Biology subjects

Luo, H.

Publications and source records attributed to Luo, H..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

Pan-sphingolipid profiling reveals differential functions of sphingolipid biosynthesis isozymes of C. elegans

Multiple isozymes are encoded in the C. elegans genome for the various sphingolipid biosynthesis reactions, but the contributions of individual isozymes are characterized only in part. We developed a simple but effective reversed-phase liquid chromatography-tandem mass spectrometry (RPLC-MS/MS) method that enables simultaneous identification and quantification of ceramides (Cer), glucosylceramides (GlcCer), and sphingomyelins (SM), three important classes of sphingolipids from the same MS run. Validating this pan-sphingolipid profiling method, we show that nearly all 47 quantifiable sphingolipid species found in young adult worms were reduced upon RNA interference (RNAi) of sptl-1 or elo-5, which are required for synthesis of the id17:1 sphingoid base. We also confirm that HYL-1 and HYL-2, but not LAGR-1, constitute the major ceramide synthase activity with different preference for fatty acid substrates, and that CGT-3 plays a greater role than CGT-1 does in producing glucosylceramides. Intriguingly, lagr-1 RNAi lowers the abundance of all sphingomyelin species and that of several glucosylceramide species, which suggests that LAGR-1 may have functions beyond what is predicted. Additionally, RNAi of sms-1, -2, and -3 all lower the abundance of sphingomyelins with an odd number of carbon atoms (mostly C21 and C23, with or without hydroxylation) in the N-acyl chain, and only sms-1 RNAi does not elevate sphingomyelins containing even-numbered N-acyl chains. This suggests that sphingolipids containing even-numbered N-acyl chains could be regulated separately, sometimes in opposite directions, with those containing odd-numbered N-acyls, presumably monomethyl branched chain fatty acyls. We also find that ceramide levels are kept in balance with those of glucosylceramides and sphingomyelins.

genetics↗

bioRxiv2023

Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04

Drug resistance poses a significant challenge in the development of effective therapies against SARS-CoV-2. Here, we identified two double mutations, M49K/M165V and M49K/S301P, in the 3C-like protease (3CLpro) that confer resistance to a novel non-covalent inhibitor, WU-04. Crystallographic analysis indicates that the M49K mutation destabilizes the WU-04 binding pocket, impacting the binding of WU-04 more significantly than the binding of 3CLpro substrates. The M165V mutation directly interferes with WU-04 binding. The S301P mutation, which is far from the WU-04 binding pocket, indirectly affects WU-04 binding by restricting the rotation of 3CLpros C-terminal tail and impeding 3CLpro dimerization. We further explored 3CLpro mutations that confer resistance to two clinically used inhibitors: ensitrelvir and nirmatrelvir, and revealed a trade-off between the catalytic activity, thermostability, and drug resistance of 3CLpro. We found that mutations at the same residue (M49) can have distinct effects on the 3CLpro inhibitors, highlighting the importance of developing multiple antiviral agents with different skeletons for fighting SARS-CoV-2. These findings enhance our understanding of SARS-CoV-2 resistance mechanisms and inform the development of effective therapeutics.

microbiology↗

bioRxiv2023

Rhodococcus equi Escapes Macrophage Autophagy: VapA Inhibits ATP6V0d1-Mediated Lysosomal Degradation

Rhodococcus equi is a gram-positive actinomycetales bacterial, which cause a pneumonia in foals and in immunocompromised humans. Virulence associated protein A (VapA) encoded from virulence plasmid is essential for intracellular proliferation in macrophage. It has reported that VapA participates in exclusion of proton-pumping vacuolar-ATPase complex from phagosome and causes membrane permeabilization, thus contributing to a pH-neutral phagosome lumen. However, there have been no reports about VapA-induced autophagy or its mechanism. In this study, we sought to determine the role of VapA in macrophage autophagy using western blotting, immunofluorescence, pull-down, Co-IP, LS/MS, pH detection LysoTracker and CFU analysis. We show that VapA inhibiting the macrophage autophagy by detecting the expression of autophagy related protein LC3II and P62 and autophagy flux in VapA treated macrophage. Furthermore, we using pull-down and MS analysis to selected ATP6V0D1 could interact with VapA, Co-IP was used to confirm its interaction. Furthermore, VapA treatment in ATP6V0D1 overexpressed cells weaken the lyso Tracker red stain comparing with ATP6V0D1 overexpressed J774A.1 cells. In addition, the expression of ATP6V0D1 significantly increased in J774A.1 post infected with vapA deletion strain, R. equi 103+/{Delta}VapA by comparing with wild type R. equi 103+ post-infection. And raise of raise of ATP6V0D1 actually reduce R. equi 103+ intracellular multiplication. These results further suggesting a decrease of ATP6V0D1 were caused the exit of VapA in R. equi. Taken those date together, we reported that VapA mediated lysosome acidification by inhibiting the expression of ATP6V0D1, which contributing the R. equi escape macrophage autophagy.

immunology↗

bioRxiv2023

Characterization of the Complete Chloroplast Genome Sequences and Phylogenetic Relationships of Four Oil-Seed Camellia spp. and related taxa

Some species in the Sect. Oleifera of the genus Camellia L. known as oil-seed camellia because of their high oil content and economic value. Additional studies aimed at clarifying the phylogenetic relationships and chloroplast genomes of Camellia species are needed to hybridization, as well as improve the breeding, selection and interspecific hybridization of Camellia species. The complete chloroplast genomes (cpDNA) of the four oil-seed camellia species C. semiserrata, C. meiocarpa, C. suaveolens, and C. osmantha were resequenced to clarify their interspecific relationships. These cpDNA had typical tetrad structures, and they were highly conserved in various structural features. The total lengths of the cpDNA ranged from 156,965 to 157,018 bp, and 134 genes were annotated, including 88 protein-coding genes, 37 transfer RNA genes, and 8 messenger RNA genes. The average GC content of these genomes was 37.3%. The codons with the highest and lowest codon usage bias were UUA (which codes for leucine) and AGC (which codes for serine), respectively. The number of simple sequences repeats of the four Camelia species ranged from 38 to 40. Mononucleotide repeats were the most common repeat type, followed by tetranucleotide, trinucleotide, and hexanucleotide repeats. Our phylogenetic analysis of cpDNA, coupled with the results of previous ploidy analyses and artificial interspecific hybridization, revealed that C. semiserrata was most closely related to C. azalea, C. suaveolens was most closely related to C. gauchowensis, C. osmantha was most closely related to C. vietnamensis, and C. meiocarpa was most closely related to C. oleifera. The phylogenetic relationships between oil-seed camellia species with high oil content and economic value were characterized. Our analysis of the cpDNA provided new insights that will aid the use of artificial distant hybridization in camellia breeding programs.

genomics↗

bioRxiv2023

Emergence of Prochlorococcus in the Tonian oceans and the initiation of Neoproterozoic oxygenation

Prochlorococcus are the smallest and most abundant photosynthetic organisms on Earth, contributing up to 50% of the chlorophyll in the oligotrophic oceans. Despite being important in regulating the carbon cycle in todays ocean, the ecological significance of Prochlorococcus in Earths history remains elusive. Our new robustly calibrated molecular clock analysis reveals that Prochlorococcus emerged in the deep photic zone of the Tonian (1,000-720 Mya) oceans. The classical light-harvesting antenna complex in Cyanobacteria, i.e., the phycobilisome, was replaced in Prochlorococcus by the chlorophyll{square}based antenna, enabling more efficient use of blue light that penetrates into deeper water. Importantly, Prochlorococcus colonization of deep water enhanced access to phosphate, which was abundant in upwelled seawater, but likely scarce in the Tonian surface ocean, promoting expansion of Prochlorococcus, displacement of incumbent low-light adapted anoxygenic photoferrotrophs, and associated increases in photosynthetic oxygen production. Colonization of deeper waters would also have improved access to ammonium, leading to the neutral loss of nitrate utilization genes. Our research thus documents the conspicuous emergence of new photosynthetic bacterial lineages in the run-up to the Neoproterozoic oxygenation event, implying an additional layer of eco-evolutionary complexity during this pivotal interval in Earths history.

microbiology↗

bioRxiv2023

Multifaceted proteome analysis at solubility, redox, and expression dimensions for target identification

Multifaceted interrogation of the proteome deepens the system-wide understanding of biological systems; however, mapping the redox changes in the proteome has so far been significantly more challenging than expression and solubility/stability analyses. Here, we devise the first high- throughput redox proteomics approach integrated with expression analysis (REX) and combine it with Proteome Integral Solubility Alteration (PISA) assay. The whole PISA-REX experiment with up to four biological replicates can be multiplexed into a single tandem mass tag TMTpro set. For benchmarking this compact tool, we analyzed HCT116 cells treated with auranofin, showing great improvement compared with previous such studies. Then we applied PISA-REX to study proteome remodeling upon stimulation of human monocytes by interferon . We also studied the proteome changes in plasmacytoid dendritic cells isolated from wild type vs. Ncf1- mutant mice treated with interferon , showing that NCF1 deficiency enhances the STAT1 pathway and modulates the expression, solubility and redox state of interferon-induced proteins. Providing comprehensive multifaceted information on the proteome, the compact PISA-REX has the potential to become an industry standard in proteomics and to open new windows into the biology of health and disease.

biochemistry↗

bioRxiv2023

Regulation of the Drosophila transcriptome by Pumilio and CCR4-NOT deadenylase

The sequence-specific RNA-binding protein Pumilio controls development of Drosophila; however, the network of mRNAs that it regulates remains incompletely characterized. In this study, we utilize knockdown and knockout approaches coupled with RNA-Seq to measure the impact of Pumilio on the transcriptome of Drosophila cells. We also used an improved RNA co-immunoprecipitation method to identify Pumilio bound mRNAs in Drosophila embryos. Integration of these datasets with the content of Pumilio binding motifs across the transcriptome revealed novel direct Pumilio target genes involved in neural, muscle, wing, and germ cell development, and cellular proliferation. These genes include components of Wnt, TGF-beta, MAPK/ERK, and Notch signaling pathways, DNA replication, and lipid metabolism. Additionally, we identified the mRNAs regulated by the CCR4-NOT deadenylase complex, a key factor in Pumilio-mediated repression, and observed concordant regulation of Pumilio:CCR4-NOT target mRNAs. Computational modeling revealed that Pumilio binding, binding site number, density, and sequence context are important determinants of regulation. Moreover, the content of optimal synonymous codons in target mRNAs exhibits a striking functional relationship to Pumilio and CCR4-NOT regulation, indicating that the inherent translation efficiency and stability of the mRNA modulates their response to these trans-acting regulatory factors. Together, the results of this work provide new insights into the Pumilio regulatory network and mechanisms, and the parameters that influence the efficacy of Pumilio-mediated regulation.

molecular biology↗

bioRxiv2023

ChromaFold predicts the 3D contact map from single-cell chromatin accessibility

The identification of cell-type-specific 3D chromatin interactions between regulatory elements can help to decipher gene regulation and to interpret the function of disease-associated non-coding variants. However, current chromosome conformation capture (3C) technologies are unable to resolve interactions at this resolution when only small numbers of cells are available as input. We therefore present ChromaFold, a deep learning model that predicts 3D contact maps and regulatory interactions from single-cell ATAC sequencing (scATAC-seq) data alone. ChromaFold uses pseudobulk chromatin accessibility, co-accessibility profiles across metacells, and predicted CTCF motif tracks as input features and employs a lightweight architecture to enable training on standard GPUs. Once trained on paired scATAC-seq and Hi-C data in human cell lines and tissues, ChromaFold can accurately predict both the 3D contact map and peak-level interactions across diverse human and mouse test cell types. In benchmarking against a recent deep learning method that uses bulk ATAC-seq, DNA sequence, and CTCF ChIP-seq to make cell-type-specific predictions, ChromaFold yields superior prediction performance when including CTCF ChIP-seq data as an input and comparable performance without. Finally, fine-tuning ChromaFold on paired scATAC-seq and Hi-C in a complex tissue enables deconvolution of chromatin interactions across cell subpopulations. ChromaFold thus achieves state-of-the-art prediction of 3D contact maps and regulatory interactions using scATAC-seq alone as input data, enabling accurate inference of cell-type-specific interactions in settings where 3C-based assays are infeasible.

bioinformatics↗

bioRxiv2023

Hummingbirds use wing inertial effects to improve maneuverability

Hummingbirds outperform other birds in terms of aerial agility at low flight speeds. To reveal the key mechanisms that enable such unparalleled agility, we reconstructed body and wing motion of hummingbird escape maneuvers from high-speed videos; then, we performed computational fluid dynamics modeling and flight mechanics analysis, in which each wingbeat was resolved. We found that the birds utilized the inertia of their wings to achieve peak body rotational acceleration within half a wingbeat before the aerodynamic forces became dominant. The aerodynamic forces instead counteracted the reversed inertial forces in the other half wingbeat, thereby to sustain body rotation, albeit at a lower acceleration. Thus, individual wingbeat cycles that generated body rotations can be split into an agility phase with rapid inertial acceleration, and a stability phase with counteracting aerodynamic and inertial acceleration. This mechanism involving inertial steering enables hummingbirds to generate instantaneous body acceleration at any phase of a wingbeat, and it is likely the key to understanding the unique dexterity distinguishing them from aircraft that solely rely on aerodynamics for maneuvering.

animal behavior and cognition↗

bioRxiv2023

Shared structure facilitates working memory of multiple sequences via neural replay

Daily experiences often involve the processing of multiple sequences, yet storing them challenges the limited capacity of working memory (WM). To achieve efficient memory storage, relational structures shared by sequences would be leveraged to reorganize and compress information. Here, participants memorized a sequence of items with different colors and spatial locations and later reproduced the full color and location sequences one after another. Crucially, we manipulated the consistency between location and color sequence trajectories. First, sequences with consistent trajectories demonstrate improved memory performance and a trajectory correlation between reproduced color and location sequences. Second, sequences with consistent trajectories show neural reactivation of common trajectories, and display spontaneous replay of color sequences when recalling locations. Finally, neural reactivation correlates with WM behavior. Our findings suggest that shared common structure is leveraged for storage of multiple sequences through compressed encoding and neural replay, together facilitating efficient information organization in WM.

neuroscience↗

bioRxiv2023

Comprehensive Assessment of Eleven de novo HiFi Assemblers on Complex Eukaryotic Genomes and Metagenomes

BackgroundPacific Bioscience HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (less than 0.01% sequencing error). While several de novo assembly tools are available for HiFi reads, there are no comprehensive studies on the evaluation of these assemblers. ResultsWe evaluated the performance of eleven de novo HiFi assemblers on (i) real data for three eukaryotic genomes, (ii) 34 synthetic datasets with different ploidy, sequencing coverage levels, heterozygosity rates and sequencing error rates, (iii) one real metagenomic dataset, and (iv) five synthetic metagenomic datasets with different composition abundance and heterozygosity rates. The nine assemblers were evaluated using QUAST (Quality Assessment Tool) and BUSCO (Benchmarking Universal Single-Copy Ortholog). We also used several additional criteria, namely, completion rate, single-copy completion rate, duplicated completion rate, average proportion of largest category, average distance difference, quality value, run-time and memory utilization. On complex eukaryotic genomes, Hifiasm had a clear advantage over the other assemblers in all tested experiments. On synthetic datasets, Hifiasm, HiCanu, and HiFlye performed equally well. Shasta and Peregrine had good performance across varying ploidy, but required high computational resources. On metagenomic datasets, Hifiasm-meta demonstrated a clear advantage over other assemblers. ConclusionWe carried out a comprehensive benchmarking study of commonly used assemblers on complex eukaryotic genomes and metagenomes. Our study will help the research community to choose the most appropriate assembler for their data and identify possible improvements in assembly algorithms.

genomics↗

bioRxiv2023

An adversarial collaboration to critically evaluate theories of consciousness

Different theories explain how subjective experience arises from brain activity1,2. These theories have independently accrued evidence, yet, confirmation bias and dependence on design choices hamper progress in the field3. Here, we present an open science adversarial collaboration which directly juxtaposes Integrated Information Theory (IIT)4,5 and Global Neuronal Workspace Theory (GNWT)6-10, employing a theory-neutral consortium approach11,12. We investigate neural correlates of the content and duration of visual experience. The theory proponents and the consortium developed and preregistered the experimental design, divergent predictions, expected outcomes, and their interpretation12. 256 human subjects viewed suprathreshold stimuli for variable durations while neural activity was measured with functional magnetic resonance imaging, magnetoencephalography, and electrocorticography. We find information about conscious content in visual, ventro-temporal and inferior frontal cortex, with sustained responses in occipital and lateral temporal cortex reflecting stimulus duration, and content-specific synchronization between frontal and early visual areas. These results confirm some predictions of IIT and GNWT, while substantially challenging both theories: for IIT, a lack of sustained synchronization within posterior cortex contradicts the claim that network connectivity specifies consciousness. GNWT is challenged by the general lack of ignition at stimulus offset and limited representation of certain conscious dimensions in prefrontal cortex. Beyond challenging the theories themselves, we present an alternative approach to advance cognitive neuroscience through a principled, theory-driven, collaborative effort. We highlight the challenges to change peoples mind 13 and the need for a quantitative framework integrating evidence for systematic theory testing and building.

neuroscience↗

bioRxiv2023

Genome reduction occurred in early Prochlorococcus with an unusually low effective population size

In the oligotrophic sunlit ocean, the most abundant free-living planktonic bacterial lineages evolve convergently through genome reduction. The cyanobacterium Prochlorococcus responsible for 10% global oxygen production is a prominent example. The dominant theory known as genome streamlining posits that they have extremely large effective population sizes (Ne) such that selection for metabolic efficiency acts to drive genome reduction. Because genome reduction largely took place anciently, this theory builds on the assumption that their ancestors Ne was similarly large. Constraining Ne for ancient ancestors is challenging because experimental measurements of extinct organisms are impossible and alternatively reconstructing ancestral Ne with phylogenetic models gives large uncertainties. Here, we develop a new strategy that leverages agent-based modeling to simulate the change of Ne proxy for ancient ancestors, the genome-wide ratio of radical to conservative nonsynonymous nucleotide substitution rate (dR/dC), in response to the change of Ne. Surprisingly, this proxy shows expected increases with decreases of Ne only when Ne falls to about 10k - 100k or lower, magnitudes characteristic of Ne of obligate endosymbiont species where drift drives genome reduction. We therefore conclude that drift, rather than selection, is the primary force that drove Prochlorococcus genome reduction.

genetics↗

bioRxiv2023

Dating the bacterial tree of life with ancient symbiosis

Obtaining a timescale for bacterial evolution is crucial to understand early life evolution but is difficult owing to the scarcity of bacterial fossils and absence of maximum age constraints of the available fossils. Here, we introduce multiple new time constraints to calibrate bacterial evolution based on ancient symbiosis. This idea is implemented using a bacterial tree constructed with mitochondria-originated genes where the mitochondrial lineage representing eukaryotes is embedded within Proteobacteria, such that the date constraints of eukaryotes established by their abundant fossils are propagated to ancient co-evolving bacterial symbionts and across the bacterial tree of life. Importantly, we formulate a new probabilistic framework that considers uncertainty in inference of the ancestral lifestyle of modern symbionts to apply 19 relative time constraints (RTC) each informed by host-symbiont association to constrain bacterial symbionts no older than their eukaryotic host. Moreover, we develop an approach to incorporating substitution mixture models that better accommodate substitutional saturation and compositional heterogeneity for dating deep phylogenies. Our analysis estimates that the last bacterial common ancestor (LBCA) occurred approximately 4.0-3.5 billion years ago (Ga), followed by rapid divergence of major bacterial clades. It is robust to alternative root ages, root positions, tree topologies, fossil ages, ancestral lifestyle reconstruction, gene sets, among other factors. The timetree obtained enables the validation of various hypotheses, such as the survival of life during the late heavy bombardment, the absence of a connection between ancient stromatolites and cyanobacteria, and the presence of aerobic enzymes before the oldest geochemical records of molecular oxygen. Significance StatementBacteria, with their vast diversity and ancient history, play a crucial role in shaping Earths biogeochemistry. However, the scarcity of fossils complicates the determination of their evolution timescale and its link to Earths history. To address this issue, we have devised and implemented novel methods that utilize ancient symbiosis and eukaryotic fossils to calibrate bacterial evolution by molecular clock. We obtain a comprehensive genus-level evolutionary timeline of bacteria that sheds light on their profound influence on the development and diversity of life on our planet, as well as its environmental dynamics. This research greatly contributes to our understanding of microbial evolution and its implications for Earths past and present.

evolutionary biology↗

bioRxiv2023

Phylogenetic and population structure of the nod-free but nodulating Bradyrhizobium phylogroup

Bradyrhizobium is a main rhizobial lineage of which most members nodulate legume plants using Nod factors (NFs) synthetized by the nod genes. However, members of the Photosynthetic supergroup (phylogroup) within Bradyrhizobium (PB) are nod-free but still capable of establishing nitrogen-fixing nodules with some tropical legumes of the Aeschynomene genus. These unusual findings are based on the genomic sequences of only 13 PB strains, and almost all were isolated from Aeschynomene nodules. Here, we investigate the diversity of Bradyrhizobium in grassland, forest, and rice field by rpoB amplicon sequencing and report that PB is mainly associated with rice root and rhizosphere. Moreover, we sequenced 209 new PB members isolated mostly from the rice field. The extended PB supergroup comprises three major clades: a basal clade with significant expansion of its diversity, followed by an intermediate clade composed by two strains, and a new clade exclusively represented by our new strains. Although the PB strains universally lack the canonical nod genes, all 28 assayed strains covering the broad diversity of these clades induced nodules on Aeschynomene indica. Interestingly, the three clades displayed significant differences in the efficiency of symbiosis, aligning well with their phylogenetic branching order. Our strain collection expands the ecological, phylogenetic and functional diversity of nod-free but nodulating Bradyrhizobium. With this expanded diversity, we conclude that the NF-independent nodulation of Aeschynomene is a common trait of this supergroup, in contrast to the photosynthetic trait originally thought as its unifying feature.

genomics↗

bioRxiv2023

ERG-driven prostate cancer emerges from basal-luminal hybrid cells

To gain insight into how ERG translocations cause prostate cancer, we performed single cell transcriptional profiling of an autochthonous mouse model at an early stage of disease initiation. Despite broad expression of ERG in all prostate epithelial cells, proliferation was enriched in a small, stem-like population with mixed-luminal basal identity (called intermediate cells). Through a series of lineage tracing and primary prostate tissue transplantation experiments, we find that tumor initiating activity resides in a subpopulation of basal cells that co-express the luminal genes Tmprss2 and Nkx3.1 (called BasalLum) but not in the larger population of classical Krt8+ luminal cells. Upon ERG activation, BasalLum cells give rise to the highly proliferative intermediate state, which subsequently transitions to the larger population of Krt8+ luminal cells characteristic of ERG-positive human cancers. Furthermore, this proliferative population is characterized by an ERG-specific chromatin state enriched for NFkB, AP-1, STAT and NFAT binding, with implications for TF cooperativity. The fact that the proliferative potential of ERG is enriched in a small stem-like population implicates the chromatin context of these cells as a critical variable for unmasking its oncogenic activity.

cancer biology↗

bioRxiv2023

Multi-Omics Integration For Disease Prediction Via Multi-Level Graph Attention Network And Adaptive Fusion

Multi-omics integration has demonstrated promising performance in complex disease prediction. However, existing research typically focuses on maximizing prediction accuracy, while often neglecting the essential task of discovering meaningful biomarkers. This issue is particularly important in biomedicine, as molecules often interact rather than function individually to influence disease outcomes. To this end, we propose a two-phase framework named GREMI to assist multi-omics classification and explanation. In the prediction phase, we propose to improve prediction performance by employing a graph attention architecture on sample-wise co-functional networks to incorporate biomolecular interaction information for enhanced feature representation, followed by the integration of a joint-late mixed strategy and the true-class-probability block to adaptively evaluate classification confidence at both feature and omics levels. In the interpretation phase, we propose a multi-view approach to explain disease outcomes from the interaction module perspective, providing a more intuitive understanding and biomedical rationale. We incorporate Monte Carlo tree search (MCTS) to explore local-view subgraphs and pinpoint modules that highly contribute to disease characterization from the global-view. Extensive experiments demonstrate that the proposed framework outperforms state-of-the-art methods in seven different classification tasks, and our model effectively addresses data mutual interference when the number of omics types increases. We further illustrate the functional- and disease-relevance of the identified modules, as well as validate the classification performance of discovered modules using an independent cohort. Code and data are available at https://github.com/Yaolab-fantastic/GREMI.

bioinformatics↗

bioRxiv2023

Phage administration with repeated intravenous doses leads to faster phage clearance in mammalian hosts

ObjectivesPhage therapy has shown a great promise for the treatment of multidrug-resistant bacterial infections. However, the lack of a thorough and organized understanding of phage-body interactions has limited its clinical application. MethodsHere, we administered different purified phages (Salmonella phage SE_SZW1, Acinetobacter phage AB_SZ6, and Pseudomonas phage PA_LZ7) intravenously to healthy animals (rats and monkeys) to evaluate the phage-induced host responses and phage pharmacokinetics (PK) with different intravenous (IV) doses in healthy animals. The plasma and the organs were sampled after different IV doses to determine the phage biodistribution, the phage-induced cytokines, and antibodies. The potential side effects of phages on animals were assessed. ResultsA non-compartment model revealed that the plasma phage titer gradually decreased over time following a single dose. Repeated doses caused that the plasma phage titer at 5 minutes dropped 2-3 Log10 compared to the first dose regardless of phage types in rats. Host innate immune responses were activated including the upregulated expression (>10-fold) of TNF- and splenic enlargement following repeated doses. Phage-specific neutralization antibodies in animals receiving phages were detected. Similar results were obtained from monkeys. ConclusionsThe mammalian bodies were well-tolerant to the administered phages. The animal responses to the phages and the phage biodistribution profiles could have a significant impact on the efficacy of phage therapy.

pharmacology and toxicology↗