Biology subjects

Tang, A.

Publications and source records attributed to Tang, A..

50 records · Page 3Linked to original sources

bioRxiv2020

Potent in vitro anti-SARS-CoV-2 activity by gallinamide A and analogues via inhibition of cathepsin L

The emergence of SARS-CoV-2 in late 2019, and the subsequent COVID-19 pandemic, has led to substantial mortality, together with mass global disruption. There is an urgent need for novel antiviral drugs for therapeutic or prophylactic application. Cathepsin L is a key host cysteine protease utilized by coronaviruses for cell entry and is recognized as a promising drug target. The marine natural product, gallinamide A and several synthetic analogues, were identified as potent inhibitors of cathepsin L activity with IC50 values in the picomolar range. Lead molecules possessed selectivity over cathepsin B and other related human cathepsin proteases and did not exhibit inhibitory activity against viral proteases Mpro and PLpro. We demonstrate that gallinamide A and two lead analogues potently inhibit SARS-CoV-2 infection in vitro, with EC50 values in the nanomolar range, thus further highlighting the potential of cathepsin L as a COVID-19 antiviral drug target.

biochemistry↗

bioRxiv2020

Phosphate dysregulation via the XPR1:KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer

Clinical outcomes for patients with ovarian and uterine cancers have not improved greatly in the past twenty years. To identify ovarian and uterine cancer vulnerabilities, we analyzed genome-scale CRISPR/ Cas9 loss-of-function screens across 739 human cancer cell lines. We found that many ovarian cancer cell lines overexpress the phosphate importer SLC34A2, which renders them sensitive to loss of the phosphate exporter XPR1. We extensively validated the XPR1 vulnerability in cancer cell lines and found that the XPR1 dependency was retained in vivo. Overexpression of SLC34A2 is frequently observed in tumor samples and is regulated by PAX8 -a transcription factor required for ovarian cancer survival. XPR1 overexpression and copy number amplifications are also frequently observed. Mechanistically, SLC34A2 overexpression and impaired phosphate efflux leads to the accumulation of intracellular phosphate and cell death. We further show that proper localization and phosphate efflux by XPR1 requires a novel binding partner, KIDINS220. Loss of either XPR1 or KIDINS220 results in acidic vacuolar structures which precede cell death. These data point to the XPR1:KIDINS220 complex - and phosphate dysregulation more broadly -as a therapeutic vulnerability in ovarian cancer.

cancer biology↗

bioRxiv2020

EEG Artifact to Signal: Predicting Horizontal Gaze Position from SOBI-DANS Identified Ocular Artifact Components

Ocular artifact in EEG has long been viewed as a problem for interpreting EEG data in basic and applied research. The removal of such artifacts has been an on-going effort over many decades. We have recently introduced a hybrid method combining second-order blind identification (SOBI) with DANS, a novel automatic identification method, to extract components containing specifically signals associated with horizontal and vertical saccadic eye movements (H and V Comps) and found that these components event-related potentials in response to saccadic eye movement are systematically modulated by movement directions and distances. Here in a case study, taking advantage of signals about gaze positions contained in the ocular artifact components, we introduced a novel concept of EEG-based virtual eye tracking (EVET) and presented its first prototype. Specifically, we determined (1) the amount of data needed for constructing models of horizontal gaze positions; (2) the asymptotic performance levels achieved with such models. We found that for the specific calibration task, 4 blocks of data (4 saccades per target position) are needed for reaching an asymptotic performance with a prediction accuracy of 0.44 and prediction reliability of 1.67. These results demonstrated that it is possible to track horizontal gaze position via EEG alone, ultimately enabling coregistration of eye movement and the neural signals.

neuroscience↗

bioRxiv2020

Nucleolin is essential for rabbit hemorrhagic disease virus replication by providing a physical link in replication complex formation

Rabbit hemorrhagic disease virus (RHDV) is an important member of the Caliciviridae family and cannot be propagated in vitro, which has greatly impeded progress of investigating its replication mechanism. Construction of an RHDV replicon system has recently provided a platform for exploring RHDV replication in host cells. Here, aided by this replicon system and using two-step affinity purification, we purified the RHDV replicase and identified its associated host factors. We identified rabbit nucleolin (NCL) as a physical link required for the formation of RHDV replication complexes (RCs), by mediating the interaction between other host proteins and the viral RNA replicase, RNA-dependent RNA polymerase (RdRp). We found that RHDV RdRp uses an amino acid (aa) region spanning residues 448-478 to directly interact with NCLs RNA-recognition motif 2. We also found that the viral p16 protein uses a highly conserved region (35Cys-Ile-Arg-Ala38 or CIRA motif) to specifically bind the N-terminal region of NCL (aa 1-110) and that RHDV p23 uses a specific domain (aa 90-145) to bind NCLs RNA-recognition motif 1. Disrupting these protein-protein interactions severely weakened viral replication. Furthermore, NCL overexpression or knockdown significantly increased or severely impaired, respectively, RHDV replication. Collectively, these results indicate that the host protein NCL is essential for RHDV replication and plays a key role in the formation of RHDV RCs. The mechanisms by which NCL promotes viral replicase assembly reported here shed light on viral RC biogenesis and may inform antiviral therapies. Author summaryRabbit hemorrhagic disease virus (RHDV) is the causative agent of highly contagious and lethal hemorrhagic disease in the European rabbit, but the host factors involved in RHDV replication remain poorly understood. In the present study, we isolated RHDV replication complex (RC) for the first time and identified its main components. We found that nucleolin (NCL) plays a key role in the formation of the RHDV RC. NCL not only interacts with viral replicase (RdRp), it also specifically binds to other important host factors. In addition, we proved that NCL is necessary for RHDV replication because the level of RHDV replication is significantly affected by knocking down the NCL gene in cells. Together, our data suggest that RHDV completes its replication by hijacking NCL to recruit other viral proteins and host factors, thereby assembling the RC of RHDV.

microbiology↗

bioRxiv2020

Antibiotic hypersensitivity signatures identify targets for attack in the Acinetobacter baumannii cell envelope

Acinetobacter baumannii is an opportunistic pathogen that is a critical, high-priority target for new antibiotic development. Clearing of A. baumannii requires relatively high doses of antibiotics across the spectrum, primarily due to its protective cell envelope. Many of the proteins that support envelope integrity and modulate drug action are uncharacterized, largely because there is an absence of orthologs for several proteins that perform essential envelope-associated processes, impeding progress on this front. To identify targets that can synergize with current antibiotics, we performed an exhaustive analysis of A. baumannii mutants causing hypersensitivity to a multitude of antibiotic treatments. By examining mutants with antibiotic hypersensitivity profiles that parallel mutations in proteins of known function, we show that the function of poorly annotated proteins can be predicted and used to identify candidate missing link proteins in essential A. baumannii processes. Using this strategy, we uncovered multiple uncharacterized proteins with critical roles in cell division or cell elongation, and revealed that a predicted cell wall D,D-endopeptidase has an unappreciated function in lipooligosaccharide synthesis. Moreover, we provide a genetic strategy that uses hypersensitivity signatures to predict drug synergies, allowing the identification of {beta}-lactams that work cooperatively based on the cell wall assembly machineries that they preferentially target. These data reveal multiple pathways critical for envelope growth in A. baumannii that can be targeted in combination strategies for attacking the pathogen.

microbiology↗

bioRxiv2020

A robust and interpretable, end-to-end deep learning model for cytometry data

Cytometry technologies are essential tools for immunology research, providing high-throughput measurements of the immune cells at the single-cell level. Traditional approaches in interpreting and using cytometry measurements include manual or automated gating to identify cell subsets from the cytometry data, providing highly intuitive results but may lead to significant information loss, in that additional details in measured or correlated cell signals might be missed. In this study, we propose and test a deep convolutional neural network for analyzing cytometry data in an end-to-end fashion, allowing a direct association between raw cytometry data and the clinical outcome of interest. Using nine large CyTOF studies from the open-access ImmPort database, we demonstrated that the deep convolutional neural network model can accurately diagnose the latent cytomegalovirus (CMV) in healthy individuals, even when using highly heterogeneous data from different studies. In addition, we developed a permutation-based method for interpreting the deep convolutional neural network model and identified a CD27-CD94+ CD8+ T cell population significantly associated with latent CMV infection. Finally, we provide a tutorial for creating, training and interpreting the tailored deep learning model for cytometry data using Keras and TensorFlow (github.com/hzc363/DeepLearningCyTOF).

bioinformatics↗

bioRxiv2019

Nanopore sequencing reveals U2AF1 S34F-associated full-length isoforms

U2AF1 S34F is one of the most recurrent splicing factor mutations in lung adenocarcinoma (ADC) and has been shown to cause transcriptome-wide pre-mRNA splicing alterations. While U2AF1 S34F-associated splicing alterations have been described, the function of altered mRNA isoform changes remains largely unexplored. To better understand the impact U2AF1 S34F has on isoform fate and function, we conducted high-throughput long-read cDNA sequencing from isogenic human bronchial epithelial cells with and without U2AF1 S34F mutation. We found that nearly 75% (49,366) of our long-read constructed multiexon isoforms do not overlap GENCODE or short-read assembled isoforms. We found 198 transcript isoforms with significant expression and usage changes caused by U2AF1 S34F mutation, including a novel lncRNA. Isoforms from immune-related genes were largely downregulated in mutant cells, none of which were found to have splicing changes. Finally, isoforms likely targeted by nonsense-mediated decay were preferentially downregulated in U2AF1 S34F cells, suggesting that the impact of observed isoform changes may alter the translational output of affected genes. Altogether, long-read sequencing provided additional insights into transcriptome alterations and downstream functional consequences associated with U2AF1 S34F mutation.

genomics↗

bioRxiv2019

Native plasmid-encoded mercury resistance genes are functional and demonstrate natural transformation in environmental bacterial isolates

Plasmid-mediated horizontal gene transfer (HGT) is a major driver of genetic diversity in bacteria. We experimentally validated the function of a putative mercury resistance operon present on an abundant 8 kilobase pair native plasmid found in groundwater samples without detectable levels of mercury. Phylogenetic analyses of the plasmid-encoded mercury reductases from the studied groundwater site show them to be distinct from those reported in proximal metal-contaminated sites. We synthesized the entire native plasmid and demonstrated that the plasmid was sufficient to confer functional mercury resistance in Escherichia coli. Given the possibility that natural transformation is a prevalent HGT mechanism in the low cell density environments of groundwaters, we also assayed bacterial strains from this environment for competence. We used the native plasmid-encoded metal resistance to design a screen and identified 17 strains positive for natural transformation. We selected 2 of the positive strains along with a model bacterium to fully confirm HGT via natural transformation. From an ecological perspective, the role of the native plasmid population in providing advantageous traits combined with the microbiomes capacity to take up environmental DNA enables rapid adaptation to environmental stresses.\n\nImportanceHorizontal transfer of mobile genetic elements via natural transformation has been poorly understood in environmental microbes. Here, we confirm the functionality of a native plasmid-encoded mercury resistance operon in a model microbe and then query for the dissemination of this resistance trait via natural transformation into environmental bacterial isolates. We identify seventeen strains including Gram-positive and Gram-negative bacteria to be naturally competent. These strains were able to successfully take up the plasmid DNA and obtain a clear growth advantage in the presence of mercury. Our study provides important insights into gene dissemination via natural transformation enabling rapid adaptation to dynamic stresses in groundwater environments.

molecular biology↗

bioRxiv2019

Multi-ATOM: Ultrahigh-throughput single-cell quantitative phase imaging with subcellular resolution

A growing body of evidence has substantiated the significance of quantitative phase imaging (QPI) in enabling cost-effective and label-free cellular assay, which provides useful insights into understanding biophysical properties of cells and their roles in cellular functions. However, available QPI modalities are limited by the loss of imaging resolution at high throughput and thus run short of sufficient statistical power at the single cell precision to define cell identities in a large and heterogeneous population of cells - hindering their utility in mainstream biomedicine and biology. Here we present a new QPI modality, coined multi-ATOM that captures and processes quantitative label-free single-cell images at ultra-high throughput without compromising sub-cellular resolution. We show that multi-ATOM, based upon ultrafast phase-gradient encoding, outperforms state-of-the-art QPI in permitting robust phase retrieval at a QPI throughput of >10,000 cell/sec, bypassing the need for interferometry which inevitably compromises QPI quality under ultrafast operation. We employ multi-ATOM for large-scale, label-free, multi-variate, cell-type classification (e.g. breast cancer sub-types, and leukemic cells versus peripheral blood mononuclear cells) at high accuracy (>94%). Our results suggest that multi-ATOM could empower new strategies in large-scale biophysical single-cell analysis with applications in biology and enriching disease diagnostics.

bioengineering↗

bioRxiv2018

Nanopore native RNA sequencing of a human poly(A) transcriptome

High throughput cDNA sequencing technologies have dramatically advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and because modifications are not carried forward in cDNA. We address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies (ONT). Our study focused on poly(A) RNA from the human cell line GM12878, generating 9.9 million aligned sequence reads. These native RNA reads had an aligned N50 length of 1294 bases, and a maximum aligned length of over 21,000 bases. A total of 78,199 high-confidence isoforms were identified by combining long nanopore reads with short higher accuracy Illumina reads. We describe strategies for assessing 3' poly(A) tail length, base modifications and transcript haplotypes from nanopore RNA data. Together, these nanopore-based techniques are poised to deliver new insights into RNA biology.\n\nDISCLOSURESMA holds shares in Oxford Nanopore Technologies (ONT). MA is a paid consultant to ONT. REW, WT, TG, JRT, JQ, NJL, JTS, NS, AB, MA, HEO, MJ, and ML received reimbursement for travel, accommodation and conference fees to speak at events organised by ONT. NL has received an honorarium to speak at an ONT company meeting. WT has two patents (8,748,091 and 8,394,584) licensed to Oxford Nanopore. JTS, ML and MA received research funding from ONT.

genomics↗

bioRxiv2018

Potential PGPR properties of cellulolytic, nitrogen-fixing, and phosphate-solubilizing bacteria of a rehabilitated tropical forest soil

In the midst of major soil degradation and erosion faced by tropical ecosystems, rehabilitated forests are established to avoid further deterioration of forest land. In this context, cellulolytic, nitrogen-fixing (N-fixing), and phosphate-solubilizing bacteria are very important functional groups in regulating the elemental cycle and plant nutrition, hence replenishing the nutrient content in forest soil. As other potential plant growth-promoting (PGP) rhizobacteria, these functional bacteria could have cross-functional abilities or beneficial traits that are essential for plants and improve their growths. This study was conducted to isolate, identify, and characterize selected PGP properties of these 3 functional groups of bacteria from tropical rehabilitated forest soils at Universiti Putra Malaysia Bintulu Sarawak Campus, Malaysia. Isolated cellulolytic, N-fixing and phosphate-solubilizing bacteria were characterized for respective functional activities, biochemical properties, molecularly identified, and assessed for PGP assays based on seed germination and indole-3-acetic acid (IAA) production. Out of 15 identified bacterial isolates exhibiting beneficial phenotypic traits, a third belong to genus Burkholderia and a fifth to Stenotrophomonas sp. with both genera consisting of members from two different functional groups. Among the tested bacterial strains, isolate Serratia nematodiphila C46d, Burkholderia nodosa NB1, and Burkholderia cepacia PC8 showed outstanding cellulase, N-fixing, and phosphate-solubilizing activities, respectively. The results of the experiments confirmed the multiple PGP traits of selected bacterial isolates based on respective high functional activities, root, shoot lengths, and seedling vigour improvements when bacterized on mung bean seeds, as well as presented some significant IAA productions. The results of this study indicated that these functional bacterial strains could potentially be included in future biotechnological screenings to produce beneficial synergistic effects via their versatile properties on improving soil fertility and possible crop growth stimulation.

microbiology↗

bioRxiv2018

Epigenome-wide study uncovers tau pathology-driven changes of chromatin organization in the aging human brain

Accumulation of tau and amyloid-{beta} are two pathologic hallmarks of Alzheimers disease (AD). Here, we conducted an epigenome-wide association study using the H3K9 acetylation (H3K9Ac) mark in 669 aged human prefrontal cortices: in contrast to amyloid-{beta}, tau protein burden had a broad effect on the epigenome, affecting 5,590 out of 26,384 H3K9Ac domains. Tau-related alterations aggregated in large genomic segments reflecting spatial chromatin organization, and the magnitude of these effects correlated with the segments nuclear lamina association. We confirmed the functional relevance of these chromatin changes by demonstrating (1) consistent transcriptional changes in three independent datasets and (2) similar findings in two AD mouse models. Finally, we found that tau overexpression in iPSC-derived neurons disrupted chromatin organization and that these effects could be blocked by a small molecule predicted to reverse the tau effect. Thus, we report large-scale tau-driven chromatin rearrangements in the aging human brain that may be reversible with HSP90 inhibitors.

neuroscience↗

bioRxiv2018

A multi-omic atlas of the human frontal cortex for aging and Alzheimer's disease research

We initiated the systematic profiling of the dorsolateral prefrontal cortex obtained from a subset of autopsied individuals enrolled in the Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP), which are jointly designed and belong to a very few prospective studies of aging and dementia with detailed, longitudinal cognitive phenotyping during life and a quantitative, structured neuropathologic examination after death for >3,322 subjects. Here, we outline the first generation of data including genome-wide genotypes (n=2,090), whole genome sequencing (n=1,179), DNA methylation (n=740), chromatin immunoprecipitation with sequencing using an anti-Histone 3 Lysine 9 acetylation (H3K9Ac) antibody (n=712), RNA sequencing (n=638), and miRNA profile (n=702). Generation of other omic data including ATACseq, proteomic and metabolomics profiles is ongoing. Thanks to its prospective design and recruitment of older, non-demented individuals, these data can be repurposed to investigate a large number of syndromic and quantitative neuroscience phenotypes. The many subjects that are cognitively non-impaired at death also offer insights into the biology of the human brain in older non-impaired individuals.

cell biology↗

bioRxiv2016

Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer’s disease

BackgroundGiven multiple studies of brain microRNA (miRNA) in relation to Alzheimers disease (AD) with few consistent results and the heterogeneity of this disease, the objective of this study was to explore their mechanism by evaluating their relation to different elements of Alzheimers disease pathology, confounding factors and mRNA expression data from the same subjects in the same brain region.\n\nResultsWe report analyses of expression profiling of miRNA (n=700 subjects) and lincRNA (n=540 subjects) from the dorsolateral prefrontal cortex of individuals participating in two longitudinal cohort studies of aging. Evaluating well-established (miR-132, miR-129), we confirm their association with pathologic AD in our dataset, and then characterize their in disease role in terms of neuritic {beta}-amyloid plaques and neurofibrillary tangle pathology. Additionally, we identify one new miRNA (miR-99) and four lincRNA that are associated with these traits. Many other previously reported associations of microRNA with AD are associated with the confounders quantified in our longitudinal cohort. Finally, by performing analyses integrating both miRNA and RNA sequence data from the same individuals (525 samples), we characterize the impact of AD associated miRNA on human brain expression: we show that the effects of miR-132 and miR-129-5b converge on certain genes such as EP300 and find a role for miR200 and its target genes in AD using an integrated miRNA/mRNA analysis.\n\nConclusionsOverall, miRNAs play a modest role in human AD, but we observe robust evidence that a small number of miRNAs are responsible for specific alterations in the cortical transcriptome that are associated with AD.

neuroscience↗