Biology subjects

Brown, C.

Publications and source records attributed to Brown, C..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Multiple stressors in the Anthropocene: Urban evolutionary history modifies sensitivity to the toxic effects of crude oil exposure in killifish

Persistence of wild species in human-altered environments is difficult, in part because challenges to fitness are complex when multiple environmental changes occur simultaneously, which is common in the Anthropocene. This complexity is difficult to conceptualize because the nature of environmental change is often highly context specific. A mechanism-guided approach may help to shape intuition and predictions about complexity; fitness challenges posed by co-occurring stressors with similar mechanisms of action may be less severe than for those with different mechanisms of action. We approach these considerations within the context of ecotoxicology because this field is built upon a rich mechanistic foundation. We hypothesized that evolved resistance to one class of common toxicants would afford resilience to the fitness impacts of another class of common toxicants that shares mechanisms of toxicity. Fundulus killifish populations in urban estuaries have repeatedly evolved resistance to persistent organic pollutants including PCBs. Since PCBs and some of the toxicants that constitute crude oil (e.g., high molecular weight PAHs) exert toxicity through perturbation of AHR signaling, we predicted that PCB resistant populations would also be resilient to crude oil toxicity. Common garden comparative oil exposure experiments, including killifish populations with different exposure histories, showed that most killifish populations were sensitive to fitness impacts (reproduction and development) caused by oil exposure, but that fish from the PCB-resistant population were insensitive. Population differences in toxic outcomes were not compatible with random-neutral expectations. Transcriptomics revealed that the molecular mechanisms that contributed to population variation in PAH resilience were shared with those that contribute to evolved variation in PCB resilience. We conclude that the fitness challenge posed by environmental pollutants is effectively reduced when those chemicals share mechanisms that affect fitness. Mechanistic considerations may help to scale predictions regarding the fitness challenges posed by stressors that may co-occur in human-altered environments.

evolutionary biology↗

bioRxiv2025

Adult killifish exposure to crude oil perturbs embryonic gene expression and larval morphology in first- and second-generation offspring

Exposures to environmental toxicants can have both immediate and long-term impacts, including those that persist into the next generation. Using Gulf killifish (Fundulus grandis), we tested whether adult progenitor exposure to crude oil caused perturbations to larval morphology and embryonic genome-wide gene expression in their first- and second-generation descendants raised in clean water. We also tracked responses of additional direct oil exposures in the F1 and F2 embryos. Exposure to oil in progenitor fish caused altered larval morphology in F1 and F2 descendants. Some perturbations were enhanced by additional oil exposure in lineages with progenitors that had been exposed to oil. Progenitor exposures altered embryonic gene expression in F1 and F2 descendants, implicating impacts on neurological and cardiovascular systems. Molecular responses to progenitor exposure were distinct between F1 and F2 offspring, suggesting complex interactions between mechanisms that contribute to the transgenerational transfer of information. In contrast, molecular responses to additional direct oil exposures during early-life development were highly conserved between generations and between progenitor exposure treatments. We conclude that exposure to crude oil causes developmental perturbations that propagate at least two generations, and we present additional hypotheses about underlying molecular mechanisms and emergent health consequences. SYNOPSISThis study shows that exposure of adult fish to crude oil perturbs development and gene expression in offspring and grand-offspring, thereby extending the timeframe necessary to consider ecotoxicological risk.

pharmacology and toxicology↗

bioRxiv2025

High-throughput chemical toxicity testing for beneficial insects: The value of coated vials

Non-target effects of insecticides used in agriculture can impact the ecosystem services provided by beneficial insects. Understanding the broader effects of chemical usage requires multi-species investigations on the impact of different insecticide active ingredients. In this work, we tested the utility of coated vials as a quick, cheap, and efficient dried residue chemical toxicity assay. This method was compared against dishes sprayed with a Potter tower, which is an industry standard instrument used to apply precise insecticide doses. Our study focused on 2 natural enemies of aphids, larval and adult Hippodamia variegata ladybird beetle, and the parasitoid wasp, Diaeretiella rapae. These natural enemies were exposed to multiple doses of 3 insecticides that are registered for aphid control in Australian agriculture: alpha-cypermethrin (pyrethroid), dimethoate (organophosphate), and sulfoxaflor (sulfoximine). Modelled dose-response relationships showed evidence of general differences in the intercepts between methods, but not in slope (rate of mortality with concentration). However, these subtle statistically significant effects did not translate into marked differences in LC50-values, which were comparable across assay methods for all natural enemies and insecticides tested. Coated vials therefore produced estimates of chemical toxicity that were consistent with those derived from Potter tower sprays. This underscores the validity of coated vials as a method for performing high-throughput chemical toxicity experiments, as required when examining different populations of multiple taxa across a range of insecticide active ingredients.

zoology↗

bioRxiv2025

CAR T-cell and oncolytic virus dynamics and determinants of combination therapy success for glioblastoma

Glioblastoma is a highly aggressive and treatment-resistant primary brain cancer. While chimeric antigen receptor (CAR) T-cell therapy has demonstrated promising results in targeting these tumors, it has not yet been curative. An innovative approach to improve CAR T-cell efficacy is to combine them with other immune modulating therapies. In this study, we investigate in vitro combination of IL-13R2 targeted CAR T-cells with an oncolytic virus (OV) and study the complex interplay between tumor cells, CAR T-cells, and OV dynamics with a novel mathematical model. We fit the model to data collected from experiments with each therapy individually and in combination to reveal determinants of therapy synergy and improved efficacy. Our analysis reveals that the virus bursting size is a critical parameter in determining the net tumor infection rate and overall combination treatment efficacy. Moreover, the model predicts that administering the oncolytic virus simultaneously with, or prior to, CAR T-cells could maximize therapeutic efficacy.

immunology↗

bioRxiv2025

Identification of a novel GREMLIN1 uptake pathway in epithelial cells that requires BMP binding

Gremlin1 is a member of a cysteine-knot containing family of secreted antagonists of bone morphogenetic protein signaling. GREM1 binding to BMP targets prevents their engagement with cognate BMP receptors, attenuating BMP-dependent gene expression. Some evidence suggests that GREM1 can directly bind to receptor tyrosine kinases on the plasma membrane, further complicating our understanding of GREM1 biology. To attempt to clarify the modalities of GREM1 signaling, we show that GREM1 protein is produced and secreted by intestinal fibroblasts and endocytosed by neighbouring epithelial cells. GREM1 uptake is a slow process and occurs by both clathrin- and caveolin-mediated endocytosis. Cell membrane heparin sulfate proteoglycans are required for GREM1 binding and uptake, and once internalised, GREM1 appears to localise to the early endosomes. Addition of BMP2 enhanced GREM1 uptake into cells. Remarkably, generation of a BMP-resistant GREM1 mutant abolished GREM1 uptake both in the presence and absence of BMP2. These data suggest that GREM1 binding and uptake into cells requires BMP binding, a process that may contribute to the antagonism of BMP signaling by GREM1. SummaryIn this article, we demonstrate differential GREM1 mRNA versus protein expression in mouse intestine. We also identify a novel GREM1 endocytosis pathway whereby mammalian cells take up GREM1 protein in what appears to be a BMP-dependent mechanism.

cell biology↗

bioRxiv2024

RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling

Ribosome profiling is a high-throughput sequencing technique that captures the positions of translating ribosomes on RNAs. Recent advancements in ribosome profiling include achieving highly-phased ribosome footprints for plant translatomes and more recently for bacterial translatomes. This substantially increases the specificity of detecting open reading frames (ORFs) that can be translated, such as small ORFs located upstream and downstream of the annotated ORFs. However, most genomes (e.g. bacterial genomes) lack the annotations for the transcription start and termination sites. This hinders the systematic discovery of novel ORFs in the untranslated regions in ribosome profiling data. Here we develop a new computational pipeline called RIBOSS. We use RIBOSS to leverage long-read and short-read data for de novo transcriptome assembly, and highly-phased ribosome profiling data for detecting novel translational events in the newly assembled transcriptome. We demonstrate the capability of RIBOSS using recently published metatranscriptome and translatome data for Salmonella enterica serovar Typhimurium. The RIBOSS Python modules are versatile and can be used to analyse prokaryotic or eukaryotic data. In sum, RIBOSS is the first computational pipeline to integrate long- and short-read sequencing technologies to investigate translation. RIBOSS is freely available at https://github.com/lcscs12345/riboss.

bioinformatics↗

bioRxiv2024

CIWARS: a web server for waterborne antibiotic resistance surveillance using longitudinal metagenomic data

The rise of antibiotic resistance (AR) is a major global health crisis, exacerbated by the overuse and misuse of antibiotics, leading to the rapid spread of antibiotic resistance genes (ARGs) in bacterial pathogens. This phenomenon poses significant threats to human and animal health, food security, and economic stability. Water bodies, particularly wastewater treatment plants (WWTPs), serve as critical reservoirs for ARGs, creating environments that favor the proliferation of resistant bacteria. Wastewater-based surveillance (WBS) has emerged as a cost-effective strategy for monitoring AR at the population level, providing real-time data to guide public health and policy decisions. Despite advancements in WBS, there are no comprehensive online analytical platforms for continuous environmental AR surveillance. This paper introduces CIWARS, a web server designed for AR analyses of longitudinal metagenomic data. CIWARS offers comprehensive ARG profiling, taxonomic annotation, and anomalous AR risk points detection. We demonstrate its capabilities through an interactive temporal data visualization, showcasing its potential for enhancing AR risk monitoring and guiding effective mitigation strategies. CIWARS is broadly applicable to longitudinal metagenomic data generated from any environment and aims to support global efforts in addressing the AR crisis by providing cyberinfrastructure for continuous AR surveillance. The web server is freely available at https://ciwars.cs.vt.edu/.

bioinformatics↗

bioRxiv2024

Generalized cell phenotyping for spatial proteomics with language-informed vision models

We present DeepCell Types, a novel approach to cell phenotyping for spatial proteomics that addresses the challenge of generalization across diverse datasets with varying marker panels collected across different platforms. Our approach utilizes a transformer with channel-wise attention to create a language-informed vision model; this models semantic understanding of the underlying marker panel enables it to learn from and adapt to heterogeneous datasets. Leveraging a curated, diverse dataset named Expanded TissueNet with cell type labels spanning the literature and the NIH Human BioMolecular Atlas Program (HuBMAP) consortium, our model demonstrates robust performance across various cell types, tissues, and imaging modalities. Comprehensive benchmarking shows that our method outperforms existing approaches on cell-type prediction and, from the same model, predicts marker positivity competitively with a dedicated specialist; it further matches manual expert gating and adapts to new data with modest fine-tuning, well past what baselines reach when trained from scratch. This work equips the spatial proteomics community with a single, continuously improvable phenotyping model that generalizes to new marker panels and can be fine-tuned efficiently when needed. We release both DeepCell Types and Expanded TissueNet as open-source resources.

bioinformatics↗

bioRxiv2024

Mitochondrial metabolism is a key determinant of chemotherapy sensitivity in Colorectal Cancer

Therapy resistance is attributed to over 80% of cancer deaths per year emphasizing the urgent need to overcome this challenge for improved patient outcomes. Despite its widespread use in colorectal cancer (CRC) treatment, resistance to 5-fluorouracil (5FU) remains poorly understood. Here, we investigate the transcriptional responses of CRC cells to 5FU treatment, revealing significant metabolic reprogramming towards heightened mitochondrial activity. Utilizing CRC models, we demonstrate sustained enhancement of mitochondrial biogenesis and function following 5FU treatment, leading to resistance in both in vitro and in vivo settings. Furthermore, we show that targeting mitochondrial metabolism, specifically by inhibiting Complex I (CI), sensitizes CRC cells to 5FU, resulting in delayed tumour growth and prolonged survival in preclinical models. Additionally, our analysis of patient data suggests that oxidative metabolism signatures may predict responses to 5FU-based chemotherapy. These findings shed light on mechanisms underlying 5FU resistance and propose a rational strategy for combination therapy in CRC, emphasizing the potential clinical benefit of targeting mitochondrial metabolism to overcome resistance and enhance patient outcomes.

cancer biology↗

bioRxiv2024

Behavioral and neural correlates of social hierarchy formation in a sex-changing fish

Social hierarchies in sex-changing fish determine which fish will change sex, yet the complexities of hierarchy formation at the neurobehavioral level are still being unraveled. Here, we investigate the formation of social hierarchies within groups of New Zealand spotty wrasse, integrating behavioral observations with neural activation patterns upon social disruption. We find that dominance hierarchies form linearly based on size, with larger fish displaying more dominant behaviors and smaller fish displaying more submissive behaviors. Disruption of the social hierarchy induced rapid behavioral changes, particularly in second-ranked fish, highlighting that second-ranked fish will opportunistically adopt a dominant position. Analysis of neural activation patterns reveals that the social decision-making network is deeply involved in the establishment of dominance, with the fish attaining dominance showing significant differences to all other ranked fish. Overall, this study underscores the complexity of social relationships and their neural underpinnings in the spotty wrasse, providing a foundation for further research into the cellular and molecular mechanisms of socially-controlled sex change, and demonstrates that disruption of the social hierarchy triggers rapid changes in both behavior and the social decision-making regions of the brain.

animal behavior and cognition↗

bioRxiv2024

Phage-plasmid hybrids are found throughout diverse environments and encode niche-specific functional traits

Phage-plasmids are unique mobile genetic elements that function as plasmids and temperate phages. While it has been observed that such elements often encode antibiotic resistance genes and defense system genes, little else is known about other functional traits they encode. Further, no study to date has documented their environmental distribution and prevalence. Here, we performed genome sequence mining of public databases of phages and plasmids utilizing a random forest classifier to identify phage-plasmids. We recovered 5,742 unique phage-plasmid genomes from a remarkable array of disparate environments, including human, animal, plant, fungi, soil, sediment, freshwater, wastewater, and saltwater environments. The resulting genomes were used in a comparative sequence analysis, revealing functional traits/accessory genes associated with specific environments. Host-associated elements contained the most defense systems (including CRISPR and anti-CRISPR systems) as well as antibiotic resistance genes, while other environments, such as freshwater and saltwater systems, tended to encode components of various biosynthetic pathways. Interestingly, we identified genes encoding for certain functional traits, including anti-CRISPR systems and specific antibiotic resistance genes, that were enriched in phage-plasmids relative to both plasmids and phages. Our results highlight that phage-plasmids are found across a wide-array of environments and likely play a role in shaping microbial ecology in a multitude of niches. IMPORTANCEPhage-plasmids are a novel, hybrid class of mobile genetic element which retain aspects of both phages and plasmids. However, whether phage-plasmids represent merely a rarity or are instead important players in horizontal gene transfer and other important ecological processes has remained a mystery. Here, we document that these hybrids are encountered across a broad range of distinct environments and encode niche-specific functional traits, including the carriage of antibiotic biosynthesis genes and both CRISPR and anti-CRISPR defense systems. These findings highlight phage-plasmids as an important class of mobile genetic element with diverse roles in multiple distinct ecological niches.

genomics↗

bioRxiv2024

Diversification of the Rho transcription termination factor in bacteria

Correct termination of transcription is essential for gene expression. In bacteria, factor-dependent termination relies on the Rho factor, that classically has three conserved domains. Some bacteria also have a functional insertion region. However, the variation in Rho structure among bacteria has not been analyzed in detail. This study determines the distribution, sequence conservation, and predicted features of Rho factors with diverse domain architectures by analyzing 2,730 bacterial genomes. About half (49.8%) of the species analyzed have the typical Escherichia coli like Rho while most of the other species (39.8%) have diverse, atypical forms of Rho. Besides conservation of the main domains, we describe a duplicated RNA-binding domain present in specific species and novel variations in the bicyclomycin binding pocket. The additional regions observed in Rho proteins exhibit remarkable diversity. Commonly, however, they have exceptional amino acid compositions and are predicted to be intrinsically disordered, to undergo phase separation, or have prion-like behavior. Phase separation has recently been shown to play roles in Rho function and bacterial fitness during harsh conditions in one species and this study suggests a more widespread role. In conclusion, diverse atypical Rho factors are broadly distributed among bacteria, suggesting additional cellular roles.

molecular biology↗

bioRxiv2024

A diverse and distinct microbiome inside living trees

Despite significant advances in microbiome research across various environments1, the microbiome of Earths largest biomass reservoir- the wood of living trees2- remains largely unexplored. This oversight neglects a critical aspect of global biodiversity and potentially key players in tree health and forest ecosystem functions. Here we illuminate the microbiome inhabiting and adapted to wood, and further specialized to individual host species. We demonstrate that a single tree can host approximately a trillion microbes in its aboveground internal tissues, with microbial communities partitioned between heartwood and sapwood, each maintaining a distinct microbiome with minimal similarity to other plant tissues or nearby ecosystem components. Notably, the heartwood microbiome emerges as a unique ecological niche, distinguished in part by endemic archaea and anaerobic bacteria that drive consequential biogeochemical processes. Our research supports the emerging idea of a plant as a "holobiont"3,4--a single ecological unit comprising host and associated microorganisms--and parallels human microbiome research in its implications for host health, disease, and functionality5. By mapping the structure, composition, and potential sources and functions of the tree internal microbiome, our findings pave the way for novel insights into tree physiology and forest ecology, and establish a new frontier in environmental microbiology.

ecology↗

bioRxiv2024

Thetis cells induce food-specific Treg cell differentiation and oral tolerance

The intestinal immune system must establish tolerance to food antigens to prevent onset of allergic and inflammatory diseases. Peripherally generated regulatory T (pTreg) cells play an essential role in suppressing inflammatory responses to allergens; however, the antigen-presenting cell (APC) that instructs food-specific pTreg cells is not known. Here, we show that antigen presentation and TGF-{beta} activation by a subset of ROR{gamma}t+ antigen-presenting cells (APC), Thetis cells IV (TC IV), is required for food-induced pTreg cell differentiation and oral tolerance. By contrast, antigen presentation by dendritic cells (DCs) was dispensable for pTreg induction but required for TH1 effector responses, highlighting a division of labor between tolerogenic TCs and pro-inflammatory DCs. While antigen presentation by TCs was required for food-specific pTreg generation both in early life and adulthood, the increased abundance of TCs in the peri-weaning period was associated with a window of opportunity for enhanced pTreg differentiation. These findings establish a critical role for TCs in oral tolerance and suggest that these cells may represent a key therapeutic target for the treatment of food-associated allergic and inflammatory diseases.

immunology↗

bioRxiv2024

The Hyaluronan Synthase isoforms direct distinct patterns of fibroblast activation linked to fibrosis progression versus resolution following renal ischaemia

BackgroundThe stroma plays a key role during renal development and in regeneration after injury. However, following injury, the stroma expands driving progressive fibrosis. Hyaluronan (HA) is a glycosaminoglycan that is absent in healthy kidney stroma but highly expressed in disease. To understand strategies to modulate stromal HA towards therapeutic advantage, this study compares HA and HA Synthase (HAS) enzyme expression in kidney development, health, disease, and recovery. MethodsRats underwent ischaemia reperfusion injury (IRI) with/without ischaemic preconditioning (IPC) and kidneys histologically analysed. Kidneys from C57BL/6 embryos and HAS1/3-/- mice were also analysed and parallel mechanistic cell studies performed using primary human fibroblasts. ResultsIn health, stromal HA was absent from the renal cortex. HAS1 was expressed in some epithelial cells, whilst HAS2 was not expressed. Following IRI there was increased stromal HA in areas of chronic fibrosis, alongside increased HAS2 (but not HAS1) expression. In contrast, during development prominent stromal HA matrices were evident in areas of tubular generation, with strong HAS1 (not HAS2) expression. Following IPC+IRI, stromal HA and HAS2 were attenuated; whilst HAS1+ cells expanded but were distinct from -SMA+ myofibroblasts. Cell studies demonstrated that HAS1+ fibroblasts had a functionally distinct phenotype, with enhanced migration and FAP expression but attenuated -SMA, EDA-FN and COL1A1 expression, whereas HAS2+ fibroblasts demonstrated a classic -SMA+ contractile myofibroblast phenotype with high EDA-FN and COL1A1. ConclusionsHA is a key regulator of stromal fibroblast heterogeneity, with HAS1 and HAS2 defining phenotypically distinct populations that may influence divergent renal outcomes following injury. SIGNIFICANCE STATEMENTHyaluronan (HA) is a matrix glycosaminoglycans that is absent in healthy kidney cortex but demonstrates increased expression in the renal stroma during progressive fibrosis. This study makes comparisons of HA accumulation, localisation, and HA Synthase (HAS) protein expression during kidney development, in health, following ischaemic kidney injury and during renal recovery. The study identifies that different HAS isoenzymes (HAS1 and HAS2) mediate distinct functional fibroblast phenotypes in vitro and are localised in distinct stromal localisations and cell sub-populations in vivo. The data provides interesting insights into HA dependent regulation of fibroblast stromal heterogeneity and identifies the novel finding that HAS1 defines cell populations that are associated with kidney recovery following ischaemic injury and are protective against progressive renal fibrosis.

pathology↗

bioRxiv2024

Expansion of pneumococcal serotype 23F and 14 lineages with genotypic changes in capsule polysaccharide locus and virulence gene profiles post introduction of pneumococcal conjugate vaccine in Blantyre, Malawi

Since the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) in Malawi in 2011, there has been persistent carriage of vaccine serotype (VT) Streptococcus pneumoniae, despite high vaccine coverage. To determine if there has been a genetic change within the VT capsule polysaccharide (cps) loci since the vaccines introduction, we compared 1,022 whole-genome-sequenced VT isolates from 1998 to 2019. We identified the clonal expansion of a multidrug-resistant, penicillin non-susceptible serotype 23F GPSC14-ST2059 lineage, a serotype 14 GPSC9-ST782 lineage and a novel serotype 14 sequence type GPSC9-ST18728 lineage. Serotype 23F GPSC14-ST2059 had an I253T mutation within the capsule oligosaccharide repeat unit polymerase Wzy protein, which is predicted in silico to alter the protein pocket cavity. Moreover, serotype 23F GPSC14-ST2059 had SNPs in the DNA binding sites for the cps transcriptional repressors CspR and SpxR. Serotype 14 GPSC9-ST782 harbour a non-truncated version of the large repetitive protein (Lrp), containing a Cna protein B-type domain which is also present in proteins associated with infection and colonisation. These emergent lineages also harboured genes associated with antibiotic resistance, and the promotion of colonisation and infection which were absent in other lineages of the same serotype. Together these data suggest that in addition to serotype replacement, modifications of the capsule locus associated with changes in virulence factor expression and antibiotic resistance may promote vaccine escape. In summary, the study highlights that the persistence of vaccine serotype carriage despite high vaccine coverage in Malawi may be partly caused by expansion of VT lineages post PCV13 rollout. Impact StatementOur findings highlight the potential for clonal expansion of multidrug-resistant, penicillin-non-susceptible vaccine serotype lineages with capsule locus modifications, within a high carriage and disease burden population. This shift has occurred among young children where there has been high vaccine coverage, posing challenges for effective vaccine scheduling and design. Furthermore, this study emphasises the importance of ongoing Streptococcus pneumoniae genomic surveillance as new or modified pneumococcal vaccines are implemented. 2. Data summaryWhole genome sequencing assemblies for the PCVPA survey have been deposited in the BioProject PRJNA1011974.

microbiology↗

bioRxiv2024

Unlocking the Genetic Potential of Solanum bulbocastanum (SB22, Selection 22): A Valuable Resource for Enhancing Disease Resistance in Commercial Potato Cultivars

Cultivated potatoes are susceptible to a host of diseases caused by various pathogens. Wild relatives of potatoes are used in breeding programs as sources of resistance introgressed into cultivated potatoes. The wild potato Solanum bulbocastanum is an essential source of resistance to Columbia root knot nematode (CRKN) and late blight. We present the initial chromosome-level assembly of SB22, produced using PacBio long reads and Dovetail Hi-C scaffolding. The final assembly size was 655.3 Mb. Using the BRAKER pipeline, 43,280 gene models were predicted, with a BUSCO completeness of about 90.3%. Repeat elements represented 63.8% of the genome, with LTR elements being the most abundant. DRAGO3 predicted 2,310 disease resistance-like genes across the 12 chromosomes of SB22; the MEME suite was used to identify their amino acid motifs. Putative candidate genes contributing to CRKN resistance were mapped on chromosome 11 of SB22. The SB22 draft genome is a valuable genomic resource for potato breeding programs.

genomics↗

bioRxiv2024

A proteome-wide quantitative guide for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs

The intricate molecular environment of the native membrane profoundly influences every aspect of membrane protein (MP) biology. Despite this, the most prevalent method of studying MPs uses detergent-like molecules that disrupt and remove this vital local membrane context. This severely impedes our ability to quantitatively decipher the local molecular context and comprehend its regulatory role in the structure, function, and biogenesis of MPs. Using a library of membrane-active polymers we have developed a platform for the high-throughput analysis of the membrane proteome. The platform enables near-complete spatially resolved extraction of target MPs directly from their endogenous membranes into native nanodiscs that maintain the local membrane context. We accompany this advancement with an open-access database that quantifies the polymer-specific extraction variability for 2065 unique mammalian MPs and provides the most optimized condition for each of them. Our method enables rapid and near-complete extraction and purification of target MPs directly from their endogenous organellar membranes at physiological expression levels while maintaining the nanoscale local membrane environment. Going beyond the plasma membrane proteome, our platform enables extraction from any target organellar membrane including the endoplasmic reticulum, mitochondria, lysosome, Golgi, and even transient organelles such as the autophagosome. To further validate this platform, we took several independent MPs and demonstrated how our resource can enable rapid extraction and purification of target MPs from different organellar membranes with high efficiency and purity. Further, taking two synaptic vesicle MPs, we show how the database can be extended to capture multiprotein complexes between overexpressed MPs. We expect these publicly available resources to empower researchers across disciplines to efficiently capture membrane nano-scoops containing a target MP and interface with structural, functional, and other bioanalytical approaches. We demonstrate an example of this by combining our extraction platform with single-molecule TIRF imaging to demonstrate how it can enable rapid determination of homo-oligomeric states of target MPs in native cell membranes.

biophysics↗