Biology subjects

Yun, H.

Publications and source records attributed to Yun, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Spontaneous Hemodynamic Oscillations during Sleep Coordinate Directional CSF Flow in the Subarachnoid Space and Ventricles

During sleep, cerebrospinal fluid (CSF) flow is enhanced and thought to facilitate clearance of metabolic waste from the brain. Human imaging has shown that sleep is associated with large waves of bulk CSF flow in the fourth ventricle; however, the CSF flow dynamics around brain tissue are unknown. Here, we investigated how CSF flow is organized across the subarachnoid space, a key site both for fluid exchange across cortical surface and for transport out of the cranium. We used an MRI technology at 7 Tesla that simultaneously measures cortical hemodynamics and slow subarachnoid CSF flow and applied this during sleep. We found that spontaneous infraslow hemodynamic oscillations were coupled to spatially structured, directional CSF flow throughout both ventricular and subarachnoid compartments. Hemodynamic oscillations and fourth-ventricle bulk flow were both associated with brain-wide CSF flow at different phases, indicating that they reflect a single coordinated CSF movement cycle. Compared to cardiac pulsations, a canonical driver of CSF movement, hemodynamic-driven CSF flow showed a distinct directional pattern and was smaller in instantaneous amplitude but produced substantially greater cumulative displacement and thus greater potential for transport within an oscillation period. Together, these findings show that hemodynamic oscillations during sleep are coupled to temporally coordinated and directional CSF flow throughout the ventricles and subarachnoid space, suggesting that sleep-dependent neuronal activity drives fluid movement across the human brain in a distinct spatial pattern.

neuroscience↗

bioRxiv2026

Clonal hematopoiesis-associated DNMT3A mutations derepress bivalent Polycomb target genes and enhance macrophage migration

Somatic mutations in the de novo DNA methyltransferase DNMT3A are frequent in clonal hematopoiesis, but how they alter the function of differentiated myeloid cells remains unclear. Here, we used isogenic human embryonic stem cell-derived macrophage models to define the consequences of DNMT3A dysfunction during myeloid differentiation. DNMT3A-mutant macrophages selectively upregulated bivalent Polycomb target genes, accompanied by DNA hypomethylation, reduced H3K27me3 and increased promoter accessibility. Despite broad epigenetic changes across bivalent promoters, transcriptional derepression occurred at a subset of loci characterized by lower baseline DNA methylation and higher H3K27me3, identifying pre-existing chromatin state as a determinant of transcriptional response. This Polycomb-associated program was conserved in murine macrophages and enriched for genes involved in cell migration and wound repair. DNMT3A-mutant macrophages exhibited enhanced migration and preferential early recruitment to injured tissue. These findings link clonal hematopoiesis-associated epigenetic alterations to selective transcriptional reprogramming and altered function of differentiated myeloid cells.

cell biology↗

bioRxiv2026

Extracellular matrix proteoglycans lumican and biglycan promote innate immune signals and viral clearance in HSV-1 infections of mouse corneas

The extracellular matrix (ECM) regulates innate immunity, but its role in HSV-1 keratitis is unclear. Here, we identify the ECM proteoglycans lumican (Lum) and biglycan (Bgn) as key regulators of early antiviral defense in the cornea. Lum-/- and BgnKO mice showed impaired viral clearance, increased corneal opacity, and worse keratitis than wild-type controls. These defects were associated with reduced early recruitment of neutrophils, monocytes, and plasmacytoid dendritic cells, and blunted induction of pro-inflammatory cytokines, chemokines, and type I interferons. In infected wild-type corneas, Lum and Bgn were upregulated, including in the basal epithelium, where Ccl2 emerged as an early epithelial response that was diminished in knockout mice. In human corneal epithelial cells, recombinant LUM or BGN enhanced HSV-1-induced CCL2 secretion, and human corneal organoids recapitulated epithelial viral tropism and CCL2 induction. Together, these findings identify Lum and Bgn as regulators of epithelial-innate immune crosstalk that promote early antiviral immunity during corneal HSV-1 infection.

immunology↗

bioRxiv2026

Genetic mapping and genomic prediction for agronomic, grain compositional, and sensing-enabled traits in a cowpea MAGIC population along an environmental gradient

Cowpea (Vigna unguiculata [L.] Walp.) is a resilient grain legume and an important global source of dietary protein, yet the genetic and environmental basis of phenological and canopy development, as well as grain composition, remains incompletely characterized across production environments. In this study, we evaluated a cowpea multi-parent advanced generation intercross (MAGIC) population along an environmental gradient in California (with contrasting daylengths, temperatures, and soil types) using agronomic, grain compositional, and uncrewed aerial vehicle (UAV) and rover-enabled phenotyping. Near-infrared spectroscopy (NIRS) enabled assessment of grain compositional traits, while sensing-enabled time-series imaging captured canopy and reproductive dynamics. Quantitative trait locus (QTL) mapping identified 267 QTL, and genome-wide association studies (GWAS) detected 1,973 marker-trait associations. Integrating QTL mapping and GWAS results identified two major genomic hotspots affecting multiple traits. A chromosome 9 hotspot (5.8-6.0 Mb) was associated with flowering time and co-localized with sensing-enabled measures of flower and pod counts, plant height, and vegetation fraction, indicating broad effects on phenological and canopy development. A chromosome 8 hotspot (37.3-37.9 Mb) contained co-localized signals for seed weight, protein, starch, phytate, and moisture. A total of 22 prioritized candidate genes were identified within these and other loci with multi-environment QTL and GWAS support. Genomic predictive abilities were moderate to high for most traits and scenarios, with multi-trait MegaLMM outperforming RR-BLUP. Together, these results define major genomic regions controlling cowpea phenology, canopy development, and grain composition, and provide targets and strategies for breeding cowpea cultivars with favorable and environmentally resilient productivity and grain composition. Significance StatementTo dissect the genetic basis of cowpea productivity, adaptation, and grain composition, and how performance for these traits varies and can be predicted across environments, we combined multi-environment phenotyping, including sensing of canopy and reproductive traits, with quantitative genetic analyses in a multi-parental population. We identified genomic hotspots for seed size/composition and reproductive phenology and an across-environment predictive advantage for multi-trait vs. single-trait genomic prediction. Overall, these findings support the comprehensive improvement of cowpea.

genetics↗

bioRxiv2025

Development and qualification of an enzyme-linked immunosorbent assay to detect human serum immunoglobulin G reactive to multiple lineages of Lassa virus nucleoprotein

Lassa fever is a severe, often fatal febrile illness endemic to West Africa caused by Lassa virus (LASV). The viral nucleoprotein (NP) is a target antigen for serological assays to identify previous exposure to LASV. To our knowledge, there is no commercially available assay that reliably quantifies anti-LASV-NP IgG antibodies in human serum. We report the development and qualification of an ELISA designed to detect and quantify anti-LASV-NP IgG in human serum samples. The assay employs recombinant Lineage IV LASV-NP immobilized on microwells to capture NP-specific IgG antibodies, which are then detected using horseradish peroxidase-conjugated anti-human IgG followed by TMB substrate and reading of optical densities. Optimal assay reagent concentrations, incubation times and temperature were determined along with assay positivity criteria and dynamic range. A reference standard prepared from pooled sera from donors in endemic Lassa fever regions was established and calibrated to the first WHO international standard for LASV antibodies. High and low positive controls for assay quality control were generated. Naive human serum was used as a negative control. Following assay optimization, performance was assessed through assay qualification. The assay positivity criteria, lower limit of detection, upper and lower limits of quantitation, inter-assay precision, selectivity and dilutional linearity were determined. Our anti-LASV-NP IgG ELISA was shown to reliably measure anti-LASV-NP IgG levels in human serum. The method demonstrated sensitivity, intra- and inter-assay precision, dilution linearity across its analytical range and specificity for anti-LASV-NP IgG. Establishing this assay represents an essential step toward strengthening LASV epidemiology research and supporting urgently needed development of a vaccine to prevent Lassa Fever.

immunology↗

bioRxiv2025

Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders

Loss-of-function mutations in DNMT3A, a DNA methyltransferase, or NSD1, a histone methyltransferase, cause overgrowth syndromes. Conversely, disruption of the DNMT3A domain that binds NSD1-deposited H3K36 dimethylation (H3K36me2) results in growth restriction. To investigate the molecular basis of these opposing growth outcomes, we generated isogenic human embryonic stem cells carrying growth syndrome-associated mutations in DNMT3A and NSD1. Unexpectedly, both overgrowth- and growth restriction- associated DNMT3A mutations led to DNA hypomethylation in a shared subset of active enhancers, implicating H3K36me2 in directing enhancer methylation maintenance. In contrast, bivalent chromatin--marked by both active and repressive chromatin modifications--showed divergent DNA methylation changes: hypermethylation in growth restriction-associated DNMT3A mutants and hypomethylation in overgrowth-associated DNMT3A or NSD1 loss-of-function mutants. These findings identify locus-specific DNA methylation defects as a common molecular feature and nominate dysregulated DNA methylation at bivalent chromatin as a potential driver of abnormal growth phenotypes.

genomics↗

bioRxiv2024

Structural basis of the catalytic and allosteric mechanism of bacterial acetyltransferase PatZ

GCN5-related N-Acetyltransferases (GNATs) play a crucial role in regulating bacterial metabolism by acetylating specific target proteins. Despite their importance in bacterial physiology, the mechanisms underlying GNATs enzymatic and regulatory functions remain poorly understood. In this study, we elucidated the structures of Escherichia coli PatZ, a type I GNAT, and investigated its ligand interactions, catalytic processes, and allosterism. PatZ functions as a homotetramer, with each subunit comprising a catalytic domain and a regulatory domain. Our findings reveal that the regulatory domain is essential for acetyltransferase activity, as it not only induces cooperative conformational changes in the catalytic domain but also directly contributes to the formation of substrate binding pockets. Furthermore, a protein structure-based analysis on the evolution of bacterial GNAT types reveals a distinct pattern of the regulatory domain across phyla, underscoring the regulatory domains critical role in responding to cellular energy status. SIGNIFICANCE STATEMENTPost-translational modifications, particularly acetylation mediated by GCN5-related N-Acetyltransferases (GNATs), play a crucial role in bacterial physiology. Protein acetyltransferase Z (PatZ) is a key GNAT with diverse substrates, essential for understanding the bacterial acetylome. This study employs cryogenic electron microscopy, X-ray crystallography, and biochemical analyses to elucidate the mechanistic regulation of Escherichia coli PatZ. Our high-resolution structures reveal PatZs homo-tetrameric architecture, with each subunit comprising regulatory and GNAT domains. We characterize ligand-PatZ interactions, demonstrating ligand-induced conformational changes that facilitate allosteric regulation of the catalytic domain. Furthermore, our analyses elucidate the regulatory domains contribution to substrate binding pocket formation, potentially enhancing substrate specificity. Structure-based phylogenetic analysis provides insights into the evolution of diverse regulatory domains in the GNAT superfamily across bacterial taxonomy. This first visualization of PatZ advances our mechanistic understanding of bacterial physiology, offering novel insights into GNAT-mediated bacterial adaptations. HIGHLIGHTS- E. coli PatZ forms a homotetramer, with each subunit possessing a GNAT catalytic domain and a regulatory domain. - Cooperative binding of acetyl-CoA to the regulatory domains is a prerequisite for inducing the structural compatibility of the catalytic domain with a substrate. - Diverse regulatory domains in GNATs evolved to adapt to varied metabolic conditions across bacterial taxonomy.

biochemistry↗

bioRxiv2024

A brain-shuttled antibody targeting alpha synuclein aggregates for the treatment of synucleinopathies

Parkinsons disease and multiple system atrophy are members of a class of devastating neurodegenerative diseases called synucleinopathies, which are characterized by the presence of alpha-synuclein (-Syn) rich aggregates in the brains of patients. Passive immunotherapy targeting these aggregates is an attractive disease-modifying strategy. Such an approach must not only demonstrate target selectivity towards -Syn aggregates, but also achieve appropriate brain exposure to have the desired therapeutic effect. Here we present preclinical data for a next-generation antibody for the treatment of synucleinopathies. SAR446159 (ABL301) is a bispecific antibody composed of an -Syn-binding immunoglobulin (IgG) and an engineered insulin-like growth factor receptor 1 (IGF1R) binding single-chain variable fragment (scFv), acting as a shuttle to transport an antibody across the blood-brain barrier (BBB). SAR446159 binds tightly and preferentially to -Syn aggregates and prevents their seeding capacity in vitro and in vivo. Incubation with SAR446159 reduced -Syn preformed fibrils (PFFs) uptake in neurons and facilitated uptake and clearance by microglia. In wild type mice injected in the striatum with -Syn PFFs, treatment with SAR446159 reduced the spread of aSyn pathology as measured by phosphorylated -Syn staining and lessened the severity of motor phenotypes. Additionally, in 9-month-old transgenic mice overexpressing -Syn (mThy1--Syn, Line 61), repeated treatment with SAR446159 reduced markers of -Syn aggregation in the brain. SAR446159 had significantly higher brain and CSF penetration over a sustained period than its monospecific counterpart (1E4) in rats and monkeys. The binding properties of SAR446159 combined with its brain-shuttle technology make it a potent, next-generation immunotherapeutic for treating synucleinopathies.

neuroscience↗

bioRxiv2024

Integrated scFv identification and CAR T cell generation for AML targeting in vivo

Cancer immunotherapy has witnessed remarkable advancements, especially in the development of chimeric antigen receptor (CAR) T cell therapy. Here, we integrated single-chain variable fragment (scFv) development with CAR T cell generation based on a newly developed scFv phagemid library. High-throughput long-read PacBio sequencing identified 4.5 x 107 unique full-length scFv proteins within the generated library. In a proof of principle, we screened for scFvs targeting C-type lectin-like molecule-1 (CLL1) with subsequent cloning into a third generation retroviral CAR backbone. Functional assays revealed the specificity and potency of these CAR T cells in targeting CLL1-positive AML cells in vitro. In vivo studies reduced tumor burden and improved survival rates compared to controls. Taken together, screening for tumor specific scFvs against CLL1 can rapidly generate AML specific CAR T cells with effective tumor killing in vivo.

immunology↗

bioRxiv2024

The long-range gene regulatory landscape of cerebellar granule neuron progenitors

Neuronal specification, expansion and differentiation are tightly regulated by the concerted actions of transcription and chromatin modifying factors that are recruited to regulatory elements in the genome. Tissue-specific distal regulatory elements are typically located tens to hundreds of kilobases from the gene they regulate. Thus, to identify the distal enhancers that directly regulate a gene, information on the localisation of enhancers relative to the gene promoter in the nucleus is crucial. Cerebellar granule cell progenitors (GCps) are important transit amplifying neuronal progenitors, giving rise to the most abundant neuronal cell type in the brain. Many of the key factors that regulate fundamental developmental processes in GCps have been identified. For instance, the proneural transcription factor Atoh1 is essential for GCp specification, proliferation and differentiation and the ATP-dependent chromatin remodeller CHD7 is necessary for normal GCp proliferation and differentiation. However, both these factors are recruited to distal regulatory elements and the direct regulatory relationships between these factors, the enhancers they are recruited to, and the genes they regulate in GCps remain uncharacterised. To identify active, long-range gene regulatory interactions in GCps, we used promoter capture Hi-C (pcHi-C), and integrated pcHi-C data with ATAC-seq and ChIP-seq data. We present a rich dataset consisting of 46,428 interactions between 22,797 putative distal regulatory regions and 12,905 protein coding gene promoters in primary mouse GCps. Using VISTA-designated hindbrain enhancers as an example, we identify the genes most likely regulated directly by these enhancers and update their annotation accordingly. Motif enrichment analyses identified a significant enrichment of proneural transcription factor motifs in CHD7-regulated enhancers. Further analyses revealed co-localisation of Atoh1 and CHD7 at gene enhancers, suggesting a novel regulatory relationship between Atoh1 and CHD7 in controlling the expression of key genes in the GCp lineage. We used our data to identify >1,500 Atoh-regulated enhancers, contacting the promoters of 577 genes in GCps, and 197 enhancers of 22 genes that appear to be co-regulated by Atoh1 and CHD7. Co-immunoprecipitation experiments showed that Atoh1 and CHD7 proteins interact with each other. These findings support the emerging picture of CHD7 as an important gene regulatory co-factor for lineage-specific transcription factors. The pcHi-C data is presented as a useful resource to the community for investigating the function of long-range enhancers in the cerebellar GCp lineage.

neuroscience↗

bioRxiv2024

An extinct clade sister to Eumetazoa: On the phylogeny of the Cambrian chancelloriids

The notable disparity of animal body plans can be traced back to the morphological innovations during the Cambrian explosion and represented by a number of exceptionally preserved soft-bodied and skeletal fossils that provide a compelling narrative for animal evolution. Chancelloriids, one of the extinct groups of Cambrian animals, have a distinctive body that characterized by a sclerite-bearing, flexible integument and a single apical opening leading into a central cavity devoid of unequivocal internal organs. Their phylogenetic position within the Metazoa, however, is controversial. Here, we describe new soft-bodied fossils of chancelloriids from the 518-million-year-old Chengjiang biota of China, which corroborate the unique bauplan pattern and reveal exquisite integument microstructures. The tiny protuberances and wrinkling structures of the integument are interpreted to be related to primitive epithelial contraction, suggesting that chancelloriids were a group of basal epitheliozoans and constitute an evolutionary clade that branched below all extant eumetazoans while above or close to the placozoans. Thus, the chancelloriid body plan likely filled one of the anatomical gaps between the Placozoa and the Eumetazoa.

paleontology↗

bioRxiv2024

Impact of exogenous aminoacyl-tRNA synthetase and tRNA on temperature sensitivity in Escherichia coli: towards a genetic code-expanded biological logic gate

Genetic code expansion (GCE) is a powerful strategy that expands the genetic code of an organism for incorporating non-canonical amino acids (ncAAs) into proteins using engineered tRNAs and aminoacyl-tRNA synthetases (aaRSs). While GCE has opened up new possibilities for synthetic biology, little is known about the potential side effects of exogenous aaRS/tRNA pairs. In this study, we investigated the impact of exogenous aaRS and amber suppressor tRNA on gene expression in Escherichia coli. We discovered that in DH10{beta} {Delta}cyaA, transformed with the F1RP/F2P two-hybrid system, high consumption rate of cellular ATP by exogenous aaRS/tRNA at elevated temperatures induces temperature sensitivity in the expression of genes regulated by the catabolite activator protein. We harnessed this temperature sensitivity to create a novel biological AND gate in E. coli, responsive to both p-benzoylphenylalanine (BzF) and low temperature, using a BzF-dependent variant of E. coli chorismate mutase and split subunits of Bordetella pertussis adenylate cyclase. Our study provides new insights into the unexpected effects of exogenous aaRS/tRNA pairs and offers a new approach for constructing a biological logic gate.

synthetic biology↗

bioRxiv2024

Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens

Recent advancements in functional genomics have provided an unprecedented ability to measure diverse molecular modalities, but learning causal regulatory relationships from observational data remains challenging. Here, we leverage pooled genetic screens and single cell sequencing (i.e. Perturb-seq) to systematically identify the targets of signaling regulators in diverse biological contexts. We demonstrate how Perturb-seq is compatible with recent and commercially available advances in combinatorial indexing and next-generation sequencing, and perform more than 1,500 perturbations split across six cell lines and five biological signaling contexts. We introduce an improved computational framework (Mixscale) to address cellular variation in perturbation efficiency, alongside optimized statistical methods to learn differentially expressed gene lists and conserved molecular signatures. Finally, we demonstrate how our Perturb-seq derived gene lists can be used to precisely infer changes in signaling pathway activation for in-vivo and in-situ samples. Our work enhances our understanding of signaling regulators and their targets, and lays a computational framework towards the data-driven inference of an atlas of perturbation signatures.

genomics↗

bioRxiv2023

Dynamic changes in subplate and cortical plate microstructure precede the onset of cortical folding in vivo

Cortical gyrification takes place predominantly during the second to third trimester, alongside other fundamental developmental processes, such as the development of white matter connections, lamination of the cortex and formation of neural circuits. The mechanistic biology that drives the formation cortical folding patterns remains an open question in neuroscience. In our previous work, we modelled the in utero diffusion signal to quantify the maturation of microstructure in transient fetal compartments, identifying patterns of change in diffusion metrics that reflect critical neurobiological transitions occurring in the second to third trimester. In this work, we apply the same modelling approach to explore whether microstructural maturation of these compartments is correlated with the process of gyrification. We quantify the relationship between sulcal depth and tissue anisotropy within the cortical plate (CP) and underlying subplate (SP), key transient fetal compartments often implicated in mechanistic hypotheses about the onset of gyrification. Using in utero high angular resolution multi-shell diffusion-weighted imaging (HARDI) from the Developing Human Connectome Project (dHCP), our analysis reveals that the anisotropic, tissue component of the diffusion signal in the SP and CP decreases immediately prior to the formation of sulcal pits in the fetal brain. By back-projecting a map of folded brain regions onto the unfolded brain, we find evidence for cytoarchitectural differences between gyral and sulcal areas in the late second trimester, suggesting that regional variation in the microstructure of transient fetal compartments precedes, and thus may have a mechanistic function, in the onset of cortical folding in the developing human brain.

neuroscience↗

bioRxiv2023

Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data

BackgroundOncometabolites, often generated as a result of a gene mutation, show pro-oncogenic function when abnormally accumulated in cancer cells. Identification of such mutation-associated metabolites will facilitate developing treatment strategies for cancers, but is challenging due to a large number of metabolites in a cell and the presence of multiple genes associated with cancer development. ResultsHere we report the development of a computational workflow that predicts metabolite-gene-pathway sets (MGPs). MGPs present metabolites and metabolic pathways significantly associated with specific somatic mutations in cancers. The computational workflow uses both cancer patient-specific genome-scale metabolic models (GEMs) and mutation data to generate MGPs. A GEM is a computational model that predicts reaction fluxes at a genome scale, and can be constructed in a cell-specific manner by using omics data (e.g., RNA-seq). The computational workflow is first validated by comparing the resulting metabolite-gene (MG) pairs with multi-omics data (i.e., mutation data, RNA-seq data, and metabolome data) from 17 acute myeloid leukemia samples and 21 renal cell carcinoma samples collected in this study. The computational workflow is further validated by evaluating the MGPs predicted for 18 cancer types, by using RNA-seq data publicly available, in comparison with the reported studies. Therapeutic potential of the resulting MGPs is also discussed. ConclusionsValidation of the MGP-predicting computational workflow indicates that a decent number of metabolites and metabolic pathways appear to be significantly associated with specific somatic mutations. The computational workflow and the resulting MGPs will help identify novel oncometabolites, and also suggest cancer treatment strategies.

systems biology↗

bioRxiv2023

Deep origin of the long root tuft: the oldest stalk-bearing sponge from the Cambrian Stage 3 black shale of South China

In virtue of remarkable tolerance on hypoxia and adaptive specialization in morphology, diverse hexactinellid sponges were prosperous in an early Cambrian living condition that characterized by dysoxic to anoxic bottom waters documented by black shales. New fossils from the black shale of Niutitang Formation (basal Stage 3 of Cambrian) in Hunan Province of China, reveal for the first time an articulated body of the sponge Hyalosinica archaica Mehl & Reitner in Steiner et al., 1993, which possesses an ovoid main body and an impressive long stalk. The specular skeleton includes large diactines that are generally organized as fan-shaped clusters, a few small stauractines and hexactines, and twisted bundles of long monaxons that form the stalk/root tuft. This hexactinellid sponge represents the oldest extinct taxon that took advantage of a long stalk to elevate the main body above the sediment surface and thus to adapt to the oxygen-deficient sea-bottom environment. The long root tuft links Hyalosinica to a series of fossil and recent sponge taxa and proves a deep origin of the stalk-bearing morphology, indicating a likely parallel evolution within the Hexactinellida in response to special environmental pressures. Furthermore, the overall skeletal organization indicates that Hyalosinica, as well as related early "rossellimorphs", are basal stem group representatives of Hexactinellida and probably branched before the extinct Reticulosa and before the two extant hexactinellid subclasses.

paleontology↗

bioRxiv2022

HOXA9 forms a repressive complex with nuclear matrix-associated protein SAFB to maintain acute myeloid leukemia

HOXA9 is commonly upregulated in acute myeloid leukemia (AML), where it confers poor prognosis. Characterising the protein interactome of endogenous HOXA9 in human AML, we identified a chromatin complex of HOXA9 with the nuclear matrix attachment protein-SAFB. SAFB perturbation phenocopied HOXA9 knockout to decrease AML proliferation, increase differentiation and apoptosis in vitro and prolonged survival in vivo. Integrated genomic, transcriptomic and proteomic analyses further demonstrated that the HOXA9-SAFB-chromatin complex associates with NuRD and HP1{gamma} to repress the expression of factors associated with differentiation and apoptosis, including NOTCH, CEBP{delta}, S100A8, and CDKN1A. Chemical or genetic perturbation of NuRD and HP1{gamma} catalytic activity also triggered differentiation, apoptosis and the induction of these tumor-suppressive genes. Importantly, this mechanism is operative in other HOXA9-dependent AML genotypes. This mechanistic insight demonstrates active HOXA9-dependent differentiation block as a potent mechanism of disease maintenance in AML, that may be amenable to therapeutic intervention via therapies targeting the HOXA9/SAFB interface and/or NuRD and HP1{gamma} activity. Key Points- Identification of the endogenous human HOXA9 protein interactome in AML - HOXA9 forms a repressive complex with S/MAR binding protein (SAFB) that is critical for the maintenance of AML by facilitating proliferation and preventing differentiation and cell death. - The HOXA9/SAFB (H9SB) complex represses gene expression via recruitment of NuRD and HP1{gamma}.

cancer biology↗

bioRxiv2022

The molecular mechanism of chloramphenicol and thiamphenicol resistance mediated by a novel oxidase CmO in Sphingomonadaceae

Antibiotic resistance mediated by bacterial enzyme inactivation plays a mysterious and crucial role for antibiotic degradation and selection pressure reduction in the environment. The enzymatic inactivation of the antibiotic chloramphenicol (CAP) involves nitro reduction, amide bond hydrolysis and acetylation modification. However, the molecular mechanism of enzymatic oxidation of CAP remains unknown. Here, a novel oxidase gene cmO was identified and confirmed biochemically to catalyze the resistance process through the oxidative inactivation at the side chain C-3 position of CAP and thiamphenicol (TAP) in Sphingomonadaceae. The oxidase CmO is highly conservative in Sphingomonadaceae and shares the highest amino acid homology of 41.05% with the biochemically identified glucose methanol choline (GMC) oxidoreductases. Molecular docking and site-directed mutagenesis analyses demonstrated that CAP was anchored inside the protein pocket of CmO with the hydrogen bonding of key residues glycine (G)99, asparagine (N)518, methionine (M)474 and tyrosine (Y)380. CAP sensitivity test demonstrated that the acetyltransferase and CmO showed higher resistance to CAP as compared with the amide bond-hydrolyzing esterase and nitroreductase. This study provides a better theoretical basis and a novel diagnostic gene for understanding and assessing the fate and resistance risk of CAP and TAP in the environment. ImportanceRising levels of antibiotic resistance undermines ecological and human health as a result of indiscriminate usage of antibiotics. Various resistance mechanisms have been revealed, for instance genes encoding proteins that degrade antibiotics, yet requiring further exploration. In this study, we reported a novel gene encoding an oxidase involved in the inactivation of typical amphenicol antibiotics (chloramphenicol and thiamphenicol), and the molecular mechanism was elucidated. The observation provides novel data to understand capabilities of bacteria to tackle antibiotic stress and suggests complex function of enzymes in the context of antibiotic resistance development and antibiotics removal. The reported gene can be further employed as an indicator to monitor amphenicols fate in the environment, benefiting the risk assessment in this era of antibiotic resistance.

microbiology↗