Biology subjects

Lu, P.

Publications and source records attributed to Lu, P..

67 records · Page 4Linked to original sources

bioRxiv2020

Repopulating Kupffer Cells Originate Directly from Hematopoietic Stem Cells

Kupffer cells (KCs) originate from yolk sac progenitors before birth. Throughout adulthood, they self-maintain independently from the input of circulating monocytes (MOs) at stead state, and are replenished within 2 weeks after having been depleted, but the origin of repopulating KCs in adult remains unclear. The current paradigm dictates that repopulating KCs originate from preexisting KCs or monocytes, but there remains a lack of fate-mapping evidence. In current study, we firstly traced the fate of preexisting KCs and that of monocytic cells with tissue-resident macrophage-specific and monocytic cell-specific fate mapping mouse models, respectively, and found no evidences that repopulating KCs originate from preexisting KCs or MOs. Secondly, we performed genetic lineage tracing to determine the type of progenitor cells involved in response to KC depletion in mice, and found that in response to KC depletion, hematopoietic stem cells (HSCs) proliferated in the bone marrow, mobilized into the blood, adoptively transferred into the liver and differentiated into KCs. Finally, we traced the fate of HSCs in a HSC-specific fate-mapping mouse model, in context of chronic liver inflammation induced by repeated carbon tetrachloride treatment, and confirmed that repopulating KCs originated directly from HSCs. Taken together, these findings provided strong in vivo fate-mapping evidences that repopulating KCs originate directly from Hematopoietic stem cells not from preexisting KCs or from MOs. SignificanceThere is a standing controversy in the field regarding the cellular origin of repopulating macrophages. This paper provides strong in vivo fate-mapping evidences that repopulating KCs originate directly from hematopoietic stem cells not from preexisting KCs or from MOs, which presenting a completely novel understanding of the cellular origin of repopulating Kupffer Cells and shedding light on the divergent roles of KCs in liver homeostasis and diseases.

cell biology↗

bioRxiv2020

Neuroinvasive potential of SARS-CoV-2 revealed in a human brain organoid model

Although COVID-19 is considered to be primarily a respiratory disease, SARS-CoV-2 affects multiple organ systems including the central nervous system (CNS). Yet, there is no consensus whether the virus can infect the brain, or what the consequences of CNS infection are. Here, we used three independent approaches to probe the capacity of SARS-CoV-2 to infect the brain. First, using human brain organoids, we observed clear evidence of infection with accompanying metabolic changes in the infected and neighboring neurons. However, no evidence for the type I interferon responses was detected. We demonstrate that neuronal infection can be prevented either by blocking ACE2 with antibodies or by administering cerebrospinal fluid from a COVID-19 patient. Second, using mice overexpressing human ACE2, we demonstrate in vivo that SARS-CoV-2 neuroinvasion, but not respiratory infection, is associated with mortality. Finally, in brain autopsy from patients who died of COVID-19, we detect SARS-CoV-2 in the cortical neurons, and note pathologic features associated with infection with minimal immune cell infiltrates. These results provide evidence for the neuroinvasive capacity of SARS-CoV2, and an unexpected consequence of direct infection of neurons by SARS-CoV-2.

microbiology↗

bioRxiv2020

Detection of SARS-CoV-2 RNA by multiplex RT-qPCR

The current RT-qPCR assay recommended for SARS-CoV-2 testing in the United States requires analysis of three genomic targets per sample: two viral and one host. To simplify testing and reduce the volume of required reagents, we developed a multiplex RT-qPCR assay to detect SARS-CoV-2 in a single reaction. We used existing N1, N2, and RP primer and probe sets by the CDC, but substituted fluorophores to allow multiplexing of the assay. The cycle threshold (Ct) values of our multiplex RT-qPCR were comparable to those obtained by the singleplex assay adapted for research purposes. Low copies (>500 copies / reaction) of SARS-CoV-2 RNA were consistently detected by the multiplex RT-qPCR. Our novel multiplex RT-qPCR improves upon current singleplex diagnostics by saving reagents, costs, time and labor.

microbiology↗

bioRxiv2020

A Mathematical Model to Simulate Intracranial Pressure and Unified Interpretation of Several Disease Entities

BACKGROUNDMany clinical phenomena related to cerebrospinal fluid(CSF) and intracranial pressure (ICP) are often contrary to common sense and difficult to explain by classical theory. Such as slit ventricle syndrome, normal intracranial pressure hydrocephalus / low pressure hydrocephalus, paradoxical herniation, and so on. Many authors have different theories about them but cant have an unified explanation. OBJECTIVEWe try to simulate the above CSF disorders and ICP conduction with a mathematical method, and make theoretical interpretations to them. METHODSWe introduced a mathematical model based on several well-accepted hypothesesto simulate human CSF physiology and propose that ICP curve should be an U-shaped curve (especially, we introduce the hypothesis that CSF also play a role of decompression). Maple software was used to draw charts according to our formula. We use the theory and intuitive charts to explain those illnesses one by one. RESULTSThe formula: ICP = {middle dot} MAP - {delta} {middle dot} V {middle dot} {middle dot} MAP + {theta} {middle dot} V{beta} {middle dot} {middle dot} MAP + C, and corresponding diagrams was conducted. CONCLUSIONThis mathematical model is a supplement to the classical Monro-Kellies theory, the curve and coordinate system can be used to analyze different pathophysiological states and give a reasonable unified explanation to them.

neuroscience↗

bioRxiv2020

Mouse model of SARS-CoV-2 reveals inflammatory role of type I interferon signaling

Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-Cov-2) has caused over 5,000,000 cases of Coronavirus disease (COVID-19) with significant fatality rate.1-3 Due to the urgency of this global pandemic, numerous therapeutic and vaccine trials have begun without customary safety and efficacy studies.4 Laboratory mice have been the stalwart of these types of studies; however, they do not support infection by SARS-CoV-2 due to the inability of its spike (S) protein to engage the mouse ortholog of its human entry receptor angiotensin-converting enzyme 2 (hACE2). While hACE2 transgenic mice support infection and pathogenesis,5 these mice are currently limited in availability and are restricted to a single genetic background. Here we report the development of a mouse model of SARS-CoV-2 based on adeno associated virus (AAV)-mediated expression of hACE2. These mice support viral replication and antibody production and exhibit pathologic findings found in COVID-19 patients as well as non-human primate models. Moreover, we show that type I interferons are unable to control SARS-CoV2 replication and drive pathologic responses. Thus, the hACE2-AAV mouse model enables rapid deployment for in-depth analysis following robust SARS-CoV-2 infection with authentic patient-derived virus in mice of diverse genetic backgrounds. This represents a much-needed platform for rapidly testing prophylactic and therapeutic strategies to combat COVID-19.

immunology↗

bioRxiv2019

PD-1 expression during acute infection is repressed through 1 a LSD1- Blimp-1 axis

During prolonged exposure to antigens, such as chronic viral infections, sustained T cell receptor (TCR) signaling can result in T cell exhaustion mediated in part by expression of Programmed cell death-1 (PD-1) encoded by the Pdcd1 gene. Here, dynamic changes in histone H3K4 modifications at the Pdcd1 locus during ex vivo and in vivo activation of CD8 T cells, suggested a potential role for the histone H3 lysine 4 demethylase LSD1 in regulating PD-1 expression. CD8 T cells lacking LSD1 expressed higher levels of Pdcd1 mRNA following ex vivo stimulation, as well as increased surface levels of PD-1 during acute but not chronic infection with lymphocytic choriomeningitis virus (LCMV). Blimp-1, a known repressor of PD-1, recruited LSD1 to the Pdcd1 gene during acute but not chronic LCMV infection. Loss of DNA methylation at Pdcd1s promoter proximal regulatory regions is highly correlated with its expression. However, following acute LCMV infection where PD-1 expression levels return to near base line, LSD1-deficient CD8 T cells failed to remethylate the Pdcd1 locus to the levels of wild-type cells. Finally, in a murine melanoma model, the frequency of PD-1 expressing tumor infiltrating LSD1-deficient CD8 T cells was greater than wild-type. Thus, LSD1 is recruited to the Pdcd1 locus by Blimp-1, downregulates PD-1 expression by facilitating the removal of activating histone marks, and is important for remethylation of the locus. Together, these data provide insight into the complex regulatory mechanisms governing T cell immunity and the regulation of a critical T cell checkpoint gene.\n\nKey PointsO_LILSD1 suppress PD-1 expression following acute infection or transient induction.\nC_LIO_LIBlimp-1 binding to the Pdcd1 locus is required to recruit LSD1.\nC_LIO_LILSD1 is required to fully remethylate the PD-1 proximal promoter region.\nC_LI

immunology↗

bioRxiv2019

Leptin deficient rats develop nonalcoholic steatohepatitis with unique disease progression

Nonalcoholic steatohepatitis (NASH) is an aggressive liver disease threatening public health, however its natural history is poorly understood. Unlike ob/ob mice, Lep{triangleup}I14/{triangleup}I14 rats develop unique NASH phenotype with steatosis, lymphocyte infiltration and ballooning after postnatal week 16. Using Lep{triangleup}I14/{triangleup}I14 rats as NASH model, we studied the natural history of NASH progression by performing an integrated analysis of hepatic transcriptome from postnatal week 4 to 48. Leptin deficiency results in a robust increase in expression of genes encoding 9 rate-limiting enzymes in lipid metabolism such as ACC and FASN. However, genes in positive regulation of inflammatory response are highly expressed at week 16 and then remain the steady elevated expression till week 48. The high expression of cytokines and chemokines including CCL2, TNF, IL6 and IL1{beta} is correlated with the phosphorylation of several key molecules in pathways such as JNK and NF-{kappa}B. Meanwhile, we observed cell infiltration of MPO+ neutrophils, CD8+ T cells, CD68+ hepatic macrophages and CCR2+ inflammatory monocyte-derived macrophages, together with macrophage polarization from M2 to M1. Importantly, Lep{triangleup}I14/{triangleup}I14 rats share more homologous genes with NASH patients than previously established mouse models and crab eating monkeys with spontaneous hepatic steatosis. Transcriptomic analysis showed that many drug targets in clinical trials can be evaluated in Lep{triangleup}I14/{triangleup}I14 rats.\n\nConclusionWe characterize Lep{triangleup}I14/{triangleup}I14 rats as a unique NASH model by performing a long-term (i.e., 4 to 48 postnatal weeks) integrated transcriptomic analysis. This work reveal the temporal dynamics of hepatic gene expression in lipid metabolism and inflammation, and shed light on understanding the natural history of NASH in human beings.

pathology↗

bioRxiv2019

Single-Cell RNA Sequencing Reveals Regulatory Mechanism for Trophoblast Cell-Fate Divergence in Human Peri-Implantation Embryo

Multipotent trophoblasts undergo dynamic morphological movement and cellular differentiation after embryonic implantation to generate placenta. However, the mechanism controlling trophoblast development and differentiation during peri-implantation development remains elusive. In this study, we modeled human embryo peri-implantation development from blastocyst to early post-implantation stages by using an in vitro coculture system, and profiled the transcriptome of individual trophoblast cells from these embryos. We revealed the genetic networks regulating peri-implantation trophoblast development. While determining when trophoblast differentiation happens, our bioinformatic analysis identified T-box transcription factor 3 (TBX3) as a key regulator for the differentiation of cytotrophoblast into syncytiotrophoblast. The function of TBX3 in trophoblast differentiation is then validated by a loss-of-function experiment. In conclusion, our results provided a valuable resource to study the regulation of trophoblasts development and differentiation during human peri-implantation development.

cell biology↗

bioRxiv2018

Spatiotemporal Gene Coexpression and Regulation in Mouse Cardiomyocytes of Early Cardiac Morphogenesis

Cardiac looping is an early morphogenic process critical for the formation of four-chambered mammalian hearts. To study the roles of signaling pathways, transcription factors (TFs) and genetic networks in the process, we constructed gene co-expression networks and identified gene modules highly activated in individual cardiomyocytes (CMs) at multiple anatomical regions and developmental stages. Function analyses of the module genes uncovered major pathways important for spatiotemporal CM differentiation. Interestingly, about half of the pathways were highly active in cardiomyocytes at outflow tract (OFT) and atrioventricular canal (AVC), including many well-known signaling pathways for cardiac development and several newly identified ones. Most of the OFT-AVC pathways were predicted to be regulated by 6 6 transcription factors (TFs) actively expressed at the OFT-AVC locations, with the prediction supported by motif enrichment analysis of the TF targets, including 10 TFs that have not been previously associated with cardiac development, e.g., Etv5, Rbpms, and Baz2b. Finally, our study showed that the OFT-AVC TF targets were significantly enriched with genes associated with mouse heart developmental abnormalities and human congenital heart defects.

genetics↗

bioRxiv2018

Reproducible evaluation of classification methods in Alzheimer’s disease: framework and application to MRI and PET data

A large number of papers have introduced novel machine learning and feature extraction methods for automatic classification of Alzheimers disease (AD). However, while the vast majority of these works use the public dataset ADNI for evaluation, they are difficult to reproduce because different key components of the validation are often not readily available. These components include selected participants and input data, image preprocessing and cross-validation procedures. The performance of the different approaches is also difficult to compare objectively. In particular, it is often difficult to assess which part of the method (e.g. preprocessing, feature extraction or classification algorithms) provides a real improvement, if any. In the present paper, we propose a framework for reproducible and objective classification experiments in AD using three publicly available datasets (ADNI, AIBL and OASIS). The framework comprises: i) automatic conversion of the three datasets into a standard format (BIDS); ii) a modular set of preprocessing pipelines, feature extraction and classification methods, together with an evaluation framework, that provide a baseline for benchmarking the different components. We demonstrate the use of the framework for a large-scale evaluation on 1960 participants using T1 MRI and FDG PET data. In this evaluation, we assess the influence of different modalities, preprocessing, feature types (regional or voxel-based features), classifiers, training set sizes and datasets. Performances were in line with the state-of-the-art. FDG PET outperformed T1 MRI for all classification tasks. No difference in performance was found for the use of different atlases, image smoothing, partial volume correction of FDG PET images, or feature type. Linear SVM and L2-logistic regression resulted in similar performance and both outperformed random forests. The classification performance increased along with the number of subjects used for training. Classifiers trained on ADNI generalized well to AIBL and OASIS, performing better than the classifiers trained and tested on each of these datasets independently. All the code of the framework and the experiments is publicly available.

neuroscience↗

bioRxiv2018

Latent-Based Imputation of Laboratory Measures from Electronic Health Records: Case for Complex Diseases

Imputation is a key step in Electronic Health Records-mining as it can significantly affect the conclusions derived from the downstream analysis. There are three main categories that explain the missingness in clinical settings-incompleteness, inconsistency, and inaccuracy-and these can capture a variety of situations: the patient did not seek treatment, the health care provider did not enter the information, etc. We used EHR data from patients diagnosed with Inflammatory Bowel Disease from Geisinger Health System to design a novel imputation that focuses on a complex phenotype. Our approach is based on latent-based analysis integrated with clustering to group patients based on their comorbidities before imputation. IBD is a chronic illness of unclear etiology and without a complete cure. We have taken advantage of the complexity of IBD to pre-process the EHR data of 10,498 IBD patients and show that imputation can be improved using shared latent comorbidities. The R code and sample simulated input data will be available at a future time.

bioinformatics↗

bioRxiv2017

Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ

RNA sequencing (RNA-seq) is a sensitive and accurate method for quantifying gene expression. Small samples or those whose RNA is degraded, such as formalin-fixed, paraffin-embedded (FFPE) tissue, remain challenging to study with nonspecialized RNA-seq protocols. Here we present a new method, Smart-3SEQ, that accurately quantifies transcript abundance even with small amounts of total RNA and effectively characterizes small samples extracted by laser-capture microdissection (LCM) from FFPE tissue. We also obtain distinct biological profiles from FFPE single cells, which have been impossible to study with previous RNA-seq protocols, and we use these data to identify possible new macrophage phenotypes associated with the tumor microenvironment. We propose Smart-3SEQ as a highly cost-effective method to enable large gene-expression profiling experiments unconstrained by sample size and tissue availability. In particular, Smart-3SEQs compatibility with FFPE tissue unlocks an enormous number of archived clinical samples, and combined with LCM it allows unprecedented studies of small cell populations and single cells isolated by their in situ context.

genomics↗

bioRxiv2017

Molecular Mapping Of YrTZ2, A Stripe Rust Resistance Gene In Wild Emmer Accession TZ-2 And Its Comparative Analyses With Aegilops tauschii

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating disease that can cause severe yield losses. Identification and utilization of stripe rust resistance genes are essential for effective breeding against the disease. Wild emmer accession TZ-2, originally collected from Mount Hermon, Israel, confers near-immunity resistance against several prevailing Pst races in China. A set of 200 F6:7 recombinant inbred lines (RILs) derived from a cross between susceptible durum wheat cultivar Langdon and TZ-2 was used for stripe rust evaluation. Genetic analysis indicated that the stripe rust resistance of TZ-2 to Pst race CYR34 was controlled by a single dominant gene, temporarily designated YrTZ2. Through bulked segregant analysis (BSA) and SSR mapping, YrTZ2 was located on chromosome arm 1BS and flanked by SSR markers Xwmc230 and Xgwm413 with genetic distance of 0.8 cM (distal) and 0.3 cM (proximal), respectively. By applying wheat 90K iSelect SNP genotyping assay, 11 polymorphic loci (consist of 250 SNP markers) closely linked with YrTZ2 were identified. YrTZ2 was further delimited into a 0.8 cM genetic interval between SNP marker IWB19368 and SSR marker Xgwm413, and co-segregated with SNP marker IWB28744 (attached with 28 SNP markers). Comparative genomics analyses revealed high level of collinearity between the YrTZ2 genomic region and the orthologous region of Aegilops tauschii 1DS. The genomic region between loci IWB19368 and IWB31649 harboring YrTZ2 is orthologous to a 24.5 Mb genomic region between AT1D0112 and AT1D0150, spanning 15 contigs on chromosome 1DS. The genetic and comparative maps of YrTZ2 provide framework for map-based cloning and marker-assisted selection (MAS) of YrTZ2.

plant biology↗