Biology subjects

Budnik, B.

Publications and source records attributed to Budnik, B..

At least 19 recordsLinked to original sources

bioRxiv2026

Firewalled synthetic commensal blocks horizontal gene transfer in the gut

Synthetic biology enables the rational reprogramming of microorganisms into living therapeutics and agents for bioremediation. However, such genetically modified organisms (GMOs) disseminate their synthetic genetic information into natural microbial communities through horizontal gene transfer (HGT), posing biosafety risks that limit clinical and environmental deployment. Reassigning sense codons to an alternative amino acid identity establishes a genetic firewall that simultaneously prevents incoming and outgoing gene flow, but reported implementations compromise fitness, precluding clinical and industrial use. Here, we overcome this limitation using genome design and laboratory evolution to create a high-fitness genetically firewalled Escherichia coli commensal. By directly altering the amino acid identity of TCA and TCG serine codons in the genetic code without an unassigned intermediate, we establish a robust genetic firewall that remains stable for thousands of generations. This firewalled commensal stably colonizes the mouse gastrointestinal tract for more than 100 days and blocks viral infections and HGT. As the long-term within-gut evolution of this firewalled organism identified adaptive mutations in genes responsible for carbon source utilization, we rationally redesigned the strain's genome to increase fitness. Together, this work establishes a genetically firewalled commensal for safer living therapeutics development and provides a strategy for designing high-fitness, virus- and gene-transfer-resistant organisms for clinical and environmental use.

synthetic biology↗

bioRxiv2026

Viscoelastic Niches Shape γδ T-Cell Phenotype and Effector Function

{gamma}{delta} T-cells, which are predominantly enriched in epithelial tissues, have been used in cancer therapy because of their capacity for rapid cytotoxicity in an MHC-independent manner. Current paradigms are largely agnostic to the role of tissue mechanical cues in regulating {gamma}{delta} T-cell function. Here, we investigated the role of matrix viscoelasticity in modulating {gamma}{delta} T-cell migration, differentiation state, phenotype, and function. Using a tunable collagen-based gel system, we found that encapsulation in highly-elastic (slow-relaxing) matrices preserved a less differentiated phenotype, as evidenced by CD27 and CD45RA expression. Slow-relaxing matrices also increased expression of Fas and PD-1, while decreasing expression of CD11a. Despite increased PD-1 expression, these cells remained functional, as demonstrated by high levels of TNF- and IFN-{gamma} relative to PD-1-negative cells. Proteomic analysis revealed that {gamma}{delta} T-cells respond to changes in viscoelasticity through actin remodeling and shifts in metabolic machinery. Overall, when compared to non-encapsulated cells (2D culture), encapsulated {gamma}{delta} T-cells showed increased expression of cytotoxic programs. Functionally, cells encapsulated in slow-relaxing gels showed improved control of tumor growth in an aggressive HCT116 tumor model. Together, these findings establish matrix viscoelasticity as an important regulator of post-thymic {gamma}{delta} T-cell differentiation and function.

bioengineering↗

bioRxiv2026

Defining Quality Control Standards for Single-Cell Proteomics by Inter-Laboratory Benchmarking

Single-cell proteomics can quantify thousands of proteins from individual mammalian cells, yet the absence of community-wide quality control limits biological interpretability. Here, the HUPO Single Cell Initiative presents the first inter-laboratory single-cell proteomics benchmarking study across seven laboratories using standardized 384-well plates acquired on Orbitrap Astral and timsTOF Ultra2 instruments. Centralized analysis across six DIA software tools revealed that software choice impacts identification depth and quantitative accuracy more than instrument vendor. Multi-layered quality control enabled the detection of cell-leakage during sorting, LC misconfiguration, column degradation and site-specific pipetting failures. Inter-lab quantitative correlations were strongest between instruments of the same vendor relative to cross-platform comparisons. Sequential correction for plate identity and well position recovered clean cell-type separation for confident downstream differential expression analysis. This study provides a data-driven quality control framework spanning plate design to batch correction for reproducible single-cell proteomics across laboratories and platforms.

biochemistry↗

bioRxiv2026

Sequestration of growth cone surface proteins by cytoplasmic Lrrtm2 induces de novo amygdala innervation by cerebral cortex associative neurons

Precise establishment of distinct cerebral cortex circuits is essential for sensorimotor function, high-level cognition, and cross-modality integration and association. Although an increasing set of molecular controls over subtype-specific cortical wiring have been identified, much less is known about how molecules in growth cones (GCs) regulate precise long-range projection of axons through complex environments, or how dysregulation of GC molecular machinery disrupts precision of circuit formation. Here, we discover a generalizable mechanism for regulation of precise circuit wiring by focusing on callosal projection neurons (CPN), which link cortical hemispheres via the corpus callosum. CPN are centrally involved in associative and cognitive function, and are often disrupted in people with autism spectrum disorders (ASD) and intellectual disabilities (ID). We identify dysregulated subcellular CPN GC proteomes in vivo after CPN-specific deletion of Bcl11a/Ctip1, a transcription factor (TF) with variants that cause ASD/ID in humans, and validate localization of dysregulated proteins to CPN GCs ex vivo. We identify that disruption of Lrrtm2 - a canonically postsynaptic transmembrane protein - in CPN GCs specifically induces de novo innervation of the amygdala, an evolutionarily ancient regulator of social behavior, cognition, and anxiety that is abnormally activated in humans with ASD. Mechanistically, we identify that deletion of Bcl11a from CPN disrupts targeting of Lrrtm2 to CPN GC membranes, causing cytoplasmic sequestration of key CPN GC surface proteins, and resulting in aberrant innervation of basolateral amygdala (BLA), which is typically targeted by evolutionarily older archicortex. Together, this work connects deletion of a causal ASD/ID TF, dysregulation of a non-canonical control over GC surface protein remodeling, and formation of a de novo, subtype-specific circuit between cerebral cortex and BLA - similar mechanisms likely generalize across neuron subtypes. These results expand conceptual understanding of how diverse circuits are precisely constructed and potentially evolve, and how coordinated dysregulation of GC molecules can disrupt precise subtype-specific circuitry, contributing to diverse neurodevelopmental and neuropsychiatric disorders.

neuroscience↗

bioRxiv2026

Human fallopian tube-on-a-chip for preclinical testing of non-hormonal contraceptives with living human sperm

The fallopian tube serves as a sperm reservoir, and it is the site where the oocytes become fertilized. Here, we describe development of an organ-on-a-chip microfluidic model of the fallopian tube (FT Chip) lined by primary human epithelial cells and stromal fibroblasts derived from the FT ampulla. Abundant tissue folds lined by hormone-responsive, epithelial cells resembling those seen in vivo formed on-chip, but not in epithelial organoids cultured in gel cultures. Comparative time-resolved analysis of human sperm versus oocyte-sized microparticles introduced into the epithelial channel in the presence of estradiol revealed that sperm movement was significantly reduced, while the oocyte-sized particles increased, relative to movements in acellular chips. When the non-hormonal contraceptive TDI-11861 was administered to the chip, dose-dependent inhibition of human sperm motility was detected. Thus, this FT Chip may offer a human preclinical tool to study FT physiology and assess the efficacy and mechanism of action of contraceptives.

cell biology↗

bioRxiv2025

Endothelial CLK2 as a therapeutic target for acute radiation syndrome

Damage to the vascular endothelium is a major contributor to acute radiation injury in multiple organs that underlies acute radiation syndrome (ARS), yet there are no FDA-approved radiation countermeasures targeting endothelial cells. Use of kinome-scale CRISPR screens performed in cultured human vascular endothelial cells isolated from different organs identified CLK2 as a potential radioprotective target. Pharmacological inhibition of CLK2 using TG003 and Cirtuvivint protected these endothelial cells against radiation injury and reversed its effects across the transcriptome and phospho-proteome. Human Organ Chip models of human intestine and lung that contain organ-specific epithelium and microvascular endothelium faithfully replicated clinical features of ARS when exposed to radiation, which were prevented when treated with CLK2 inhibitors. Thus, CLK2 inhibitors may represent a new class of radiation countermeasure drugs that can protect multiple organs against radiation-induced toxicities in patients with ARS.

molecular biology↗

bioRxiv2025

Induction of cervical dysfunction associated with preterm birth by IL-1 and dysbiotic microbiome revealed in human endocervix chips

Cervical dysfunction, a major contributor to preterm labor and neonatal mortality, remains poorly understood due to the absence of physiologically relevant human models. Here, we show that a microfluidic human Endocervix Chip lined by primary endocervical epithelium interfaced with stromal cells and cultured under pregnancy-like hormonal conditions recapitulates key aspects of the biology of the endocervix, including formation of a mucus plug-like structure with antimicrobial properties. Culturing a dysbiotic cervico-vaginal microbiome on-chip increased secretion of pro-inflammatory cytokines observed in patients with preterm labor and enhanced production of matrix metalloproteinases (MMPs) that degrade stromal extracellular matrix (ECM). Perfusion with inflammatory cytokines at clinically relevant concentrations altered cervical mucus composition, upregulated prostaglandin-endoperoxide synthase 2 expression, increased MMP secretion, and reduced collagen production, which together drive dissolution of the stromal ECM and promote cervical ripening. Addition of circulating peripheral blood mononuclear cells (PBMCs) amplified these effects. Administration of a clinically approved drug for prevention of preterm labor that the Food and Drug Administration (FDA) recently deemed ineffective was also found to be inactive in the chip, while an approved therapeutic antagonist of the IL-1 receptor successfully protected against cervical dysfunction in this model. These findings demonstrate that IL-1 acts directly on human cervical tissues to promote changes associated with initiation of labor and that primary human endocervix chips may represent a useful preclinical model for studies on cervical dysfunction associated with preterm birth. One Sentence SummaryHuman endocervix chip modeling of cervical dysfunction suggests that IL-1 receptor antagonists may prevent preterm labor.

bioengineering↗

bioRxiv2025

Altered Protein Phosphorylation in a Novel Midbrain Organoid Model for Bipolar Disorder

Bipolar disorder (BD) is a severe psychiatric condition marked by episodes of mania and depression, with neurotransmitter imbalance in the midbrain believed to play a critical role in its pathophysiology. Despite this, there is currently no validated midbrain model for examining BD-associated molecular changes available. Leveraging recent advances in stem cell technology, we developed a midbrain organoid model using human induced pluripotent stem cells (hiPSCs) from BD patients and healthy controls (CTR). To address issues of variability and enhance the throughput in organoid production, we implemented liquid handling and high-content imaging techniques. Quality control metrics were established to identify organoids unsuitable for further study. Electrophysiological analysis via high-density microelectrode arrays (MEAs) revealed significantly elevated neuronal properties in individual BD organoids, including increased mean amplitude, conduction velocity, and extended axonal and dendritic growth. Transcriptome and proteome analyses indicated significant dysregulation of BD-relevant signaling pathways--such as those involving phosphatidylinositol, glycogen synthase kinase-3 beta, and AKT. Notably, we identified dysregulated casein kinase 2 (CSNK2A1) and calmodulin 3 (CALM3) in BD organoids, which were reversed by lithium treatment, highlighting potential novel targets for therapeutic intervention. This study validates the midbrain organoid model as a valuable tool for exploring the molecular underpinnings of BD and identifying new treatment avenues.

cell biology↗

bioRxiv2024

Cortical projection neurons with distinct axonal connectivity employ ribosomal complexes with distinct protein compositions

Diverse subtypes of cortical projection neurons (PN) form long-range axonal projections that are responsible for distinct sensory, motor, cognitive, and behavioral functions. Translational control has been identified at multiple stages of PN development, but how translational regulation contributes to formation of distinct, subtype-specific long-range circuits is poorly understood. Ribosomal complexes (RCs) exhibit variations of their component proteins, with an increasing set of examples that confer specialized translational control. Here, we directly compare the protein compositions of RCs in vivo from two closely related cortical neuron subtypes-cortical output "subcerebral PN" (SCPN) and interhemispheric "callosal PN" (CPN)- during establishment of their distinct axonal connectivity. Using retrograde labeling of subtype-specific somata, purification by fluorescence-activated cell sorting, ribosome immunoprecipitation, and ultra-low-input mass spectrometry, we identify distinct protein compositions of RCs from these two subtypes. Strikingly, we identify 16 associated proteins reliably and exclusively detected only in RCs of SCPN. 11 of these proteins have known interaction with components of ribosomes; we further validated ribosome interaction with protein kinase C epsilon (PRKCE), a candidate with roles in synaptogenesis. PRKCE and a subset of SCPN-specific candidate ribosome-associated proteins also exhibit enriched gene expression by SCPN. Together, these results indicate that ribosomal complexes exheq]ibit subtype-specific protein composition in distinct subtypes of cortical projection neurons during development, and identify potential candidates for further investigation of function in translational regulation involved in subtype-specific circuit formation.

neuroscience↗

bioRxiv2024

Preventing escape and malfunction of recoded cells due to tRNA base changes

Engineering the genetic code restricts DNA transfer (cellular bioisolation) and enables new chemistries via non-standard amino acid incorporation. These distinct properties make recoded cells state-of-the-art safe technologies. However, evolutionary pressures may endanger the longevity of the recoding. Here, we reveal that recoded Escherichia coli lacking 18,214 serine codons and two tRNASer can express wild-type antibiotic resistance genes and escape up to seven orders of magnitude faster than expected. We show a two-step escape process whereby recoded cells mistranslate antibiotic resistance genes to survive until modified or mutated tRNAs reintroduce serine into unassigned codons. We developed genetic-code-sensitive kill switches that sense serine incorporation and prevent cellular escape while preserving encoding of three distinct non-standard amino acids. This work lays the foundation for the long-term controlled function of cells that incorporate new chemistries, with implications for the design, use, and biosafety of synthetic genomes in clinical and environmental applications where physical containment is insufficient.

synthetic biology↗

bioRxiv2024

Synthetic genomes unveil the effects of synonymous recoding

Engineering the genetic code of an organism provides the basis for (i) making any organism safely resistant to natural viruses and (ii) preventing genetic information flow into and out of genetically modified organisms while (iii) allowing the biosynthesis of genetically encoded unnatural polymers1-4. Achieving these three goals requires the reassignment of multiple of the 64 codons nature uses to encode proteins. However, synonymous codon replacement--recoding--is frequently lethal, and how recoding impacts fitness remains poorly explored. Here, we explore these effects using whole-genome synthesis, multiplexed directed evolution, and genome-transcriptome-translatome-proteome co-profiling on multiple recoded genomes. Using this information, we assemble a synthetic Escherichia coli genome in seven sections using only 57 codons to encode proteins. By discovering the rules responsible for the lethality of synonymous recoding and developing a data-driven multi-omics-based genome construction workflow that troubleshoots synthetic genomes, we overcome the lethal effects of 62,007 synonymous codon swaps and 11,108 additional genomic edits. We show that synonymous recoding induces transcriptional noise including new antisense RNAs, leading to drastic transcriptome and proteome perturbation. As the elimination of select codons from an organisms genetic code results in the widespread appearance of cryptic promoters, we show that synonymous codon choice may naturally evolve to minimize transcriptional noise. Our work provides the first genome-scale description of how synonymous codon changes influence organismal fitness and paves the way for the construction of functional genomes that provide genetic firewalls from natural ecosystems and safely produce biopolymers, drugs, and enzymes with an expanded chemistry.

synthetic biology↗

bioRxiv2024

Identification of markers for the isolation of neuron-specific extracellular vesicles

Extracellular vesicles (EVs) are released by all cells and contain RNA and protein from their cell of origin. EVs in biofluids could be used as diagnostic biomarkers to non-invasively report the state of inaccessible cells, such as neurons in the brain. As biofluids such as cerebrospinal fluid (CSF) and plasma contain EVs originating from many different cells, isolating cell type-specific EVs and measuring their cargo could help determine the state of specific cell types. Here, we demonstrate an approach aiming to immuno-isolate EVs from neurons based on neuron-derived protein surface markers. We first developed a framework to select transmembrane proteins suitable as neuron-specific EV markers based on gene expression and EV proteomics data. Leveraging a novel, high-purity EV isolation method we developed, we further cataloged the proteins present on EVs in human CSF and plasma. Using ultrasensitive immunoassays against several of the predicted neuron-specific proteins, we confirmed one marker, NRXN3 as present on EVs in CSF and plasma by size exclusion chromatography (SEC) and density gradient centrifugation (DGC). Finally, we developed efficient EV immuno-isolation methods and applied them to isolate NRXN3+ EVs. Our study provides a general methodology for the isolation of cell-type specific EVs and paves the way for the use of neuron-derived EVs to study and diagnose neurological disease.

molecular biology↗

bioRxiv2024

Control of Molecular Biochemistry and Cell Injury Responses through Highly Ordered Supramolecular Assembly of Flavonoids

Flavonoids are phytonutrients commonly found in plant-based foods and are generally known for their health benefits. However, their utility as potential therapeutics has not been explored because their presence in drug development tests can lead to false positives due to non-specific binding. Here, we employed molecular dynamic simulations (MDS) to examine flavonoid behavior and discovered that they form highly organized supramolecular assemblies that physically interact with disordered regions of enzymatic proteins and can physically interlink multiple protein molecules. These flavonoid assemblies adopt secondary structural patterns like those found in proteins and nucleic acids, and they physically influence molecular movement and tertiary protein structure, thereby modulating the biochemical activities of a diverse range of enzymes. Moreover, in the presence of flavonoids, human cells are protected against injury caused by ultraviolet radiation. These findings unveil a novel form of biochemical regulation wherein small molecules can modulate the function of larger proteins by forming supramolecular assemblies which results in enhanced molecular and cellular resilience. Single Sentence SummaryMolecular dynamic simulations led to the discovery that flavonoid phytonutrients can self-assemble into highly ordered supramolecular structures that interact with enzymatic proteins, slow biochemical activities, and protect cells against injury.

biochemistry↗

bioRxiv2024

Symmetry in levels of axon-axon homophilic adhesion establishes topography in the corpus callosum and development of connectivity between brain hemispheres

Specific and highly diverse connectivity between functionally specialized regions of the nervous system is controlled at multiple scales, from anatomically organized connectivity following macroscopic axon tracts to individual axon target-finding and synapse formation. Identifying mechanisms that enable entire subpopulations of related neurons to project their axons with regional specificity within stereotyped tracts to form appropriate long-range connectivity is key to understanding brain development, organization, and function. Here, we investigate how axons of the cerebral cortex form precise connections between the two cortical hemispheres via the corpus callosum. We identify topographic principles of the developing trans-hemispheric callosal tract that emerge through intrinsic guidance executed by growing axons in the corpus callosum within the first postnatal week in mice. Using micro-transplantation of regionally distinct neurons, subtype-specific growth cone purification, subcellular proteomics, and in utero gene manipulation, we investigate guidance mechanisms of transhemispheric axons. We find that adhesion molecule levels instruct tract topography and target field guidance. We propose a model in which transcallosal axons in the developing brain perform a "handshake" that is guided through co-fasciculation with symmetric contralateral axons, resulting in the stereotyped homotopic connectivity between the brains hemispheres.

neuroscience↗

bioRxiv2023

A blood-brain-barrier penetrant AAV gene therapy rescues neurological deficits in mucolipidosis IV mice.

Mucolipidosis IV (MLIV) is a rare, autosomal recessive, lysosomal disease characterized by intellectual disability, motor deficits and progressive vision loss. Using AAV9 and AAV-PHP.B as delivery vectors, we previously demonstrated the feasibility of modifying disease course in a mouse model of MLIV by the human MCOLN1 gene transfer. Here, using a primate-enabling capsid AAV.CPP.16 (CPP16), we constructed a new, clinic-oriented MCOLN1 gene expression vector and demonstrated its efficacy in the preclinical model of MLIV. Systemic administration of CPP16-MCOLN1 in adult symptomatic Mcoln1-/- mice at a dose of 1e12 vg per mouse resulted in MCOLN1 expression in the brain and peripheral tissues, alleviated brain pathology, rescued neuromotor function, and completely prevented paralysis. Notable expression of MCOLN1 transcripts was also detected in the retina of the mouse that had exhibited significant degeneration at the time of the treatment. However, no increase of retinal thickness was observed after the gene therapy treatment. Our results suggest a new AAV-based systemic gene replacement therapy for the treatment of MLIV that could be translated into clinical studies.

genetics↗

bioRxiv2023

Brain cell type specific proteomics approach to discover pathological mechanisms in the childhood CNS disorder mucolipidosis type IV

1 Mucolipidosis IV (MLIV) is an ultra-rare, recessively inherited lysosomal disorder resulting from inactivating mutations in MCOLN1, the gene encoding the lysosomal cation channel TRPML1. The disease primarily affects the central nervous system (CNS) and manifests in the first year with cognitive and motor developmental delay, followed by a gradual decline in neurological function across the second decade of life, blindness, and premature death in third or fourth decades. Brain pathology manifestations in MLIV are consistent with hypomyelinating leukodystrophy with brain iron accumulation. Presently, there are no approved or investigational therapies for MLIV, and pathogenic mechanisms remain largely unknown. The MLIV mouse model, Mcoln1-/- mice, recapitulates all major manifestations of the human disease. Here, to better understand the pathological mechanisms in the MLIV brain, we performed cell type specific LC-MS/MS proteomics analysis in the MLIV mouse model and reconstituted molecular signatures of the disease in either freshly isolated populations of neurons, astrocytes, oligodendrocytes, and neural stem cells, or whole tissue cortical homogenates from young adult symptomatic Mcoln1-/- mice. Our analysis confirmed on the molecular level major histopathological hallmarks of MLIV universally present in Mcoln1-/- tissue and brain cells, such as hypomyelination, lysosomal dysregulation, and impaired metabolism of lipids and polysaccharides. Importantly, pathway analysis in brain cells revealed mitochondria-related alterations in all Mcoln1-/- brain cells, except oligodendrocytes, that was not possible to resolve in whole tissue. We also report unique proteome signatures and dysregulated pathways for each brain cell population used in this study. These data shed new light on cell-intrinsic mechanisms of MLIV and provide new insights for biomarker discovery and validation to advance translational studies for this disease.

neuroscience↗

bioRxiv2023

Improved Isolation of Extracellular Vesicles by Removal of Both Free Proteins and Lipoproteins

Extracellular vesicles (EVs) are released by all cells into biofluids such as plasma. The separation of EVs from highly abundant free proteins and similarly-sized lipoproteins remains technically challenging. We developed a digital ELISA assay based on Single Molecule Array (Simoa) technology for ApoB-100, the protein component of several lipoproteins. Combining this ApoB-100 assay with previously developed Simoa assays for albumin and three tetraspanin proteins found on EVs (Ter-Ovanesyan*, Norman* et al., 2021), we were able to measure the separation of EVs from both lipoproteins and free proteins. We used these five assays to compare EV separation from lipoproteins using size exclusion chromatography (SEC) with resins containing different pore sizes. We also developed improved methods for EV isolation based on combining several types of chromatography resins in the same column. We present a simple approach to quantitatively measure the main contaminants of EV isolation in plasma and apply this approach to develop novel methods for isolating highly-pure EVs from human plasma. These methods will enable applications where high purity EVs are required to both understand EV biology and profile EVs for biomarker discovery.

bioengineering↗

bioRxiv2022

Swapped genetic code blocks viral infections and gene transfer

Removing cellular transfer RNAs (tRNAs), making their cognate codons unreadable, creates a genetic firewall that prevents viral replication and horizontal gene transfer. However, numerous viruses and mobile genetic elements encode parts of the translational apparatus, including tRNAs, potentially rendering a genetic-code-based firewall ineffective. In this paper, we show that such horizontally transferred tRNA genes can enable viral replication in Escherichia coli cells despite the genome-wide lack of three codons and the previously essential cognate tRNAs and release factor 1. By repurposing viral tRNAs, we then develop recoded cells bearing an amino-acid-swapped genetic code that reassigns two of the six serine codons to leucine during translation. This amino-acid-swapped genetic code renders cells completely resistant to viral infections by mistranslating viral proteomes and prevents the escape of synthetic genetic information by engineered reliance on serine codons to produce leucine-requiring proteins. Finally, we also repurpose the third free codon to biocontain this virus-resistant host via dependence on an amino acid not found in nature.

synthetic biology↗