Biology subjects

Kim, A.

Publications and source records attributed to Kim, A..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Deep Mining of the Human Antibody Repertoire Identifies Frequent and Immunogenetically Diverse CDRH3 Topologies Targetable by Vaccination

Germline targeting vaccination strategies against highly variable pathogens such as HIV aim to elicit broadly neutralizing antibodies (bnAbs) with particular immunogenetic or structural features. The V2 apex of the HIV Env protein is a promising target for a class of bnAbs that contain conserved structural motifs in the heavy chain complementarity determining region 3 (CDRH3). Here, we show that these structural motifs are targetable by vaccination by characterizing V2 apex axe-like CDRH3s in the human repertoire and developing new immunogens capable of engaging them. We determined the frequency and diversity of axe-like CDHR3s in healthy human donors using a series of structural informatics approaches, finding these precursors in nearly 90% of donors. Axe-targeting immunogens based on the HIV Env Q23.17 bound axe-like precursors in cryo-EM structures, induced V2 apex-specific antibody responses in humanized mice, and induced axe-like heterologous neutralizing antibodies in rhesus macaques infected with a germline-targeted simian-human immunodeficiency virus. These results illustrate a new structure-guided immunoinformatic vaccine design paradigm that can be employed to elicit immunogenetically diverse yet structurally conserved classes of antibodies. Significance StatementMany broadly neutralizing antibodies (bnAbs) utilize modes of epitope recognition dominated by the antibody complementarity determining region 3 (CDRH3). The CDRH3 is the most diverse part of the antibody, posing a challenge for germline targeting vaccine designs that aim to elicit antibodies with particular immunogenetic features. Vaccine design strategies that accommodate CDRH3 variability are therefore needed. Many HIV Env V2 apex bnAbs share "axe-like" CDRH3 microfolds that arise from diverse immunogenetic origins. Here we determined the frequency in humans of B cells with such CDRH3 topologies and designed immunogens to engage their precursors. This work opens a path toward vaccines that engage specific structural classes of B cells, thereby advancing the rational design of immunogens for HIV and other pathogens.

immunology↗

bioRxiv2024

Targets of influenza Human T cell response are mostly conserved in H5N1

Frequent recent spillovers of subtype H5N1 clade 2.3.4.4b highly pathogenic avian influenza (HPAI) virus into poultry and mammals, especially dairy cattle, including several human cases, increased concerns over a possible future pandemic. Here, we performed an analysis of epitope data curated in the Immune Epitope Database (IEDB). We found that the patterns of immunodominance of seasonal influenza viruses circulating in humans and H5N1 are similar. We further conclude that a significant fraction of the T cell epitopes is conserved at a level associated with cross-reactivity between avian and seasonal sequences, and we further experimentally demonstrate extensive cross-reactivity in the most dominant T cell epitopes curated in the IEDB. Based on these observations, and the overall similarity of the neuraminidase (NA) N1 subtype encoded in both HPAI and seasonal H1N1 influenza virus as well as cross-reactive group 1 HA stalk-reactive antibodies, we expect that a degree of pre-existing immunity is present in the general human population that could blunt the severity of human H5N1 infections.

immunology↗

bioRxiv2024

Evolution of drought resistance strategies following the introduction of white clover (Trifolium repens L.)

Background and AimsSuccess during colonization likely depends on growing quickly and tolerating novel and stressful environmental conditions. However, rapid growth, stress avoidance, and stress tolerance are generally considered divergent physiological strategies. MethodsWe evaluate how white clover (Trifolium repens) has evolved to a divergent water regime following introduction to North America. We conduct RNAseq within a dry-down experiment utilizing accessions from low and high latitude populations from native and introduced ranges, and assess variation in dehydration avoidance (avoidance of wilting) and dehydration tolerance (ability to survive wilting). Key ResultsIntroduced populations are better at avoiding dehydration, but poorer at tolerating dehydration than native populations. There is a strong negative correlation between avoidance and tolerance traits and expression of most drought-associated genes exhibits similar tradeoffs. Candidate genes with expression strongly associated with dehydration avoidance are linked to stress signaling, closing stomata and producing osmoprotectants. However, genes with expression linked to dehydration tolerance are associated with avoiding excessive ROS production and toxic bioproducts of stress responses. Several candidate genes show differential expression patterns between native and introduced ranges, and could underlie differences in drought resistance syndromes between ranges. ConclusionsThese results suggest there has been strong selection following introduction for dehydration avoidance at the cost of surviving dehydration.

evolutionary biology↗

bioRxiv2024

The primary sclerosing cholangitis and ulcerative colitis colonic mucosa defined through paired microbial and single-cell RNA sequencing

Primary sclerosing cholangitis (PSC) is a chronic progressing cholestatic disease that often co-occurs with inflammatory bowel disease (PSC-IBD). PSC-IBD affecting the colon (PSC-UC) is likened clinically to ulcerative colitis (UC), however differences include a right colon dominance, less severe inflammatory presentation and a greater lifetime risk of colorectal cancer. To understand the basis of clinical differences, we combine single-cell mRNA and antigen receptor sequencing, 16S ribosomal DNA analysis and spatial transcriptomics on biopsies from multiple colon regions of both PSC-UC and UC patients in remission or at the time of relapse. We discover disease-specific cell and microbial profiles between these cohorts, highlighting a distinct landscape in the right colon of PSC-UC patients and an epithelial-endothelial cell state that may contribute to intestinal permeability in UC. We show the expansion of an activated mast cell state in both diseases during flare, and demonstrate the requirement of TMEM176B in sustaining this activated state. Together this work demonstrates that PSC-UC and UC are distinct diseases with common cell mechanisms during inflammation, providing cellular and microbial insights to improve treatment of both patient cohorts.

cell biology↗

bioRxiv2024

Genome Restructuring around Innate Immune Genes in Monocytes in Alcohol-associated Hepatitis

Many inflammatory genes in the immune system are clustered in the genome. The 3D genome architecture of these clustered genes likely plays a critical role in their regulation and alterations to this structure may contribute to diseases where inflammation is poorly controlled. Alcohol-associated hepatitis (AH) is a severe inflammatory disease that contributes significantly to morbidity in alcohol associated liver disease. Monocytes in AH are hyper-responsive to inflammatory stimuli and contribute significantly to inflammation. We performed high throughput chromatin conformation capture (Hi-C) technology on monocytes isolated from 4 AH patients and 4 healthy controls to better understand how genome structure is altered in AH. Most chromosomes from AH and healthy controls were significantly dissimilar from each other. Comparing AH to HC, many regions of the genome contained significant changes in contact frequency. While there were alterations throughout the genome, there were a number of hotspots containing a higher density of changes in structure. A few of these hotspots contained genes involved in innate immunity including the NK-gene receptor complex and the CXC-chemokines. Finally, we compare these results to scRNA-seq data from patients with AH challenged with LPS to predict how chromatin conformation impacts transcription of clustered immune genes. Together, these results reveal changes in the chromatin structure of monocytes from AH patients that perturb expression of highly clustered proinflammatory genes.

immunology↗

bioRxiv2024

scSNViz: a user-friendly toolset for visualization and analysis of Cell-Specific Expressed SNVs

SummaryAccurately characterizing expressed genetic variation at the single-cell level is essential for understanding transcriptional heterogeneity, allelic regulation, and mutational dynamics within complex tissues. However, few tools enable comprehensive visualization and quantitative analysis of expressed variants across individual cells. scSNViz is an R package for the exploration, quantification, and visualization of expressed single-nucleotide variants (SNVs) from cell-barcoded single-cell RNA sequencing (scRNA-seq) data. The software supports estimation of variant allele fractions, clustering of SNV expression profiles, and 2D and 3Dl visualization of individual SNVs or user-defined SNV groups. Beyond visualization, scSNViz facilitates investigation of cell-, cluster-, or lineage-specific variant expression patterns, as well as allelic dynamics including imprinting, random allele inactivation, and transcriptional bursting. It interoperates seamlessly with established single-cell frameworks - Seurat for clustering, Slingshot for trajectory inference, scType for cell-type annotation, and CopyKat for copy-number profiling - enabling integrative multi-omic analyses of expressed variation. Availability and ImplementationscSNViz is implemented in R and freely available at https://github.com/HorvathLab/scSNViz (DOI: 10.5281/zenodo.17307516). The package includes comprehensive documentation and example workflows designed for users with limited bioinformatics experience.

genomics↗

bioRxiv2024

Investigation of expression of genes encoding glycogen degrading enzymes in Gardnerella swidsinskii and identification of reference genes for quantitative real-time PCR

Gardnerella spp. express and export enzymes for the breakdown of glycogen into glucose, maltose, and malto-oligosaccharides for consumption by the vaginal microbiota but how the expression of these "public goods" is affected by substrate and product levels in the environment is not known. Accurate measurement of relative gene expression using real-time quantitative PCR relies on the identification of appropriate reference genes whose expression levels remain constant under the conditions of the study. Currently, no reference genes have been identified for gene expression analysis of Gardnerella spp. The objectives of this study were to identify reference genes and apply them in determining the relative gene expression levels of genes encoding -amylase and -amylase-pullulanase in media supplemented with substrate (glycogen) or a preferred product (maltotriose). Ten candidate reference genes were evaluated and analysis of Cq values from qPCR using multiple algorithms identified uppS (encoding polyprenyl diphosphate synthase) as the top comprehensively ranked reference gene followed by gatA (encoding Asp-tRNA/Glu-tRNA amidotransferase subunit gatA). Interpretation of the Cq values for -amylase and -amylase-pullulanase was performed by applying these two reference genes in the calculation of relative gene expression levels. -amylase-pullulanase gene expression was upregulated in media supplemented with 1% glycogen in comparison to media supplemented with 1% maltotriose suggesting a regulatory mechanism in G. swidsinskii that responds to nutrient availability. No significant difference in gene expression of -amylase was observed suggesting expression is not influenced by substrate availability. The RNA purification protocol and reference genes validated in this study will be useful in future studies of gene expression in Gardnerella. ImportanceKnowledge of the factors affecting growth of vaginal microbiota is critical to understanding how vaginal dysbiosis is initiated and maintained. Overgrowth of Gardnerella species including G. swidsinskii is a hallmark of bacterial vaginosis. These organisms break down vaginal glycogen and the products become available for uptake by Gardnerella and other microbiota. Measuring how expression of genes encoding glycogen degrading enzymes relates to relative abundance of substrate and products in the environment requires development of protocols for RNA purification and identification of reference genes for RT-qPCR.

microbiology↗

bioRxiv2024

BMI1 regulates human erythroid self-renewal through both gene repression and gene activation

The limited proliferative capacity of erythroid precursors is a major obstacle to generate sufficient numbers of in vitro-derived red blood cells (RBC) for clinical purposes. We and others have determined that BMI1, a member of the polycomb repressive complex 1 (PRC1), is both necessary and sufficient to drive extensive proliferation of self-renewing erythroblasts (SREs). However, the mechanisms of BMI1 action remain poorly understood. BMI1 overexpression led to 10 billion-fold increase BMI1-induced (i)SRE self-renewal. Despite prolonged culture and BMI1 overexpression, human iSREs can terminally mature and agglutinate with typing reagent monoclonal antibodies against conventional RBC antigens. BMI1 and RING1B occupancy, along with repressive histone marks, were identified at known BMI1 target genes, including the INK-ARF locus, consistent with an altered cell cycle following BMI1 inhibition. We also identified upregulated BMI1 target genes with low repressive histone modifications, including key regulator of cholesterol homeostasis. Functional studies suggest that both cholesterol import and synthesis are essential for BMI1-associated self-renewal. These findings support the hypothesis that BMI1 regulates erythroid self-renewal not only through gene repression but also through gene activation and offer a strategy to expand the pool of immature erythroid precursors for eventual clinical uses.

cell biology↗

bioRxiv2024

Neural substrates underlying the expectation of rewards resulting from effortful exertion

Decisions to exert effort for reward are often conceptualized as reflecting a trade-off between anticipated benefits and effort costs. However, economic theories propose that valuation is reference-dependent, such that behavior is shaped relative to expected outcomes rather than absolute reward magnitude. Whether reward expectations influence effort expenditure through such reference-dependent mechanisms, and how these computations are represented in the brain, remains unclear. Using an incentivized grip-force task during functional magnetic resonance imaging, we experimentally manipulated reward expectations independently of reward outcomes. Behavioral results showed that effort exertion varied systematically with reward expectations, indicating that individuals evaluated exertion relative to a reference point. Neural activity in the ventral striatum tracked both prospective reward expectations and deviations between expected and realized earnings. Moreover, these neural signals predicted individual differences in reference-dependent modulation of effort. Together, these findings identify ventral striatal representations associated with reference-dependent effort valuation and suggest that reference-dependent computations contribute to motivated behavior. Significance statementDecisions to exert effort are commonly described as reflecting a trade-off between reward and effort cost. However, whether effort valuation is shaped by reward expectations rather than absolute incentives remains unclear. Using functional magnetic resonance imaging and an incentivized grip-force task, we show that reward expectations serve as a reference point that systematically influences effort expenditure. Neural signals in the ventral striatum tracked both reward expectations and deviations between expected and realized outcomes, and these signals predicted individual differences in reference-dependent effort behavior. These findings suggest that reference-dependent valuation contributes to the neural control of motivated action.

neuroscience↗

bioRxiv2023

Using a decision tree to predict COVID case numbers: a tutorial for beginners

This manuscript describes the development of a module that is part of a learning platform named "NIGMS Sandbox for Cloud-based Learning" https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox at the beginning of this Supplement. This module delivers learning materials on machine learning and decision tree concepts in an interactive format that uses appropriate cloud resources for data access and analyses. Machine learning (ML) is an important tool in biomedical research and can lead to improvements in diagnosis, treatment, and prevention of diseases. During the COVID pandemic ML was used for predictions at the patient and community levels. Given its ubiquity, it is important that future doctors, researchers and teachers get acquainted with ML and its contributions to research. Our goal is to make it easier for everyone to learn about machine learning. The learning module we present here is based on a small COVID dataset, videos, annotated code and the use of Google Colab or the Google Cloud Platform (GCP). The benefit of these platforms is that students do not have to set up a programming environment on their computer which saves time and is also an important democratization factor. The module focuses on learning the basics of decision trees by applying them to COVID data. It introduces basic terminology used in supervised machine learning and its relevance to research. Our experience with biology students at San Francisco State University suggests that the material increases interest in ML.

scientific communication and education↗

bioRxiv2023

Activation of Protein Kinase R (PKR) Plays a Pro-Viral Role in Mammarenavirus Infected Cells

Many viruses, including mammarenaviruses, have evolved mechanisms to counteract different components of the host cell innate immunity, which is required to facilitate robust virus multiplication. The double strand (ds)RNA sensor protein kinase receptor (PKR) pathway plays a critical role in the cell antiviral response. Whether PKR can restrict the multiplication of the Old World mammarenavirus lymphocytic choriomeningitis virus (LCMV) and the mechanisms by which LCMV may counteract the antiviral functions of PKR have not yet been investigated. Here we present evidence that LCMV infection results in very limited levels of PKR activation, but LCMV multiplication is enhanced in the absence of PKR. In contrast, infection with a recombinant LCMV with a mutation affecting the 3-5 exonuclease (ExoN) activity of the viral nucleoprotein (NP) resulted in robust PKR activation in the absence of detectable levels of dsRNA, which was associated with severely restricted virus multiplication that was alleviated in the absence of PKR. However, pharmacological inhibition of PKR activation resulted in reduced levels of LCMV multiplication. These findings uncovered a complex role of the PKR pathway in LCMV-infected cells involving both pro-and anti- viral activities. IMPORTANCEAs with many other viruses, the prototypic Old World mammarenavirus lymphocytic choriomeningitis virus (LCMV) can interfere with the host cell innate immune response to infection, which includes the double strand (ds)RNA sensor protein kinase receptor (PKR) pathway. A detailed understanding of LCMV-PKR interactions can provide novel insights about mammarenavirus-host cell interactions and facilitate the development of effective antiviral strategies against human pathogenic mammarenaviruses. In the present work, we present evidence that LCMV multiplication is enhanced in PKR- deficient cells, but pharmacological inhibition of PKR activation unexpectedly resulted in severely restricted propagation of LCMV. Likewise, we document a robust PKR activation in LCMV-infected cells in the absence of detectable levels of dsRNA. Our findings have revealed a complex role of the PKR pathway during LCMV infection and uncovered the activation of PKR as a druggable target for the development of antiviral drugs against human pathogenic mammarenaviruses.

microbiology↗

bioRxiv2023

A visual efference copy-based navigation algorithm in Drosophila for complex visual environments

How flies adjust their flight direction in response to visual cues has been intensively studied, leading to a detailed understanding of individual neural circuits. However, how these circuits operate collectively in complex visual environments remains unclear. To understand how a mixture of visual stimuli--including those caused by the flys own actions--jointly determines its motor program, we developed an integrative model of Drosophila visuomotor processing. In particular, we derived simple models from flies wing responses to individual visual patterns and combined them through different internal models. We compared the steering behavior of these "virtual flies" with those of flying flies that freely changed their orientation. The results of these experiments supported the idea that, for selective visual patterns, flies employ suppressive mechanisms between competing visuomotor reflexes, consistent with an efference copy-based internal model. Our model provides a formal description of vision-based navigation strategies of Drosophila under complex visual environments.

neuroscience↗

bioRxiv2023

Postglacial genomes from foragers across Northern Eurasia reveal prehistoric mobility associated with the spread of the Uralic and Yeniseian languages

The North Eurasian forest and forest-steppe zones have sustained millennia of sociocultural connections among northern peoples. We present genome-wide ancient DNA data for 181 individuals from this region spanning the Mesolithic, Neolithic and Bronze Age. We find that Early to Mid-Holocene hunter-gatherer populations from across the southern forest and forest-steppes of Northern Eurasia can be characterized by a continuous gradient of ancestry that remained stable for millennia, ranging from fully West Eurasian in the Baltic region to fully East Asian in the Transbaikal region. In contrast, cotemporaneous groups in far Northeast Siberia were genetically distinct, retaining high levels of continuity from a population that was the primary source of ancestry for Native Americans. By the mid-Holocene, admixture between this early Northeastern Siberian population and groups from Inland East Asia and the Amur River Basin produced two distinctive populations in eastern Siberia that played an important role in the genetic formation of later people. Ancestry from the first population, Cis-Baikal Late Neolithic-Bronze Age (Cisbaikal_LNBA), is found substantially only among Yeniseian-speaking groups and those known to have admixed with them. Ancestry from the second, Yakutian Late Neolithic-Bronze Age (Yakutia_LNBA), is strongly associated with present-day Uralic speakers. We show how Yakutia_LNBA ancestry spread from an east Siberian origin [~]4.5kya, along with subclades of Y-chromosome haplogroup N occurring at high frequencies among present-day Uralic speakers, into Western and Central Siberia in communities associated with Seima-Turbino metallurgy: a suite of advanced bronze casting techniques that spread explosively across an enormous region of Northern Eurasia [~]4.0kya. However, the ancestry of the 16 Seima-Turbino-period individuals--the first reported from sites with this metallurgy--was otherwise extraordinarily diverse, with partial descent from Indo-Iranian-speaking pastoralists and multiple hunter-gatherer populations from widely separated regions of Eurasia. Our results provide support for theories suggesting that early Uralic speakers at the beginning of their westward dispersal where involved in the expansion of Seima-Turbino metallurgical traditions, and suggests that both cultural transmission and migration were important in the spread of Seima-Turbino material culture.

genomics↗

bioRxiv2023

4R-Tau seeding activity unravels molecular subtypes in patients with Progressive Supranuclear Palsy

Progressive Supranuclear palsy (PSP) is a 4-repeat (4-R) tauopathy. We hypothesized that the molecular diversity of tau could explain the heterogeneity seen in PSP disease progression. To test this hypothesis, we performed an extensive biochemical characterisation of the high molecular weight tau species (HMW-Tau) in 20 different brain regions of 25 PSP patients. We found a correlation between the HMW-Tau species and tau seeding capacity in the primary motor cortex, where we confirmed that an elevated 4R-Tau seeding activity correlates with a shorter disease duration. To identify factors that contribute to these differences, we performed proteomic and spatial transcriptomic analysis that revealed key mechanistic pathways, in particular those involving the immune system, that defined patients demonstrating high and low tau seeding capacity. These observations suggest that differences in the tau seeding activity may contribute to the considerable heterogeneity seen in disease progression of patients suffering from PSP.

neuroscience↗

bioRxiv2023

A Pooled Cell Painting CRISPR Screening Platform Enables de novo Inference of Gene Function by Self-supervised Deep Learning

Pooled CRISPR screening has emerged as a powerful method of mapping gene functions thanks to its scalability, affordability, and robustness against well or plate-specific confounders present in array-based screening 1-6. Most pooled CRISPR screens assay for low dimensional phenotypes (e.g. fitness, fluorescent markers). Higher-dimensional assays such as perturb-seq are available but costly and only applicable to transcriptomics readouts 7-11. Recently, pooled optical screening, which combines pooled CRISPR screening and microscopy-based assays, has been demonstrated in the studies of the NFkB pathway, essential human genes, cytoskeletal organization and antiviral response 12-15. While the pooled optical screening methodology is scalable and information-rich, the applications thus far employ hypothesis-specific assays. Here, we enable hypothesis-free reverse genetic screening for generic morphological phenotypes by re-engineering the Cell Painting 16 technique to provide compatibility with pooled optical screening. We validated this technique using well-defined morphological genesets (124 genes), compared classical image analysis and self-supervised learning methods using a mechanism-of-action (MoA) library (300 genes), and performed discovery screening with a druggable genome library (1640 genes) 17. Across these three experiments we show that the combination of rich morphological data and deep learning allows gene networks to emerge without the need for target-specific biomarkers, leading to better discovery of gene functions.

genomics↗

bioRxiv2023

Competition between stochastic neuropeptide signals calibrates the rate of satiation

We investigated how transmission of hunger- and satiety-promoting neuropeptides, NPY and MSH, is integrated at the level of intracellular signaling to control feeding. Receptors for these peptides use the second messenger cAMP, but the messengers spatiotemporal dynamics and role in energy balance are controversial. We show that AgRP axon stimulation in the paraventricular hypothalamus evokes probabilistic and spatially restricted NPY release that triggers stochastic cAMP decrements in downstream MC4R-expressing neurons (PVHMC4R). Meanwhile, POMC axon stimulation triggers stochastic, MSH-dependent cAMP increments. NPY and MSH competitively control cAMP, as reflected by hunger-state-dependent differences in the amplitude and persistence of cAMP transients evoked by each peptide. During feeding bouts, elevated MSH release and suppressed NPY release cooperatively sustain elevated cAMP in PVHMC4R neurons, thereby potentiating feeding-related excitatory inputs and promoting satiation across minutes. Our findings highlight how state-dependent integration of opposing, quantal peptidergic events by a common biochemical target calibrates energy intake.

neuroscience↗

bioRxiv2023

Olfactory fear conditioning biases olfactory stem cell receptor fate

The main olfactory epithelium initiates the process of odor encoding. Recent studies have demonstrated intergenerationally inherited changes in the olfactory system in response to fear conditioning, resulting in increases in olfactory sensory neuron frequencies and altered responses to odors. We investigated changes in the cellular composition of the olfactory epithelium in response to an aversive stimulus. Here, we achieve volumetric cellular resolution to demonstrate that olfactory fear conditioning increases the number of odor-encoding neurons in mice that experience odor-shock conditioning (F0), as well as their unconditioned offspring (F1). We demonstrate that the increase in F0 is due, in part, to the biasing of the stem cell layer of the main olfactory epithelium. Detailed analysis of F1 behavior revealed subtle odor-specific differences between the offspring of unconditioned and conditioned parents, despite the absence of an active aversion to the conditioned odor. Thus, we reveal intergenerational regulation of olfactory epithelium composition in response to olfactory fear conditioning, providing insight into the heritability of acquired phenotypes. One-Sentence SummaryOlfactory fear conditioning induces heritable changes to the mouse olfactory system and biases neurogenesis and behavior in both parent and offspring.

neuroscience↗

bioRxiv2022

Targeted degradation of PRC1 components, BMI1 and RING1B, via a novel protein complex degrader strategy

Polycomb repressive complex 1 (PRC1) is an essential epigenetic regulator that mainly controls histone H2A Lys119 mono-ubiquitination (H2AK119ub). BMI1 and RING1B are PRC1 core components and play critical roles in the development of various cancers. However, therapeutic agents targeting PRC1 are very limited, and small-molecule inhibitors of PRC1 displayed limited effectiveness in killing cancer cells. In this study, MS147, the first degrader of PRC1 core components, BMI1 and RING1B, was discovered via a novel protein complex degradation strategy that utilizes the target proteins interacting partner protein (EED) to degrade BMI1 and RING1B. MS147, which comprises an EED small-molecule binder linked to a ligand of the E3 ligase VHL, degrades BMI1 and RING1B in an EED-, VHL-, ubiquitination- and time-dependent manner. MS147 is selective and preferentially degrades BMI1 and RING1B over PRC2 core components: EED, EZH2 and SUZ12. Consequently, MS147 effectively reduces H2AK119ub, but not H3K27me3, which is catalyzed by PRC2. Furthermore, MS147, but not the parent EED binder or known PRC2 degraders, effectively inhibits the proliferation of cancer cell lines that are insensitive to EZH2 knockout or PRC2 degraders. Overall, this study provides a novel degrader targeting BMI1 and RING1B, which is a useful chemical tool to further investigate the roles of PRC1 in cancer, and a novel protein complex degradation strategy, which could potentially expand the degradable human proteome.

biochemistry↗