Biology subjects

Yuan, X.

Publications and source records attributed to Yuan, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

The m6A reader protein YTHDF2 facilitates HTLV-1 infectious and mitotic propagation by stabilizing Tax RNA

N6-methyladenosine (m6A) is one of the important RNA modifications that affect RNA abundance and function and has also been implicated in viral infection. In this study, we identify a number of m6A modification sites within human T-cell leukemia virus type 1 (HTLV-1) RNAs, particularly in the RNA of the Tax oncogene. We demonstrate that YTH domain family, member 2 (YTHDF2), a key m6A reader protein that binds m6A-modified RNAs and influences RNA metabolism, is required for HTLV-1 replication in both de novo and persistently infected cells. Mechanistically, YTHDF2 interacts with and stabilizes Tax RNA in an m6A-dependent manner, thereby promoting Tax-driven HTLV-1 replication. Importantly, YTHDF2 activates oncogenic cellular pathways and promotes proliferation in HTLV-1 infected cells, aligning with the functions of Tax. Overall, our findings characterize YTHDF2 as a host factor critical to HTLV-1 RNA metabolism and viral propagation, offering novel insights into the understanding of HTLV-1 life cycle and the development of targeted interventions. Importancem6A is an RNA modification that plays crucial roles in physiological and pathological conditions; however, its roles in HTLV-1 infection are poorly understood. In this study, we identify that m6A modification is widely present in HTLV-1 RNAs including Tax. We demonstrate that YTHDF2, a prominent m6A reader protein, enhances the stability of Tax RNA, thereby promoting both de novo and persistent HTLV-1 replication. Our findings position YTHDF2 as an essential factor for HTLV-1 persistence and suggest it as a potential therapeutic target for viral clearance.

microbiology↗

bioRxiv2025

Susceptibility to Task-irrelevant Auditory Distractors in Relation to Visual Working Memory in Children With and Without ADHD

ObjectiveAttention-deficit/hyperactivity disorder (ADHD) is a prevalent neurodevelopmental disorder in children and is often associated with increased distractibility. Previous research has reported that susceptibility to task-irrelevant visual distractions is associated with visual working memory (WM) capacity. However, how neural responses to task-irrelevant auditory distractors are related to visual WM capacity in children with and without ADHD remains poorly understood. MethodsIn this study, we collected electroencephalography (EEG) signals from 72 children with ADHD and 88 typically developing (TD) children across two experiments, during which they performed visual tasks of varying difficulty while task-irrelevant auditory distractors were presented. The mismatch negativity (MMN) amplitude was measured as a neural index of susceptibility to auditory distractors, and the K score was assessed as a behavioral indicator of visual WM capacity. ResultsTD children showed opposite patterns across the two experiments: under low audiovisual competition, those with higher visual working memory capacity were more susceptible to task-irrelevant sounds, whereas under high competition, children with lower capacity showed greater susceptibility to distraction. In contrast, children with ADHD showed a stable association, with lower visual WM capacity consistently predicting higher susceptibility to task-irrelevant auditory distractors regardless of competition level. ConclusionsThese findings provide novel evidence that susceptibility to task-irrelevant auditory distraction is closely related to visual WM capacity in both children with and without ADHD, but the patterns of this relationship differ between typical and atypical neurodevelopment and are modulated by audiovisual competition.

neuroscience↗

bioRxiv2025

MELO-ED: learning locality-sensitive multi-embeddings for edit distance

Edit distance is a fundamental metric for quantifying similarity between biological sequences, but its high computational cost limits large-scale applications. Previously, we proposed learned locality-sensitive bucketing (LSB) functions that achieved superior performance and efficiency compared to classical seeding methods for identifying similar and dissimilar sequences. How-ever, each component of an LSB function is represented as a one-dimensional hash value that can only be compared for identity, which constrains the methods accuracy. Here, we intro-duce MELO-ED, a multi-embedding locality-sensitive framework that upgrades each hash value to a higher-dimensional embedding capable of efficiently approximating edit distance. MELO-ED employs a Siamese convolutional neural architecture that learns complementary embeddings capturing both global sequence context and fine-grained edit operations. By integrating locality-sensitive bucketing with multi-embedding representations, MELO-ED achieves near-perfect ac-curacy without increasing the number of buckets required. Leveraging mature indexing methods in the embedding space, MELO-ED transforms time-consuming edit distance computations into scalable similarity searches across massive genomic databases. Comprehensive evaluations on simulated DNA sequences and real barcode datasets demonstrate that MELO-ED outperforms both traditional alignment-free methods and contemporary machine learning approaches, in-cluding our previously developed learned LSB functions. These results establish MELO-ED as a state-of-the-art framework for fast and accurate classification of similar and dissimilar sequences. MELO-ED is available at https://github.com/Shao-Group/MELO-ED.

bioinformatics↗

bioRxiv2025

The origin and molecular evolution of the mammalian liver cell architecture

The liver is a central organ with essential roles in processes such as nutritional metabolism, detoxification, and immune defense1-6. It has been instrumental in the adaptation of mammalian species to diverse environments, as reflected by its rapid molecular evolution7,8. However, the origins and evolutionary dynamics of liver cell types and their structural organization remain largely unexplored. Here we report evolutionary analyses of transcriptome and chromatin accessibility data for liver cells from 17 species, spanning all major feeding strategies (herbivory, omnivory, carnivory, insectivory), great apes (including humans), placental clades (Afrotheria, Xenarthra, Laurasiatheria, Euarchontoglires), major mammalian lineages (placentals, marsupials, monotremes), and a bird as outgroup. Integrated with spatial transcriptomics, our data reveal that liver zonation--the compartmentalization of hepatocyte functions along the lobule, the livers fundamental anatomical and functional unit--is conserved across mammals but absent in other vertebrates. We find that zonation originated in the mammalian ancestor, driven by the emergence of WNT and R-spondin signaling from central vein endothelial cells, which activate central hepatocyte gene expression via the transcription factor TCF7L2. Despite this conserved architecture and signaling, genes with zonated expression exhibit rapid evolutionary turnover. Consistently, hepatocytes evolve fast, likely due to reduced selective constraints, enabling adaptive changes under positive selection. Alongside immune cells, hepatocytes are therefore key drivers of the livers rapid evolution and functional innovations. In great apes, we identify human-specific shifts in zonation and cell-type-specific expression linked to recent cis-regulatory changes, particularly in genes involved in lipid metabolism, likely contributing to human-specific metabolic traits. Our study uncovers the origins of a mammal-specific liver cell architecture, within which reduced constraints facilitated molecular changes underlying ecological adaptations.

evolutionary biology↗

bioRxiv2025

Discrete interneuron subsets participate in GluN1/GluN3A excitatory glycine receptor (eGlyR)-mediated regulation of hippocampal network activity throughout development and evolution.

Decades of studies implicating GluN3A N-methyl-D-aspartate receptor (NMDAR) subunits in physiological and pathological function have largely been interpreted through direct regulation of conventional glutamatergic NMDARs. However, emerging evidence indicates that GluN3A frequently assembles with GluN1 forming unconventional glutamate-insensitive NMDARs that operate as native excitatory glycine receptors (eGlyRs). Here we demonstrate that hippocampal somatostatin and neurogliaform interneurons (Sst-INs and NGFCs) express functional eGlyRs from early postnatal through adult ages. In the developing hippocampus eGlyR-mediated excitation of NGFCs with ambient glycine dramatically increases GABAergic tone, with consequences for the generation of giant depolarizing potentials (GDPs). In the mature hippocampus, eGlyR- mediated excitation of Sst-INs regulates sharp wave ripples (SWRs). Finally, we reveal evolutionary conservation of hippocampal Sst-IN eGlyRs and eGlyR- mediated SWR regulation in non-human primates confirming functional eGlyR availability for therapeutic potential in higher species. Our findings underscore that eGlyR mediated regulation of cell and circuit excitability through both cell autonomous and cell non-autonomous mechanisms must be considered to understand GluN3A roles in brain development, plasticity, and disease.

neuroscience↗

bioRxiv2025

Essential roles of HGT-derived sterol biosynthesis in trypanosomatid growth and parasitism

Horizontal gene transfer (HGT) has played a major role in the evolution of kinetoplastids, but its scope and functional significance remain incompletely understood. We performed a comparative genomic analysis of 12 trypanosomatid parasites together with the free-living kinetoplastid Bodo saltans as an outgroup, using the DarkHorse algorithm to identify putative HGT candidates. B. saltans encoded the largest number of HGT-derived genes (980; 5.2% of coding sequences), whereas parasitic Leishmania species retained the fewest (67-71; 0.8-0.9%), consistent with extensive gene loss accompanying the transition to parasitism. Dollo parsimony reconstruction indicated that the kinetoplastid ancestor acquired numerous horizontally transferred genes, many of which were subsequently lost, but several functionally important families were retained in trypanosomatids. Among these, we identified a bacterial-derived aspartate ammonia ligase that, together with aspartate ammonia lyase, likely supports redox balance and succinate fermentation under anaerobic conditions in the insect gut. Phylogenetic analyses also revealed bacterial or archaeal origins of multiple enzymes in ergosterol biosynthesis, an essential pathway in trypanosomatids. Functional characterization in Lotmaria passim demonstrated that sterol C-8 isomerase is indispensable, whereas sterol C-5 desaturase is nonessential in vitro but critical for parasite growth at low temperature, amphotericin B sensitivity, and successful colonization of the honey bee hindgut. These findings illustrate the dual evolutionary trajectory of HGT in kinetoplastids: extensive gene loss during the transition to parasitism, coupled with the retention of lineage-specific innovations essential for survival in host environments. Significance StatementKinetoplastids include both free-living species such as Bodo saltans and parasitic trypanosomatids, the latter responsible for devastating human, animal, and insect diseases. While trypanosomatids have streamlined their genomes during host adaptation, free-living relatives retained a broader genetic repertoire shaped by environmental gene acquisition. By systematically tracing horizontally transferred genes (HGTs) across kinetoplastids, we reveal how free-living B. saltans accumulated diverse HGT candidates, whereas parasitic trypanosomatids lost many of these genes but selectively retained or acquired others critical for their specialized niches. We show that HGT contributed to the evolution of sterol biosynthesis and metabolic pathways supporting parasite survival in anaerobic insect guts. Functional analyses in Lotmaria passim, a honey bee parasite, demonstrate that HGT-dependent ergosterol biosynthesis is essential for gut colonization and influence sensitivity to amphotericin B. These findings highlight how horizontal gene transfer not only shaped the metabolic architecture of kinetoplastids but also underpins parasite adaptation to host environments.

microbiology↗

bioRxiv2025

Telomere 3'-overhang attrition and persistent telomeric DNA damage response in failing human hearts

BackgroundTelomere homeostasis is critical for normal cellular and organ function, and its dysregulation is implicated in aging and chronic diseases. Although telomere length (TL) is critical for normal telomere function, its functional status can also be altered by many other factors. The organization and protective status of telomere in failing human heart (FHH) remains incompletely understood. MethodsUsing left ventricular tissues from patients with idiopathic dilated cardiomyopathy (IDC), ischemic heart disease (IHD), and non-failing heart (NFH), we performed a comprehensive analysis that included measurements of overall TL and 3 overhang length in left ventricles and cardiomyocytes (CM), assessment of telomere-binding protein associations, and transcriptomic profiling through RNA sequencing. ResultsAlthough TL varied among individuals, reduced median TL was observed only in IDC, while both IDC and IHD showed an increased frequency of very short telomeres, falling below the 5th percentile, in CMs. Strikingly, significant telomere 3-overhang attrition was detected in both disease groups and strongly correlated with elevated H2AX phosphorylated on serine 139 ({gamma}H2AX) in heart tissues, indicating DNA damage. This was accompanied by persistent activation of ataxia telangiectasia mutated (ATM) protein-mediated DNA damage responses and the formation of telomere dysfunction-induced foci (TIFs) in CMs from FHH. Concomitantly, the association of telomeres with the single-stranded telomere-binding protein, Protection of Telomeres 1 (POT1), and the double-stranded telomere-interacting protein, telomere repeat-binding factor 2 (TERF2), was markedly reduced, accompanied by an increase in association of {gamma}H2AX and ssDNA binding protein, RPA with telomeres in IDC and IHD relative to NFH, signifying telomere de-protection. ConclusionsCM telomere dysfunction, characterized by 3 overhang attrition and de-protection, is a common feature in FHH, leading to persistent DNA damage response in telomeres. Better understanding of telomere biology throughout the progression of different heart diseases to heart failure will provide more effective prevention and treatment strategies. GRAPHICAL ABSTRACTHuman telomeres safeguard chromosome ends through a higher-order telomere-loop (t-loop) structure and the shelterin complex, preventing their recognition as DNA double-strand breaks (DSBs). In the failing human heart (FHH) with idiopathic dilated cardiomyopathy (IDC) and ischemic heart disease (IHD), cardiomyocyte telomeres lose protection due to disruption of the shelterin complex, driven by oxidative DNA damage from reactive oxygen species (ROS) targeting G-rich telomeric sequences. This leads to t-loop unfolding, DDR cascade activation, 3 overhang excision, and persistent DNA damage responses with Telomere Dysfunction-Induced Foci (TIFs) formation at the telomeric regions of cardiomyocytes in FHH. The ATM-mediated DDR, along with engagement of both classical non-homologous end joining (cNHEJ) and homologous recombination (HDR) repair pathways, is integral to FHH progression. This study underscores the significance of telomere 3 overhang attrition in the pathogenesis of FHH with IDC and IHD. Unlike changes in overall telomere length, 3 overhang shortening directly correlates with increased DNA damage in human myocardial tissue. Preventing telomere 3 overhang attrition and oxidative damage offers a promising avenue for attenuating heart disease progression toward heart failure. In particular, selective ATM inhibition, as opposed to ATR inhibition, presents a potential therapeutic strategy for patients with IDC and IHD. Future efforts to pinpoint deficiencies in cNHEJ and HDR pathways in failing human hearts may reveal novel targets for heart failure prevention and treatment, providing new strategies in the management of this patient population. CMs, cardiomyocytes; DDR, DNA double-strand break repair; FHH, failing human heart; ROS, reactive oxygen species; t-loop, telomere-loop. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/669993v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@1d21937org.highwire.dtl.DTLVardef@757f54org.highwire.dtl.DTLVardef@1fa7472org.highwire.dtl.DTLVardef@1f2e961_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Platelets drive immune suppression and glioblastoma growth in a sex-dependent manner via PAR4 signaling

Sex differences in cancer outcome, including that of glioblastoma (GBM), are shaped by biological, hormonal, and immunological factors and impact disease progression, treatment responses, survival, and tumor microenvironment (TME) interactions. Platelets regulate the immune responses and tumor progression in many cancers, but it is not clear how they contribute to these sex-based differences by affecting the dynamics of the TME. Here, we show that GBM patients exhibit heightened platelet reactivity driven by PAR4 signaling. In murine GBM models, both pharmacological inhibition of PAR4 using BMS986120 and genetic deletion of PAR4 significantly prolong survival in females but not males. This survival advantage is estrogen dependent: it is preserved in chromosomal male-hormonal female mice within the four-core genotype model and is rescued in ovariectomized mice treated with estrogen. The survival benefit is TME specific and is mediated by platelet-driven enhancement of CD8 T cell infiltration into the tumor. Inhibition of platelet PAR4 signaling increases calcium signaling through an estrogen-dependent interaction between PAR4 and estrogen receptor {beta} (ER{beta})--a receptor interaction not previously described. PAR4-activated platelets within the TME suppress CD8 T cell function, and depletion of CD8 T cells abolishes both the tumor-induced platelet reactivity and the survival benefit conferred by PAR4 inhibition. These findings establish platelet-mediated PAR4 signaling as a critical driver of tumor progression and identify sex-specific immune responses as key to therapeutic efficacy.

cancer biology↗

bioRxiv2025

Rationally Engineered Coronavirus-mimicking Protein Nanocage Platform for Glioblastoma Targeted Delivery and Immunity Regulation

Glioblastoma (GBM) is one of the most aggressive and treatment-resistant brain tumors, owing to the dual challenges of the blood-brain barrier (BBB) and a profoundly immunosuppressive tumor microenvironment. However, few existing strategies are capable of simultaneously overcoming these two barriers, underscoring a critical scientific gap and the need for innovative therapeutic platforms that enable both effective BBB traversal and tumor immune reprogramming. Here, we present a coronavirus-mimicking protein nanocage platform (EcomPC) derived from Thermotoga maritima encapsulin, rationally engineered for the targeted and sustained delivery of interferon- (IFN-) to GBM lesions. Through strategic insertion of flexible linkers, cysteine-to-serine mutations, and modular surface functionalization via SpyTag/SpyCatcher chemistry, EcomPC enables intracellular self-assembly of IFN- and glioma-specific targeting. In orthotopic GBM models, EcomPC-IFN demonstrates efficient BBB translocation, selective tumor accumulation, and potent anti-tumor efficacy. Mechanistically, localized IFN- release induces tumor cell apoptosis and reprograms the immune microenvironment--characterized by increased CD8 T cell infiltration, decreased Foxp3 regulatory T cells, and a favorable chemokine shift. These therapeutic effects are not recapitulated by free IFN- or untargeted nanocages, underscoring the essential role of both structural mimicry and ligand-guided delivery. Collectively, this work establishes EcomPC as a programmable, virus-inspired protein delivery platform capable of overcoming key physiological barriers in brain tumor immunotherapy, and lays the foundation for its broader application in CNS-targeted biologic delivery.

bioengineering↗

bioRxiv2025

MGMG: Cell Morphology-Guided Molecule Generation for Drug Discovery

Designing novel molecules with desired bioactivity remains a fundamental challenge in drug discovery. Most molecular design methods follow target-based drug discovery paradigms that rely on well-defined drug targets, thereby limiting their applicability to diseases lacking known targets or reference compounds. Here we introduce Morphology-Guided Molecule Generation (MGMG), a phenotypic drug discovery-oriented approach that integrates cellular morphological profiles from compound treatments with molecular textual descriptions without requiring molecular target information. Cell morphology offers the guidance on desired bioactivity-relevant phenotypic effects, while textual descriptions provide direct and interpretable cues about molecular structure. Leveraging complementary structural and bioactivity context, MGMG significantly enhances molecule generation performance, especially in scenarios where textual descriptions are under-informative or morphological signals are weak. MGMG can also be applied to genetic perturbations, enabling activator design from gene overexpression morphology without requiring knowledge of reference compound structure. In addition, in silico docking demonstrates that MGMG-generated molecules, despite lacking target information, exhibit binding affinities comparable to reference compounds, preserving key interactions while introducing structural diversity. Overall, MGMG jointly utilizes morphological and textual description inputs to guide molecule generation, enabling diverse, bioactivity-aware compound design in a target-agnostic fashion.

bioinformatics↗

bioRxiv2025

A novel, evolutionarily conserved inhibitory circuit selectively regulates dentate gyrus mossy cell function.

The mammalian dentate gyrus contributes to mnemonic function by parsing similar events and places. The disparate activity patterns of mossy cells and granule cells is believed to enable this function yet the mechanisms that drive this circuit dynamic remain elusive. We identified a novel inhibitory interneuron subtype, characterized by VGluT3 expression, with overwhelming target selectivity for mossy cells while also revealing that CCK, PV, SOM and VIP interneurons preferentially innervate granule cells. Leveraging pharmacology and novel enhancer viruses, we find that this target-specific inhibitory innervation pattern is evolutionarily conserved in non-human primates and humans. In addition, in vivo chemogenetic manipulation of VGluT3+ interneurons selectively alters the activity and functional properties of mossy cells. These findings establish that mossy cells and granule cells have unique, evolutionarily conserved inhibitory innervation patterns and suggest selective inhibitory circuits may be necessary to maintain DG circuit dynamics and enable pattern separation across species.

neuroscience↗

bioRxiv2025

Modeling cellular influence delineates functionally relevant cellular neighborhoods in primary and metastatic pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer, with liver metastases significantly worsening outcomes. However, distinct features of the tumor microenvironment (TME) between primary and metastatic sites remain poorly defined. Cellular neighborhoods within the TME are recognized as functional units that influence tumor behavior. Conventional spatial methods, which assign equal weights to all cells in a region, fail to capture the nuances of cellular interactions. To address this, we developed Functional Cellular Neighborhood (FunCN) quantification, which integrates both the proportion and proximity of surrounding cells. Applying FunCN to PDAC imaging mass cytometry data, we identified neutrophil-enriched interactions in liver metastases compared to primary tumors, correlating with elevated VISTA expression by tumor cells. Additionally, FunCN clusters around CD8+ T cells in pancreas and liver were associated with higher TIGIT and LAG3, respectively. These findings demonstrate the importance of spatial immune landscapes in PDAC and identify potential therapeutic opportunities.

systems biology↗

bioRxiv2025

Cryo-EM Structure of Photosystem I from mangroves in their natural environment

Photosystem I (PSI) is a multi-subunit pigment-protein supercomplex responsible for light driven electron transport in photosynthesis. Its structural plasticity under natural environmental stress remains poorly understood. Here, we present a 2.1 [A] cryo-EM structure of the PSI-LHCI supercomplex from Avicennia marina, a halotolerant, dominant mangrove species native to the Arabian Gulf that thrives in harsh coastal environments. Unlike structures derived from laboratory grown specimens, our analysis captures PSI directly from wild-grown plant leaves, offering an in-situ snapshot of plant adaptation. The core architecture comprising twelve protein subunits and four Lhca antenna proteins coordinating 157 chlorophylls, 36 carotenoids and 24 lipids is highly conserved relative to model angiosperms yet exhibits subtle shifts in antenna core coupling and pigment organization. Red-shifted chlorophylls in Lhca3, conserved among far red adapted plants, suggest an ancestral photoprotective mechanism retained in high light, high-salinity environments. Lipid mediated stabilization at interfaces likely counteracts salinity-induced membrane fluidity changes enhancing resilience under fluctuating light and salt stress. Comparative analysis with PSI structures from other vascular plants highlights both evolutionary conservation and distinct ecological tuning of LHCI organization and cofactor binding in mangroves. These insights reveal molecular strategies enabling A. marina to maintain efficient photosynthesis under extreme conditions, offering strategies for engineering photosystems in crops.

plant biology↗

bioRxiv2025

Features fusion or not: harnessing multiple pathological foundation models using Meta-Encoder for downstream tasks fine-tuning

The emergence of diverse pathological foundation models has empowered computational pathology tasks, including tumor classification, biomarker prediction, and RNA expression prediction. However, variations in model architecture and data sources lead to inconsistent downstream performance and complicate centralized training. Specifically, the lack of data sharing makes retraining foundation models with pooled data infeasible. Alternatively, the release of model parameters enables combining multiple models during fine-tuning. Inspired by the meta-analysis method, we propose the Meta-Encoder framework, which integrates features from multiple foundation models to generate a comprehensive representation, improving downstream fine-tuning task performance. Comparative experiments demonstrate that Meta-Encoder is more effective than individual foundation models, with its strengths more pronounced in handling complex tasks. While single models may perform sufficiently well for simple tasks, Meta-Encoder can match or even surpass the best-performing single model, alleviating concerns over model selection. Moderately challenging tasks benefit from Meta-Encoders concatenation or self-attention strategies, with the latter demonstrating superior performance in more challenging scenarios. For highly complex tasks, such as high-dimensional gene expression prediction, self-attention proves to be the most effective Meta-Encoder strategy, balancing feature integration and computational efficiency. For three patch-level spatial gene expression prediction tasks (HEST-Benchmark, CRC-inhouse, and Her2ST), the self-attention strategy improved the Pearson correlation by 38.58%, 26.06%, and 20.39%, respectively, compared to the average performance of three patch-level single models. Similarly, for the TCGA-BRCA, TCGA-NSCLC, and TCGA-CRC WSI-level bulk gene expression prediction tasks, the Pearson correlation increased by 14.36%, 9.27%, and 42.55%, respectively, compared to the average performance of two WSI-level single models. By leveraging multiple pathological foundation models using Meta-Encoder, it can further improve molecular characterization in pathology images to advance precision oncology.

bioinformatics↗

bioRxiv2025

The mutational landscape defines the proteome and spatial organization of tumor, stroma and immune cells in ovarian cancer

High-grade serous ovarian cancer (HGSOC) is a highly aggressive and lethal form of ovarian cancer. Challenges to diagnosis and treatment include a lack of effective screening methods for early detection, the absence of cancer-specific symptoms, and the development of chemoresistance. The genomic instability of HGSOC, further complicated by homologous recombination deficiency (HRD), leads to heterogeneity in HGSOC tumors and patient response to treatment. This makes it challenging to develop a single, effective diagnostic and treatment approach for this disease. Proteogenomic studies have provided some insight into HGSOC biology, but a deeper understanding of the tumor proteome through chemotherapy and disease recurrence is needed. Here we have profiled the proteome of tumors from 29 HGSOC patients before and after multiple rounds of chemotherapy. The proteome of HGSOC tumors remained unchanged for individual patients even after numerous rounds of chemotherapy. Differential expression analysis revealed known and novel proteins associated with chemoresistance and HRD status, further supported by similar changes at the genetic and epigenetic levels. We found that HRD affected proteins related to immune pathways. HRD was also associated with more shared T cell receptor (TCR) CDR3 repertoires of tumor-infiltrating T cells and increased neoantigen counts. ERAP1, a protein involved in peptide trimming before antigen presentation to immune cells via MHC-class I, was overexpressed in homologous recombination proficient (HRP) tumors and negatively correlated to neoantigen count. Its potential role in immune suppression in HRP tumors makes it an attractive therapeutic target that may be effective in combination with immunotherapy, particularly for HRP tumors. 26-plex immunostaining of HGSOC whole tissues further revealed significant differences in the spatial proximities of immune cells to each other and to tumor cells based on HRD status. Through proteomic and imaging analysis, this work has shown that the immune landscape of HGSOC tumors is influenced by homologous recombination status and identified candidate drivers of HGSOC biology.

cancer biology↗

bioRxiv2025

In situ structure of bacterial 50S ribosomes at 2.98 A resolution from vitreous sections.

In situ high-resolution structure determination is limited to samples thin enough to be penetrated by the electron beam during imaging. Sample thinning involves focused ion or plasma beam milling of specimens to produce lamellae with thicknesses as low as 100-150 nm. However, surface damage caused by the milling process can extend 30-60 nm deep, restricting the usable lamella thickness. This imposes limitations on single-particle analysis of macromolecular complexes due to elevated structural noise, which cannot be avoided in situ because of the dense cellular environment. Alternative methods capable of producing thinner samples are needed to reduce background. Here, we demonstrate that high-resolution structures at side-chain level, free of orientation bias, can be obtained from vitreous sections prepared by cryo-ultramicrotomy, both in vitro and in situ. We optimized the method to produce sections as thin as [~]40 nm, free from significant surface damage. Using this approach, we determined the structure of the 50S ribosomal subunit in vitro at 2.8 [A] and in situ at 3 [A] from bacterial cells. These results lay the foundation for future in situ studies of smaller complexes using CEMOVIS, as well as for methodological advances aimed at achieving compression-free sectioning.

biochemistry↗

bioRxiv2025

Divergent MIC of Clarithromycin and Azithromycin Against Clinical Isolates of Mycobacterium abscessus Complex

Current treatment guidelines for Mycobacterium abscessus complex (MAB) infections recommend macrolides (clarithromycin/CAM and azithromycin/AZM) as cornerstone therapies, considering them clinically interchangeable without distinction. This study evaluated the comparative in vitro activity of clarithromycin (CAM) and azithromycin (AZM) against 146 clinical isolates of Mycobacterium abscessus complex organisms. MIC distributions revealed significantly higher resistance to AZM (94.5% resistant at [≥]8 g/mL) compared to CAM (77.4% resistant at [≥]8 g/mL), with only 4.8% of isolates susceptible to both drugs. Notably, 26 strains (17.8% of total) showed AZM resistance despite being non-resistant to CAM (MIC <8 g/mL) among 146 clinical isolates. Among the 33 CAM-non-resistant isolates (including susceptible and intermediate strains), 78.8% (26/33) were AZM-resistant, demonstrating frequent discordance in susceptibility profiles. These findings contrast with current treatment guidelines that recommend using CAM and AZM interchangeably without distinction. Subspecies analysis showed three distinct susceptibility profiles: isolates susceptible to both antibiotics (n=3, M. massiliense), isolates resistant to both antibiotics (n=3, M. massiliense), and M. bolletii with CAM-susceptible/AZM-resistant phenotypes (n=2). This differential resistance pattern suggests that while both drugs face substantial resistance challenges, CAM retains meaningful activity against certain strains that are AZM-resistant-particularly in M. bolletii. These findings indicate that AZM and CAM should not be used interchangeably to treat MAB infections and emphasize the need to prioritize CAM over AZM in treatment regimens.

microbiology↗

bioRxiv2025

The HORMA-domain protein ASY1 recruits the plant-specific cyclin SDS to promote DMC1-mediated meiotic recombination

The chromosome axis is a proteinaceous scaffold essential for crossover formation in meiosis. While the axis associated HORMA-domain protein ASY1 is known to be necessary for the localization of the recombinase DMC1 to the axis, the molecular mechanism linking ASY1 to DMC1 loading remains unclear. Here, we demonstrate that ASY1 directly recruits the plant-specific cyclin SDS to chromosomes, which ensures efficient DMC1 localization and interhomolog recombination. Live-cell imaging and immunodetection revealed that SDS localizes to chromosomes from leptotene to zygotene and dissociates from chromosomes after pachytene resembling DMC1 dynamics. Biochemical assays demonstrated a direct interaction between ASY1 and SDS. Further analyses revealed that ASY1s closure motif, a conformational regulatory element, is required for SDS recruitment despite being dispensable for ASY1s own chromosome association. Moreover, unlike in sds mutants, depletion of the DMC1 inhibitor FIGL1-FLIP complex failed to restore DMC1 foci in asy1 mutants, positioning ASY1 upstream of both positive (SDS) and negative (FIGL1-FLIP) regulators of DMC1. These findings establish ASY1 as a key coordinator of meiotic recombination, bridging chromosome axis architecture with recombinase dynamics to control crossover formation and genome stability.

plant biology↗