Biology subjects

Tran, Q.

Publications and source records attributed to Tran, Q..

10 recordsLinked to original sources

bioRxiv2026

Tumor cell specific total mRNA expression informed neural networks predicts cancer progression

Inferring tumor molecular phenotypes from high-dimensional multi-omic data is a fundamental challenge in computational biology. Current methods for estimating tumor cell-specific total mRNA expression (TmS) require matched DNA and RNA sequencing data and rely on computationally intensive deconvolution pipelines. We present TmSNet, a deep learning framework that predicts TmS using mRNA, DNA methylation, miRNA, and immune cell proportions as input features. TmSNet integrates structured feature selection (gradient boosting, LASSO, elastic net) with specialized neural architectures to predict continuous TmS. Across 12 TCGA cancer types, TmSNet achieved cross-validated performance up to concordance correlation coefficient (CCC) = 0.93 and correlation R{superscript 2} = 0.88 and generalized to external cohorts with correlations of 0.54 (SCAN-B) and 0.43 (FUSCC). Predicted TmS values effectively stratify patients by risk and preserve known transcriptional profiles across tumor subtypes. These results demonstrate that TmSNet can infer biologically meaningful phenotypes from multi-omic data and provide a scalable framework for modeling tumor transcriptional activity in heterogeneous cohorts.

bioinformatics↗

bioRxiv2025

Pooled single-cell CRISPRa/i screens for functional genomics in bacteria at scale

Pooled CRISPR screens using single-cell RNA sequencing (scRNA-seq) have emerged as powerful tools to uncover gene function, map regulatory networks, and identify genetic interactions. However, the inherent sparsity of bacterial scRNA-seq data has posed a major challenge toward applying these approaches to bacteria. Here, we present mapSPLiT, a pooled bacterial CRISPR activation and interference (CRISPRa/i) screening platform that enables large-scale experiments that simultaneously link hundreds of perturbations to their corresponding single-cell transcriptomes. By targeting 52 known or putative transcription factors with 118 perturbations in a pooled experiment, we expanded the E. coli regulatory network map, determined the function of putative regulators, and identified emergent global phenotypes. By targeting combinations of transcription factors simultaneously, we uncovered genetic interactions and regulatory logic between them. Mapping regulatory networks for carbon utilization in P. putida revealed control points that could expand metabolic flexibility and improve biomanufacturing. Together, these results establish mapSPLiT as a generalizable platform for single-cell functional genomics in bacteria.

genomics↗

bioRxiv2025

Engineering HIV antibodies with enhanced breadth and potency of neutralization through multistate affinity maturation

Broadly neutralizing antibodies (bnAbs) against HIV hold promise as therapeutic and prophylactic agents, but realizing this potential requires antibodies that function across the antigenic heterogeneity of the HIV envelope glycoprotein (Env). Although numerous bnAbs have been isolated from infected individuals, their breadth and potency may not be sufficient to tackle global viral diversity, motivating efforts to further improve their neutralization capacity. Here, we address this challenge using a multistate antibody engineering approach integrating deep mutational scanning with combinatorial library screening across diverse Env variants. This strategy enables identification of mutation patterns that confer improved binding across antigenically distinct targets. Starting from one of the best-in-class CD4-binding site bnAbs, we performed iterative optimization to increase binding affinity across diverse Env variants. The resulting lead candidate exhibited improved breadth and up to 100-fold higher potency against pseudoviruses from large cross-clade historical and contemporary panels while maintaining biophysical and pharmacokinetic profiles conducive to clinical development. Structural and molecular dynamics analyses revealed a unique tri-tyrosine aromatic triad and reinforced electrostatic contacts that stabilized the bnAb/Env interface. These findings demonstrate that systematic in vitro engineering can generate bnAbs with enhanced breadth and potency, providing a generalizable strategy for developing therapeutic antibodies against highly diverse pathogens.

bioengineering↗

bioRxiv2024

Pan-cancer subclonal mutation analysis of 7,827 tumors predicts clinical outcome

Intra-tumor heterogeneity is characterized by a diverse population of tumor clones and subclones which are important drivers of tumor evolution and therapeutic response. However, accurate subclonal reconstruction at scale remains challenging. We developed a machine learning tool, CliPP, and surveyed 9,972 tumors from 32 cancer types. We found that high subclonal mutation load (sML), the fraction of subclonal single nucleotide variants (SNVs) to all SNVs in the coding region, was prognostic of survival (progression free survival or overall survival) in 18 cancer types. In 14 cancers with low to moderate tumor mutation burden (TMB), high sML was associated with better prognosis. In immunotherapy trials for 42 metastatic prostate cancer (mCRPC), high sML was predictive of favorable response to ipilimumab and associated with increased CD8+ T-cell infiltration and decreased macrophage population. A validation using 613 whole-genomes of esophageal adenocarcinoma confirms the favorable effect of high sML and the observed tumor-associated macrophage. Our study identifies sML as a key feature of cancer, suggesting a biphasic relationship between evolutionary dynamics and differential immune environments. Finally, sML may serve as an orthogonal approach to identify likely responders of immune checkpoint blockade in low to moderate TMB tumors.

genomics↗

bioRxiv2024

The interplay between dormant mutated cells and tumor promotion by chronic tissue damage in determining cancer risk.

While the causal role of mutagenic carcinogens in tumor development is well established, the relative contribution of environmental tumor promoting factors, wounding, and chronic inflammation is still unclear. Recent sequencing studies have suggested that most environmental carcinogens act as promoters rather than through mechanisms that involve direct induction of point mutations, but whether cancer risk factors such as obesity, chronic inflammation, wounding, or tumor promoters contribute directly or indirectly to mutation burden, or induce novel signatures, has not been investigated. Here, we present WGS analysis of over 100 mouse skin tumors to compare the effects of exposure to mutagens, the tumor promoter TPA, chronic wounding, obesity, or chemotherapy, on mutational burden and cancer risk. All tumors initiated by the carcinogen Dimethylbenzanthracene (DMBA) show a very strong A>T mutational signature (SBS.DMBA) attributable to a single exposure to this carcinogen. The number of SBS.DMBA mutations also showed a strong correlation with the "clock" signature SBS5, suggesting that one treatment with this mutagen can induce mutational signatures attributed to endogenous processes. No specific signatures could be attributed to obesity, high fat diet, wounding, or TPA. Cells carrying thousands of mutations persist over very long periods without inducing tumors or causing pathological changes but can give rise to tumors after short term exposure to TPA. Furthermore, normal cell turnover and proliferation during fetal and adult growth, is not sufficient for promotion, but tissue damage followed by regenerative proliferation seems to be required for tumor development. We conclude that tumor promoters, chronic inflammation, wounding, and obesity do not contribute significantly to tumor mutational burden, and that the rate-limiting determinant of tumor growth is exposure to a tumor promoter rather than the nature or number of genomic point mutations. These data are highly relevant to the recent demonstration of persistent oncogenic mutations in histologically normal human tissues during ageing.

cancer biology↗

bioRxiv2022

Engineering SARS-CoV-2 neutralizing antibodies for increased potency and reduced viral escape

The rapid spread of SARS-CoV-2 variants poses a constant threat of escape from monoclonal antibody and vaccine countermeasures. Mutations in the ACE2 receptor binding site on the surface S protein have been shown to disrupt antibody binding and prevent viral neutralization. Here, we use a directed evolution-based approach to engineer three neutralizing antibodies for enhanced binding to S protein. The engineered antibodies showed increased in vitro functional activity in terms of neutralization potency and/or breadth of neutralization against viral variants. Deep mutational scanning revealed that higher binding affinity reduced the total number of viral escape mutations. Studies in the Syrian hamster model showed two examples where the affinity matured antibody provided superior protection compared to the parental antibody. These data suggest that monoclonal antibodies for anti-viral indications could benefit from in vitro affinity maturation to reduce viral escape pathways and appropriate affinity maturation in vaccine immunization could help resist viral variation.

bioengineering↗

bioRxiv2021

A Transparent Ultrasound Array for Real-time Optical, Ultrasound and Photoacoustic Imaging

Objective and Impact StatementSimultaneous imaging of ultrasound and optical contrasts can help map structural, functional and molecular biomarkers inside living subjects with high spatial resolution. There is a need to develop a platform to facilitate this multimodal imaging capability to improve diagnostic sensitivity and specificity. IntroductionCurrently, combining ultrasound, photoacoustic and optical imaging modalities is challenging because con-ventional ultrasound transducer arrays are optically opaque. As a result, complex geometries are used to co-align both optical and ultrasound waves in the same field of view. MethodsOne elegant solution is to make the ultrasound transducer transparent to light. Here, we demonstrate a novel transparent ultrasound transducer (TUT) liner array fabricated using a transparent lithium niobate piezoelectric material for real-time multimodal imaging. ResultsThe TUT array consisted of 64 elements and centered at [~] 6 MHz frequency. We demonstrate a quad-mode ultrasound, Doppler ultrasound, photoacoustic and fluorescence imaging in real-time using the TUT array directly coupled to the tissue mimicking phantoms. ConclusionThe TUT array successfully showed a multimodal imaging capability, and has potential applications in diagnosing cancer, neuro and vascular diseases, including image-guided endoscopy and wearable imaging.

bioengineering↗

bioRxiv2020

Treatment of the X chromosome in mapping multiple quantitative trait loci

Statistical methods to map quantitative trait loci (QTL) often neglect the X chromosome and may focus exclusively on autosomal loci. But the X chromosome often requires special treatment: sex and cross-direction covariates may need to be included to avoid spurious evidence of linkage, and the X chromosome may require a separate significance threshold. In multiple-QTL analyses, including the consideration of epistatic interactions, the X chromosome also requires special care and consideration. We extend a penalized likelihood method for multiple-QTL model selection, to appropriately handle the X chromosome. We examine its performance in simulation and by application to a large eQTL data set. The method has been implemented in the package R/qtl.

genetics↗

bioRxiv2020

Cryo-Electron Microscopy Visualization of a Large Insertion in the 5S ribosomal RNA of the Extremely Halophilic Archaeon Halococcus morrhuae.

The extreme halophile Halococcus morrhuae (ATCC(R) 17082) contains a 108-nucleotide insertion in its 5S rRNA. Large rRNA expansions in Archaea are rare. This one almost doubles the length of the 5S rRNA. In order to understand how such an insertion is accommodated in the ribosome, we obtained a cryo-electron microscopy reconstruction of the native large subunit at subnanometer resolution. The insertion site forms a four-way junction that fully preserves the canonical 5S rRNA structure. Moving away from the junction site, the inserted region is conformationally flexible and does not pack tightly against the large subunit.

microbiology↗

bioRxiv2019

Regulation of KRAS4A/B splicing in cancer stem cells by the RBM39 splicing complex.

The KRAS oncogene is expressed as major KRAS4B and minor KRAS4A splice isoforms, the distinct functions of which in cancer are unknown. We demonstrate here that KRAS4A is enriched in cancer stem-like cells, and is activated by hypoxia, whereas KRAS4B is more widely expressed and responds to ER stress. Mice completely lacking either isoform are viable but resistant to lung cancer development, as are Kras4A/B double heterozygous mice expressing both isoforms, but in which splice regulation has been uncoupled. Splicing of KRAS4A, but not KRAS4B, in human tumor cells can be inhibited by treatment with the splice inhibitor indisulam, or by CRISPR/Cas inhibition of the RBM39 splicing complex. Our data suggest that control of KRAS4A/B splicing is a targetable vulnerability in KRAS mutant tumors.

cancer biology↗