Biology subjects

Phan, N.

Publications and source records attributed to Phan, N..

15 recordsLinked to original sources

bioRxiv2026

Experimentally Tuned Protein-RNA Rosetta Score Function using Bayesian Optimization

Protein-RNA complexes drive fundamental cellular processes such as transcription and translation. Despite the prevalence and importance of protein-RNA interactions, the field lacks reliable and accessible methods to quantify the energetic favorability of these interactions. We propose an experimentally tuned protein-RNA score function that can be directly implemented into ROSETTA. Fine-tuning these score functions for predictive tasks requires repeated evaluations on a set of protein-RNA complexes, which can be computationally expensive given the number of parameters to tune. We used Bayesian Optimization to efficiently improve the energetic agreement between ROSETTA and experimentation. We observe significant interactions for specific RNA subclasses, serving as further confirmation of the physical validity of the score function. Beyond protein-RNA interaction prediction, we establish a framework to efficiently fine-tune ROSETTA score functions for any protein-class interaction using Bayesian Optimization. TOC FIGURE O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/739244v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@c7d3edorg.highwire.dtl.DTLVardef@12a8fe2org.highwire.dtl.DTLVardef@14c4c5dorg.highwire.dtl.DTLVardef@297169_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

CovSite: A High-Throughput Blind Covalent Screening Framework for Reactive Site Detection

Targeted covalent inhibitors are a powerful, yet underexplored, class of therapeutics, and current computational covalent screeners are constrained in early drug discovery due to the need for prior knowledge of the target site and limited throughput. We present CovSite, a blind covalent screening tool that identifies candidate reactive residues across the entire protein surface, utilizing only the protein structure and electrophile SMILES. CovSite applies a pipeline of four orthogonal physicochemical filters (nucleophile identification, solvent accessibility, environment-dependent deprotonation prediction, and semi-quantum-mechanical reactivity ranking) to identify potential small-molecule candidate inhibitors. Validated against 2,062 diverse covalent protein-ligand complexes spanning six nucleophilic residue types, CovSite achieves a 98.5% blind target site hit on a held-out benchmark set of 207 cysteine-targeted complexes while reducing the search space by 97.8%. The target-site hit detection exceeds the 53-62% accuracy of popular covalent screening tools operating under non-blind conditions on the same benchmark set. By extending nucleophilic coverage beyond cysteine to include serine, threonine, lysine, histidine, and tyrosine, and completing a screening of a 200-residue protein in two to three minutes on standard hardware, CovSite serves as a platform technology with the potential to address critical gaps in throughput, generalizability, and accuracy in this field of covalent screening. We demonstrate this capability by using CovSite as a blind, ligand-specific approach that enables iterative, machine-learning-driven covalent inhibitor generation that is impractical with existing tools, establishing a foundation for computationally guided covalent drug discovery for novel and understudied targets. TOC Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/739288v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@139335forg.highwire.dtl.DTLVardef@5bd9feorg.highwire.dtl.DTLVardef@44d6c8org.highwire.dtl.DTLVardef@1710154_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Air-driven aldehyde synthesis in engineered bacteria via gene deletion and aryl-alcohol oxidase profiling

Engineered bacterial routes for oxidation of non-native alcohols face three challenges: Nicotinamide-dependent enzymes are coupled to cellular redox metabolism, nicotinamide-independent aryl-alcohol oxidases (AAOs) usually express poorly in bacteria, and aldehyde products are rapidly modified by host enzymes. Here, we address these limitations by engineering aldehyde-retaining Escherichia coli for discovery and application of soluble bacterial AAOs. Screening 51 candidates revealed a high-expression sequence cluster containing enzymes that are active on diverse aromatic and furan-based alcohols. Pairing the top-performing AAO with designer pathways in aldehyde-retaining cells enabled modular C-N and C-C bond forming cascades starting from supplied alcohols. By making both the oxidase and its product compatible with the host, this work advances air-driven oxidation of diverse alcohols as a programmable entry point to aldehyde-derived chemistry in engineered bacteria.

synthetic biology↗

bioRxiv2026

circPMS1-mediated LIM protein scaffolding promotes cytoskeletal remodeling and melanoma metastasis

Circular RNAs (circRNAs) have been implicated in diverse biological processes and diseases such as cancer; however, their functional roles in tumor biology remain incompletely understood. Here, we identify circPMS1 as an aberrantly upregulated, pro-metastatic circRNA in melanoma. Overexpression and silencing studies revealed that circPMS1 promotes migration and invasion of non-transformed melanocytes and melanoma cells, enhances metastasis in xenograft models, and drives spontaneous dissemination and lymph node metastases in a genetically engineered melanoma mouse model. circPMS1 pro-metastatic activity depends on its circularization and is mediated by a putative secondary structure spanning the back-splice junction and the canonical start codon of the linear PMS1 mRNA. Proteomic analysis identified LIM domain proteins, including ABLIM1, LMO7, and PDLIM7, as circPMS1-bound factors. Mechanistic studies demonstrate that circPMS1 scaffolds these LIM proteins, enhancing their association with actin filaments inducing focal adhesion and cytoskeletal remodeling. This remodeling is associated with RhoA activity, and inhibition of the RhoA pathway attenuates circPMS1-induced migration. Together, these findings establish circPMS1 as a pro-metastatic circRNA that drives melanoma progression by scaffolding LIM domain proteins and regulating cytoskeletal dynamics and cell motility.

Cancer Biology↗

bioRxiv2025

Viral non-coding RNAs hijack host Pumilio proteins to regulate host transcripts

Viral non-coding RNAs (ncRNAs) often perform multiple functions during persistent infection, but how they interface with host RNA-binding proteins remains incompletely understood. Herpesvirus saimiri (HVS), a T-tropic {gamma}-herpesvirus that induces aggressive lymphomas in primates, during its latency expresses abundant small nuclear RNAs HSUR1 and HSUR2. HSUR1 is known to trigger target-directed microRNA decay (TDMD) of host miR-27a, and HSUR2 can function as a miRNA-dependent adaptor; here we show that both HSURs also bind host Pumilio proteins (PUM1 and PUM2) via perfectly conserved Pumilio response elements (PREs). PUM proteins are potent post-transcriptional regulators that bind PREs usually located in 3' UTRs of mRNAs to repress protein production. In Jurkat T cells, wild-type HSUR1/2, but not PRE-mutant variants, shift cells from a naive-like toward an effector/memory-like state. This PRE-dependent shift is evidenced by increased surface expression of CXCR3, a chemokine receptor of activated effector T cells, and CD57, a marker of terminally differentiated T and NK cells. Our data support a model in which HSURs sequester a fraction of PUM proteins. Consistently, depletion of PUM1 or PUM2 phenocopies HSUR-induced changes, with more abundant PUM1 exerting the dominant effect. Consistently, depletion of PUM1 or PUM2 phenocopies HSUR-induced changes, with more abundant PUM1 exerting the dominant effect. In BJAB B cells, HSUR1 still drives PRE-dependent gene regulation, but the affected genes only partially overlap with those in Jurkat cells, and some transcripts even show reversed direction of change, revealing strong cell-type specificity. By identifying PUM1/2 as key host partners of HSUR ncRNAs, this work uncovers an underappreciated role for PUM proteins in shaping T- and B-cell states and reveals an additional way in which{gamma} -herpesviral ncRNAs reprogram lymphocytes to promote viral persistence.

cell biology↗

bioRxiv2025

Modular Nanobody Conjugates with Controlled Topology Using Genetically Encoded Non-canonical Amino Acids

Bispecific antibody-based derivatives are traditionally generated by fusing short, flexible peptides to two variable heavy and light chain pairs that recognize distinct antigens. However, this method limits domain joining to the amino (N) or carboxyl (C) termini, thereby restricting our ability to study the role of domain orientation in key properties of bispecific molecules, such as affinity and specificity. Here, we present an adaptable, plug-and-play application of genetic code expansion technology for the rapid, modular creation of bispecific nanobody conjugates from non-canonical amino acid (ncAA)- integrated nanobody domains, offering precise control over domain topology. We implement this strategy using a single-plasmid genetic code expansion system and computation-guided ncAA site selection to preserve nanobody expression and target binding. We demonstrate the effective incorporation and crosslinking of azide- and tetrazine-modified lysine and phenylalanine, respectively, at four engineered positions within an anti-PD-L1 nanobody and two positions within an anti-CTLA-4 nanobody in a panel of immune cell- and cancer-cell-binding nanobodies. Using this approach, we demonstrate the modular synthesis of a library of bispecific nanobodies, comprising four PD-L1xCD16 immune synapse engagers and eight PD-L1xCTLA-4 immune checkpoint bispecifics. This work enables a new dimension of control over protein crosslinking for rapidly constructing immune cell engagers for dual immune checkpoint blockade therapy and to bridge the synapse between immune cells and cancer cells.

bioengineering↗

bioRxiv2025

PUM2 binds SARS-CoV-2 RNA and PUM1 mildly reduces viral RNA levels, but neither protein affects progeny virus production

Pumilio proteins (PUM1 and PUM2) are essential post-transcriptional regulators of gene expression found across plants, animals, and yeast. They bind Pumilio Response Elements (PREs) on messenger RNAs (mRNAs) to modulate mRNA stability and translation. PUMs have been implicated in diverse cellular processes, including stem cell maintenance, neurogenesis, and cell cycle regulation. They have also been reported to negatively regulate innate immunity genes and to participate in viral RNA sensing. Previous high-throughput interactome studies revealed that PUMs bind SARS-CoV-2 RNA. We found that SARS-CoV-2 transcripts contain multiple conserved PREs, some of which are preferentially bound by PUM2. Surprisingly, altering PUM levels does not affect the production of progeny virions. However, depletion of PUM1 slightly increases intracellular viral RNA levels, suggesting that PUM1 either plays a mild antiviral role against SARS-CoV-2 or regulates a host factor that promotes viral replication. Notably, PUM1 also negatively regulates innate immunity gene expression both at steady state and during SARS-CoV-2 infection. Our findings support a complex immunomodulatory role for PUM1, acting both as a negative regulator of innate immunity genes and a mild inhibitor of SARS-CoV-2 RNA accumulation. However, in cell culture, these roles appear negligible based on viral progeny output. Whether the multiple PREs found in the SARS-CoV-2 genome contribute to evasion of PUM1 activity remains an open question.

microbiology↗

bioRxiv2023

Methods for constructing and evaluating consensus genomic interval sets

The amount of genomic region data continues to increase. Integrating across diverse genomic region sets requires consensus regions, which enable comparing regions across experiments, but also by necessity lose precision in region definitions. We require methods to assess this loss of precision and build optimal consensus region sets. Here, we introduce the concept of flexible intervals and propose 3 novel methods for building consensus region sets, or universes: a coverage cutoff method, a likelihood method, and a Hidden Markov Model. We then propose 3 novel measures for evaluating how well a proposed universe fits a collection of region sets: a base-level overlap score, a region boundary distance score, and a likelihood score. We apply our methods and evaluation approaches to several collections of region sets and show how these methods can be used to evaluate fit of universes and build optimal universes. We describe scenarios where the common approach of merging regions to create consensus leads to undesirable outcomes and provide principled alternatives that provide interoperability of interval data while minimizing loss of resolution. Software is available at https://github.com/databio/geniml.

genomics↗

bioRxiv2023

Targeted therapies prime oncogene-driven lung cancers for macrophage-mediated destruction

Macrophage immune checkpoint inhibitors, such as anti-CD47 antibodies, show promise in clinical trials for solid and hematologic malignancies. However, the best strategies to use these therapies remain unknown and ongoing studies suggest they may be most effective when used in combination with other anticancer agents. Here, we developed a novel screening platform to identify drugs that render lung cancer cells more vulnerable to macrophage attack, and we identified therapeutic synergy exists between genotype-directed therapies and anti-CD47 antibodies. In validation studies, we found the combination of genotype-directed therapies and CD47 blockade elicited robust phagocytosis and eliminated persister cells in vitro and maximized anti-tumor responses in vivo. Importantly, these findings broadly applied to lung cancers with various RTK/MAPK pathway alterations--including EGFR mutations, ALK fusions, or KRASG12C mutations. We observed downregulation of {beta}2-microglobulin and CD73 as molecular mechanisms contributing to enhanced sensitivity to macrophage attack. Our findings demonstrate that dual inhibition of the RTK/MAPK pathway and the CD47/SIRPa axis is a promising immunotherapeutic strategy. Our study provides strong rationale for testing this therapeutic combination in patients with lung cancers bearing driver mutations. Brief summaryUnbiased drug screens identify targeted therapies as drugs that make lung cancers with driver mutations more vulnerable to macrophage attack.

cancer biology↗

bioRxiv2022

Three-dimensional cilia structures from animals' closest unicellular relatives, the Choanoflagellates

In most eukaryotic organisms, cilia perform a variety of life-sustaining roles related to environmental sensing and motility. Cryo-electron microscopy has provided considerable insight into the morphology and function of ciliary structures, but studies have been limited to less than a dozen of the millions of known eukaryotic species. Ultrastructural information is particularly lacking for unicellular organisms in the opisthokont clade, leaving a sizeable gap in our understanding of cilia evolution between unicellular species and multicellular metazoans (animals). Choanoflagellates are important aquatic heterotrophs, uniquely positioned within the opisthokonts as the metazoans closest living unicellular relatives. We performed cryo-focused ion beam milling and cryo-electron tomography on cilia from the choanoflagellate species Salpingoeca rosetta. We show that the axonemal dyneins, radial spokes, and central pair complex in S. rosetta more closely resemble metazoan structures than those of unicellular organisms from other suprakingdoms. In addition, we describe unique features of S. rosetta cilia, including microtubule holes, microtubule inner proteins, and the ciliary vane: a fine, net-like extension that has been notoriously difficult to visualize using other methods. Furthermore, we report barb-like structures of unknown function on the extracellular surface of the ciliary membrane. Together, our findings provide new insights into choanoflagellate biology and cilia evolution between unicellular and multicellular opisthokonts.

cell biology↗

bioRxiv2022

Ingestible capsule for detecting labile inflammatory biomarkers in situ

Transient molecules in the gastrointestinal (GI) tract, such as nitric oxide and hydrogen sulfide, are key signals and mediators of inflammatory bowel disease (IBD). Because these molecules are extremely short-lived in the body, they are difficult to detect. To track these reactive molecules in the GI tract, we have developed a miniaturized device that integrates genetically-engineered probiotic biosensors with a custom-designed photodetector and readout chip. Leveraging the molecular specificity of living sensors, we genetically encoded bacteria to respond to IBD-associated molecules by luminescing. Low-power electronic readout circuits (nanowatt power) integrated into the device convert the light from just 1 L of bacterial culture into a wireless signal. We demonstrate biosensor monitoring in the GI tract of small and large animal models and integration of all components into a sub-1.4 cm3 ingestible form factor capable of supporting wireless communication. The wireless detection of short-lived, disease-associated molecules could support earlier diagnosis of disease than is currently possible, more accurate tracking of disease progression, and more timely communication between patient and their care team supporting remote personalized care.

synthetic biology↗

bioRxiv2021

Structural organization of the C1b projection within the ciliary central apparatus

9+2 motile cilia contain 9 doublet microtubules and a central apparatus (CA) composed of two singlet microtubules with associated projections. The CA plays crucial roles in regulating ciliary motility. Defects in CA assembly or function usually result in motility-impaired or paralyzed cilia, which in humans causes disease. Despite their importance, the protein composition and functions of most CA projections remain largely unknown. Here, we combined genetic approaches and quantitative proteomics with cryo-electron tomography and subtomogram averaging to compare the CA of wild-type Chlamydomonas with those of two CA mutants. Our results show that two conserved proteins, FAP42 and FAP246, are localized to the L-shaped C1b projection of the CA. We also identified another novel CA candidate protein, FAP413, which interacts with both FAP42 and FAP246. FAP42 is a large protein that forms the peripheral beam of the C1b projection, and the FAP246-FAP413 subcomplex serves as the bracket between the beam (FAP42) and the C1b pillar that attaches the projection to the C1 microtubule. The FAP246-FAP413-FAP42 complex is essential for stable assembly of both the C1b and C1f projections, and loss of any of these proteins leads to ciliary motility defects. Our results provide insight into the subunit organization and 3D structure of the C1b projection, suggesting that the FAP246-FAP413-FAP42 subcomplex is part of a large interconnected CA-network that provides mechanical support and may play a role in mechano-signaling between the CA and radial spokes to regulate dynein activity and ciliary beating. Summary StatementThe present work provides insight into the subunit organization and 3D structure of the C1b projection of CA and the mechanism by which it regulates dynein activity and ciliary beating.

cell biology↗

bioRxiv2021

APOBEC3A drives acquired resistance to targeted therapies in non-small cell lung cancer

Acquired drug resistance to even the most effective anti-cancer targeted therapies remains an unsolved clinical problem. Although many drivers of acquired drug resistance have been identified1-6, the underlying molecular mechanisms shaping tumor evolution during treatment are incompletely understood. The extent to which therapy actively drives tumor evolution by promoting mutagenic processes7 or simply provides the selective pressure necessary for the outgrowth of drug-resistant clones8 remains an open question. Here, we report that lung cancer targeted therapies commonly used in the clinic induce the expression of cytidine deaminase APOBEC3A (A3A), leading to sustained mutagenesis in drug-tolerant cancer cells persisting during therapy. Induction of A3A facilitated the formation of double-strand DNA breaks (DSBs) in cycling drug-treated cells, and fully resistant clones that evolved from drug-tolerant intermediates exhibited an elevated burden of chromosomal aberrations such as copy number alterations and structural variations. Preventing therapy-induced A3A mutagenesis either by gene deletion or RNAi-mediated suppression delayed the emergence of drug resistance. Finally, we observed accumulation of A3A mutations in lung cancer patients who developed drug resistance after treatment with sequential targeted therapies. These data suggest that induction of A3A mutagenesis in response to targeted therapy treatment may facilitate the development of acquired resistance in non-small-cell lung cancer. Thus, suppressing expression or enzymatic activity of A3A may represent a potential therapeutic strategy to prevent or delay acquired resistance to lung cancer targeted therapy.

cancer biology↗

bioRxiv2019

Structural organization of the C1a-e-c supercomplex within the ciliary central apparatus

Nearly all motile cilia contain a central apparatus (CA) composed of two connected singlet-microtubules with attached projections that play crucial roles in regulating ciliary motility. Defects in CA assembly usually result in motility-impaired or paralyzed cilia, which in humans causes disease. Despite their importance, the protein composition and functions of the CA projections are largely unknown. Here, we integrated biochemical and genetic approaches with cryo-electron tomography to compare the CA of wild type Chlamydomonas with CA mutants. We identified a large (>2 MDa) complex, the C1a-e-c supercomplex, that requires the PF16 protein for assembly and contains the CA components FAP76, FAP81, FAP92, and FAP216. We localized these subunits within the supercomplex using nanogold-labeling and show that loss of any one of them results in impaired ciliary motility. These data provide insight into the subunit organization and three-dimensional (3D) structure of the CA, which is a prerequisite for understanding the molecular mechanisms by which the CA regulates ciliary beating.\n\nSummaryFu et al. use a wild-type vs. mutant comparison and cryo-electron tomography of Chlamydomonas flagella to identify central apparatus (CA) subunits and visualize their location in the native 3D CA structure. The study provides a better understanding of the CA and how it regulates ciliary motility.

cell biology↗

bioRxiv2017

Miniring approach for high-throughput drug screenings in 3D tumor models

There is increasing interest in developing 3D tumor organoid models for drug development and personalized medicine applications. While tumor organoids are in principle amenable to high-throughput drug screenings, progress has been hampered by technical constraints and extensive manipulations required by current methodologies. Here, we introduce a miniaturized, fully automatable, flexible high-throughput method using a simplified geometry to rapidly establish 3D organoids from cell lines and primary tissue and robustly assay drug responses. As proof of principle, we use our miniring approach to establish organoids of high-grade serous tumors and one carcinosarcoma of the ovaries and screen hundreds of protein kinase compounds currently FDA-approved or in clinical development. In all cases we could identify drugs causing significant reduction in cell viability, number and size of organoids within a week from surgery, a timeline compatible with therapeutic decision making.

cancer biology↗