Biology subjects

Mueller, C.

Publications and source records attributed to Mueller, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Evolutionary history and polyploidization lead to rapid shifts in chemodiversity of Hypericum

Polyploidization can profoundly affect plant metabolite biosynthesis, yet its influence on chemodiversity remains poorly understood, despite the central role of chemodiversity in mediating plant interactions with the environment. The coexistence of facultative apomictic and sexual reproductive systems across ploidy levels in Hypericum provides an excellent model for investigating the evolution of chemodiversity following polyploidization. We analyzed ploidy levels and leaf metabolic fingerprints across selected populations of three Hypericum taxa, H. maculatum, H. perforatum subsp. perforatum and H. perforatum subsp. veronense. Polyploidization was common across all three taxa. Leaf metabolic fingerprints were more pronouncedly differentiated by the ploidy level of the mother plant (F0) than that of the offspring (F1). Although unique metabolic features emerged in plants of most ploidy levels, diploid plants exhibited fewer metabolic features than polyploid plants. Higher Shannon diversity, functional Hill diversity, and intensities of features belonging to specific chemical families were associated with higher F0 ploidy levels in H. perforatum subsp. perforatum, but not in H. maculatum and H. perforatum subsp. veronense. Our findings demonstrate that polyploidization can lead to rapid shifts in chemodiversity across generations in Hypericum. The fast divergence in chemodiversity associated with polyploidization in H. perforatum may contribute to its remarkable invasive potential.

plant biology↗

bioRxiv2026

Comprehensive ctDNA Profiling Enables Tissue-of-Origin Prediction and Actionable Biomarker Detection in Cancer of Unknown Primary

Most patients with cancer of unknown primary (CUP) still receive platinum-based chemotherapy and have a poor prognosis, with overall survival of less than one year. Recent studies suggest improved outcomes with molecularly guided or site-specific therapies informed by molecular tissue profiling. Here, we analyzed ctDNA from 190 CUP patients using an integrated genomic and epigenomic assay to identify actionable alterations and predict tissue-of-origin (ToO). Integration of actionable biomarkers, ToO prediction and clinical data yielded diagnostic, prognostic or therapeutic information in 90% of unfavorable CUP cases and 88% of patients analyzed at first diagnosis. High ctDNA tumor fraction was associated with poorer prognosis in both favorable and unfavorable CUP. These findings highlight the clinical utility of ctDNA analysis for therapeutic decision-making in CUP and support its incorporation into the diagnostic work-up, particularly when tissue samples are unavailable or insufficient for molecular testing.

Cancer Biology↗

bioRxiv2026

Genetic analysis of maize seedling root traits under chilling highlights their importance for early field development

Characterizing the genetic basis of root system architecture and its role in early plant development is essential for developing maize varieties with improved nutrient uptake, enhanced early vigour, and higher yield potential in temperate regions. Landraces represent an invaluable source of allelic diversity that can be leveraged to enrich the genetic basis of modern breeding material. In this study, we used a high throughput phenotyping platform to characterize genetic variation for seedling root traits under chilling conditions relevant for early plant establishment in a large doubled haploid (DH) library derived from two European maize landraces. We dissected the quantitative genetic architecture of twelve seedling root traits using a haplotype-based genome-wide association study, identifying large-effect haplotypes specific to the individual landraces as well as numerous small-effect haplotypes present in both landraces. We validated the effects of four QTL in a biparental population, demonstrating their stability across genetic backgrounds. We found highly significant correlations between haplotype effects on seedling root traits evaluated in the phenotyping platform and early plant height evaluated in multi environment field trials, demonstrating the relevance of seedling root architecture for early plant establishment. In particular, haplotypes associated with seminal and lateral root length were the major determinants of early plant height under field conditions. Several of the haplotypes increasing seedling root length were absent from a broad panel of flint breeding lines, highlighting their potential as targets for introgression to improve early plant establishment under temperate growing conditions. Key messageSeedling root QTL discovered in a high throughput phenotyping platform under chilling conditions influence early plant development in the field.

genetics↗

bioRxiv2026

Influence of different pharmaceuticals on the germination and early development of two leafy vegetable species

Pharmaceuticals are becoming increasingly prevalent in the environment, yet their effects on terrestrial plants, especially during early development, are poorly investigated. In this context, leafy vegetables are of particular interest because they tend to accumulate more pharmaceuticals than other crops. This study investigated the impacts of six pharmaceuticals of different classes commonly detected in soils and water on seed germination and early seedling growth of the leafy vegetables bok choy (Brassica rapa subsp. chinensis) and spinach (Spinacia oleracea) under controlled conditions. Seeds were exposed to different concentrations of the non-steroidal anti-inflammatory drugs (NSAIDs) ibuprofen, naproxen, diclofenac, or salicylic acid, the antiepileptic drug carbamazepine, or the antibiotic ciprofloxacin, and germination rates, root and shoot lengths, biomass allocation, cotyledon development, and lateral root formation (in bok choy only) measured after seven days. While germination was unaffected, early development parameters showed species-specific responses. In bok choy, high concentrations of NSAIDs and ciprofloxacin led to an increased shoot biomass and cotyledon area but a reduced primary root growth and lateral root formation, while carbamazepine had no effect. The contrasting effects on aboveground versus belowground organs of different pharmaceuticals suggest an interference with hormonal regulation, especially auxin. Spinach showed less responses than bok choy, with root length being rather increased by some NSAIDs. These results indicate that sensitivity to pharmaceuticals begins after germination and depends on both the chemical properties of the compound and the plant species. The study highlights the value of systematic comparative testing of pharmaceuticals across plant species.

pharmacology and toxicology↗

bioRxiv2026

Common, species-specific, and accession-specific responses of foliar phytohormones and morphological traits to drought and herbivory

BackgroundPlants are exposed to various environmental challenges. With ongoing climate change, droughts and insect outbreaks are expected to become more frequent. Thus, a better understanding is needed of how different plant species respond to such single and combined challenges. This study investigated common versus species-specific responses to environmental challenges in three perennial plant species of different growth forms and whether responses differ intraspecifically among accessions. Clones of different accessions of the herbaceous species Tanacetum vulgare, the woody vine Solanum dulcamara, and the tree Populus nigra were subjected to similar control, herbivory, drought, and combined (drought and herbivory) treatments for the same periods. After the exposure, concentrations of foliar phytohormones and various morphological traits were measured. ResultsAcross all species, several foliar phytohormones and one of ten morphological traits responded consistently to the environmental challenges. Jasmonoyl-isoleucine was induced by herbivory and the combined treatment, abscisic acid (ABA) by drought and the combined treatment, and indole acetic acid by the combined treatment in all species. Root mass remained unchanged in all species. However, structural equation models (SEMs) revealed a shared regulatory pathway across species in which ABA connected treatment and root mass, indicating a common hormonal response potentially linking challenges to growth responses. Despite these common patterns, species-specific responses were pronounced. In P. nigra, a unique induction of salicylic acid was found under the combined treatment, while aboveground mass and root-shoot ratio remained unaffected by any treatment, in contrast to the other two species. Species-specific SEMs further indicated distinct phytohormone-mediated pathways underlying morphological variation. Phenotypic plasticity reflected these species-specific patterns, with none of the phytohormones or morphological traits exhibiting uniform plasticity across species. Intraspecific variation further shaped responses, as phytohormone and morphological trait plasticity depended on accession, indicating substantial accession-specific plant responses. ConclusionsOur results indicate that some responses to comparable challenges may be conserved across species, while others are species-specific. The combined treatment elicited the most pronounced responses, and such complex responses may become more frequent under current global change. Our study highlights that comprehensive understanding of plant responses requires systematic comparisons at both interspecific and intraspecific scales.

ecology↗

bioRxiv2025

The Microbiotas Response to Host Adaptive Evolution

Over the past two decades, experimental evolution has significantly advanced our understanding of evolutionary patterns and mechanisms of genomic change. One critically underexplored dimension is the role of microbiota in host adaptive evolution. In this research we investigate the microbiota from forty laboratory-selected Drosophila melanogaster populations exhibiting four distinct aging trajectories, ranging from extremely-short lifespans to -long lifespans. Using metagenomic sequencing and colony forming unit (CFU) counts in both conventional and gnotobiotic conditions, we uncover substantial microbiota differentiation among these populations. The most striking pattern is the consistent loss of Wolbachia in populations selected for rapid aging, in contrast to its near complete dominance in long-lived populations. This suggests a positive association between relative abundance of Wolbachia and lifespan, alongside a negative correlation between Wolbachia and Acetic Acid Bacteria (AAB) titres. These findings position the microbiota, and particularly Wolbachia, as a potentially integral component in host life history evolution, with implications for understanding the microbial contributions to aging and adaptation. SignificanceFruit flies bred for short lifespans consistently lose the bacterial symbiote Wolbachia, while the microbiota of long-lived flies are almost entirely dominated by it. There is a stable, recurring link between this microbe and lifespan, and traits associated with lifespan. This persistent pattern suggests that microbiota, Wolbachia in particular, may play a direct role in shaping the evolution of lifespan.

microbiology↗

bioRxiv2025

Exploring contemporary and historic effective population sizes in Atlantic beluga whale populations

Ongoing global environmental changes will require animals to adapt to new conditions, as their necessary resources for survival may shift or decline. Understanding population dynamics in wildlife informs conservation strategies by providing context for genetic diversity and current population abundances. Here, we use whole genome data to reconstruct past demographic trends and estimate contemporary effective population sizes in the beluga whale (Delphinapterus leucas), an Arctic endemic species with significant cultural importance, that is an integral part of the marine ecosystem along the Canadian coast. In line with previous work, we identified six genetic populations: 1) St. Lawrence Estuary, 2) Eastern High Arctic, 3) James Bay, 4) Cumberland Sound, 5) Hudson Bay-Strait Complex and 6) Little and Great Whale Rivers. Demographic history in the deep (up to 1,000,000 years) past revealed all but the Hudson Bay-Strait Complex population declined in effective population sizes following the last glacial period. Within the last several centuries, the Eastern High Arctic and Hudson Bay-Strait Complex populations have shown evidence for an increase in effective population size and have contemporary estimates greater than 2,000. The other four populations have contemporary estimates below 400. The very low effective population size estimates in Cumberland Sound, Little and Great Whale Rivers and James Bay, as well as the high inbreeding in the St. Lawrence Estuary indicate that these populations are in need of protective measures for long-term sustainability. These results have advanced our understanding of the dynamics of beluga genetics across eastern Canada and provide valuable metrics for conservation strategies.

evolutionary biology↗

bioRxiv2025

Ergosterol-depleted clinical isolates of Nakaseomyces glabratus can develop multi-drug resistance without apparent fitness and virulence defects

ObjectivesNakaseomyces glabratus (formerly Candida glabrata) is a leading cause of invasive candidiasis and rapidly develops antifungal drug resistance during treatment. An increasing number of clinical isolates shows reduced susceptibility to echinocandins and azoles, leaving amphotericin B (AMB) as a last therapeutic option. Resistance of N. glabratus to this drug is rare and its underlying mechanisms are still not fully understood. Here, we describe two independent multidrug resistant (MDR) bloodstream isolates displaying resistance to AMB and anidulafungin (ANF) as well as a reduced susceptibility to azoles. MethodsWhole-genome sequencing and sterol profiling were performed on nine clinical N. glabratus isolates which were resistant to ANF and displayed resistance or low susceptibility to fluconazole (FLU) and AMB. The transcriptional response of reference strain CBS138 and an AMBR+ANFR isolate was analyzed by RNA-seq. Furthermore, PDR1 was deleted in the latter isolate to examine its influence on efflux pump gene expression. Additionally, fitness and virulence of the AMBR+ANFR isolate were examined in growth assays and a Galleria mellonella infection model. ResultsLoss of function mutations in the genes ERG3 and ERG4 is linked to ergosterol depletion and AMB resistance. Ergosterol depletion also contributed to a Pdr1-mediated up-regulation of ERG and ABC transporter genes which was associated with low FLU susceptibility. The AMBR isolates displayed no fitness defects and one of them was fully virulent in a G. mellonella infection model. ConclusionsThese findings demonstrate that ergosterol depletion in N. glabratus leads to AMB resistance without affecting fitness or virulence.

microbiology↗

bioRxiv2025

Contractility governs cardiomyocyte cell cycle activity

The hearts rhythmic contractions keep blood flowing to deliver the oxygen and nutrients that sustain life, but this very strength may also explain why the heart has so little capacity to regenerate. Whereas embryonic and neonatal hearts can repair themselves, this ability is rapidly lost after birth as heart muscle cells (cardiomyocytes) exit the cell cycle. We tested whether the force-generating machinery of the heart acts as a barrier to regeneration. Across human cardiomyocytes, engineered heart tissue, and myocardial slices, we found that active force generation suppresses proliferation, whereas its inhibition, through chemogenetic or pharmacological modulation, enabled cell cycle re-entry. These findings identify contractility as a central regulator of regenerative potential, highlighting new directions for strategies to restore repair in the diseased heart.

cell biology↗

bioRxiv2025

AAV gene therapy for GBA-PD and Gaucher Disease

Mutations in GBA1, the gene encoding glucocerebrosidase (GCase), are the most common risk factor for Parkinsons Disease (PD). GBA-PD patients are a genetic subpopulation of PD carrying heterozygous mutations in GBA1. Additionally, bi-allelic mutations in GBA1 cause Gaucher Disease (GD), a lysosomal storage disorder. Loss of GCase activity, a lysosomal enzyme leads to the accumulation of lipid substrates, disrupting lipid homeostasis and promoting cellular toxicity. Here, we report an AAV-mediated GBA1 replacement strategy to treat GD and GBA-PD by a one-time infusion via intravenous (GD Type 1) or intra-CSF (GBA-PD) route of administration. We engineered human GCase to be readily secretable to facilitate broad cross-correction. We developed CBE (conduritol {beta}-epoxide) induced lipid accumulation models to assess efficacy in mice and non-human primates (NHPs) to assess efficacy of our engineered constructs. Based on data across species, across different routes of administration, we nominated AAV.GMU01 SS3-GBA1 as our lead candidate. SS3-GBA1 is robustly secreted, cross-corrected across tissues and promotes lipid clearance. By comparing human GCase levels in AAV-treated NHP brains to healthy human donor brains, we demonstrate that AAV.GMU01 SS3-GBA1 replenishes the GCase deficit seen in GBA-PD patients, thus, restoring GCase to near-physiological levels Importantly, AAV.GMU01 SS3-GBA1 is well-tolerated with no adverse findings. Collectively, we establish a therapeutic strategy for the treatment of Gaucher Disease and GBA-PD with a single gene therapy product. One Sentence SummaryA novel gene therapy strategy for GBA1-PD and Gaucher disease with an engineered payload that robustly cross-corrects enhancing therapeutic footprint

neuroscience↗

bioRxiv2025

AAV-mediated ARSA replacement for the treatment of Metachromatic Leukodystrophy

Metachromatic leukodystrophy (MLD) is an autosomal recessive neurodegenerative disorder caused by mutations in the arylsulfatase A (ARSA) gene, resulting in lower sulfatase activity and the toxic accumulation of sulfatides in the central and peripheral nervous system. Children account for 70% of cases and become progressively disabled with death occurring within 10 years of disease onset. Gene therapy approaches to restore ARSA expression via adeno-associated viral vectors (AAV) have been promising but hampered by limited brain biodistribution. We report the development of a novel capsid AAV.GMU01, demonstrating superior biodistribution and transgene expression in the central nervous system of non-human primates (NHPs). Next, we show that AAV.GMU01-ARSA treated MLD mice exhibit persistent, normal levels of sulfatase activity and a concomitant reduction in toxic sulfatides. Treated mice also show a reduction in MLD-associated pathology and auditory dysfunction. Lastly, we demonstrate that treatment with AAV.GMU01-ARSA in NHPs is well-tolerated and results in potentially therapeutic ARSA expression in the brain. In summary, we propose AAV.GMU01-ARSA mediated gene replacement as a clinically viable approach to achieve broad and therapeutic levels of ARSA.

neuroscience↗

bioRxiv2025

From larval stage to adulthood? Habitat type-specific chemical fingerprints of fire salamander larvae might give first indication for adult mate preference

Assortative mating can play a major role in the divergence of a population with gene flow. In a fire salamander population near Bonn, Germany, the larvae differ genetically according to the habitat type they are found in, i.e. ponds or streams. Neither sound nor vision are a source for assortative mating in fire salamanders, but it is known that females can discriminate between sexes and habitat types of the males based on chemical cues. The adults share the same terrestrial habitat which leads to the question whether there is a habitat type-specific chemical fingerprint already existing in the larvae that may be used in the adult stage as the base for assortative mating. We took water samples and captured larvae at two ponds and two streams and used polydimethylsiloxane and TD-GC-MS to collect and analyze samples of the environmental background as well as from the surface of the larvae. We found a significantly different composition of chemical features in the environmental back-ground samples. Additionally, we found the larvae to carry habitat type-specific chemical features. These finding allow to speculate that the features on the larval surface may be used

ecology↗

bioRxiv2024

Organic opto-nanobiointerface enables multiscale biomodulation

Virtually all organic material on Earth has been produced converting solar energy through photosynthesis in chloroplasts, a sack-like, double membrane organelle in plants and algae, where transmembrane electron transfer occurs from lumen to stroma. Although animals hardly harness the power of photosynthesis, their bioelectrical signals extensively regulate complex electrophysiological behaviors, rendering it a superior target for biomedical innovation. Here, a crude structural mimicry of chloroplast has led us to discover that hollow sphere graphitic carbon nitride nanoparticles (hg-C3N4 NPs) endowed non-genetic, subcellular and intercellular photo-modulation of various excitable and non-excitable cells, accumulatively achieving modulation at tissue/organ function level. The homogeneous hg-C3N4 NPs showed responsiveness to light via both photoelectrochemical and photothermal mechanisms. The hg-C3N4 NPs can be spontaneously internalized with excellent cytocompatibility. Using a focusing laser, the hg-C3N4 NPs enable intracellular optical stimulation with subcellular resolution, inducing calcium transient release in multiple cells and propagation in primary cardiomyocytes and cardiac fibroblasts. At multicellular scale, optical pacing and synchronization of cardiomyocyte beating is readily achieved by LED. Further, we demonstrate that hg-C3N4 nanoparticles can be safely delivered into the mouse eye and elicit measurable cortical and behavioral light responses in a subset of animals in a model of advanced retinal degeneration. Finally, application of hg-C3N4 NPs to porcine retinal tissue ex vivo confirmed their modulation capability to directly activate RGCs activity under LED photostimulation. Taken together, these nanostructured biomimetic photocatalytic NPs offer high resolution, leadless optical probing, non-invasive delivery and great biocompatibility, serving as a versatile tool for addressing a range of complex biomedical challenges through subcellular, intercellular and tissue-level photo-modulation across a broad spectrum of scales.

bioengineering↗

bioRxiv2024

Electromagnetic Stimulated Microfillamented Hydrogels for Guided Neuronal Morphogenesis

Biohybrid materials that integrate structural and bioelectronic cues across scales offer new routes to regulate neural development and repair. We present a hybrid, hydrogel-electromagnetic stimulation platform with a 3D hierarchically anisotropic structure, combining FLight bioprinted hydrogel microfilaments with a melt-electrowritten wireless electromagnetic stimulation system, to guide neural morphogenesis across central and peripheral systems at cellular and tissue scale. In the central nervous system, the soft microfilaments selectively promoted healthy, white-matter-like neurite extension rather than glioblastoma-derived outgrowth in human cortical brain tissues, while the electrically stimulation further enhanced the hippocampal neurosphere networking along the microfilaments. As a peripheral nerve conduit, the system directs dorsal root ganglion alignment in vitro and, in rat sciatic defects, drives a coordinated pro-regenerative response that improves axonal guidance, remyelination, and functional recovery. This multiscale biohybrid strategy demonstrates how synergistic integration of soft biomaterials and systematic, wireless bioelectric cues can non-invasively regulate neural morphogenesis, establishing new design principles for next-generation bioelectronic interfaces and regenerative medicine.

bioengineering↗

bioRxiv2024

Self-driving development of perfusion processes for monoclonal antibody production

The development of autonomous agents in bioporcess development is crucial for advancing biopharma innovation, as it can significantly reduce the time and resources required to transition from product to process. While robotics and machine learning have greatly accelerated drug discovery and initial screening, the later stages of development have primarily benefited from experimental automation, lacking advanced computational tools for experimental planning and execution. For example, in the development of new monoclonal antibodies, the search for optimal upstream conditions (such as feeding strategy, pH, temperature, and media composition) is often conducted using sophisticated high-throughput (HT) mini-bioreactor systems, while the integration of machine learning tools for experimental design and operation in these systems have not matured accordingly. In this work, we introduce an integrated user-friendly software framework that combines a Bayesian experimental design algorithm, a cognitive digital twin of the cultivation system, and an advanced 24-parallel mini-bioreactor perfusion experimental setup. This results in an autonomous experimental machine capable of: (1) embedding existing process knowledge, (2) learning during experimentation, utilizing information from similar processes, (4) predicting future events, and (5) autonomously operating the parallel cultivation setup to achieve challenging objectives. As proof of concept, we present experimental results from 27-day-long cultivations operated by the autonomous software agent, which successfully achieved challenging goals such as increasing the viable cell volume (VCV) and maximizing the viability throughout the experiment.

bioengineering↗

bioRxiv2024

Life stage- and sex-specific sensitivity to nutritional stress in a holometabolous insect

O_LIOver the course of their lives, organisms can be repeatedly exposed to stress, which shapes their phenotype. At certain life stages, known as sensitive phases, individuals might be more receptive to such stress than at others. One of these stresses is nutritional stress, such as food limitation. However, little is known about how plastic responses differ between individuals experiencing nutritional stress early versus later in life or repeatedly, particularly in species with distinct ontogenetic niches. Moreover, there may be sex-specific differences due to distinct physiology. C_LIO_LIThe turnip sawfly, Athalia rosae (Hymenoptera: Tenthredinidae), is a holometabolous herbivore, whose larvae consume leaves and flowers, while the adults take up nectar. We examined the effects of starvation experienced at different life stages on life-history traits as well as adult behavioural and metabolic traits to determine which life-stage may be more sensitive to nutritional stress and how specific these traits respond. We exposed individuals to four distinct nutritional regimes, no, larval, or adult starvation, or starvation periods during both larval and adult stage. C_LIO_LILarvae exposed to starvation had a prolonged developmental time, and starved females reached a lower initial adult body mass than non-starved individuals. However, males did not differ in initial adult body mass regardless of larval starvation, suggesting the ability to conform well to poor nutritional conditions, possibly through changes in development and metabolism. C_LIO_LIAdult behaviour, measured as activity, was not significantly impacted by larval or adult starvation in either sex. Individuals starved as larvae had similar carbohydrate and lipid (i.e. fatty acid) contents as non-starved individuals, potentially due to building up energy reserves during their prolonged development, while starvation during adulthood or at both stages led to reduced energy reserves in males. C_LIO_LIThis study indicates that the sensitivity of a life stage to nutritional stress depends on the specific trait under consideration. Life-history traits were mainly affected by larval nutritional stress, while activity appeared to be more robust and metabolism mostly impacted by the adult nutritional conditions. Individuals differed in their ability to conform to the given environment, with the responses being life stage- and sex-specific. C_LI

ecology↗

bioRxiv2024

Systematic Characterization of Transport Regulation in Escherichia coli across defined environmental cues

Transport of small molecules across the bacterial cell envelope is essential to ensure nutrient uptake and protect bacteria from toxic compounds. Due to its decisive role, transport is controlled by complex regulatory networks, knowledge of which - in particular across external cues - remains poorly understood. Here we investigate transcriptional regulation of seven prominent transport genes in Escherichia coli across 94 defined chemical cues, and simultaneously map the contributions of the key regulators MarA, SoxS and Rob to promoter activity. One third of all tested compounds triggered transcriptional changes, the vast majority of which previously unknown. Importantly, we exposed main drivers of transport control in E. coli, e.g. bacteriostatic, but not bactericidal, antibiotics trigger expression of efflux pumps, and that Rob contributes to [~]1/3 of all measured transcriptional changes, thereby emerging as a more prominent transport regulator than previously thought. We showcase the potential of our resource by elucidating the molecular mechanism of antibiotic antagonisms with widely consumed caffeine in E. coli. Altogether, our resource capitalizes on providing a quantitative overview of transport determinants across environments, and brings perspective to long-term prevailing concepts in the field.

microbiology↗

bioRxiv2024

Prediction of Adeno-Associated Virus Fitness with a Protein Language Based Machine Learning Model

Adeno-associated viral (AAV)-based therapeutics have the potential to transform the lives of patients by delivering one-time treatments for a variety of diseases. However, a critical challenge to their widespread adoption and distribution is the high cost of goods (CoGS). Reducing manufacturing costs by developing AAV capsids with improved yield, or fitness, is key to making gene therapies more affordable. AAV fitness is largely determined by the amino acid sequence of the capsid, however, engineered AAVs are rarely optimized for manufacturability. Here, we report a state-of-the art machine learning (ML) model that predicts the fitness of AAV capsid mutants based on the amino acid sequence of the capsid monomer. By combining a protein language model (PLM) and classical ML techniques, our model achieved a significantly high prediction accuracy (Pearson correlation = 0.818) for capsid fitness. Importantly, tests on completely independent datasets showed robustness and generalizability of our model, even for multi-mutant AAV capsids. Our accurate ML-based model can be used as a surrogate for laborious in vitro experiments, thus saving time and resources, and can be deployed to increase fitness of clinical AAV capsids to make gene therapies economically viable for patients.

bioinformatics↗