stress responses against Pseudomonas syringae in Arabidopsis progenies

Systemic acquired resistance (SAR) is an induced immune mechanism in plants, involving epigenetic regulation by chromatin remodeling and DNA methylation, which can be inherited to progeny following stress exposure. Intersexual epigenetic conflict sometimes leads to unequal expression of maternal and paternal alleles in offspring, resulting in parent-of-origin effects of inheritance. To better understand the parental contributions of epialleles in plant defense, isogenic Arabidopsis parental lines were mock-treated (M) and Pseudomonas syringae (Pst)-treated (P) for reciprocal crosses to produce F1 progenies (MP, PM). Together with their self-fertilized F1 descendants (MM, PP), the genome-wide inherited DNA methylation and transcriptomic changes against Pst were analyzed. F1 descendants shared widespread DNA methylation and transcriptional changes at transposable elements (TEs) and genes. The confrontation of epigenomes triggers the reprogramming of DNA methylation in reciprocal crosses, resulting in transgressive segregation that also shows the parental effect of Pst treatment. Compared to PM, the MP (Pst-primed paternal genome) was found to contributes to CHH hypermethylation, which is associated with processes in plant-pathogen interaction, including carbohydrate metabolism, glutathione metabolism and stronger translation process, which potentially contribute to improved disease resistance in MP in response to Pst challenge. Our data suggested a parent-of-origin effect of defense priming that contributes differently toward improved defense response in progenies.

genetics↗

bioRxiv2022

Capturing the Hierarchically Assorted Modules of Protein Interaction in the Organized Nucleome

Nuclear proteins are major constituents and key regulators of the topological organization of nucleome. To elucidate the global connectivity of nucleomic proteins and to decipher the hierarchically organized modules of protein interaction that are involved in nucleomic organization and nuclear events, both formaldehyde and CBDPS crosslinkers were applied sequentially on the in vivo prefixed nuclei to perform a double chemical crosslinking with mass spectrometry (XL-MS) analysis. The integration of dimethyl-labelling with XL-MS generated a quantitative XL-MS workflow (qXL-MS) that consequently identified 5,340 cross-linked peptides (crosslinks) from nucleome. These crosslinks were construed into 1,297 nuclear protein-protein interactions (PPIs), from which discovered were 250 and 26 novel interactors of histones and nucleolar box C/D snoRNP complex, respectively. MONET-based modulomic analysis of their Arabidopsis orthoglous PPIs constructed 27 and 24 master nuclear protein interaction modules (NPIMs) that contain the condensate-forming protein(s) and the intrinsically disordered region (IDR)-containing proteins, respectively. These NPIMs successfully captured the previously reported nuclear protein complexes and nuclear bodies in nucleome. Surprisingly, modulomic analysis showed that these NPIMs were hierarchically assorted into four communities of NPIMs in nucleome including Genome Community and Nucleolus Community. The qXL-MS-based quantitative interactomics finally revealed 17 Hormone-specific module variants participating in a broad range of nuclear events. Thus, this integrated pipeline of qXL-MS and MONET modulomics, named as CHAMPION, is capable of capturing both nuclear protein complexes and nuclear bodies, constructing the topological architecture of protein interaction modules and module variants in nucleome and probably of mapping the protein compositions of condensates. HighlightsO_LIThe formaldehyde and CBDPS crosslinkers coupled qXL-MS discovered 5,340 crosslinked peptides. These crosslinks were construed into 1,297 nuclear protein-protein interactions (PPIs), protein components of which contained 250 and 26 novel interactors of histone octamer and nucleolar box C/D snoRNP complex, respectively, in the intricately organized nucleome. C_LIO_LIThe MONET-based modulomic analysis of these crosslinks captured 95 nuclear protein interaction modules (NPIMs), a portion of which contain both the condensate-forming and the intrinsically disordered region (IDR)-containing proteins. Especially, some NPIMs captured 6 previously reported nuclear protein complexes. C_LIO_LIA number of Hormone-specific module variants were identified by modulomics upon hormone treatment using the hormone significantly up-regulated crosslinks from qXL-MS. Several PPIs and NPIMs have been substantiated with alternative biological experiments. C_LIO_LIThis CHAMPION pipeline has partitioned these NPIMs into four hierarchically and topologically organized communities in nucleome. The molecular functions of those proteins partitioned into C1 and C2 community are specialized in genome organization and nucleolar functions, respectively. C_LI

bioinformatics↗

bioRxiv2022

On-target inhibition of Cryptosporidium parvum by nitazoxanide (NTZ) and paclitaxel (PTX) validated using a novel MDR1-transgenic host cell model and algorithms to quantify on/off-target rates

Cryptosporidium parvum is a globally distributed zoonotic protozoan parasite that causes moderate to severe, sometime deadly, watery diarrhea in humans and animals, for which fully effective treatments are yet unavailable. In the study of mechanism of action of drugs against intracellular pathogens, it is important to validate whether the observed anti-infective activity is attributed to the drug action on the pathogen (on-target effect) or host cells (off-target effect). For the epicellular Cryptosporidium, we have previously developed a concept that the host cells with significantly increased drug tolerance by transient overexpression of the multidrug resistance protein-1 (MDR1) could be utilized to evaluate whether an observed anti-cryptosporidial activity of an inhibitor was attributed to the action of the inhibitor on the parasite or host cell targets. However, the transient transfection model was only applicable to evaluating inhibitors that were MDR1 substrates. Here we report an advanced model using stable MDR1-transgenic HCT-8 cells that allowed continuous application of drug pressure for rapid development of novel resistance to non-MDR1 substrates. Using the new model, we successfully validated that nitazoxanide, the only FDA-approved drug to treat human cryptosporidiosis and non-MDR1 substrate, killed C. parvum by fully acting on the parasite target (100% on-target). We also confirmed that paclitaxel acted fully on-target, while several other inhibitors including mitoxantrone, doxorubicin, vincristine and ivermectin acted partially on-target. Additionally, we developed mathematical models to quantify the proportional contributions of on-target and off-target effects to the observed anti-cryptosporidial activity and to evaluate the relationships between antiparasitic efficacy (ECi), cytotoxicity (TCi), safety interval (SI) and Hill slope (h) parameters. Owning to the promiscuity of the MDR1 efflux pump, the MDR1-transgenic host cell model could be applied to assess the on/off-target effects of newly hits/leads, either substrates or non-substrates of MDR1, against Cryptosporidium or other epicellular pathogens. Author SummaryCryptosporidium parvum is an important zoonotic parasite, for which fully effective treatments are unavailable. Anti-cryptosporidial drug discovery faces many challenges and technical difficulties. One obstacle is the lack of tools to assess whether the killing of C. parvum by an inhibitor is attributed to the action of the inhibitor on the parasite or on host cells. To address this question, we developed an MDR1-transgenic host cell line that allowed rapid development of drug resistance by applying continuous drug pressure. By analyzing the antiparasitic activity and cytotoxicity between wild-type and drug-resistant host cells, we verified that nitazoxanide (the only FDA-approved drug for treating cryptosporidiosis) and paclitaxel (anti-cryptosporidial lead) killed the parasite by acting fully on the parasite, whereas mitoxantrone, doxorubicin, vincristine and ivermectin killed the parasite by acting on both the parasite and host cells. We also developed algorithms to quantify the percent contributions of actions on the parasite and host cells to the observed anti-cryptosporidial activity. In summary, we developed novel in vitro and mathematical models for evaluating/quantifying the on/off-target effects of anti-cryptosporidial drugs. The models are also applicable to evaluate/quantify the drug actions on other epicellular pathogens.

microbiology↗

bioRxiv2021

Genome-wide association analyses of individual differences in quantitatively assessed reading- and language-related skills in up to 34,000 people

The use of spoken and written language is a capacity that is unique to humans. Individual differences in reading- and language-related skills are influenced by genetic variation, with twin-based heritability estimates of 30-80%, depending on the trait. The relevant genetic architecture is complex, heterogeneous, and multifactorial, and yet to be investigated with well-powered studies. Here, we present a multicohort genome-wide association study (GWAS) of five traits assessed individually using psychometric measures: word reading, nonword reading, spelling, phoneme awareness, and nonword repetition, with total sample sizes ranging from 13,633 to 33,959 participants aged 5-26 years (12,411 to 27,180 for those with European ancestry, defined by principal component analyses). We identified a genome-wide significant association with word reading (rs11208009, p=1.098 x 10-8) independent of known loci associated with intelligence or educational attainment. All five reading-/language-related traits had robust SNP-heritability estimates (0.13-0.26), and genetic correlations between them were modest to high. Using genomic structural equation modelling, we found evidence for a shared genetic factor explaining the majority of variation in word and nonword reading, spelling, and phoneme awareness, which only partially overlapped with genetic variation contributing to nonword repetition, intelligence and educational attainment. A multivariate GWAS was performed to jointly analyse word and nonword reading, spelling, and phoneme awareness, maximizing power for follow-up investigation. Genetic correlation analysis of multivariate GWAS results with neuroimaging traits identified association with cortical surface area of the banks of the left superior temporal sulcus, a brain region with known links to processing of spoken and written language. Analysis of evolutionary annotations on the lineage that led to modern humans showed enriched heritability in regions depleted of Neanderthal variants. Together, these results provide new avenues for deciphering the biological underpinnings of these uniquely human traits.

genomics↗

bioRxiv2021

Identification of Significant Gene Expression Changes in Multiple Perturbation Experiments using Knockoffs

MotivationLarge-scale multiple perturbation experiments have the potential to reveal a more detailed understanding of the molecular pathways that respond to genetic and environmental changes. A key question in these studies is which gene expression changes are important for the response to the perturbation. ResultsWe present here a method based on the model-X knockoffs framework to identify significant gene expression changes in multiple perturbation experiments. This approach makes no assumptions on the functional form of the dependence between the responses and the perturbations and provides finite sample false discovery rate control for the set of important gene expression responses. In a large-scale multiple perturbation gene expression data set from the Library of Integrated Network-Based Cellular Signature (LINCS) NIH program, we identified important genes whose expression is modulated in response to perturbation with anthracycline, vorinostat, trichostatin-a, geldanamycin, and sirolimus. Furthermore, we compared the set of important genes that respond to these small molecules to identify co-responsive pathways. Availability and Implementationhttps://github.com/flahertylab/deepYknockoff Contactpflaherty@umass.edu and zhaott0416@gmail.com Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2021

Brain Injury Localization in Electromagnetic Imaging using Symmetric Crossing Lines Method

To avoid death or disability, patients with brain injury should undertake a diagnosis at the earliest time and accept frequent monitoring after starting any medical intervention. This paper presents a novel approach to localize brain injury using the intersection of pairs of signals from symmetrical antennas based on the hypothesis that healthy brains are approximately symmetric that the bleeding targets will lead to significantly different amplitude and phase changes if one of pair of transmit signals cross targets. The scattered signals (S-parameters) are acquired using 100 realistic brain models and 150 experimental data measurements. Firstly, three pair of horizontal antennas are used to detect target crossing which line and in which hemisphere in low frequency bands and estimate the size using high frequency bands. Then, an intersection of two pairs of antennas are identified the position of the target. Finally, a heat map is used to visualise the stroke brain. The results indicate that crossing pairs of antenna signals from the hemisphere with a blood mass exhibit significantly different signal amplitude in the graph features compared to those without the target (p<0.003). The experiments show that our novel localization algorithm can achieve an accuracy of 0.85{+/-}0.08 Dice similarity coefficient based on 150 experimental measurements using an elliptical container, which is suitable for brain injury localization.

biophysics↗

bioRxiv2021

Mosaic Evolution of Beta Barrel Porin Encoding Genes in Escherichia coli

Bacterial porins serve as the interface interacting with extracellular environment, and are often found under positive selection to fit in different environmental stresses. Local recombination has been identified in a handful of porin genes to facilitate the rapid adaptation of bacterial cells. It remains unknown whether it is a common evolutionary mechanism in gram-negative bacteria for all or a majority of the outer membrane proteins. In this research, we investigated the {beta}-barrel porin encoding genes in Escherichia coli that were reported under positive Darwinia selection. Besides fhuA that was found with ingenic local recombination predominantly previously, we identified four other genes, i.e., lamB, ompA, ompC and ompF, all showing the similar mosaic evolution patterns as in fhuA. Comparative analysis of the protein sequences disclosed a list of highly variable regions in each protein family, which are mostly located in the convex of extracellular loops and coinciding with the binding sites of various bacteriophages. For each of the porin family, mosaic recombination leads to various combinations of the HVRs with different sequence patterns, generating diverse protein groups. Structure modeling further indicated the conserved global topology for various groups of each porin family, but the extracellular surface varies a lot that is formed by individual or combinatorial HVRs. The conservation of global tertiary structure ensures the channel activity while the wide diversity of HVRs may assist bacteria avoiding the invasion of phages, antibiotics or immune surveillance factors. In summary, the study identified multiple bacterial porin genes with mosaic evolution, a likely general strategy, by which outer membrane proteins could facilitate the host bacteria to both maintain normal life processes and evade the attack of unflavored environmental factors rapidly. ImportanceMicroevolution studies can disclose more elaborate evolutionary mechanisms of genes, appearing especially important for genes with multifaceted function such as those encoding outer membrane proteins. However, in most cases, the gene is considered as a whole unit and the evolutionary patterns are disclosed. In this research, we reported that multiple bacterial porin proteins follow mosaic evolution, with local ingenic recombination combined with spontaneous mutations based positive Darwinia selection, and conservation for most of the other regions. It could represent a common mechanism for bacterial outer membrane proteins. The study also provides insights on development of new anti-bacterial agent or vaccines.

microbiology↗