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Cao, H.

Publications and source records attributed to Cao, H..

At least 73 records · Page 4Linked to original sources

New tree shrew Parkinson's model: a cost-effective alternative to monkey models

The surge in demand for experimental monkeys has led to a rapid increase in their associated costs. Consequently, there is a growing need for the development of a cost-effective model for Parkinsons disease (PD) that exhibits all core clinical and pathological phenotypes of PD. Evolutionarily, tree shrews (Tupaia belangeri) are much closer to primates in comparison to rodents and share more similar PD-related brain structures and movement ability with monkeys. As such, tree shrews represent an ideal small animal species for modeling PD. To develop a tree shrew PD model, we used the 1-Methyl-4-phenylpyridinium (MPP+) metabolite, derived from the well-established PD modeling drug 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), to induce lesions in the dopaminergic neurons of the unilateral substantia nigra. After determining the optimal modeling dosage, the tree shrews consistently exhibited and maintained all classic clinical manifestations of PD for a 5-month period. The symptoms closely resembled the ones observed in PD monkeys and included bradykinesia, rest tremor, postural instability, and apomorphine-induced rotations, a classic phenotype of unilateral PD models. Immunostaining showed a significant loss of dopaminergic neurons (approximately 95%) in the substantia nigra on the lesioned side of the brain, a crucial pathological marker of PD. Further cytomorphological analysis revealed that the size of nigral dopaminergic neurons in tree shrews exceeded that of rodents and more closely approximated that of macaques. Based on the principle that structure determines function, the morphological similarity between tree shrews and monkeys may be an important structural basis for the manifestation of the highly similar phenotypes between monkey and tree shrew PD models. Collectively, this study successfully developed a PD model in a small animal species that faithfully recapitulated the classical clinical symptoms and key pathological indicators of PD monkeys. In addition to the well-recognized monkey models, the tree shrew model provides a novel avenue for the evaluation of PD treatments and underlying mechanisms.

neuroscience↗

Immunities Specific to Both of the M Protein Ectodomain and RBD Synergize to Confer Cross-protection against SARS-CoV-2 Infections

The effectiveness of the prototypic SARS-CoV-2 vaccine largely decreased overtime against the emerging virus strains, necessitating the universal vaccine development. The most abundant structural membrane (M) protein is highly conserved in amino acid sequence, which arouses our research interests in developing a universal immunogen based on it. Serological analysis showed that IgG responses specific to its N-terminal peptides can be strongly detected in many serum samples from both convalescent patients and vaccinees receiving inactivated vaccines, indicating the potential existence of human B-cell epitopes in reactive peptides. Microneutralization assays showed that the N-terminal peptide S2M2-30-specific hyperimmune serum was capable of cross-neutralizing the authentic viruses including wild-type HKU-001a, B.1.617.2/Delta, and Omicron subvariant BQ.1.1, and synergized with RBD-specific serum in reinforcing antiviral activities. Strong S2M2-30-specific immunities elicited in hACE2-transgenic mice could effectively inhibit B.1.1.7/Alpha (UK) infections. Our results suggest the potentiality of conserved M peptides as vaccine targets for conferring cross-protections against sarbecoviruses.

immunology↗

Single transcript-level metabolic responsive landscape of human liver transcriptome

Direct knowledge of gene regulation in human liver by metabolic stimuli could fundamentally advance our understanding of metabolic physiology. This information, however, is largely unknown, and this void is deeply rooted in a paradox that is caused by the inaccessibility of human liver to treatments and the insufficient annotation of liver transcriptome. Recent advances have uncovered immense complexity of transcriptome, i.e., multiple transcripts produced from one gene and extensive RNA modifications, which are all highly regulated and often condition-dependent. Establishing an inclusive annotation to study liver transcriptome dynamics thus requires human liver samples of diverse conditions, which are paradoxically unavailable due to the inaccessibility of human liver to treatments. In this work, we addressed these challenges by coupling an isogenic humanized mouse model with Nanopore single-molecule direct RNA sequencing (DRS). We first generated mice that carried humanized livers of identical genetic background, which were equivalent to clones of a single human liver, and then subjected the mice to representative metabolic treatments. We then analyzed the humanized livers with Nanopore DRS, which directly reads full-length native RNAs to determine the expression level, m6A modification and poly(A) tail length of all RNA transcript isoforms. Thus, our system allows for constructing a de novo annotation of human liver transcriptomes reflecting metabolic responses and studying transcriptome dynamics in conjunction. Our analysis uncovered a vast number of novel genes and transcripts that have not been previously reported. Our transcript-level analysis of human liver transcriptomes also identified a multitude of regulated metabolic pathways that were otherwise invisible using conventional short read RNA-seq. We also revealed for the first time the dynamic changes in m6A and poly(A) tail length of human liver transcripts many of which are transcribed from key metabolic genes. Furthermore, we performed comparative analyses of gene regulation between human and mouse and between two individuals using the liver-specific humanized mice. This revealed that transcriptome dynamics are highly species- and genetic background-dependent, which may only be faithfully studied in a humanized system that entails clones of the same human liver. Hence our work revealed a complex metabolic responsive landscape of human liver transcriptome and also provided a framework to understand transcriptome dynamics of human liver in response to physiologically relevant metabolic stimuli.

systems biology↗

ASD mutation of Katnal2 impairs ependymal ciliary motion and causes hydrocephalus

Katanin catalytic subunit A1 like 2 (KATNAL2) is a high-risk gene associated with autism spectrum disorders (ASD), however its impact on brain development and disease remains unclear. The present study revealed an unexpected role of KATNAL2 in regulating ependymal ciliary motion and cerebrospinal fluid flow during brain development, an important contributing factor for ASD. We discovered a distinct expression pattern of KATNAL2 in multiciliated ependymal cells of both human and mouse brains. Notably, an ASD-associated mutation of Katnal2 disrupted its molecular function and resulted in ASD-related behavioral deficits in mice. Additionally, this mutation affected the polarized organization and beating of ependymal cilia, leading to delayed cerebrospinal fluid flow and sustained ventricular enlargement from the early postnatal stage. Conditional ablation of Katnal2 specifically in the ependymal cells of neonatal mice is sufficient to cause ventricular dilation, whereas no such effect was observed in adult mice. Our findings highlight the importance of ependymal motile cilia and hydrocephalus in ASD, offering insights into its pathogenesis and potential intervention.

neuroscience↗

Consecutive treatments of methamphetamine promote the 4 development of cardiac pathological symptoms in zebrafish

Chronic methamphetamine use, a widespread drug epidemic, has been associated with cardiac morphological and electrical remodeling, leading to the development of numerous cardiovascular diseases. While methamphetamine has been documented to induce arrhythmia, most results originate from clinical trials from users who experienced different durations of methamphetamine abuse, providing no documentation on the use of methamphetamine in standardized settings. Additionally, the underlying molecular mechanism on how methamphetamine affects the cardiovascular system remains elusive. A relationship was sought between cardiotoxicity and arrhythmia with associated methamphetamine abuse in zebrafish to identify and to understand the adverse cardiac symptoms associated with methamphetamine. Zebrafish were first treated with methamphetamine 3 times a week over a 2-week duration. Immediately after treatment, zebrafish underwent electrocardiogram (ECG) measurement using an in-house developed acquisition system for electrophysiological analysis. Subsequent analyses of cAMP expression and Ca2+ regulation in zebrafish cardiomyocytes were conducted. cAMP is vital to development of myocardial fibrosis and arrhythmia, prominent symptoms in the development of cardiovascular diseases. Ca2+ dysregulation is also a factor in inducing arrhythmias. During the first week of treatment, zebrafish that were administered with methamphetamine displayed a decrease in heart rate, which persisted throughout the second week and remained significantly lower than the heart rate of untreated fish. Results also indicate an increased heart rate variability during the early stage of treatment followed by a decrease in the late stage for methamphetamine-treated fish over the duration of the experiment, suggesting a biphasic response to methamphetamine exposure. Methamphetamine-treated fish also exhibited reduced QTc intervals throughout the experiment. Results from the cAMP and Ca2+ assays demonstrate that cAMP was upregulated and Ca2+ was dysregulated in response to methamphetamine treatment. Collagenic assays indicated significant fibrotic response to methamphetamine treatment. These results provide potential insight into the role of methamphetamine in the development of fibrosis and arrhythmia due to downstream effectors of cAMP.

physiology↗

STAREG: an empirical Bayesian approach to detect replicable spatially variable genes in spatial transcriptomic studies

Identifying replicable genes that display spatial expression patterns from different yet related spatially resolved transcriptomic studies provides stronger scientific evidence and more powerful inference. We present an empirical Bayesian method, STAREG, for identifying replicable spatially variable genes in data generated from various spatially resolved transcriptomic techniques. STAREG models the joint distribution of p-values from different studies with a mixture model and accounts for the heterogeneity of different studies. It provides effective control of the false discovery rate and has higher power by borrowing information across genes and different studies. Moreover, it provides different rankings of important spatially variable genes. With the EM algorithm in combination with pool-adjacent-violator-algorithm (PAVA), STAREG is scalable to datasets with tens of thousands of genes measured on tens of thousands of spatial spots without any tuning parameters. Analyzing three pairs of spatially resolved transcriptomic datasets using STAREG, we show that it makes biological discoveries that otherwise cannot be obtained by using existing methods.

bioinformatics↗

Effects of phase encoding direction on test-retest reliability of human functional connectome

The majority of human connectome studies in the literature based on functional magnetic resonance imaging (fMRI) data use either an anterior-to-posterior (AP) or a posterior-to-anterior (PA) phase encoding direction. However, whether and how phase encoding direction would affect test-retest reliability of functional connectome is unclear. Here, in a sample of healthy subjects with two sessions of fMRI scans separated by 12 weeks (two runs per session, one with AP, the other with PA), we tested the influence of phase encoding direction on global and nodal connectivity in the constructed brain networks. All data underwent the state-of-the-art Human Connectome Project (HCP) pipeline to correct for phase-encoding-related distortions before entering analysis. We found that at the global level, the PA scans showed significantly higher intraclass correlation coefficients (ICCs) for global connectivity compared with AP scans, which was particularly prominent when using the Seitzman-300 atlas (versus the CAB-NP-718 atlas). At the nodal level, regions most strongly affected by phase encoding direction were consistently mapped to the cingulate cortex and temporal lobe, with significantly higher ICCs during PA scans compared with AP scans, regardless of atlas. Further, we demonstrated that the observed reliability differences between phase encoding directions may relate to a similar effect on the reliability of temporal signal-to-noise ratio (tSNR) in the same regions (that PA scans were associated with higher reliability of tSNR than AP scans). Averaging the connectivity outcome from the AP and PA scans could slightly, but overall have limited value to boost the ICCs. These results were largely replicated in an independent, public dataset from the HCP-Early Psychosis (HCP-EP) study with a similar design but a much shorter scan session interval. Our findings suggest that phase encoding direction has significant effects on the reliability of connectomic estimates in fMRI studies. We urge that these effects need to be carefully considered in future neuroimaging designs, especially in longitudinal studies such as those related to neurodevelopment or clinical intervention.

neuroscience↗

Hypothalamic thyroid hormone deficiency underlies reversible anorexia in a mammalian hibernator

Mammalian hibernators survive prolonged periods of cold and resource scarcity by temporarily modulating normal physiological functions, but the mechanisms underlying these adaptations are poorly understood. The hibernation cycle of thirteen-lined ground squirrels (Ictidomys tridecemlineatus) lasts for 5-7 months and comprises weeks of hypometabolic, hypothermic torpor interspersed with 24-48-hour periods of an active-like interbout arousal (IBA) state. We show that ground squirrels, who endure the entire hibernation season without food, have negligible hunger during IBAs. These squirrels exhibit reversible inhibition of the hypothalamic feeding center, such that hypothalamic arcuate nucleus neurons exhibit reduced sensitivity to the orexigenic and anorexigenic effects of ghrelin and leptin, respectively. However, hypothalamic infusion of thyroid hormone during an IBA is sufficient to rescue hibernation anorexia. Our results reveal that thyroid hormone deficiency underlies hibernation anorexia and demonstrate the functional flexibility of the hypothalamic feeding center.

physiology↗

CTLA-4 tail fusion enhances CAR-T anti-tumor immunity

Chimeric antigen receptor (CAR) T cells are powerful therapeutics; however, their efficacy is often hindered by critical hurdles. Here, utilizing the endocytic feature of the cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4) cytoplasmic tail (CT), we reprogram CAR function and substantially enhance CAR-T efficacy in vivo. CAR-T cells with monomeric, duplex, or triplex CTLA-4 CTs (CCTs) fused to the C-terminus of CAR exhibit a progressive increase in cytotoxicity under repeated stimulation, accompanied by reduced activation and production of pro-inflammatory cytokines. Further characterization reveals that CARs with increasing CCT fusion show a progressively lower surface expression, regulated by their constant endocytosis, recycling and degradation under steady state. The molecular dynamics of reengineered CAR with CCT fusion results in reduced CAR-mediated trogocytosis, loss of tumor antigen, and improved CAR-T survival. CARs with either monomeric (CAR-1CCT) or duplex CCTs (CAR-2CCT) have superior anti-tumor efficacy in a relapsed leukemia model. Single-cell RNA sequencing and flow cytometry analysis reveal that CAR-2CCT cells retain a stronger central memory phenotype and exhibit increased persistence. These findings illuminate a unique strategy for engineering therapeutic T cells and improving CAR-T function through synthetic CCT fusion, which is orthogonal to other cell engineering techniques.

immunology↗

Cas12a/Cpf1 knock-in mice enable efficient multiplexed immune cell engineering

Cas9 transgenic animals have drastically accelerated the discovery of novel immune modulators. But due to its inability to process its own CRISPR RNAs (crRNAs), simultaneous multiplexed gene perturbations using Cas9 remains limited, especially by pseudoviral vectors. Cas12a/Cpf1, however, can process concatenated crRNA arrays for this purpose. Here, we created conditional and constitutive LbCas12a knock-in transgenic mice. With these mice, we demonstrated efficient multiplexed gene editing and surface protein knockdown within individual primary immune cells. We showed genome editing across multiple types of primary immune cells including CD4 and CD8 T cells, B cells, and bone-marrow derived dendritic cells. These transgenic animals, along with the accompanying viral vectors, together provide a versatile toolkit for a broad range of ex vivo and in vivo gene editing applications, including fundamental immunological discovery and immune gene engineering.

genetics↗

JUMP: statistical analysis of replicability across two studies

MotivationReplicability is the cornerstone of scientific research. The current statistical method for high-dimensional replicability analysis either cannot control the false discovery rate (FDR) or is too conservative. ResultsWe propose a statistical method, JUMP, for the high-dimensional replicability analysis of two studies. The input is a high dimensional paired sequence of p-values from two studies and the test statistic is the maximum of p-values of the pair. JUMP uses four states of the p-value pairs to indicate whether they are null or non-null. Conditional on the hidden states, JUMP computes the cumulative distribution function of the maximum of p-values for each state to conservatively approximate the probability of rejection under the composite null of replicability. JUMP estimates unknown parameters and uses a step-up procedure to control FDR. By incorporating different states of composite null, JUMP achieves a substantial power gain over existing methods while controlling the FDR. Analyzing two pairs of spatially resolved transcriptomic datasets, JUMP makes biological discoveries that otherwise cannot be obtained by using existing methods. AvailabilityAn R package JUMP implementing the JUMP method is available on CRAN (https://CRAN.R-project.org/package=JUMP).

bioinformatics↗

Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function

MotivationMillions of protein sequences have been generated by numerous genome and transcriptome sequencing projects. However, experimentally determining the function of the proteins is still a time consuming, low-throughput, and expensive process, leading to a large protein sequence-function gap. Therefore, it is important to develop computational methods to accurately predict protein function to fill the gap. Even though many methods have been developed to use protein sequences as input to predict function, much fewer methods leverage protein structures in protein function prediction because there was lack of accurate protein structures for most proteins until recently. ResultsWe developed TransFun - a method using a transformer-based protein language model and 3D-equivariant graph neural networks to distill information from both protein sequences and structures to predict protein function. It extracts feature embeddings from protein sequences using a pre-trained protein language model (ESM) via transfer learning and combines them with 3D structures of proteins predicted by AlphaFold2 through equivariant graph neural networks. Benchmarked on the CAFA3 test dataset and a new test dataset, TransFun outperforms several state-of-the-art methods, indicating the language model and 3D-equivariant graph neural networks are effective methods to leverage protein sequences and structures to improve protein function prediction. Combining TransFun predictions and sequence similarity-based predictions can further increase prediction accuracy. AvailabilityThe source code of TransFun is available at https://github.com/jianlin-cheng/TransFun Contactchengji@missouri.edu

bioinformatics↗

PD-L1 regulates inflammatory macrophage development from human pluripotent stem cells by maintaining interferon-gamma signal

PD-L1 (programmed death-ligand 1) serves as a pivotal immune checkpoint in both the innate and adaptive immune systems. PD-L1 is expressed in macrophages in response to interferon-gamma (IFN{gamma}). We examined whether PD-L1 might regulate macrophage development. We established PD-L1-/- human pluripotent stem cells, differentiated them into macrophages, and observed a 60% reduction of CD11B+CD45+ macrophages in PD-L1-/-, orthogonally verified with PD-L1 inhibitor BMS-1166 reduced macrophages to the same fold. Single-cell RNA sequencing further confirmed the 60% reduction of macrophages as well as the down-regulation of macrophage-defining transcription factors SPI1, KLF6, and MAFB. Further, PD-L1-/- macrophages reduced the level of inflammatory signals such as NF{kappa}B, TNF, and chemokines CXCL and CCL families. Whilst anti-inflammatory TGF-{beta} was upregulated. Finally, we identified that PD-L1-/- macrophages significantly down-regulated interferon-stimulated genes (ISGs) despite IFN{gamma} in differentiation media. Mechanistically, PD-L1-/- macrophages reduced IFNGR1 expression explaining that cells could not respond to IFN{gamma}. These data suggest that PD-L1 regulates inflammatory macrophage development by maintaining the IFN{gamma} signal.

immunology↗

Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane

Entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into host cells depends on refolding of the virus-encoded spike protein from a prefusion conformation, metastable after cleavage, to a lower energy, stable postfusion conformation. This transition overcomes kinetic barriers for fusion of viral and target cell membranes. We report here a cryo-EM structure of the intact postfusion spike in a lipid bilayer that represents single-membrane product of the fusion reaction. The structure provides structural definition of the functionally critical membraneinteracting segments, including the fusion peptide and transmembrane anchor. The internal fusion peptide forms a hairpin-like wedge that spans almost the entire lipid bilayer and the transmembrane segment wraps around the fusion peptide at the last stage of membrane fusion. These results advance our understanding of the spike protein in a membrane environment and may guide development of intervention strategies.

biochemistry↗

Transcriptional programs controlling lineages specification of mandibular epithelium during tooth initiation

Tooth development starts with formation of the dental lamina, a localized thickening of the maxillary and mandibular epithelium, at specific location of oral cavity. How this dental lamina is specified within the continuous naive maxillary and mandibular epithelium, remains as a critical and unresolved question. To identify potential genes and transcriptional regulatory networks that controlling dental lamina formation, we utilized single-cell Multiome-seq and Laser Microdissection coupled RNA-seq to profile gene expression and open chromatin of mandibular epithelium during tooth initiation. We comprehensively identified transcription factors (TFs) and signaling pathways that are differentially expressed among different domains (including dental lamina) along dorsal-ventral axis of mandibular epithelium. Specifically, we found Sox2 and Tfap2a/Tfap2b forming two complementary domains along the dorsal-ventral axis of mandibular epithelium. Furthermore, dental lamina specific or enriched TFs such as Pitx1, Pitx2 and Zfp536 are presented around the interface of Sox2 and Tfap2a/Tfap2b. We also identified correlation between signaling pathways and domain specific TFs. Through computational analysis of single-cell Multiome-seq dataset, we identified potential key/driver TFs and core transcriptional regulatory networks (TRNs) for lineages (oral, dental, skin) specification during tooth initiation. Our computational analysis also reveals a potential cross repression interactions between different groups of TFs (i.e. Pitx1/Pitx2 and Tfap2a/Tfap2b) that might be essential for dental lamina specification.

developmental biology↗

Early life sleep disruption has long lasting, sex specific effects on later development of sleep in prairie voles

In mammals, sleep duration is highest in the early postnatal period of life and is critical for shaping neural circuits that control the development of complex behaviors. The prairie vole is a wild, highly social rodent that serves as a unique model for the study of complex, species-typical social behaviors. Previous work in our laboratory has found that early life sleep disruption (ELSD) in prairie voles during a sensitive window of postnatal development leads to long lasting changes in social and cognitive behaviors as well as structural changes in excitatory and inhibitory neural circuits in the brain. However, it is currently unknown how later sleep is impacted by ELSD, both shortly after ELSD and over the long term. Therefore, the aim of this study was to describe the effects of ELSD on later life sleep, compared to sleep in normally developing prairie voles. First, we conducted tethered electroencephalogram/electromyogram (EEG/EMG) recordings in juvenile prairie voles undergoing ELSD, compared to Control conditions. Second, we conducted 24 hours of home cage tethered EEG/EMG recordings in either adolescent or adult male and female prairie voles that had previously undergone ELSD or Control conditions as juveniles. We found that, as adults, male ELSD prairie voles showed persistently lower REM sleep duration and female ELSD prairie voles showed persistently higher NREM sleep duration compared to Controls, but no other sleep parameters differed. We concluded that 1) persistent effects of ELSD on sleep into adulthood may contribute to the social and cognitive deficits observed in adult voles, and 2) sleep disruption early in life can influence later sleep patterns in adulthood.

neuroscience↗

Genetic and histological correlation between the musk gland and skin of Chinese forest musk deer

Chinese forest musk deer (FMD, Moschus berezovskii) glands have the ability to secrete musk, which plays an important role in attracting females during the breeding season. Sebaceous glands (SGs) are exocrine skin glands associated with hair follicles that continuously release a mixture of sebum, lipids and cellular debris, by holocrine secretion. Both the musk glands and the skin tissues of the FMD contain abundant sebaceous glands, and Sox9, Caveolin1, and Androgen receptor (AR) are all involved in the regulation of sebum secretion by the sebaceous glands. However, there are fewer studies on the correlation between skin and musk glands and the expression of Sox9, Caveolin1, and AR in the musk glands and skin tissue of FMD. To address this gap, we analyzed biochemical data from FMD skin tissues and musk glands using transcriptomic data, hematoxylin-eosin (HE) staining, western blotting (WB), immunohistochemistry (IHC), tissue dissection, and RT-qPCR. Anatomical results show that only adult male FMD had complete glandular part and sachets, while 4-month-old FMD do not have well-developed sachets. Transcriptomic data showed that 88.24% of genes were co-expressed in the skin and musk glands tissues of FMD. The WB, IHC, and RT-qPCR results showed that the genes involved in regulating sebum secretion, Sox9, Caveolin1, and AR were expressed in the skin tissues and musk glands. In summary, skin tissues and musk glands tissue have a strong correlation, and Sox9, Caveolin1, and AR may play important roles in skin tissues and musk glands tissue.

biochemistry↗

Kynurenic acid promotes A1 to A2 astrocyte conversion against HIV-associated neurocognitive disorder

Although extensive astrocyte activation is present in the CNS of patients suffering from HIV-associated neurocognitive disorder (HAND), little is known about the contribution of reactive astrocytes to HAND neuropathology. Here, we report that the imbalance between neurotoxic (A1 astrocytes) and protective astrocytes (A2 astrocytes) occurring in HIV-1 gp120 transgenic mice impedes the resolution of inflammation in the CNS, perpetuating neuron damage and cognitive deficits. Kynurenic acid (KYNA), a tryptophan metabolite with 7 nicotinic acetylcholine receptors (7nAChR) inhibitory property, blunts gp120-induced A1 astrocyte activation while promoting A2 astrocyte formation through blockade of 7nAChR/JAK2/STAT3 signaling activation. Meanwhile, we provide evidence that 7nAChR deletion and tryptophan administration convert astrocyte phenotypes, ultimately facilitating neuronal and cognitive improvement in the gp120tg mice. These initial and determinant findings mark a turning point in our understanding of the role of 7nAChR in gp120-mediated astrocyte activation, which opens new opportunities to control reactive astrocyte generation through KYNA and tryptophan administration as a pharmacological approach for treating HAND.

microbiology↗