Biology subjects

Hu, J.

Publications and source records attributed to Hu, J..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

Dual Targeting of BRAFV600E and Ferroptosis Results in Synergistic Anticancer Activity via Iron Overload and Enhanced Oxidative Stress

PurposeWhile combination BRAF and MEK inhibitor treatment in BRAFV600E-mutant cancers results in a response, treatment resistance and toxicity are common. Ferroptosis is an iron-dependent form of non-apoptotic cell death. BRAF inhibition has been associated with increased sensitivity to ferroptosis that is dependent on Glutathione Peroxidase 4 (GPX4). Experimental DesignIn vitro, ex vivo, and in vivo models of anaplastic thyroid cancer (ATC) were used to evaluate the anticancer activity of combination BRAF inhibition and ferroptosis induction. ResultsTargeting key regulators of ferroptosis--GPX4, using RSL3 and ML162, and system Xc-, using erastin--induced significant cell death in all ATC cell lines. Combination of dabrafenib and RSL3 synergistically increased cell death in BRAFV600E-mutant ATC cells, and significantly inhibited cellular migration and colony formation. Mechanistically, lipid peroxidation, reactive oxygen species levels, and intracellular Fe2+ increased significantly with combination treatment compared with each agent alone. Analysis of cell membrane iron importers and exporters showed significantly lower expression of ferroportin-1 (an iron exporter), suggesting the synergistic anticancer activity was due to increased iron accumulation and oxidative stress, leading to enhanced ferroptotic cell death. BRAFV600E-mutant ATC cell spheroids showed synergistic cell death with dabrafenib and RSL3 treatment. In vivo, combination dabrafenib and ferroptosis induction (by targeting GPX4 using C18, and system Xc- with IKE) significantly inhibited tumor growth in an orthotopic ATC mouse model. Additionally, dabrafenib-resistant BRAFV600E-mutant ATC cells were more sensitive to ferroptosis induction than parental cells. ConclusionsDual targeting of BRAFV600E and ferroptosis results in synergistic anticancer activity and overcomes resistance to BRAF inhibition.

cancer biology↗

bioRxiv2025

CRISPR-Based Gene Dependency Screens reveal Mechanism of BRAF Inhibitor Resistance in Anaplastic Thyroid Cancer

Anaplastic thyroid cancer (ATC) is the most aggressive form of thyroid cancer. Despite recent advances in treating BRAFV600E-driven ATC, therapy resistance remains a significant challenge, often resulting in disease progression and death. Leveraging a focused CRISPR/KO screen in parallel with a CRISPR/activation screen, both tailored on response to BRAFV600E inhibitor treatment, we identified TAZ (encoded by the WWTR1 gene) deficiency as synthetically lethal with BRAF inhibitor in ATC. TAZ is overexpressed in ATC compared to well-differentiated thyroid tumors. We demonstrate that TAZ-deficient ATC cells display heightened sensitivity to BRAF inhibitors both in vitro and in vivo. Using gene essentiality score across a large panel of cancer cell lines, we found that BRAFV600E-driven cancers are highly sensitive to TAZ loss, unlike their counterparts with wild-type BRAF and non-BRAFV600E. Mechanistically, we demonstrate that dabrafenib triggers the Unfolded Protein Response (UPR) under ER stress and suppresses protein synthesis. TAZ loss represses the UPR, reverses the inhibition of protein synthesis, and triggers increased cell death by ferroptosis in dabrafenib-treated ATC. Collectively, our findings unveil TAZ as a new target to overcome resistance to BRAF inhibitors in undifferentiated thyroid cancer.

cancer biology↗

bioRxiv2025

Self-inactivating AAV-CRISPR at different ages enables sustained amelioration of Huntington's disease deficits in BAC226Q mice

Huntingtons disease (HD) is a monogenic autosomal dominant neurodegenerative disorder caused by a CAG repeat expansion in the first exon of the HTT gene, yielding a gain-of-toxic-function mutant Huntingtin protein mHTT. CRISPR/Cas9 is a potentially powerful therapeutic tool for treating HD by eliminating mutant HTT (mHTT) gene. We developed a specific SaCas9 guide RNA to target human mHTT, and a self-inactivating gene editing system that abolishes SaCas9 after a short transient expression for high gene editing efficiency and maximal safety to prevent off-target effects. Both conventional and the new self-inactivating gene editing systems achieved successful elimination of mHTT gene, 60-90% mHTT protein and 90% of mHTT aggregation in BAC226Q HD mouse brains, which resulted in significant long-term rescue of neural pathology, motor deficits, weight loss and shortened lifespan. These beneficial effects were observed when gene editing was applied before, at and well after the on-set of pathological and behavioral abnormalities. These proof-of-concept data demonstrate that gene editing can be a highly effective therapeutic approach for HD and other inherited neurodegenerative diseases. One Sentence SummarySelf-inactivating CRISPR for mutant huntingtin in HD mice achieved long-term rescue of neural pathology, motor deficits, weight loss and survival.

neuroscience↗

bioRxiv2025

Widespread distribution of the BpfA-carrying bacteria involved in the bisphenol F degradation in Pseudomonadota and Actinomycetota

The global use of bisphenol F (BPF) has led to widespread environmental contamination, posing significant threats to ecosystems and human health. However, the genes involved in BPF degradation remained unknown. In this study, a novel oxidase gene, bpfA, was obtained from strain Microbacterium sp. F2 through a four-step purification strategy. BpfA is classified as a member of the 4-phenol oxidizing (4PO) subfamily and contains a conserved FAD-binding domain (Asp152 and His393) as well as a Tyr-Tyr-Arg triad (Tyr93, Tyr474, Arg475). BpfA catalyzes the conversion of BPF to 4,4-dihydroxydibenzophenone (DHBP) through a series of three consecutive reactions. In addition, BpfA exhibits catalytic activity towards 4-alkylphenols, such as vanillyl alcohol (VA), 4-n-propylguaiacol (4PG), and 4-(methoxymethyl)phenol (4MOP). BpfA homologs are widely distributed in the environment, particularly in soil. Bioinformatics-based taxonomic profiling revealed that BpfA homologs are widely distributed in metagenomes from cultivated land and forests, mainly belonging to Pseudomonadota and Actinomycetota. This study enhances our understanding of the microbial degradation mechanism of BPF, elucidates the catalytic function of the novel oxidase gene bpfA and its distribution pattern in the environment, and provides important insights into the evolutionary origin of BPF degradation genes and the targeted mining of environmental microbial resources.

microbiology↗

bioRxiv2025

Joint Modeling of Longitudinal Biomarker and Survival Outcomes with the Presence of Competing Risk in Nested Case-Control Studies with Application to the TEDDY Microbiome Dataset

MotivationLarge-scale prospective cohort studies collect longitudinal biospecimens alongside time-to-event outcomes to investigate biomarker dynamics in relation to disease risk. The nested case-control (NCC) design provides a cost-effective alternative to full cohort biomarker studies while preserving statistical efficiency. Despite advances in joint modeling for longitudinal and time-to-event outcomes, few approaches address the unique challenges posed by NCC sampling, non-normally distributed biomarkers, and competing survival outcomes. ResultsMotivated by the TEDDY study, we propose "JM-NCC", a joint modeling framework designed for NCC studies with competing events. It integrates a generalized linear mixed-effects model for potentially non-normally distributed biomarkers with a cause-specific hazard model for competing risks. Two estimation methods are developed. fJM-NCC leverages NCC sub-cohort longitudinal biomarker data and full cohort survival and clinical metadata, while wJM-NCC uses only NCC sub-cohort data. Both simulation studies and an application to TEDDY microbiome dataset demonstrate the robustness and efficiency of the proposed methods.

bioinformatics↗

bioRxiv2025

Targeting the selectivity filter to drastically alter the activity and substrate spectrum of a promiscuous metal transporter

d-Block metal transporters play a crucial role in maintaining the homeostasis of life-essential trace elements and are attractive targets for protein engineering aimed to selectively enriching or excluding metals in living organisms. However, systematic efforts to engineer these transporters have been hindered by limited understanding of their transport mechanism and substrate specificity. In this study, we applied a focused-screen approach to human ZIP8, a promiscuous d-block divalent metal transporter, by systematically changing three key residues that form the selectivity filter at the entrance of the transport pathway. Screening a library of 48 constructs using an ICP-MS-based transport assay, we identified variants with significantly altered transport activities and/or substrate preferences. The E343D variant exhibited dramatically enhanced activity for all tested metal substrates, a shift in substrate preference, and an expanded substrate spectrum including the non-substrate metals VO2+ and Cu2+. Additionally, we identified lead ion (Pb2+) as a substrate of wild-type ZIP8. These findings suggest that the ZIP fold is highly adaptable and amenable for transporting a wide range of metals with diverse physicochemical properties, making it a promising scaffold to generate novel metal transporters for applications.

biochemistry↗

bioRxiv2025

Nuclear Argonaute:miRNA complexes recognize target sequences within chromatin and silence gene expression

RNA interference (RNAi) in mammalian cells involves recognition of mRNA in the cytoplasm and inhibition of translation. Both protein RNAi factors and miRNAs, however, are present in mammalian cell nuclei. It is unclear how this nuclear localization affects endogenous gene expression. Here, we use chimeric eCLIP to identify complexes of Argonaute 2 (AGO2) and miRNAs. We identify the most abundant miRNAs associated with chromatin and their chromatin-associated RNA targets. Chimeric eCLIP revealed that High mobility group AT-Hook A (HMGA2) was the most compelling target for miRNA-mediated gene binding. There are four confirmed let-7 miRNA sites within the 3-UTR in the cytoplasm or nucleus and three within chromatin-associated RNA. The expression of mature HMGA2 mRNA was repressed by let-7 in the cytoplasm and nucleus. let-7 had little effect splicing or transcription. Our data validate chimeric eCLIP as a powerful method for experimentally identifying promising miRNA:RNA interactions. Rather than a solely cytoplasmic event, binding of RNAi factors to mRNA targets may begin in the nucleus through a mechanism that can reduce RNA levels in both the cytoplasm and the nucleus. miRNA-mediated silencing of mRNAs may be influenced by both nuclear and cytoplasmic interactions.

biochemistry↗

bioRxiv2025

Targeted Molecular MRI of Colorectal Cancer by Antibody Functionalized Hyperpolarized Silicon Particles

The development of non-invasive, non-ionizing sensitive molecular targeting approaches to detect colorectal cancer (CRC) lesions is warranted to improve high risk patient outcomes. Hyperpolarized silicon nanoparticles and microparticles are potentially well-suited to act as targeted molecular imaging agents because of their overall biocompatibility and long-lasting enhanced magnetic resonance imaging (MRI) signals. In this study, dynamic nuclear polarization was performed on silicon particles functionalized with an antibody to Mucin-1 (MUC1), a surface mucin glycoprotein aberrantly expressed in CRC. Antibody conjugation to the particle surface did not affect 29Si hyperpolarization characteristics. Similarly, conjugation and the dynamic nuclear polarization process did not adversely affect the affinity of the targeting antibody. In vivo MRI scans performed 10-15 minutes after luminal administration of targeted hyperpolarized particles into human MUC1-expressing orthotopic CRC mouse models showed that particles actively targeted tumor sites. These results were supported by chemical and biological controls and blocking experiments as well as correlative immunohistochemical analysis. These surface-functionalized silicon particles are under development as a platform technology that will allow non-invasive molecular targeting of CRC using hyperpolarized MRI. Single Sentence SummaryTargeted molecular MR imaging of colorectal cancer by hyperpolarized silicon particles functionalized with mucin 1 antibody.

cancer biology↗

bioRxiv2025

Small molecule inhibition of CPSF3 impacts R-loop distribution

R-loops are three-stranded nucleic acid structures consisting of an RNA/DNA hybrid and a displaced strand of DNA. These structures have been implicated in a variety of regulatory cellular processes. Their untimed or excess accumulation, however, can cause genomic instability and induce DNA damage. Most R-loops form co-transcriptionally when the nascent transcript reanneals to unwound DNA duplex. Changes in the rate of transcription have the potential to impact R-loop formation, and compounds that modulate R-loop formation would be useful molecular tools and therapeutic leads. Cleavage and Polyadenylation Specific Factor 3 (CPSF3) recognizes the pre-mRNA 3 cleavage site, cleaves the transcript prior to polyadenylation, and has been linked to R-loop formation. Inhibition of CPSF3 has been found to induce transcriptional readthrough and cell proliferation defects. A previous report suggested that inhibition of CPSF3 with a small molecule causes a global increase in R-loop abundance. Here we test the impact of YT-II-100, a novel inhibitor of CPSF3. We find that addition of YT-II-100 increases global R-loop formation but does not change R-loop formation at specific genes that are normally used as positive controls for R-loop formation. We performed parallel assays using previously reported compound JTE-607 and observed similar results. Our data emphasize the need for cautious interpretation of experiments using JTE-607 and YT-II-100. There may be different mechanisms of R-loop formation depending on gene loci, with the control of R-loop formation at some genes diverging from the regulation of global R-loop formation.

biochemistry↗

bioRxiv2025

Loss of age-associated increase in m6A-modified RNA contributes to GABAergic dysregulation in Alzheimer's disease

Dysregulated RNA metabolism is a significant feature of Alzheimers disease (AD), yet how post-transcriptional RNA modifications like N6-methyladenosine (m6A) are altered in AD is unknown. Here, we performed deamination adjacent to RNA modification targets (DART-seq) on human dorsolateral prefrontal cortices to assess changes in m6A with nucleotide resolution. In non-AD brains, m6A sites increased with age, predominantly within the 3'UTR of transcripts encoding tripartite synapse proteins. In contrast, AD brains lost the age-associated m6A site increase and exhibited global hypomethylation of transcripts, including MAPT and APP. Hypomethylated genes involved with GABAergic signaling, glutamate transport, and ubiquitin-mediated proteolysis exhibited reduced expression, connecting m6A to synaptic excitotoxicity and disrupted proteostasis in AD. Site-specific m6A levels were linked with GABRA1 expression and protein levels, but this relationship was abolished in AD. Our findings provide insight into post-transcriptional mechanisms of dysregulated RNA metabolism in AD that are related to aging and GABAergic regulation. HIGHLIGHTSO_LIWith age, the number of m6A sites increases among Control cases (lacking AD pathology) but remains unchanged in AD cases. C_LIO_LITranscripts are globally hypomethylated in AD cases. C_LIO_LIHypomethylation is linked to decreased mRNA expression of transcripts related to synaptic and proteostatic function in AD. C_LIO_LI3UTR-localized m6A sites lack typical association with transcript metabolism of GABRA1 in AD. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/651974v3_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@995c55org.highwire.dtl.DTLVardef@7d0619org.highwire.dtl.DTLVardef@1b6a20org.highwire.dtl.DTLVardef@1d47dce_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Endocytosis of a zinc transceptor ZIP4 is mediated by AP2 through an atypical dileucine motif

Human ZIP4 is an essential zinc transporter for dietary zinc absorption and also a transceptor that undergoes zinc-dependent endocytosis to regulate cellular zinc uptake capacity in response to changes in zinc availability. However, the detailed molecular mechanism of this post-translational regulation remains elusive. In this work, we focus on the LxL motif (formerly LQL motif), which is located in the longest cytosolic loop and indispensable for ZIP4 endocytosis, to elucidate how it is involved in ZIP4 endocytosis in a zinc-responsive manner. Integrating a combination of biochemical, cell/molecular biology and modelling approaches, our data collectively support a working model that the LxL motif, which is found to be more exposed and/or less ordered upon increased zinc availability, acts as an atypical dileucine motif to interact with the adaptor protein complex 2 for clathrin-mediated endocytosis. These findings provide insights into the molecular basis of zinc-dependent ZIP4 endocytosis, advancing the understanding of cellular zinc homeostasis and providing a paradigm for mechanistic studies of substrate-induced endocytosis of other nutrient transceptors. HighlightsO_LIHydrophobicity of the LxL motif is essential for ZIP4 endocytosis C_LIO_LIEndocytosis of endogenously expressed ZIP4 depends on Clathrin and AP2 C_LIO_LIThe LxL motif binds to the {sigma}2 subunit of AP2 C_LIO_LICellular zinc levels regulate the structure of the LxL motif C_LI

cell biology↗

bioRxiv2025

Maximal Efficacy of Alternative Splicing is Ensured by Balanced Efficiency of U1 and U2AF

Alternative splicing (AS) significantly increases the diversity of gene function by enabling a single gene to produce multiple protein isoforms. U1 and U2AF are proteins responsible for the recognition and splicing of an introns donor and acceptor sites, respectively. Here, we used RNA- seq to explore these fundamental splicing events to separately calculate the splicing efficiency of U1 and U2AF. The expression levels of splice sites were directly calculated by the number of uniquely mapped reads spanning the splice junction. We found that the scaled expression levels of donor and acceptor sites both follow a type III extreme value Weibull distribution with the same shape parameter of 0.14. These observations significantly extend our previous findings by revealing that AS follows a Weibull distribution at the levels of both the fundamental splicing event and the mature transcript isoform. A simple transform of the shape parameter a, 1/(1+a), ranges between 0 and 1, and positively correlates with the dominance of the major splicing product and therefore represents an index of the splicing machinery efficiency. Importantly, the equal splicing efficiency of U1 and U2AF ensure that their combined efficacy reaches a maximum.

bioinformatics↗

bioRxiv2025

A role of villin-dependent F-actin organization in peroxisome motility in Arabidopsis cells

Actin microfilaments (F-actin) serve as the track for directional movement of organelles in plants. To understand how the F-actin network is employed for the movement of peroxisomes, essential organelles in plant metabolism, we analyzed mutants of three villin (VLN) genes, which encode the primary actin-bundling factor and are most actively expressed in vegetative tissues in Arabidopsis thaliana. We found that the vln4 mutation greatly exacerbated the growth and subcellular defects in vln2 vln3. Compared to the wild-type cells, the double and triple vln mutants exhibit progressive reduction of stable F-actin bundles and rapid remodeling of the fine filaments. The defective F-actin network did not prevent peroxisomes from taking on both rapid and slow movements along the tracks but caused significantly reduced speed of movement and displacement distance of peroxisomes. Using a correlation analysis method, we classified the complex heterogeneous peroxisome movement patterns into clusters reflecting distinct movement directionalities. The vln triple mutant had significantly reduced number of peroxisomes with long-range and linear movement. Our results provide insights into how VLN-dependent F-actin organization is coupled with the complex pattern of peroxisome movement.

plant biology↗

bioRxiv2025

ER fusogens maintain membrane reservoir to ensure brain function

How the morphological dynamics of the endoplasmic reticulum (ER) are linked to its functions is unclear. Atlastins (ATLs), a class of GTPases, mediate ER fusion, and human mutations in ATL1 cause hereditary spastic paraplegia (HSP). Here, we show that ATL2-knockout mice are embryonic lethal with compromised development, particularly of the cerebellum. ATL2 is highly expressed in neuroglia, though ATL1 is dominant in the brain. Lack of ATL2 disorganizes the positioning of Bergmann glia, which in turn interferes with granule cell migration. These cells have significant shrinkage in the intracellular membrane area, which is associated with decreased phosphatidylcholine and cholesterol synthesis. When tested in calyx-type synapses in ATL-deleted mice, a reduced membrane reservoir, represented by fewer presynaptic vesicles, leads to defective synaptic function and deafness. Collectively, these findings suggest that ER-shaping activity by ATL is essential for sustained lipid synthesis, and boosted lipid uptake is potentially beneficial for HSP patients.

neuroscience↗

bioRxiv2025

Accelerated, Accurate, Hybrid Short and Long Reads Alignment and Variant Calling

BackgroundIntegrating short-read and long-read sequencing technologies has become a promising approach for achieving accurate and comprehensive genomic analysis. While short-read sequencing (Illumina, etc.) offers high base accuracy and cost efficiency, it struggles with structural variation (SV) detection and complex genomic regions. In contrast, long-read sequencing (PacBio HiFi) excels in resolving large SVs and repetitive sequences but is limited by throughput, higher Indel error rates, and sequencing costs. Hybrid approaches may combine these technologies and leverage their complementary strengths and different sources of error to provide higher accuracy, more comprehensive results, and higher throughput by lowering the coverage requirement for the long reads. MethodsThis study benchmarks the DNAscope Hybrid pipeline, a novel integrated alignment and variant calling framework that combines short- and long-read data sequenced from the same sample. We evaluate its performance across multiple human genome reference datasets (HG002-HG004) using the draft Q100 and Genome in a Bottle v4.2.1 benchmarks. The pipelines ability to detect small variants (SNPs/Indels), structural variants (SVs), and copy number variations (CNVs) is assessed using data from the Illumina and Pacbio sequencing systems at varying read depths (5x-30x). Benchmark results are compared to DeepVariant. ResultsThe DNAscope Hybrid pipeline significantly improves SNP and Indel calling accuracy, particularly in complex genomic regions. At lower long-read depths (e.g., 5x-10x), the hybrid approach outperforms standalone short- or long-read pipelines at full sequencing depths (30x-35x). Additionally, the DNAscope Hybrid outperforms leading open-source tools for SV and CNV detection, enhancing variant discovery in challenging genomic regions. The pipeline also demonstrates clinical utility by identifying disease- associated variants. Moreover, DNAscope Hybrid is highly efficient, achieving less than 90 minutes runtimes at single standard instance. ConclusionThe DNAscope Hybrid pipeline is a computationally efficient, highly accurate variant calling framework that leverages the advantages of both short- and long-read sequencing. By improving variant detection in challenging genomic regions and offering a robust solution for clinical and large-scale genomic applications, it holds significant promise for genetic disease diagnostics, population-scale studies, and personalized medicine.

bioinformatics↗

bioRxiv2025

Benchmarking single cell transcriptome matching methods for incremental growth of reference atlases

BackgroundThe advancement of single cell technologies has driven significant progress in constructing a multiscale, pan-organ Human Reference Atlas for healthy human cells. Many multi-faceted cell atlases for different organs, species, and diseases now exist, though challenges remain in harmonizing cell types and unifying nomenclature among respective cell atlases. Multiple machine learning and artificial intelligence methods, including models pre-trained on large-scale cell atlas datasets, are publicly available for single cell community users to computationally map their cell clusters to the cell atlases. ResultsThis study benchmarks seven computational tools for cell type matching and label transfer - Azimuth, CellTypist, CellHint, FR-Match, scArches, scPred, and singleR - in ten organ systems. Using healthy lung as an exemplary organ, when matching the well-annotated cell types in two atlases - the Human Lung Cell Atlas (HLCA) and the LungMAP Single-Cell Reference (CellRef), variations in the matching accuracy were observed, especially in rare cell types, underlining the need for a consensus strategy using a selective set of computational methods. In the meta-analysis, the benchmarked methods were used to incrementally integrate 61 cell types from HLCA and 48 from CellRef, resulting in a cell meta-atlas of 41 matched, 20 HLCA-, and 7 CellRef-specific cell types. Similar approach revealed 25 matched cell types existed in two independent kidney atlases. Generalizability of the benchmarking performances were further demonstrated in a variety of organ systems. ConclusionThis study reveals complementing strengths of the benchmarked methods and presents a framework for incremental growth of cell types in cell atlases.

bioinformatics↗

bioRxiv2025

A biGWAS strategy reveals the genetic architecture of the interaction between wheat and Blumeria graminis f. sp. tritici

BackgroundWheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt) is one of the most significant diseases affecting global wheat production. Breeding for disease resistance (R) genes against Bgt often follows a boom-bust cycles, where cultivars with effective resistance are widely deployed on an expanding area until virulence emerges in the avirulence (Avr) pathogen population. While extensive effort has been devoted to identifying and cloning R genes, Avr genes remain relatively understudied, limiting our understanding of R-Avr interactions. That said, understanding R-Avr interactions is crucial for developing durable resistance strategies. ResultsWe conducted whole genome sequencing on 245 Bgt isolates collected from major wheat-growing regions in China, identifying 120 genetically unique isolates. Each of these unique isolates was inoculated and phenotyped on a diverse panel of wheat germplasm. Through Genome-Wide Association Analysis (GWAS) in both Bgt and wheat, we identified 65 Avr loci and 251 R loci overlapping with nine and eight cloned Avr or R genes, respectively. On average, each isolate carries eight Avr alleles, ranging from one to 17. Little geographical preference for Avr alleles or their combinations was observed, suggesting that disease resistance breeding against this pathogen should be coordinated at the national level. The level of resistance level is positively correlated with the number of R alleles carried by a wheat line, and the average frequency of an R allele is 2% among the wheat panel, indicating the potential for accumulating R alleles in breeding programs. We mapped 212 R-Avr interactions based on joint GWAS using both plant and pathogen genomes and cross-species epistasis, where a network of interactions was formed between wheat and Bgt. These interactions indicate that pyramiding five major R loci has the potential to confer resistance to half of the Avr loci. As a proof of concept, we successfully verified two previously described R-Avr pairs using tobacco experiments. Furthermore, we provided molecular validation evidence for three new Avr genes, including Bgt-50651, BgtE-5826 and BgtE-20009, and two new R-Avr interactions. Among them, Bgt-50651 interacts with Pm1a, Pm2a, and another unidentified R gene located near the Pm6/Pm52 interval. ConclusionOur study provides a framework for understanding the genetic interaction between plants and pathogens. The discovery of novel R/Avr loci and their complex interaction network underscores the need to integrate crop and pathogen genetic background, particularly the R/Avr allele composition, into breeding program design. These findings have significant implications for developing durable resistance strategies in wheat alongside offering valuable insights into the broader dynamics of plant-pathogen interactions.

genomics↗

bioRxiv2025

A class of COPI adaptors regulates processing of transmembrane receptors by reinforcing their Golgi retention

Many transmembrane (TM) receptors undergo essential post-translational modification in the Golgi prior to their delivery to the plasma membrane. Whether and how the passage and accompanied modification of these receptors across the Golgi is controlled remains unclear. Here, we show that leptin receptor overlapping transcript (LEPROT) and LEPROT-like 1 (LEPROTL1) regulate receptor activation by securing their sufficient Golgi retention. LEPROTs localize to cis and medial Golgi in a COPI-dependent manner. Deletion of LEPROTs in cells causes expedited release of receptors transiting through the Golgi, and leakage of some Golgi-enriched proteins into the endomembrane compartments. LEPROTs interact directly with COPI coats and simultaneously engage a variety of integral membrane proteins with relatively long TM domains at acidic pH. Loss of LEPROTs dysregulates receptor activity, including that of EGFR and TFRC, due to defective modification. Collectively, LEPROTs serve as a class of COPI adaptors for TM receptors, ensuring adequate preparation, which is vital for subsequent action on the plasma membrane.

cell biology↗