Biology subjects

Pang, Z.

Publications and source records attributed to Pang, Z..

26 records · Page 2Linked to original sources

bioRxiv2020

Developing Human Pluripotent Stem Cell-Based Cerebral Organoids with a Controllable Microglia Ratio for Modeling Brain Development and Pathology

Microglia, as brain-resident macrophages, play critical roles in brain development, homeostasis, and disease. Microglia in animal models cannot accurately model the properties of human microglia due to notable transcriptomic and functional differences between human and other animal microglia. Efficient generation of microglia from human pluripotent stem cells (hPSCs) provides unprecedented opportunities to study the function and behavior of human microglia. Particularly, incorporating hPSCs-derived microglia into brain organoids facilitates their development in a 3-dimensional context, mimicking the brain environment. However, an optimized method that integrates an appropriate amount of microglia into brain organoids at a proper time point, resembling in vivo brain development, is still lacking. Here, we report the development of a new brain region-specific, microglia-containing organoid model by co-culturing hPSCs-derived primitive neural progenitor cells (pNPCs) and primitive macrophage progenitors (PMPs). In these organoids, hPSCs-derived pNPCs and PMPs interact with each other and develop into functional neurons, astroglia, and microglia, respectively. Importantly, the numbers of human microglia in the organoids can be controlled, resulting in a cell type ratio similar to that seen in the human brain. Using super-resolution microscopy, we demonstrate that these human microglia are able to phagocytize neural progenitor cells (NPCs) and apoptotic cells, as well as to prune synapses at different developmental stages of the organoids. Furthermore, these human microglia respond to Zika virus infection of the organoids, as indicated by amoeboid-like morphology, increased expression of gene transcripts encoding inflammatory cytokines, and excessive pruning of synaptic materials. Together, our findings establish a new microglia-containing brain organoid model that will serve to study human microglial function in a variety of neurological disorders.

neuroscience↗

bioRxiv2020

Turning the stimulus on and off dynamically changes the direction of alpha travelling waves

Traveling waves have been studied to characterize the complex spatiotemporal dynamics of the brain. Several studies have suggested that the propagation direction of alpha traveling waves can be task-dependent. For example, a recent EEG study from our group found that forward waves (i.e. occipital to frontal, FW waves) were observed during visual processing, whereas backward waves (i.e. frontal to occipital, BW waves) mostly occurred in the absence of sensory input. These EEG recordings, however, were obtained from different experimental sessions and different groups of subjects. To further examine how the waves direction changes between task conditions, 13 participants were tested on a target detection task while EEG signals were recorded simultaneously. We alternated visual stimulation (5 s display of visual luminance sequences) and resting state (5 s of black screen) within each single trial, allowing us to monitor the moment-to-moment progression of traveling waves. As expected, the direction of alpha waves was closely linked with task conditions. First, FW waves from occipital to frontal regions, absent during rest, emerged as a result of visual processing, while BW waves in the opposite direction dominated in the absence of visual inputs, and were reduced (but not eliminated) by external visual inputs. Second, during visual stimulation (but not rest), both waves coexisted on average, but were negatively correlated. In summary, we conclude that the functional role of alpha traveling waves is closely related with their propagating direction, with stimulus-evoked FW waves supporting visual processing and spontaneous BW waves involved more in top-down control.

neuroscience↗

bioRxiv2020

Citrus vascular proteomics highlights the role of peroxidases and serine proteases during Huanglongbing disease progression

Huanglongbing (HLB) is the most devastating and widespread citrus disease. All commercial citrus varieties are susceptible to the HLB-associated bacterium, Candidatus Liberibacter asiaticus (CLas), which resides in the phloem. The phloem is part of the plant vascular system and is involved in sugar transport. To investigate the plant response to CLas, we enriched for proteins surrounding the phloem in an HLB susceptible sweet orange variety, Washington navel (Citrus sinensis (L) Osbeck). Quantitative proteomics revealed global changes in the citrus proteome after CLas inoculation. Plant metabolism and translation were suppressed, while defense-related proteins such as peroxidases, proteases and protease inhibitors were induced in the vasculature. Transcript accumulation and enzymatic activity of plant peroxidases in CLas infected sweet orange varieties under greenhouse and field conditions were assessed. While peroxidase transcript accumulation was induced in CLas infected sweet orange varieties, peroxidase enzymatic activity varied. Specific serine proteases were upregulated in Washington navel in the presence of CLas based on quantitative proteomics. Subsequent activity-based protein profiling revealed increased activity of two serine proteases, and reduced activity of one protease in two C. sinensis sweet orange varieties under greenhouse and field conditions. The observations in the current study highlight global reprogramming of the citrus vascular proteome and differential regulation of enzyme classes in response to CLas infection. These results open an avenue for further investigation of diverse responses to HLB across different environmental conditions and citrus genotypes.

plant biology↗

bioRxiv2019

Allele-specific open chromatin in human iPSC neurons elucidates functional non-coding disease variants

Functional interpretation of noncoding disease variants, which likely regulate gene expression, has been challenging. Chromatin accessibility strongly influences gene expression during neurodevelopment; however, to what extent genetic variants can alter chromatin accessibility in the context of brain disorders/traits is unknown. Using human induced pluripotent stem cell (iPSC)-derived neurons as a neurodevelopmental model, we identified abundant open-chromatin regions absent in adult brain samples and thousands of genetic variants exhibiting allele-specific open-chromatin (ASoC). ASoC variants are overrepresented in brain enhancers, transcription-factor-binding sites, and quantitative-trait-loci associated with gene expression, histone modification, and DNA methylation. Notably, compared to open chromatin regions and other commonly used functional annotations, neuronal ASoC variants showed much stronger enrichments of risk variants for various brain disorders/traits. Our study provides the first snapshot of the neuronal ASoC landscape and a powerful framework for prioritizing functional disease variants.\n\nOne Sentence SummaryAllele-specific open chromatin informs functional disease variants

genetics↗

bioRxiv2019

Extraordinary diversity of HLA class I gene expression in single cells contribute to the plasticity and adaptability of human immune system

HLA, the coding genes of human major histocompatibility (MHC) proteins, play a crucial role in the human adaptive immune system by presenting antigenic peptides to T cell receptors on T cells. HLA-A, HLA-B and HLA-C, these 3 Class I HLA genes are one of the most polymorphic loci in the human genome. For decades, HLA typing has been performed prior to tissue and stem cell transplantation. However, beyond the role in tissue matching, HLA has also been implicated in a wide array of autoimmune diseases and HLA genotypes and expression levels are closely associated with cancer patients prognosis as recent studies have revealed. Recently methods have been developed to perform HLA typing and HLA expression quantification together by using RNA-seq techniques. However, these bulk RNA-seq experiments are measuring an averaged signal of cell populations. Single-cell RNA-seq (scRNA-seq) has regained its popularity due to its power to reliably resolve single RNA transcriptomes at large scales. In our present study, we did HLA typing using three independent scRNA-seq datasets. Interestingly, we found that single cells from the same donor could be classified into different groups where each group has a distinct expressed HLA genotype (e.g., HLA-A, heterozygous or homozygous); in other words, HLA class I genes show abundant allele specific expression in single cells. This phenomenon has been repeatedly observed in a total of 14 donors from 3 independent datasets (one is breast epithelium, another two are multiple myeloma). Our systematic analysis of HLA class I gene expression using multiple scRNA-seq datasets has uncovered a putative mechanism, where by fine tuning HLA class I expressions both at the quantity and allele levels, our immune system is able to handle various internal challenges through single cells equipped with extraordinary diverse HLA expression patterns.

immunology↗

bioRxiv2019

Corticotropin-Releasing Hormone Signaling in the Oval Bed Nucleus of the Stria Terminalis Mediates Chronic Stress-Induced Negative Valence Behaviors Associated with Anxiety

The bed nucleus of stria terminalis (BNST) is a forebrain region highly sensitive to stress that expresses corticotropin-releasing hormone (CRH) neuropeptide at high levels and regulates negative valence behaviors associated with anxiety. However, how chronic stress modulates CRH signaling and neuronal activity in BNST remains unknown. We subjected C57BL6/J mice to a 6-week chronic variable mild stress (CVMS) paradigm and investigated the effects on behavior, BNST cellular neurophysiology, and BNST CRH signaling. We also utilized pharmacological infusions and optogenetics to decipher and mimic the effects of CVMS on BNST cellular neurophysiology and behavior. CVMS elevated plasma corticosterone levels, induced negative valence behaviors associated with anxiety, diminished M-currents (voltage-gated K+ currents that stabilize membrane potential and regulate neuronal excitability), and increased mEPSC amplitude in ovBNST. Additionally, the number of c-fos+, CRH+, and CRH activator pituitary adenylate cyclase-activating polypeptide (PACAP)+ cells were increased while CRH inhibitor striatal-enriched protein tyrosine phosphatase (STEP)+ cells were decreased in ovBNST. These expression data were confirmed with qPCR. CVMS also activated PKA in BNST and the electrophysiological and behavioral effects of CVMS were reversed by ovBNST infusion of the PKA-selective antagonist H89. Moreover, optogenetic activation of ovBNST directly induced negative valence behaviors associated with anxiety, mimicking the effects of CVMS. CVMS mediates effects on negative valence behaviors associated with anxiety by activating CRH signaling components and cellular excitability in ovBNST Our findings decipher an important CRH-associated stress molecular signature in BNST and advance our understanding of the neural circuitry underlying stress-induced disorders.

neuroscience↗

bioRxiv2018

Reversing Abnormal Neural Development by Inhibiting OLIG2 in Down Syndrome Human iPSC Brain Organoids and Neuronal Mouse Chimeras

Down syndrome (DS) is a common neurodevelopmental disorder, and cognitive defects in DS patients may arise form imbalances in excitatory and inhibitory neurotransmission. Understanding the mechanisms underlying such imbalances may provide opportunities for therapeutic intervention. Here, we show that human induced pluripotent stem cells (hiPSCs) derived from DS patients overproduce OLIG2+ ventral forebrain neural progenitors. As a result, DS hiPSC-derived cerebral organoids excessively produce specific subclasses of GABAergic interneurons and cause impaired recognition memory in neuronal chimeric mice. Increased OLIG2 expression in DS cells directly upregulates interneuron lineage-determining transcription factors. shRNA-mediated knockdown of OLIG2 largely reverses abnormal gene expression in early-stage DS neural progenitors, reduces interneuron production in DS organoids and chimeric mouse brains, and improves behavioral deficits in DS chimeric mice. Thus, altered OLIG2 expression may underlie neurodevelopmental abnormalities and cognitive defects in DS patients.

neuroscience↗

bioRxiv2018

Addiction associated N40D mu-opioid receptor variant modulates synaptic function in human neurons

BackgroundThe OPRM1 A118G gene variant (N40D) encoding the {micro}-opioid receptor (MOR) has been associated with dependence on opiates and other abused drugs but its mechanism is unknown. With opioid abuse-related deaths rising at unprecedented rates, understanding these mechanisms may provide a path to therapy.\n\nMethodsSeven human induced pluripotent stem (iPS) cell lines from homozygous N40D subjects (4 with N40 and 3 with D40 variants) were generated and human induced neuronal cells (iNs) were derived from these iPS cell lines. Morphological, gene expression as well as synaptic physiology analyses were conducted in human iN cells carrying N40D MOR variants; Two pairs of isogenic pluripotent stem cells carrying N40D were generated using CRISPR/Cas9 genome-editing and iN cells derived from them were analyzed.\n\nResultsInhibitory human neurons generated from subjects carrying N40D MOR gene variants show mature properties in morphological and functional analyses. Gene expression revealed that they express mature neuronal marker and MORs. Activation of MORs suppressed inhibitory synaptic transmission in human neurons carrying both N40 or D40 MOR variants but D40 show stronger effects. To mitigate the confounding effects of background genetic variation on neuronal function, the regulatory effects of MORs on synaptic transmission were validated in two sets of independently generated isogenic N40D iNs.\n\nConclusionsActivations of N40D MOR variants show different regulatory effects on synaptic transmission in inhibitory human neurons. This study identifies neurophysiological differences between human MOR variants that may predict altered opioid responsivity and/or dependence in this subset of individuals.

neuroscience↗