Biology subjects

Pham, N. T.

Publications and source records attributed to Pham, N. T..

12 recordsLinked to original sources

bioRxiv2024

Supervised non-negative matrix factorization on cell-free DNA fragmentomic features enhances early cancer detection

BackgroundCell-free circulating DNA (cfDNA) fragments exhibit non-random patterns in their length (FLEN), end-motif (EM), and distance to nucleosome position (ND). While these cfDNA features have shown promise as inputs for machine learning and deep learning models in early cancer detection, most studies utilize them as raw inputs, overlooking the potential benefits of pre-processing to extract cancer-specific features. This study aims to enhance cancer detection accuracy by developing a novel approach to feature extraction from cfDNA fragmentomics. MethodsWe implemented a supervised non-negative matrix factorization (SNMF) algorithm to generate embedding vectors capturing cancer-specific signals within cfDNA fragmentomic features. These embeddings served as input for a machine learning model to classify cancer patients from healthy individuals. ResultsWe validated our framework using two datasets: an in-house cohort of 431 cancer patients and 442 healthy individuals (dataset 1), and a published cohort comprising 90 hepatocellular carcinoma (HCC) patients and 103 individuals with cirrhosis or hepatitis B (dataset 2). In dataset 1, we achieved an AUC of 94% in pan-cancer detection. In dataset 2, our framework achieved an AUC of 100% for HCC vs healthy classification, 99% for HCC vs non-HCC patients classification, and 96% for identifying HCC patients among a mixed group of non-HCC patients and healthy donors. ConclusionThis study demonstrates the efficiency of SNMF-transformed features in improving both pan-cancer detection and specific HCC detection. Our approach offers a significant advancement in leveraging cfDNA fragmentomics for early cancer detection, potentially enhancing diagnostic accuracy in clinical settings.

bioinformatics↗

bioRxiv2023

Estradiol propionate reduction of nuclear size in prostate cancer lines lacking DHRS7suggests DHRS7 absence as a biomarker for the effectiveness of estrogen therapy

Increased nuclear size correlates with lower survival rates for prostate cancer and is a hallmark of late-stage androgen-insensitive tumors. The short-chain dehydrogenase/reductase (SDR) family member DHRS7 was suggested as a marker for prostate cancer grading because it is lost in late-stage androgen-insensitive tumors. Here we find that loss of DHRS7 from the early-stage LNCaP prostate cancer cell line increases nuclear size, potentially explaining the nuclear size increase observed in higher-grade prostate tumors. Exogenous expression of DHRS7 in the late-stage PC3 prostate cancer cell line correspondingly decreases nuclear size. We separately tested 80 compounds from the Microsource Spectrum library for their ability to restore normal nuclear size to PC3 cells, finding estradiol propionate had the same effect as re-expression of DHRS7 in the PC3 cells. However, the drug had no effect on LNCaP cells or PC3 cells re-expressing DHRS7. We speculate that reported beneficial effects of estrogens in late-stage prostate cancer may target a pathway which is only active in cells lacking DHRS7 that have increased nuclear size and propose DHRS7 as a potential biomarker for the likely effectiveness of estrogen-based treatments.

cancer biology↗

bioRxiv2023

Long-term epidemiology and evolution of swine influenza viruses in Vietnam

Swine influenza virus (SwIV) surveillance in Hanoi, Vietnam from 2013-2019 found gene pool enrichment from imported swine from Asia and North America. Long-term maintenance, persistence and reassortment of SwIV lineages was observed. Co-circulation of H1-{delta}1a viruses with other SwIV genotypes raises concern due to its zoonotic potential.

microbiology↗

bioRxiv2022

Nanoscaled discovery of a shunt rifamycin from Salinispora arenicola using a three-colour GFP-tagged Staphylococcus aureus macrophage infection assay.

Antimicrobial resistance has emerged as an urgent global public health threat, and development of novel therapeutics for treating infections caused by multi-drug resistant bacteria is urgent. Staphylococcus aureus is a major human and animal pathogen, responsible for high levels of morbidity and mortality worldwide. The intracellular survival of S. aureus in macrophages contributes to immune evasion, dissemination, and resilience to antibiotic treatment. Here, we present a confocal fluorescence imaging assay for monitoring macrophage infection by GFP-tagged Staphylococcus aureus as a front-line tool to identify antibiotic leads. The assay was employed in combination with nanoscaled chemical analyses to facilitate the discovery of a novel, active rifamycin analogue. Our findings indicate a promising new approach to the identification of anti-microbial compounds with macrophage intracellular activity. The novel antibiotic identified here may represent a useful addition to our armoury in tackling the silent pandemic of antimicrobial resistance.

cell biology↗

bioRxiv2022

Preclinical assessment of Fibroblast Activation Protein-specific MRI as an alternative to PSMA for image-guided focal therapy of prostate cancer

Accurate and precise delineation of gross tumour volumes remains a barrier to radiotherapy dose escalation and boost dosing in the treatment of solid tumours, such as prostate cancer. Magnetic resonance imaging of tumour molecular targets has the power to enable focal dose boosting, particularly when combined with technological advances such as MRI-LINAC. Fibroblast activation protein (FAP) is a transmembrane protein overexpressed in stromal components of >90% of epithelial carcinomas. Herein we compare targeted MRI of gold standard PSMA with FAP in the delineation of orthotopic tumours in a mouse model of prostate cancer. Control (no ligand), FAP and PSMA-targeting iron oxide nanoparticles were prepared with modification of an MRI agent (FerroTrace). Mice with orthotopic LNCaP tumours underwent T2-weighted 3D MRI 24 hours after intravenous injection of contrast agents. FAP and PSMA nanoparticles produced contrast enhancement on MRI when compared to control nanoparticles, which was most pronounced on the tumour periphery. FAP-targeted MRI increased the proportion of tumour contrast enhancing black pixels by 13.37% when compared to PSMA. Furthermore, analysis of changes in R2 values between healthy prostates and LNCaP tumours indicated an increase in contrast enhancing pixels in the tumour border of 15%, when targeting FAP, in contrast to PSMA This study demonstrates preclinical feasibility of PSMA and FAP-targeted MRI which can enable targeted image-guided focal therapy of localized prostate cancer.

bioengineering↗

bioRxiv2021

RNA pull-down-Confocal Nanoscanning (RP-CONA) detects quercetin as pri-miR-7/HuR interaction inhibitor that decreases α-Synuclein levels

RNA-protein interactions are central to all gene expression processes and contribute to variety of human diseases. Therapeutic approaches targeting RNA-protein interactions have shown promising effects on some diseases that are previously regarded as incurable. Here we developed a fluorescent on-bead screening platform: RNA pull-down-Confocal Nanoscanning (RP-CONA), to identify RNA-protein interaction modulators in eukaryotic cell extracts. Using RP-CONA, we identified small molecules that disrupt the interaction between HuR, an inhibitor of brain-enriched miR-7 biogenesis, and the conserved terminal loop of pri-miR-7-1. Importantly, miR-7s primary target is an mRNA of -Synuclein, which contributes to aetiology of Parkinsons disease. Our method identified a natural product quercetin as a molecule able to upregulate cellular miR-7 levels and downregulate the expression of -Synuclein. This opens up new therapeutic avenues towards treatment of Parkinsons disease as well as provides novel methodology to search for RNA-protein interaction modulators.

molecular biology↗

bioRxiv2020

PyBindingCurve, simulation and curve fitting to complex binding systems at equilibrium.

Understanding multicomponent binding interactions in protein-ligand, protein-protein and competition systems is essential for fundamental biology and drug discovery. Hand deriving equations quickly becomes unfeasible when the number of components is increased, and direct analytical solutions only exist to a certain complexity. To address this problem and allow easy access to simulation, plotting and parameter fitting to complex systems at equilibrium, we present the Python package PyBindingCurve. We apply this software to explore homodimer and heterodimer formation culminating in the discovery that under certain conditions, homodimers are easier to break with an inhibitor than heterodimers and may also be more readily depleted. This is a potentially valuable and overlooked phenomenon of great importance to drug discovery. PyBindingCurve may be expanded to operate on any equilibrium binding system and allows definition of custom systems using a simple syntax. PyBindingCurve is available under the MIT license at: https://github.com/stevenshave/pybindingcurve as Python source code accompanied by examples and as an easily installable package within the Python Package Index.

biophysics↗

bioRxiv2020

A Rad51-Independent P{-}ath{-}way Promotes Single-Strand Template Repair in Gene Editing

The Rad51/RecA family of recombinases perform a critical function in typical repair of double-strand breaks (DSBs): strand invasion of a resected DSB end into a homologous double-stranded DNA (dsDNA) template sequence to facilitate repair. However, repair of a DSB using single stranded DNA (ssDNA) as a template, a common method of CRISPR/Cas9-mediated gene editing, is Rad51-independent. We have analyzed the genetic requirements for these Rad51-independent events in Saccharomyces cerevisiae in two different assays. Gene editing events were carried out either by creating a DSB with the site-specific HO endonuclease and repairing the DSB with 80-nt single-stranded oligonucleotides (ssODNs) or by using a bacterial retron system that produces ssDNA templates in vivo in combination with DSBs created by Cas9. We show that single strand template repair (SSTR), is dependent on Rad52, Rad59, Srs2 and the Mre11-Rad50-Xrs2 (MRX) complex, but not Rad51, Rad54 or Rad55. Srs2 acts to prevent overloading of Rad51 on the ssDNA filament, whereas Rad59 appears to alleviate the inhibition of Rad51 on Rad52s strand annealing activity; thus, deletion of RAD51 suppresses both the srs2{Delta} and rad59{Delta} phenotypes. This same suppression by rad51{Delta} of rad59{Delta} is found in another DSB repair pathway, single strand annealing (SSA). In contrast, gene targeting using an 80-bp dsDNA template of the same sequence is Rad51-dependent. We also examined SSTR events in which the ssODN carried several mismatches. In the absence of the mismatch repair protein, Msh2, we found that the fate of mismatches carried on the ssDNA template are very different at the 3 end, which can anneal directly to the resected DSB end, compared to the 5 end. We also find that DNA polymerase Pol{delta}s 3 to 5 proofreading activity frequently excises a mismatch close to the 3 end of the template, similar to its removal of heterologies close to the 3 invading end of the DSB. We further report that SSTR is accompanied by a 600-fold increase in mutations in a region adjacent to the sequences directly undergoing repair. These DNA polymerase {zeta}-dependent mutations may compromise the accuracy of gene editing.

genetics↗

bioRxiv2020

Chemical-Genetic Interrogation of Nuclear Size Control Reveals Cancer-Specific Effects on Cell Migration and Invasion

Lower survival rates for many cancer types correlate with increases or decreases in nuclear size/scaling in a tumor-type/tissue-specific manner. Postulating that nuclear size changes confer a fitness advantage on tumor cells, we screened for FDA/EMA-approved compounds that reverse tumor nuclear size changes in cell lines from three such tumor types: prostate adenocarcinoma, colonic adenocarcinoma, and small-cell squamous lung cancer. We found distinct, largely non-overlapping sets of compounds that either rectify or exacerbate nuclear size changes for each tumor type. Nuclear size phenotypes across cell lines clustered particular classes of compounds including serotonin uptake inhibitors, cyclo-oxygenase inhibitors, beta-adrenergic receptor agonists, monoamine oxidase inhibitors, and Na+/K+ ATPase inhibitors. Nearly all compounds selected for further investigation inhibited cell migration and/or invasion, suggesting that targeting nuclear size control pathways in chemotherapy regimens could improve patient survival.

cancer biology↗

bioRxiv2019

Asparagine deprivation causes a reversible inhibition of Human Cytomegalovirus acute virus replication

As obligate intracellular pathogens, viruses rely on the host cell machinery to replicate efficiently, with the host metabolism extensively manipulated for this purpose. High throughput siRNA screens provide a systematic approach for the identification of novel host-virus interactions. Here, we report a large-scale screen for host factors important for human cytomegalovirus (HCMV), consisting of 6,881 siRNAs. We identified 47 proviral factors and 68 antiviral factors involved in a wide range of cellular processes including the mediator complex, proteasome function and mRNA splicing. Focused characterisation of one of the hits, asparagine synthetase (ASNS), demonstrated a strict requirement for asparagine for HCMV replication which leads to an early block in virus replication before the onset of DNA amplification. This effect is specific to HCMV, as knockdown of ASNS had little effect on herpes simplex virus-1 or influenza A virus replication, suggesting the restriction is not simply due to a failure in protein production. Remarkably, virus replication could be completely rescued seven days post-infection with addition of exogenous asparagine, indicating that while virus replication is restricted at an early stage, it maintains the capacity for full replication days after initial infection. This study represents the most comprehensive siRNA screen for the identification of host factors involved in HCMV replication and identifies the non-essential amino acid, asparagine as a critical factor in regulating HCMV virus replication. These results have implications for control of viral latency and the clinical treatment of HCMV in patients.\n\nImportanceHCMV accounts for more than 60% of complications associated with solid organ transplant patients. Prophylactic or preventative treatment with antivirals, such as ganciclovir, reduces the occurrence of early onset HCMV disease. However, late onset disease remains a significant problem and prolonged treatment, especially in patients with suppressed immune systems, greatly increases the risk of antiviral resistance. Very few antivirals have been developed for use against HCMV since the licensing of ganciclovir, and of these, the same viral genes are often targeted, reducing the usefulness of these drugs against resistant strains. An alternative approach is to target host genes essential for virus replication. Here we demonstrate that HCMV replication is highly dependent on levels of the amino acid asparagine and knockdown of a critical enzyme involved in asparagine synthesis results in severe attenuation of virus replication. These results suggest that reducing asparagine levels through dietary restriction or chemotherapeutic treatment could limit HCMV replication in patients.

microbiology↗

bioRxiv2019

Genome sequence of the model rice variety KitaakeX

Here, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We identified 331,335 genomic variations between KitaakeX and Nipponbare (ssp. japonica), and 2,785,991 variations between KitaakeX and Zhenshan97 (ssp. indica). We also compared Kitaake resequencing reads to the KitaakeX assembly and identified 219 small variations. The high-quality genome of the model rice plant KitaakeX will accelerate rice functional genomics.

genomics↗

bioRxiv2017

The Sequence of 1504 Mutants in the Model Rice Variety Kitaake Facilitates Rapid Functional Genomic Studies

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitates functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa L. ssp. japonica), which completes its life cycle in 9 weeks. We sequenced 1,504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. Using this mutant population, we identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line with a small segregating population. This result reveals the usefulness of the resource for efficient identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks, enabling rapid functional genomic studies of rice.\n\nOne-sentence summaryWe have sequenced 1,504 mutant lines generated in the short life cycle rice variety Kitaake (9 weeks) and established a publicly available database, enabling rapid functional genomic studies of rice.

plant biology↗