Biology subjects

Zhao, W.

Publications and source records attributed to Zhao, W..

At least 19 recordsLinked to original sources

bioRxiv2026

Comprehensive characterization of genomic, transcriptomic and epigenomic artifacts introduced in formalin-fixed, paraffin-embedded tissues.

Genomic, transcriptomic and epigenomic characterization has accelerated the discovery of clinically-relevant alterations in cancer, predominantly using fresh frozen (FF) specimens. However, clinical molecular pathology laboratories prefer formalin-fixed paraffin-embedded (FFPE) methods, known to introduce artifacts at the nucleic acid level, over fresh frozen methods. Extending the multi-platform analysis to FFPE specimens for comprehensive clinical molecular diagnosis requires a thorough understanding of the consequence of formalin-fixation. We present a detailed multi-platform characterization of FFPE preservation using paired FF specimens as the 'gold standard'. DNA and RNA were obtained from 38 patients across 6 cancer types using a FFPE optimized co-isolation. The impact of FFPE on exome sequencing was dependent on filtering, where a minimum coverage or supporting read filter can mitigate FFPE-specific false positives. Copy number alterations, MSI assessment, mutational signatures, and DNA methylation were comparable between FFPE and FF. FFPE biases in RNA expression can be overcome when using biology-relevant genes and we describe a novel consequence of FFPE on miRNA species diversity. Collectively, this data provides a broad view of FFPE artifact and offers best practices for overcome these biases.

bioinformatics↗

bioRxiv2018

A global map of RNA binding protein occupancy guides functional dissection of post-transcriptional regulation of the T cell transcriptome

RNA binding proteins (RBPs) mediate constitutive RNA metabolism and gene specific regulatory interactions. To identify RNA cis-regulatory elements, we developed GCLiPP, a biochemical technique for detecting RBP occupancy transcriptome-wide. GCLiPP sequence tags corresponded with known RBP binding sites, specifically correlating to abundant cytosolic RBPs. To demonstrate the utility of our occupancy profiles, we performed functional dissection of 3' UTRs with CRISPR/Cas9 genome editing. Two RBP occupied sites in the CD69 3' UTR destabilized the transcript of this key regulator of lymphocyte tissue egress. Comparing human Jurkat T cells and mouse primary T cells uncovered hundreds of biochemically shared peaks of GCLiPP signal across homologous regions of human and mouse 3' UTRs, including a cis-regulatory element that governs the stability of the mRNA that encodes the proto-oncogene PIM3 in both species. Our GCLiPP datasets provide a rich resource for investigation of post-transcriptional regulation in the immune system.

genomics↗

bioRxiv2018

Impaired cognitive performance under psycho-social stress in cannabis dependence is mediated by attenuated precuneus activity

BackgroundDeficient regulation of stress plays an important role in the escalation of substance use, addiction and relapse. Accumulating evidence suggests dysregulations in cognitive and reward-related processes and the underlying neural circuitry in cannabis dependence. However, despite the important regulatory role of the endocannabinoid system in the stress response, associations between chronic cannabis use and altered stress processing on the neural level have not been systematically examined. MethodsAgainst this background, the present functional magnetic resonance imaging (fMRI)study examined psycho-social stress processing in cannabis-dependent males (n = 28) and matched controls (n = 23) using an established stress-induction paradigm (Montreal Imaging Stress Task) that combines computerized (adaptive) mental arithmetic challenges with social evaluative threat. ResultsDuring psycho-social stress exposure, but not the no-stress condition, cannabis users demonstrated impaired performance relative to controls. In contrast, levels of experienced stress and cardiovascular stress responsivity did not differ from controls. Functional MRI data revealed that stress-induced performance deteriorations in cannabis users were accompanied by decreased precuneus activity and increased connectivity of this region with the dorsal medial prefrontal cortex. LimitationsOnly male cannabis-dependent users were examined, the generalizability in female users remains to be determined. ConclusionTogether, the present findings provide first evidence for exaggerated stress-induced cognitive performance deteriorations in cannabis users. The neural data suggest that deficient stress-related dynamics of the precuneus may mediate the deterioration of performance on the behavioral level.

neuroscience↗

bioRxiv2018

Collection of continuous rotation MicroED Data from Ion Beam Milled Crystals of Any Size

Microcrystal electron diffraction (MicroED) allows for macromolecular structure solution from nanocrystals. To create crystals of suitable size for MicroED data collection, sample preparation typically involves sonication or pipetting a slurry of crystals from a crystallization drop. The resultant crystal fragments are fragile and the quality of the data that can be obtained from them is sensitive to subsequent sample preparation for cryoEM as interactions in the water-air interface can damage crystals during blotting. Here, we demonstrate the use of a focused ion beam to generate lamellae of macromolecular protein crystals for continuous rotation MicroED that are of ideal thickness, easy to locate, and require no blotting optimization. In this manner, crystals of nearly any size may be scooped and milled to ideal dimensions prior to data collection, thus streamlining the methodology for sample preparation for MicroED.

biochemistry↗

bioRxiv2018

Can pharmacological enhancement of the placebo effect be a novel therapy for working memory impairments?

Working memory is considered as a core aspect of cognitive function and its impairment in a wide range of mental disorders has resulted in it being considered as an important transdiagnostic feature. To date pharmacological and behavioural strategies for augmenting working memory have achieved only moderate success. Here we have taken a different approach by combining expectancy effects with intranasal oxytocin as an adjunct given previous evidence that it may enhance placebo effects. In a randomised controlled clinical trial we demonstrate that while working memory performance is not influenced by expectancy per se when it is given in conjunction with oxytocin performance in terms of accuracy can be significantly enhanced following positive expectancy induction (placebo effect) and impaired following negative expectancy induction (nocebo effect). Thus combining expectancy effects with intranasal oxytocin may represent a radical new approach for improving working memory function in mental disorders.

neuroscience↗

bioRxiv2018

Oxytocin amplifies sex differences in human mate choice

Infidelity is the major cause of breakups and individuals with a history of infidelity are more likely to repeat it, but may also present a greater opportunity for short-term sexual relationships. Here in a pre-registered, double-blind study involving 160 subjects we report that while both sexes valued faithful individuals most for long-term relationships, both single men and those in a relationship were more interested in having short-term relationships with previously unfaithful individuals than women. Oxytocin administration resulted in men rating the faces of unfaithful women as more attractive but in women rating those of unfaithful men as less attractive and also finding them less memorable. Oxytocin also increased mens interest in having short-term relationships with previously unfaithful women whereas it increased womens interest in having long-term relationships with faithful men. Thus, oxytocin release during courtship may first act to amplify sex-dependent priorities in attraction and mate choice before subsequently promoting romantic bonds.

neuroscience↗

bioRxiv2018

Oxytocin modulates the intrinsic dynamics between attention-related large scale networks

Attention and salience processing have been linked to the intrinsic between- and within-network dynamics of large scale networks engaged in internal (default mode network, DN) and external attention allocation (dorsal attention, DAN, salience network, SN). The central oxytocin (OXT) system appears ideally organized to modulate widely distributed neural systems and to regulate the switch between internal attention and salient stimuli in the environment. The current randomized placebo (PLC) controlled between-subject pharmacological resting-state fMRI study in N = 187 (OXT, n = 94; n = 93; single-dose intranasal administration) healthy male and female participants employed an independent component analysis (ICA) approach to determine the modulatory effects of OXT on the within- and between-network dynamics of the DAN-SN-DN triple network system. OXT increased the functional integration between subsystems within SN and DN and increased functional segregation of the DN with the SN and DAN engaged in attentional control. Whereas no sex differences were observed, OXT effects on the DN-SN interaction were modulated by autism traits. Together, the findings suggest that OXT may facilitate efficient attentional allocation towards social cues by modulating the intrinsic functional dynamics between DN components engaged in social processing and large-scale networks involved in external attentional demands (SN, DAN).

neuroscience↗

bioRxiv2018

Auditory attention reduced ear-canal noise in humans, but not through medial olivocochlear efferent inhibition: Implications for measuring otoacoustic emissions during behavioral task performance

Otoacoustic emissions (OAEs) are often measured to non-invasively determine activation of medial olivocochlear (MOC) efferents in humans. Usually these experiments assume that ear-canal noise remains constant. However, changes in ear-canal noise have been reported in some behavioral experiments. We studied the variability of ear-canal noise in eight subjects who performed a two-interval-forced-choice (2IFC) sound-level-discrimination task on monaural tone pips in masking noise. Ear-canal noise was recorded directly from the unstimulated ear opposite the task ear. Recordings were also done with similar sounds presented, but no task done. In task trials, ear-canal noise was reduced at the time the subject did the discrimination, relative to the noise level earlier in the trial. In two subjects, there was a decrease in ear-canal noise, primarily at 1-2 kHz, with a time course similar to that expected from inhibition by MOC activity elicited by the task-ear masker noise. These were the only subjects with spontaneous OAEs (SOAEs). We hypothesize that the SOAEs were inhibited by MOC activity elicited by the task-ear masker. Based on the standard rationale in OAE experiments that large bursts of noise are artifacts due to subject movement, noise bursts above a sound-level criterion were removed. As the criterion was lowered and more high-and moderate-level noise bursts were removed, the reduction in noise level from the beginning of the trial to the time of the 2IFC discrimination became less. This pattern is opposite that expected from MOC inhibition (which is greater on lower-level sounds), but can be explained by the hypothesis that subjects move less and create fewer bursts of noise when they concentrate on doing the task. In contrast, for the six subjects with no SOAEs, in no-task trials the noise level was little changed throughout the trial. Our results show that measurements of MOC effects on OAEs must measure and account for changes in ear-canal noise, especially in behavioral experiments. The results also provide a novel way of showing the time course of the buildup of attention in ear-canal noise during a 2IFC task.

neuroscience↗

bioRxiv2018

Radiogenomics-based Risk Prediction of Glioblastoma Multiforme with Clinical Relevance

GBM is the most common and aggressive primary brain tumor. Although the TMZ-based radiochemotherapy improves overall GBM patients survival, it also increases the frequency of false positive post-treatment magnetic resonance imaging (MRI) assessments for tumor progression. Pseudoprogression is a treatment-related reaction with an increase in contrast-enhancing lesion size at the tumor site or resection margins which mimics tumor recurrence on MRI. Accurate and reliable prognostication of GBM progression is urgently needed in the clinical management of GBM patients. Clinical data analysis indicates that the patients with PsP had superior overall and progression-free survival rates. In this study, we aimed to develop a prognostic model to evaluate tumor progression potential of GBM patients following standard therapies. We applied a dictionary learning scheme to obtain imaging features of GBM patients with PsP or TTP from the Wake dataset. Based on these radiographic features, we then conducted radiogenomics analysis to identify the significantly associated genes. These significantly associated genes were then used as features to construct a 2YS logistic regression model. GBM patients were classified into low-and high-survival risk groups based on the individual 2YS scores derived from this model. We tested our model using an independent TCGA dataset and found that 2YS scores were significantly associated with the patients overall survival. We further used two cohorts of the TCGA data to train and test our model. Our results show that 2YS scores-based classification results from the training and testing TGCA datasets were significantly associated with the overall survival of patients. We also analyzed the survival prediction ability of other clinical factors (gender, age, KPS, normal cell ratio) and found that these factors were not related or weakly correlated with patients survival. Overall, our studies have demonstrated the effectiveness and robustness of the 2YS model in predicting clinical outcomes of GBM patients after standard therapies.

bioinformatics↗

bioRxiv2018

Single-cell Transcriptomic Landscape of Nucleated Cells in Umbilical Cord Blood

Umbilical cord blood (UCB) transplant is a therapeutic option for both pediatric and adult patients with a variety of hematologic diseases such as several types of blood cancers, myeloproliferative disorders, genetic diseases, and metabolic disorders. However, the level of cellular heterogeneity and diversity of nucleated cells in the UCB has not yet been assessed in an unbiased and systemic fashion. In the current study, nucleated cells from UCB were subjected to single-cell RNA sequencing, a technology enabled simultaneous profiling of the gene expression signatures of thousands of cells, generating rich resources for further functional studies. Here, we report the transcriptomic maps of 19,052 UCB cells, covering 11 major cell types. Many of these cell types are comprised of distinct subpopulations, including distinct signatures in NK and NKT cell types in the UCB. Pseudotime ordering of nucleated red blood cells (NRBC) identifies wave-like activation and suppression of transcription regulators, leading to a polarized cellular state, which may reflect the NRBC maturation. Progenitor cells in the UBC also consist two subpopulations with divergent transcription programs activated, leading to specific cell-fate commitment. Collectively, we provide this comprehensive single-cell transcriptomic landscape and show that it can uncover previously unrecognized cell types, pathways and gene expression regulations that may contribute to the efficacy and outcome of UCB transplant, broadening the scope of research and clinical innovations.

genomics↗

bioRxiv2018

Oxytocin facilitates empathic- and self-embarrassment ratings by attenuating amygdala and anterior insula responses

The hypothalamic neuropeptide oxytocin has been reported to enhance emotional empathy in association with reduced amygdala activation, although to date studies have not investigated empathy for individuals expressing self-conscious, moral emotions which engage mentalizing as well as emotion processing networks. In the current randomized, double-blind placebo controlled functional MRI experiment on 70 male and female subjects we have therefore investigated the effects of intranasal oxytocin (40 IU) on behavioral and neural responses to embarrassment experienced by others or by self. Results showed that oxytocin significantly increased ratings of both empathic and self-embarrassment and concomitantly decreased skin conductance response and activation in the right amygdala and insula but not in the medial prefrontal cortex. The amygdala effects of oxytocin were associated with the magnitude of the skin conductance response and trait anxiety scores. Overall our results demonstrate that oxytocin increases ratings of self- and other embarrassment and that this is associated with reduced physiological arousal and activity in neural circuitry involved in emotional arousal. The neural effects of oxytocin are also stronger in individuals with high trait anxiety suggesting that it may particularly reduce their anxiety in embarrassing situations.

neuroscience↗

bioRxiv2018

PARPi triggers STING-dependent immune response and enhances therapeutic efficacy of immune checkpoint blockade independent of BRCAness

Poly-(ADP-ribose) polymerase (PARP) inhibitors (PARPis) have shown remarkable therapeutic efficacy against BRCA1/2 mutant cancers through a synthetic lethal interaction. PARPis are believed to exert their therapeutic effects mainly through the blockade of single-strand DNA damage repair, which leads to the accumulation of toxic DNA double strand breaks, specifically in cancer cells with DNA repair deficiency (BCRAness), including those harboring BRCA1/2 mutations. Here, we show that PARPis modulate immune reposes, which contribute to their therapeutic effects independent of BRCA1/2 mutations. The mechanism underlying this PARPi-induced reprogramming of anti-tumor microenvironment involves a promoted accumulation of cytosolic DNA fragments due to unresolved DNA lesions. This in turn activates the DNA sensing cGAS-STING pathway and stimulates production of type I interferons. Ultimately, these events promote PARPi-induced antitumor immunity independent of BRCAness, which can be further enhanced by immune checkpoint blockade. Our results may provide a mechanistic rationale for using PARPis as immunomodulatory agents to harness therapeutic efficacy of immune checkpoint blockade.

cancer biology↗

bioRxiv2018

Real-time functional connectivity-based neurofeedback of amygdala-frontal pathways reduces anxiety

Deficient emotion regulation and exaggerated anxiety represent a major transdiagnostic psychopathological marker. On the neural level these deficits have been closely linked to impaired, yet treatment-sensitive, prefrontal regulatory control over the amygdala. Gaining direct control over these pathways could therefore provide an innovative and promising strategy to regulate exaggerated anxiety. To this end the current proof-of-concept study evaluated the feasibility, functional relevance and maintenance of a novel connectivity-informed real-time fMRI neurofeedback training. In a randomized within-subject sham-controlled design high anxious subjects (n = 26) underwent real-time fMRI-guided training to enhance connectivity between the ventrolateral prefrontal cortex (vlPFC) and the amygdala (target pathway) during threat exposure. Maintenance of regulatory control was assessed after three days and in the absence of feedback. Training-induced changes in functional connectivity of the target pathway and anxiety ratings served as primary outcomes. Training of the target, yet not the sham-control, pathway significantly increased amygdala-vlPFC connectivity and decreased subjective anxiety levels. On the individual level stronger connectivity increases were significantly associated with anxiety reduction. At follow-up, volitional control over the target pathway and decreased anxiety level were maintained in the absence of feedback. The present results demonstrate for the first time that successful self-regulation of amygdala-prefrontal top-down regulatory circuits may represent a novel strategy to control anxiety. As such, the present findings underscore both the critical contribution of amygdala-prefrontal circuits to emotion regulation and the therapeutic potential of connectivity-informed real-time neurofeedback.

clinical trials↗

bioRxiv2018

Oxytocin enhancement of emotional empathy: generalization across cultures and effects on amygdala activity

Accumulating evidence suggests that the neuropeptide oxytocin can enhance empathy although it is unclear which specific behavioral and neural aspects are influenced, and whether the effects are modulated by culture, sex and trait autism. Based on previous findings in Caucasian men, we hypothesized that a single intranasal dose of oxytocin would specifically enhance emotional empathy via modulatory effects on the amygdala in an Asian (Chinese) population and explored the modulatory role of sex and trait autism on the effects. We first conducted a double-blind, randomized between-subject design experiment using a modified version of the multifaceted empathy task (MET) to determine whether oxytocins facilitation of emotional empathy can be replicated in Chinese men (n = 60). To further explore neural mechanisms behind and potential sex differences, functional MRI and skin conductance measures were acquired in an independent experiment incorporating men and women (n = 72). Oxytocin enhanced emotional empathy across experiments and sex, an effect that was accompanied by reduced amygdala activity and increased skin conductance responses. On the network level oxytocin enhanced functional coupling of the right amygdala with the insula and posterior cingulate cortex for positive valence stimuli but attenuated coupling for negative valence stimuli. The effect of oxytocin on amygdala functional connectivity with the insula was modulated by trait autism. Overall, our findings provide further support for the role of oxytocin in facilitating emotional empathy and demonstrate that effects are independent of culture and sex and involve modulatory effects on the amygdala and its interactions with other key empathy regions.

neuroscience↗

bioRxiv2018

Colonization of phosphate-solubilizing Pseudomonas sp. strain P34-L in the wheat rhizosphere and its effects on wheat growth and the expression of phosphate transporter gene TaPT4 in wheat

The ability to colonize the rhizosphere is an important basics requirement for field application of plant growth-promoting rhizobacteria (PGPR) strains. There are complex signal exchanges and mutual recognition between microbes and plants. In this study, phosphate-solubilizing Pseudomonas sp. P34, a PGPR strain with affinity to wheat, was isolated from the wheat rhizosphere by wheat germ agglutinin (WGA). The plasmid pTR102 harboring the luciferase luxAB gene was transferred into P34 to create P34-L. The labeled strain was used to track the temporal and spatial characteristics of colonization in wheat rhizosphere and its effects on wheat development. The transcript level of phosphate transporter gene TaPT4, a phosphorus deficiency indicator gene, in wheat roots was monitored by quantitative reverse-transcription PCR. The experimental results indicated that there was a high density of stain P34-L within the top 8-cm depth of the wheat rhizosphere on day 36 of wheat growth. The strain could survive in the wheat rhizosphere for a long time, and colonize new spaces in wheat rhizosphere following the extension of wheat roots. Compared with uninoculated wheat plants, those inoculated with P34-L showed significantly increased phosphorus accumulation in leaves, seedling fresh and dry weight, root fresh and dry weight, total root length, and number of root tips, forks, crossings, which showed a great value of application of the strain on wheat production by promoting the root growth and dry matter accumulation. Strain P34-L down-regulated the transcript level of TaPT4 in wheat roots, which means a well phosphorus supplementation environment was established by P34-L.\n\nImportanceMany PGPR strains often failed to achieve the desired effects when applied in the field. One major reason for the failure is lack of a special affinity between a certain strain and the target host plant, so those strains have low competitive ability with the indigenous microorganism, and unable to survive constantly in rhizosphere. In this work, a new technique to isolate wheat-specific phosphate-solubilizing PGPR strain by WGA was established. The isolate P34 was confirmed can colonize the wheat rhizosphere, and have significantly ability in promoting phosphorus absorption and wheat growth by luminescence labeling techniques. Furthermore, the phosphate-solubilizing ability of this affinity PGPR strain was verified in gene level by quantitative reverse-transcription PCR. These results lay a firm foundation for further research on the relationships between PGPR and their host plants. Meanwhile, this work supplied a potential ideal biofertilizer producing strain for sustainable agriculture.

microbiology↗

bioRxiv2018

Sex- and Context-dependent Effects of Oxytocin on Social Reward Processing

We interact socially and form bonds with others because such experiences are rewarding. However, an insecure attachment style or social anxiety can reduce these rewarding effects. The neuropeptide oxytocin (OXT) may facilitate social interactions either by increasing their rewarding experience or by attenuating anxiety, although effects can be sex- and attachment-style dependent. In this study, 64 pairs of same-sex friends completed a social sharing paradigm in a double-blind, placebo-controlled, between-subject design with one friend inside an MRI scanner and the other in a remote behavioral testing room. In this way we could examine whether intranasal-OXT differentially modulated the emotional impact of social sharing and associated neural processing. Additionally, we investigated if OXT effects were modulated by sex and attachment style. Results showed that in women, but not men, OXT increased ratings for sharing stimuli with their friend but not with a stranger, particularly in the friend in the scanner. Corresponding neuroimaging results showed that OXT decreased both amygdala and insula activity as well as their functional connectivity in women when they shared with friends but had the opposite effect in men. On the other hand, OXT did not enhance responses in brain reward circuitry. In the PLC treated group amygdala responses in women when they shared pictures with their friend were positively associated with attachment anxiety and OXT uncoupled this. Our findings demonstrate that OXT facilitates the impact of sharing positive experiences with others in women, but not men, and that this is associated with differential effects on the amygdala and insula and their functional connections. Furthermore, OXT particularly reduced increased amygdala responses during sharing in individuals with higher attachment anxiety. Thus, OXT effects in this context may be due more to reduced anxiety when sharing with a friend than to enhanced social reward.

neuroscience↗

bioRxiv2018

Cell atlas of human uterus

The human uterus is a highly dynamic tissue that undergoes repeated damage repair and regeneration during the menstrual cycle, which make it ideal model to study tissue regeneration and pathological process. Stem/progenitors were speculated to be involved in the regeneration of endometrial epithelial and pathogenesis of endometriosis. But the identity, microenvironment and regulatory mechanisms of the uterus epithelial stem/progenitors in vivo remain unclear. Here, we dissected the cell heterogeneities of the full-thickness human uterus epithelial cells (11 clusters), stroma cells (6 clusters), endothelial cells (5 clusters), smooth muscle cells (2 clusters), myofibroblasts (2 clusters) and immune cells (6 clusters) from 2735 single cell by single cell RNA-seq. Further analysis identified a unique ciliated epithelial cell cluster showing characteristics of stem/progenitors with properties of epithelial-mesenchymal transition (EMT) that mainly localized in the upper functionalis of the endometrium. Ordering the cell subpopulations along the pseudo-space revealed cell clusters possess cellular states of stress, inflammation and apoptosis in the upper functionalis cellular ecosystem of the endometrium. Connectivity map between the human uterus subpopulations revealed potential inflammatory (cytokines and chemokines) and developmental (WNT, FGF, VEGF) signals within the upper functionalis cellular ecosystem of the endometrium, especially from other epithelial clusters, regulating cell plasticity of the EMT-epithelial clusters. This study reconstructed the heterogeneities, space-specific distribution and connectivity map of human uterus atlas, which would provide insight in the regeneration of uterus endometria and reference for the pathogenesis of uterus.

cell biology↗

bioRxiv2018

Phosphorothioate-modified DNA oligonucleotides inactivate CRISPR-Cpf1 mediated genome editing

CRISPR-Cpf1, a microbial adaptive immune system discovered from Prevotella and Francisella 1, employs a single-stranded CRISPR RNA (crRNA) to induce double stranded DNA breaks1. To modulate genome editing activity of Cpf1 in human cells, we designed a series of crRNA variants including DNA-crRNA and RNA-crRNA duplexes, and identified that phosphorothioate (PS)-modified DNA-crRNA duplex completely blocked the function of Cpf1 mediated gene editing. More importantly, without prehybridization, this PS-modified DNA was able to regulate Cpf1 activity in a time-and dose-dependent manner. Mechanistic studies indicate that PS-modified DNA oligonucleotides hinder the binding between Cpf1-crRNA complex and target DNA substrate. Consequently, phosphorothioate-modified DNA oligonucleotides provide a tunable platform to inactivate Cpf1 mediated genome editing.

bioengineering↗