Biology subjects

Lu, L.

Publications and source records attributed to Lu, L..

At least 181 records · Page 10Linked to original sources

bioRxiv2020

The Molecular Landscape of the Aging Mouse Liver

Systems biology approaches often use inferred networks of gene expression and metabolite data to identify regulatory factors and pathways connected with phenotypic variance. Generally, study-specific multi-layer "Omics" datasets are used to contextualize generic molecular networks. In this regard separating upstream causal mechanisms, downstream biomarkers, and incidental correlations remains a significant challenge, yet it is essential for designing mechanistic experiments. To address this, we designed a study following a population of 2157 individuals from 89 isogenic BXD mouse strains across their lifespan to identify molecular interactions among genotype, environment, age (GxExA) and metabolic fitness. Each strain was separated into two cohorts, one fed low fat (6% cal/fat) and the other high fat (60% cal/fat) diets. Tissues were collected for 662 individuals (309 cohorts) diverging across age (7, 12, 18, and 24 months), diet, sex, and strain. Transcriptome, proteome, and metabolome data were generated for liver. Of these we identified linear relations among these molecular data with lifespan for the same genomes of mice (Roy et al. 2020), and we defined [~]1100 novel protein-coding genes associated with longevity. We knocked down the ortholog of Ctsd in C. elegans. The treatment reduced longevity both in wildtype and in mutant long-lived strains, thus validating the prediction. Next, to assess the molecular impact of GxExA on gene expression, the multi-omics data was parsed into metabolic networks where connectivity varied due to the independent variables. Differences in edge strengths connecting nodes in these molecular networks according to each variable enabled causal inference by using stability selection, with roughly 21% of novel gene-pathway connections being causally affected by diet and/or age. For instance, Chchd2 is activated by aging and drives changes in the proteasome, oxidative phosphorylation, and mitochondrial translation transcriptional networks. Together, we have developed a large multi-omics resource for studying aging in the liver, and a resource for turning standard associations into causal networks.

systems biology↗

bioRxiv2020

Genetic signatures for lineage/sublineage classification of HPV16, 18, 52 and 58 variants

Increasing evidences indicate that high-risk HPV variants are heterogeneous in carcinogenicity and ethnic dispersion. In this work, we identified genetic signatures for convenient determination of lineage/sublineage of HPV16, 18, 52 and 58 variants. Using publicly available genomes, we found that E2 of HPV16, L2 of HPV18, L1 and LCR of HPV52, and L2, LCR and E1 of HPV58 contain the proper genetic signature for lineage/sublineage classification. Sets of hierarchical signature nucleotide positions (SNPs) were further confirmed for high accuracy (>98%) by classifying HPV genomes obtained from Chinese females, which included 117 HPV16 variants, 48 HPV18 variants 117 HPV52 variants and 89 HPV58 variants. The circulation of HPV variants posing higher cancer risk in Eastern China, such as HPV16 A4 and HPV58 A3, calls for continuous surveillance in this region. The marker genes and signature nucleotide positions may facilitate cost-effective diagnostic detections of HPV variants in clinical settings.

evolutionary biology↗

bioRxiv2020

Spritz: A Proteogenomic Database Engine

Proteoforms are the workhorses of the cell, and subtle differences between their amino acid sequence or post-translational modifications (PTMs) can change their biological function. To most effectively identify and quantify proteoforms in genetically diverse samples by mass spectrometry (MS), it is advantageous to search the MS data against a sample-specific protein database that is tailored to the sample being analyzed, in that it contains the correct amino acid sequences and relevant PTMs for that sample. To this end, we have developed Spritz (https://smith-chem-wisc.github.io/Spritz/), an open-source software tool for generating protein databases annotated with sequence variations and PTMs. We provide a simple graphical user interface (GUI) for Windows and scripts that can be run on any operating system. Spritz automatically sets up and executes approximately 20 tools, which enable construction of a proteogenomic database from only raw RNA sequencing data. Sequence variations that are discovered in RNA sequencing data upon comparison to the Ensembl reference genome are annotated on proteins in these databases, and PTM annotations are transferred from UniProt. Modifications can also be discovered and added to the database using bottom-up mass spectrometry data and global PTM discovery in MetaMorpheus. We demonstrate that such sample-specific databases allow the identification of variant peptides, modified variant peptides, and variant proteoforms by searching bottom-up and top-down proteomic data from the Jurkat human T lymphocyte cell line and demonstrate the identification of phosphorylated variant sites with phosphoproteomic data from the U2OS human osteosarcoma cell line.

bioinformatics↗

bioRxiv2020

How to quantitatively measure, assess and correct the fluorescence crosstalk in the wide-field microscopy

During the multi-color fluorescence imaging, a fluorophore can be detected in the non-corresponding channel due to the broad spectra of the fluorophore and filters, resulting in the artefact called the crosstalk (crossover or bleed-through). Unfortunately, the fluorescence crosstalk is ubiquitous for the conventional fluorescence microscopy. Significant crosstalk can distort the image and lead to incorrect interpretation. Here, we introduce a simple quantitative metric, the crosstalk factor, to measure the crosstalk effect of a fluorophore on a channel in the wide-field fluorescence microscopy. We describe a cell biologist friendly protocol which should be easily implemented by cell biologists using commonly available image processing software such as ImageJ.

biophysics↗

bioRxiv2020

O-Pair Search with MetaMorpheus for O-glycopeptide Characterization

We report O-Pair Search, a new approach to identify O-glycopeptides and localize O-glycosites. Using paired collision- and electron-based dissociation spectra, O-Pair Search identifies O-glycopeptides using an ion-indexed open modification search and localizes O-glycosites using graph theory and probability-based localization. O-Pair Search reduces search times more than 2,000-fold compared to current O-glycopeptide processing software, while defining O-glycosite localization confidence levels and generating more O-glycopeptide identifications. O-Pair Search is freely available: https://github.com/smith-chem-wisc/MetaMorpheus.

bioinformatics↗

bioRxiv2020

Glycans function as a Golgi export signal to promote the constitutive exocytic trafficking

Most proteins in the secretory pathway are glycosylated. However, the role of glycans in the membrane trafficking is still unclear. Here, we discovered that transmembrane secretory cargos, such as interleukin 2 receptor subunit or Tac, transferrin receptor and cluster of differentiation 8a, unexpectedly displayed substantial Golgi localization when their O-glycosylation was compromised. By quantitatively measuring their Golgi residence times, we found that the apparent Golgi localization of these O-glycan deficient cargos is due to their slow Golgi export. The super-resolution microscopy method that we previously developed revealed that O-glycan deficient Tac chimeras localize at the interior of the trans-Golgi cisternae. The O-glycan was observed to be both necessary and sufficient for the efficient Golgi export of Tac chimeras. By sequentially introducing O-glycosylation sites to {beta}-galactoside -2,6-sialyltransferase1, we demonstrated that the O-glycans effect on the Golgi export is probably additive. Finally, the finding that N-glycosylated GFP substantially reduces the Golgi residence time of Tac chimera suggests that the N-glycan might have a similar effect. Therefore, both O- and N-glycan might function as a generic Golgi export signal at the trans-Golgi to promote the constitutive exocytic trafficking.

cell biology↗

bioRxiv2020

Single-cell RNA-sequencing of peripheral neuroblastic tumors reveals an aggressive transitional cell state at the junction of an adrenergic-mesenchymal transdifferentiation trajectory

Peripheral neuroblastic tumors (PNTs) are the most common extracranial solid tumors in early childhood. They represent a spectrum of neural crest derived tumors including neuroblastoma, ganglioneuroblastoma and ganglioneuroma. PNTs exhibit heterogeneity due to interconverting malignant cell states described as adrenergic/nor-adrenergic or mesenchymal/neural crest cell in origin. The factors determining individual patient levels of tumor heterogeneity, their impact on the malignant phenotype, and the presence of other cell states are unknown. Here, single-cell RNA-sequencing analysis of 4267 cells from 7 PNTs demonstrated extensive transcriptomic heterogeneity. Trajectory modelling showed that malignant neuroblasts move between adrenergic and mesenchymal cell states via a novel state that we termed a "transitional" phenotype. Transitional cells are characterized by gene expression programs linked to a sympathoadrenal development, and aggressive tumor phenotypes such as rapid proliferation and tumor dissemination. Among primary bulk tumor patient cohorts, high expression of the transitional gene signature was highly predictive of poor prognosis when compared to adrenergic and mesenchymal expression patterns. High transitional gene expression in neuroblastoma cell lines identified a similar transitional H3K27-acetylation super-enhancer landscape, supporting the concept that PNTs have phenotypic plasticity and transdifferentiation capacity. Additionally, examination of PNT microenvironments, found that neuroblastomas contained low immune cell infiltration, high levels of non-inflammatory macrophages, and low cytotoxic T lymphocyte levels compared with more benign PNT subtypes. Modeling of cell-cell signaling in the tumor microenvironment predicted specific paracrine effects toward the various subtypes of malignant cells, suggesting further cell-extrinsic influences on malignant cell phenotype. Collectively, our study reveals the presence of a previously unrecognized transitional cell state with high malignant potential and an immune cell architecture which serve both as potential biomarkers and therapeutic targets.

cancer biology↗

bioRxiv2020

De Novo Assembly of the Northern Cardinal (Cardinalis cardinalis) Genome Reveals Candidate Regulatory Regions for Sexually Dichromatic Red Plumage Coloration

Northern cardinals (Cardinalis cardinalis) are common, mid-sized passerines widely distributed in North America. As an iconic species with strong sexual dichromatism, it has been the focus of extensive ecological and evolutionary research, yet genomic studies investigating the evolution of genotype-phenotype association of plumage coloration and dichromatism are lacking. Here we present a new, highly contiguous assembly for C. cardinalis. We generated a 1.1 Gb assembly comprised of 4,762 scaffolds, with a scaffold N50 of 3.6 Mb, a contig N50 of 114.4 kb and a longest scaffold of 19.7 Mb. We identified 93.5% complete and single-copy orthologs from an Aves dataset using BUSCO, demonstrating high completeness of the genome assembly. We annotated the genomic region comprising the CYP2J19 gene, which plays a pivotal role in the red coloration in birds. Comparative analyses demonstrated non-exonic regions unique to the CYP2J19 gene in passerines and a long insertion upstream of the gene in C. cardinalis. Transcription factor binding motifs discovered in the unique insertion region in C. cardinalis suggest potential androgen-regulated mechanisms underlying sexual dichromatism. Pairwise Sequential Markovian Coalescent (PSMC) analysis of the genome reveals fluctuations in historic effective population size between 100,000-250,000 in the last 2 millions years, with declines concordant with the beginning of the Pleistocene epoch and Last Glacial Period. This draft genome of C. cardinalis provides an important resource for future studies of ecological, evolutionary, and functional genomics in cardinals and other birds.

evolutionary biology↗

bioRxiv2020

Evaluating rehabilitation progress using motion features identified by machine learning

Evaluating progress throughout a patients rehabilitation episode is critical for determining effectiveness of the selected treatments and contributing to the evidence-based practice. The evaluation process is complex due to the inherent large human variations in motor recovery and the limitations of commonly used clinical measurement tools. Information recorded during a robot-assisted rehabilitation process can provide an effective means to continuously quantitatively assess movement performance and rehabilitation progress. However, selecting appropriate motion features for rehabilitation evaluation has always been challenging. This paper exploits unsupervised feature learning techniques to reduce the complexity of building the evaluation model of patients progress. A new feature learning technique is developed to select the most significant features from a large amount of kinematic features measured from robotics, providing clinically useful information to health practitioners with reduction of modeling complexity. A novel indicator that can reflect monotonicity and trendability is proposed to evaluate the suitability of kinematic features, which are derived from the collected data of a population of stroke patients participating in robot-aided rehabilitation. The selected kinematic features allow for human variations across a population of patients as well as over the sequence of rehabilitation sessions. The study is based on data records pertaining to 41 stroke patients using three different robot assisted exercises for upper limb rehabilitation. Consistent with the literature, the results indicate that features based on movement smoothness are the best measures among 17 kinematic features used to evaluate rehabilitation progress.

bioengineering↗

bioRxiv2020

Identification of 38 novel loci for systemic lupus erythematosus and genetic heterogeneity that may underly population disparities in this disease

Systemic lupus erythematosus (SLE), a worldwide autoimmune disease with high heritability, shows differences in prevalence, severity and age of onset among different ancestral groups. Previous genetic studies have focused more on European populations, which appear to be the least affected. Consequently, the genetic variations that underly the commonalities, differences and treatment options in SLE among ancestral groups have not been well elucidated. To address this, we undertook a genome-wide association study, increasing the sample size of Chinese populations to the level of existing European studies. Thirty-eight novel SLE-associated loci and incomplete sharing of genetic architecture were identified. Nine disease loci showed clear ancestral group heterogeneity and implicated antibody production as a potential mechanism for differences in disease manifestation. Polygenic risk scores performed significantly better when trained on matched ancestral data sets. These analyses help to reveal the genetic bases for disparities in SLE among ancestral groups.

genetics↗

bioRxiv2020

Fully human single-domain antibodies against SARS-CoV-2

The COVID-19 pandemic is spreading rapidly, highlighting the urgent need for an efficient approach to rapidly develop therapeutics and prophylactics against SARS-CoV-2. We describe here the development of a phage-displayed single-domain antibody library by grafting naive CDRs into framework regions of an identified human germline IGHV allele. This enabled the isolation of high-affinity single-domain antibodies of fully human origin. The panning using SARS-CoV-2 RBD and S1 as antigens resulted in the identification of antibodies targeting five types of neutralizing or non-neutralizing epitopes on SARS-CoV-2 RBD. These fully human single-domain antibodies bound specifically to SARS-CoV-2 RBD with subnanomolar to low nanomolar affinities. Some of them were found to potently neutralize pseudotyped and live virus, and therefore may represent promising candidates for prophylaxis and therapy of COVID-19. This study also reports unique immunogenic profile of SARS-CoV-2 RBD compared to that of SARS-CoV and MERS-CoV, which may have important implications for the development of effective vaccines against SARS-CoV-2.

microbiology↗

bioRxiv2020

Inhibition of SARS-CoV-2 infection (previously 2019-nCoV) by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion

The recent outbreak of coronavirus disease (COVID-19) caused by SARS-CoV-2 infection in Wuhan, China has posed a serious threat to global public health. To develop specific anti-coronavirus therapeutics and prophylactics, the molecular mechanism that underlies viral infection must first be confirmed. Therefore, we herein used a SARS-CoV-2 spike (S) protein-mediated cell-cell fusion assay and found that SARS-CoV-2 showed plasma membrane fusion capacity superior to that of SARS-CoV. We solved the X-ray crystal structure of six-helical bundle (6-HB) core of the HR1 and HR2 domains in SARS-CoV-2 S protein S2 subunit, revealing that several mutated amino acid residues in the HR1 domain may be associated with enhanced interactions with HR2 domain. We previously developed a pan-coronavirus fusion inhibitor, EK1, which targeted HR1 domain and could inhibit infection by divergent human coronaviruses tested, including SARS-CoV and MERS-CoV. We then generated a series of lipopeptides and found that the EK1C4 was the most potent fusion inhibitor against SARS-CoV-2 S protein-mediated membrane fusion and pseudovirus infection with IC50s of 1.3 and 15.8 nM, about 241- and 149-fold more potent than that of EK1 peptide, respectively. EK1C4 was also highly effective against membrane fusion and infection of other human coronavirus pseudoviruses tested, including SARS-CoV and MERS-CoV, as well as SARSr-CoVs, potently inhibiting replication of 4 live human coronaviruses, including SARS-CoV-2. Intranasal application of EK1C4 before or after challenge with HCoV-OC43 protected mice from infection, suggesting that EK1C4 could be used for prevention and treatment of infection by currently circulating SARS-CoV-2 and emerging SARSr-CoVs.

microbiology↗

bioRxiv2020

Effective Assessments of a Short-duration Poor Posture on Upper Limb Muscle Fatigue before Physical Exercise

A forward head and rounded shoulder posture is a poor posture that is widely seen in everyday life. It is known that sitting in such a poor posture with long hours will bring health issues such as muscle pain. However, it is not known whether sitting in this poor posture for a short period of time will affect human activities. This paper investigates the effects of a shortduration poor posture before some typical physical activities such as push-ups. The experiments are set up as follows. Fourteen male subjects are asked to do push-ups until fatigue with two surface electromyography (sEMG) at the upper limb. Two days later, they are asked to sit in this poor posture for 15 mins with 8 sEMG sensors located at given back muscles. Then they do the push-ups after the short-duration poor posture. The observations from the median frequency of sEMG signals at the upper limb indicate that the short-duration poor posture does affect the fatigue procedure of push-ups. A significant decreasing trend of the performance of push-ups is obtained after sitting in this poor posture. Such effects indicate that some parts of the back muscles indeed get fatigued with only 15 minutes sitting in this poor posture. By further investigating the time-frequency components of sEMG of back muscles, it is observed that the low and middle frequencies of sEMG signals from the infraspinatus muscle of the dominant side are demonstrated to be more prone to fatigue with the poor posture. Although this study focuses only on push-ups, similar experiments can be arranged for other physical exercises as well. This study provides new insights into the effect of a short-duration poor posture before physical activities. These insights can be used to guide athletes to pay attention to postures before physical activities to improve performance and reduce the risk of injury.

bioinformatics↗

bioRxiv2020

Three-dimensional genome structure and chromatin accessibility reorganization during in vivo induction of human T cell tolerance

Achieving T cell tolerance is a pivotal goal for the field of transplantation and autoimmune diseases. Here, we characterized the gene expression profiles, 3D genome architecture and chromatin accessibility in human steady-state and tolerant T cells, which had been induced in healthy donors by granulocyte-colony-stimulating factor in vivo. We provided the first high-resolution 3D genomic landscape of human tolerant T cells in vivo and identified highly expressed suppressor of cytokine signaling 1 (SOCS1), which is essential for maintaining T cell tolerance and was validated by ex vivo experiments. Mechanistically, SOCS1 is activated by STAT3, which mediates a new interaction between the SOCS1 locus and downstream super-enhancers and is accompanied by the disruption of the CTCF loop between the SOCS1 locus and upstream heterochromatin. This competitive regulation pattern between STAT3 and CTCF is present in the whole genome. Our study defines a regulatory model of transcription factors and provides insight into the induction of immune tolerance.

bioinformatics↗

bioRxiv2020

Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody

The newly identified 2019 novel coronavirus (2019-nCoV) has caused more than 800 laboratory-confirmed human infections, including 25 deaths, posing a serious threat to human health. Currently, however, there is no specific antiviral treatment or vaccine. Considering the relatively high identity of receptor binding domain (RBD) in 2019-nCoV and SARS-CoV, it is urgent to assess the cross-reactivity of anti-SARS-CoV antibodies with 2019-nCoV spike protein, which could have important implications for rapid development of vaccines and therapeutic antibodies against 2019-nCoV. Here, we report for the first time that a SARS-CoV-specific human monoclonal antibody, CR3022, could bind potently with 2019-nCoV RBD (KD of 6.3 nM). The epitope of CR3022 does not overlap with the ACE2 binding site within 2019-nCoV RBD. Therefore, CR3022 has the potential to be developed as candidate therapeutics, alone or in combination with other neutralizing antibodies, for the prevention and treatment of 2019-nCoV infections. Interestingly, some of the most potent SARS-CoV-specific neutralizing antibodies (e.g., m396, CR3014) that target the ACE2 binding site of SARS-CoV failed to bind 2019-nCoV spike protein, indicating that the difference in the RBD of SARS-CoV and 2019-nCoV has a critical impact for the cross-reactivity of neutralizing antibodies, and that it is still necessary to develop novel monoclonal antibodies that could bind specifically to 2019-nCoV RBD.

microbiology↗

bioRxiv2020

Bayesian copy number detection and association in large-scale studies

Germline copy number variants (CNVs) increase risk for many diseases, yet detection of CNVs and quantifying their contribution to disease risk in large-scale studies is challenging. We developed an approach called CNPBayes to identify latent batch effects, to provide probabilistic estimates of integer copy number across the estimated batches, and to fully integrate the copy number uncertainty in the association model for disease. We demonstrate this approach in a Pancreatic Cancer Case Control study of 7,598 participants where the major sources of technical variation were not captured by study site and varied across the genome. Candidate associations aided by this approach include deletions of 8q24 near regulatory elements of the tumor oncogene MYC and of Tumor Supressor Candidate 3 (TUSC3). This study provides a robust Bayesian inferential framework for estimating copy number and evaluating the role of copy number in heritable diseases.

genetics↗

bioRxiv2020

Characterization of a novel NDM-5-harboring plasmid from a carbapenem-resistant Escherichia coli isolate from China

A carbapenem-resistant Escherichia coli (sequence type 5415) strain was isolated from a male patient. S1-PFGE and Southern blotting showed that the blaNDM-5 gene was located on a novel 66-kb IncFII [F2:A-:B-] plasmid. Conjugation assays revealed that the blaNDM-5-bearing plasmid was self-transferrable. Genomic sequencing and comparative analysis suggested that plasmid p2947-NDM5 likely originated from a combination of an IncFII-type backbone and the blaNDM-5 flanking genetic elements. This study highlights the genetic complexity of an NDM-5 carbapenemase and the urgent need for continuous active monitoring. IMPORTANCECarbapenem resistance due to the NDM enzyme has become a serious clinical problem in medical care and public health. We here identified a blaNDM-5-positive E. coli strain ST5414. The blaNDM-5 gene was located on a novel self-transferrable IncFII type plasmid p2947-NDM5. Genomic sequencing and comparative analysis suggested that plasmid p2947-NDM5 likely originated from a combination of an IncFII-type backbone and the blaNDM-5 flanking genetic elements. The genetic context of NDM-5 is highly similar to that of animal origins, and we speculate that the blaNDM-harboring IncFII plasmid has a potential risk of being transmitted from animals to humans and should be paid more attention. Our findings highlight the threat of NDM-5 carbapenemase circulation and the urgency of stringent surveillance and control measures.

genomics↗

bioRxiv2019

Modulation of longevity by diet, and youthful body weight, but not by weight gain after maturity

Diet and environment profoundly modulate lifespan. We measured longevity as a function of diet and weight gain across a genetically diverse family of mice. We followed 1348 females from two parental strains--C57BL/6J and DBA/2J--and 146 cohorts of BXD isogenic progeny strains (n = 73) across their lifespan on a low fat chow diet (CD, 18% calories from fat) and on a high fat diet (HFD, 60% calories from fat). On average, HFD shortens lifespan by 85 days or 12%, roughly equivalent to an 8-10 year decrease in humans. However, strain variation in the response of diet on longevity is remarkably high, ranging from a longevity loss of 54% in BXD65 to a gain of 37% in BXD8. Baseline weights and early weight gain are both associated with a mean decrease in longevity of [~]4 days/g. By 500 days-of-age, cases fed HFD gained four times as much weight as control on average. However, strain-specific variation was substantial, thus weight gain did not correlate well with lifespan. In summary, high fat had a strong negative effect on longevity, but genetic interactions effects were even stronger. This highlights the unequivocal importance of genetic differences in making dietary recommendations.

genetics↗