Biology subjects

Zhao, R.

Publications and source records attributed to Zhao, R..

At least 19 recordsLinked to original sources

bioRxiv2026

NeuroPack: Advanced Learnable Packaging Toolkit Towards Ultra-High Compression Ratio for Volumetric Neuroimaging

High-throughput 3D microscopic imaging generates brain-volume datasets at terabyte to petabyte scale, posing significant storage challenges for large-scale neuroimaging data. In this study, we introduce NeuroPack, a hyperprior-driven 3D deep-learning-based packaging toolkit specifically designed for compressing 3D microscopic volumes at the mesoscale. NeuroPack encodes a compact hyperprior stream that conditions its entropy model on local voxel-wise variance, adaptively allocating bits to preserve mesoscale anatomical details for an optimal rate-distortion balance. To ensure reproducible deployment across heterogeneous microscopy datasets and computing environments, NeuroPack implements model integerization for the hyperprior side-information pathway, whose hyper-decoder predicts the Gaussian mean and scale parameters used by the arithmetic coder. By replacing platform-dependent floating-point hyper-decoding with deterministic fixed-point integer convolutions, NeuroPack produces bit-exact entropy models across CPUs, GPUs, local workstations, and cloud servers, thereby preventing decoding drift caused by floating-point rounding, fused-multiply-add ordering, or library-specific kernels. This integerized design preserves rate-distortion behavior while maintaining efficient encoding and decoding for large anisotropic 3D microscopy volumes. Our method enables high-fidelity microscopy reconstruction at 100- to 1000-fold compression across diverse modalities and species. Quantitatively, NeuroPack delivers the strongest overall rate-distortion performance in both BD-PSNR and BD-MSSSIM, with average relative gains of 73.4% and 50.8%, respectively, over the best competing codec. Importantly, NeuroPack preserves image fidelity required for downstream morphological reconstruction and analysis, as validated by simultaneous human annotation of original and decompressed confocal whole-brain zebrafish microscopy images. Together, NeuroPack provides a learning-based compression framework explicitly tailored for microscopy data, establishing a scalable storage solution for data-intensive neuroimaging and AI-empowered biological discovery.

bioengineering↗

bioRxiv2026

Novel extracellular, extra-embryonic and intercellular γ-tubulin assemblies in mouse oocytes and preimplantation embryos

{gamma}-tubulin is a core component of microtubule-organizing centers (MTOCs), which are traditionally known as intracellular. Here, we report previously unrecognized extracellular, intercellular, and extra-embryonic {gamma}-tubulin assemblies in mouse oocytes and preimplantation embryos in three distinct categories: the {gamma}-tubulin extracellular satellite ({gamma}-TES), {gamma}-tubulin intercellular bridge girdle ({gamma}-IBG), and {gamma}-tubulin nucleation center ({gamma}-TNC). {gamma}-TESs are punctate structures outside the plasma membrane of oocytes and pre-hatching embryos. {gamma}-IBGs are transient, ring-like structures that, together with F-actin, encircle nascent intercellular bridges, suggesting a previously unrecognized role for {gamma}-tubulin in early intercellular bridge formation. {gamma}-TNCs are large, dynamic extracellular assemblies that emerge after fertilization and undergo stage-specific spatial and morphological reorganization during cleavage and blastocyst development. Both {gamma}-TESs and {gamma}-TNCs disappear after embryo hatching. Furthermore, {gamma}-TNCs and {gamma}-IBGs may represent large and ring-like aggregates of {gamma}-TESs, respectively, suggesting that {gamma}-TESs may serve as a local {gamma}-tubulin reservoir for higher order formations. {gamma}-IBGs and {gamma}-TNCs also exhibit close spatial association with microtubules, which form a peri-embryonic web lining the edge of the embryo exterior from zygotes to morulae. Together, our findings reveal a non-canonical, extra-embryonic {gamma}-tubulin organization system that may coordinate an embryonic skeleton architecture across blastomeres for critical embryo-wide developmental events such as polyspermy prevention, polarity establishment, morula and blastocyst formation, and embryo hatching.

developmental biology↗

bioRxiv2026

Expanding Therapeutic Target Space from Genes to Disease-Relevant Molecular Forms with Agent3Diso

Therapeutic targets are commonly defined at the gene or canonical protein level, yet therapeutic effects are ultimately exerted through specific molecular states operating in specific biological contexts. Alternative splicing generates diverse RNA and translated protein forms whose functional consequences, disease relevance, and therapeutic vulnerabilities can differ substantially within the same gene. Resolving these disease-relevant molecular forms creates opportunities for selective intervention across complementary RNA- and protein-directed modalities, but requires reasoning across tightly coupled molecular layers, heterogeneous evidence, explicit biological constraints, and modality-specific therapeutic requirements. Here, we present Agent3Diso, a hybrid deterministic--agent multimodal framework for molecular-form-resolved therapeutic discovery. Agent3Diso establishes cross-layer molecular coherence from transcript identity and translation to structure, function, and disease context; enforces explicit molecular and therapeutic constraints through deterministic computation; and applies specialized agentic reasoning to evidence synthesis, mechanistic interpretation, conflict resolution, hypothesis critique, and experimental design. The framework evaluates therapeutic opportunities across multiple intervention modalities and translates prioritized disease-relevant molecular states into traceable hypotheses linking molecular identity, therapeutic rationale, modality, concrete intervention, uncertainty, and experimental validation. By integrating molecular resolution with constraint-aware and modality-conditioned agentic reasoning, Agent3Diso provides a framework for extending therapeutic discovery beyond gene-level targets toward disease-relevant molecular forms.

cancer biology↗

bioRxiv2026

SWELL1 channel-mediated D-2HG export promotes immune evasion and metabolic fitness in IDH-mutant gliomas

Isocitrate dehydrogenase (IDH) is the most frequently mutated metabolic enzyme in human cancers. Mutant IDH produces the oncometabolite D-2-hydroxyglutarate (D-2HG), which promotes tumorigenesis in part through epigenetic alterations. Beyond its cell-autonomous effects, tumor-derived D-2HG acts as a potent immunosuppressant that establishes an immune-cold tumor microenvironment. However, the mechanism by which D-2HG is released from tumors remains largely unknown. Here, we identify the SWELL1 (LRRC8A)/LRRC8C-containing volume-regulated anion channel (VRAC) as a principal pathway for D-2HG efflux from IDH-mutant cells. Genetic deletion of SWELL1, the essential VRAC subunit, markedly reduces D-2HG release and reverses associated immunosuppression in an orthotopic mouse model of IDH-mutant glioma. Strikingly, loss of VRAC causes intracellular accumulation of D-2HG, which paradoxically limits tumor cell proliferation by driving epigenetic remodeling and mitochondrial metabolic stress. Pharmacological inhibition of VRAC with dicumarol suppresses IDH-mutant glioma growth, enhances intratumoral T cell activation, synergizes with immune checkpoint blockade, and prolongs survival in tumor-bearing mice. In human IDH-mutant lower-grade gliomas, elevated LRRC8C expression correlates with DNA hypermethylation and an immunosuppressive tumor microenvironment (TME), and predicts poor overall survival. Together, these findings establish VRAC-mediated D-2HG export as a central mechanism regulating both immune evasion and tumor cell fitness, uncovering new therapeutic opportunities across IDH-mutant cancers.

cancer biology↗

bioRxiv2026

Widespread exon definition is promoted by the U1 snRNP 70K subunit and requires sites of contact with RNA Polymerase II

Much pre-mRNA splicing initiates co-transcriptionally, but its mechanism is unclear. We investigated this process by degron depletion of the U1-70K subunit of U1 snRNP that contacts transcribing RNA polymerase II (RNAPII). U1-70K deficiency caused extensive exon skipping consistent with widespread exon definition. Surprisingly, exons with the strongest 5' splice sites (SSs) are skipped. Furthermore, strengthening of non-canonical 5' splice sites with a complementary mutant U1 snRNA or a splice modifying drug induced exon skipping in response to U1-70K depletion. We suggest that U1-70K plays a previously unappreciated role in destabilizing the U1-5'SS interaction to facilitate the transition to the U6-5'SS interaction required for productive splicing following exon definition. Consistent with this idea, knock- down of Prp28/DDX23 that exchanges U1 for U6 at the 5'SS also promotes exon skipping mimicking U1-70K depletion. Replacing WT U1-70K in degron-containing cells with a mutant in the RNAPII interface caused widespread exon skipping. We propose that frequent exon definition occurs at the transcription elongation complex and is enabled by U1-70K contact with transcribing RNAPII.

molecular biology↗

bioRxiv2026

Synergistic targeting of EP300/CBP and EYA co-activators collapses the rhabdomyosarcoma core regulatory circuit

Rhabdomyosarcoma (RMS) is a multi-subtype, high-risk pediatric sarcoma with a low mutational burden. The mutations found in RMS often alter genes involved in transcriptional control. Approaches to target dysregulated RMS transcription have remained elusive. Here, we develop a novel approach to target RMS transcription comprising simultaneous targeting of two distinctly acting transcriptional co-activators. We discover a common identity-controlling pan-RMS core regulatory circuit (CRC) composed of oncogenic and lineage-specific myogenic master transcription factors (mTFs). Using a super-enhancer-based reporter screen, we identify the EP300/CBP inhibitor A485 as a potent inhibitor of the pan-RMS CRC, though with efficacy-limiting toxicities. To enhance efficacy, we identify the mTF-binding co-activator EYA2 as a co-factor of this pan-RMS CRC and exploit a new second-generation EYA1/2 inhibitor, LG1-34, to disrupt its function. Combined co-activator inhibition inactivates the CRC and synergistically reduces RMS growth. This strategy dually targets CRC-associated co-activators to cooperatively suppress the RMS transcriptome and enforce cell death.

cancer biology↗

bioRxiv2026

RECON infers regions of interest from H&E images and reconstructs whole-slide molecular profiles at single-cell resolution

Spatial omics technologies resolve molecular expression and spatial architecture at single-cell resolution, but profiling whole slides remains costly. In practice, only a few regions of interest (ROIs) are profiled, leaving the rest of the tissue unmeasured. S2-omics was the first framework to unify ROI selection with out-of-ROI prediction, but it operates on superpixels rather than individual cells and predicts discrete cell types rather than continuous molecular profiles. Superpixel-based representations do not explicitly preserve cell boundaries, while categorical cell-type labels cannot quantify molecular expression within cells. Here we present RECON, a two-stage framework that performs ROI inference and whole-slide molecular reconstruction at single-cell resolution, predicting both continuous molecular profiles and discrete cell-type labels. In the first stage, RECON extracts morphological and microenvironmental features from individual cells to identify a representative ROI for spatially resolved single-cell molecular profiling. In the second stage, RECON trains deep learning models on molecular measurements acquired within the selected ROI and reconstructs transcriptomic or proteomic profiles for all remaining cells on the slide. Benchmarked against pathologist annotations, RECONs ROI selection outperforms the superpixel-based S2-omics approaches (IoU: 0.75 versus 0.64). For transcriptomics, refining the modeling unit from superpixels to single cells improves per-gene Pearson correlation by 22%. For proteomics, RECON surpasses the current state-of-the-art method, ROSIE, across all 16 markers, with a median per-cell Pearson correlation of 0.91 versus 0.84. Moreover, RECON delineates tumour boundaries and regions with distinct immune-cell densities, and highlights candidate tertiary lymphoid structures. Together, these results demonstrate that RECON enables informative ROI selection and whole-slide molecular reconstruction at single-cell resolution for both spatial transcriptomics and spatial proteomics.

bioinformatics↗

bioRxiv2026

The function of human PIF1 in G quadruplex formation and replication stress response at ALT telomeres

Cancers maintain their telomeres through two telomere maintenance mechanisms: 85-90% of cancers rely on telomerase (TEL+), while 10-15% of cancers adopt the Alternative Lengthening of Telomeres (ALT) pathway. The Break-Induced Replication (BIR) pathway plays a critical role in maintaining telomere length in the ALT+ cells. In both yeast and human, PIF1, a 5' to 3' helicase, is required for the robust activity of BIR. However, the extent of human PIF1 (hPIF1) involvement in the ALT pathway remains unknown. Here we showed that hPIF1 can be recruited to damaged telomeres in ALT+ cells. In addition, we demonstrated that inhibition of hPIF1 induced DNA damage and G quadruplex (G4) accumulation at ALT telomeres, leading to a moderate reduction of the mean telomere length. Most interestingly, we demonstrated that inhibition of hPIF1 also attenuates checkpoint activation, BLM recruitment, single-stranded DNA (ssDNA) formation, DNA damage, and G4s at telomeres in the FANCM deficient ALT+ cells. Finally, we showed that inactivation of hPIF1 affects the viability of both ALT+ and TEL+ cancers, suggesting that hPIF1 is a potential drug target for cancer therapy.

molecular biology↗

bioRxiv2026

NIR-II squeezed light-field microscopy enables high-speed volumetric imaging of deep-tissue dynamics in vivo

High-speed three-dimensional imaging in scattering biological tissues remains challenging because volumetric microscopy generally requires scanning, whereas snapshot light-field approaches divide limited detector pixels among multiple views. This constraint is particularly severe in the second near-infrared window (NIR-II), where InGaAs cameras have small sensor formats and high detector noise. Here we introduce NIR-II squeezed light-field microscopy (NIR-II SLIM), which optically rotates and compresses multiple perspective views before detection, allowing efficient use of camera pixels while retaining complementary spatial information for three-dimensional reconstruction. NIR-II SLIM acquires up to 600 volumes s-1 with a reconstructed lateral sampling grid of 512 x 512 pixels. We use this method for label-free imaging of cardiac dynamics in pigmented late-larval zebrafish, resolving chamber deformation and millisecond-scale atrioventricular-valve motion, and for NIR-II fluorescence imaging of vascular and lymphatic transport in mice. NIR-II SLIM provides a detector-efficient approach for high-speed volumetric imaging of rapid biological dynamics in scattering tissues.

bioengineering↗

bioRxiv2026

Hidden genetic diversity in 320 nearly-complete East Asian genome assemblies

East Asian populations, representing over 20% of the global population, remain critically underrepresented in human genomic studies, limiting our understanding of population-stratified genetic variation and its implications for health and disease. Here we present the first phase of the Asian Pan-Genome project (APG), comprising 320 nearly complete, fully phased haploid genome assemblies from 160 East Asian individuals. These assemblies achieve unprecedented quality, with an average contig N50 of 144.3 megabase pairs and an average quality value of 64.5. Leveraging these superior assemblies, we reveal previously uncharacterized diversity in human repeatome, including population-stratified patterns in centromere satellites and rDNA arrays. Compared to existing global human genome assemblies, the newly generated genomes supplement 152 million base pairs of novel sequences, 355 gene gains, 18,300 structural variation loci and 26 large euchromatic inversions missing from current human pangenomes. We perform population stratification analyses of structural variations, and further resolve the structural haplotypes of complex genomic regions such as Major Histocompatibility Complex and Survival Motor Neuron loci across global pangenomes, exemplifying tandem-duplicate and inversion-rich complex locus architectures in the human genome, respectively. This resource provides a critical foundation for human genetic studies, especially for East Asian populations, promoting more accurate variant discovery, reducing bias, and ultimately advancing the equity and efficacy of genomic medicine.

genomics↗

bioRxiv2026

Genetic and Pharmacologic Targeting of Eya3 in Macrophages Drives Anti-Tumor Immunity in Triple-Negative Breast Cancer

Triple negative breast cancer (TNBC) is an aggressive form of breast cancer that remains difficult to treat despite its relatively high immunogenicity, as tumors frequently evade immune destruction through poorly understood mechanisms. Here, we discover a previously unrecognized role for Eya3 within macrophages in the tumor immune microenvironment, where its expression is elevated. Using macrophage Eya3 knockdown and conditional knockout models, we show that Eya3 depletion induces coordinated transcriptional and functional changes in macrophages, enhancing migration, antigen processing, and inflammatory signaling associated with anti-tumor immunity. Strikingly, macrophage-targeted deletion of Eya3 reprograms the immune response in TNBC, increasing CD8+ T cell infiltration, suppressing primary tumor growth, and prolonging survival. Pharmacologic inhibition of Eya3 tyrosine phosphatase activity with a novel allosteric inhibitor, LG1-34, mirrors this effect, dramatically reducing primary TNBC growth through immune-mediated mechanisms that likely act both though targeting tumor and immune cells. These findings identify Eya3 as a macrophage-intrinsic checkpoint on anti-tumor immunity, identifying a new potential vulnerability in TNBC. Significance StatementTargeting Eya3 tyrosine phosphatase activity in tumor-associated macrophages reprograms the TNBC immune microenvironment and restores anti-tumor immunity, identifying a new potential therapeutic vulnerability in a cancer that has limited treatment targeted options.

cancer biology↗

bioRxiv2026

A DNA-scaffolded Retron Ring Mediates Antiphage Immunity

Retrons are a diverse family of bacterial defence systems that couple reverse transcriptase (RT) activity to antiphage immunity by producing multicopy single-stranded DNA (msDNA). Yet, the molecular mechanisms by which most systems detect infection and execute immunity remain unknown. Here, we define the structure, immune sensing and effector mechanisms of retron type IX, composed of an RT, a non-coding RNA, a tandem KH-HTH subunit and a HEPN RNase effector. Retron IX confers robust protection against diverse bacteriophages. Cryo-EM and biochemical analyses reveal a supramolecular ring assembly composed of 8-10 repeating modules, spanning up to 230 [A] in diameter. Within this assembly, the msDNA scaffolds the outer rim inhibiting the HEPN ribonuclease in a catalytically poised state, with the active site occluded within the inner layer. We identify a phage-encoded PD-(D/E)XK nuclease as the immune trigger that cleaves the exposed msDNA stem-loop, leading to ring disassembly and HEPN effector release. Upon activation, the HEPN ribonucleases cleave tRNAs indiscriminately, inducing dormancy and blocking phage propagation. Our findings unveil how ring-shaped higher-order assembly controls enzymatic activities while allowing signal-specific activation and establish the ncRNA as an evolvable scaffold underlying the remarkable structural and defensive diversity of bacterial retron immune complexes.

microbiology↗

bioRxiv2026

Depleting prion protein using splice-switching small molecules

Prion diseases are fatal neurodegenerative disorders driven by prion protein (PrP) misfolding, and lowering cellular PrP represents a promising therapeutic strategy. Here we report a small-molecule approach that reduces PrP by modulating pre-mRNA splicing of the PRNP gene. Through chemical modification of the clinically approved splicing modulator risdiplam, we generated CP3, the first class of compounds that selectively activate a cryptic exon in PRNP and routes its mRNA product for degradation, reducing PrP by [~]70% in cells. We demonstrate that CP3 activity critically depends on alternative splicing factor Luc7L, revealing a novel requirement for alternative splicing factors in small molecule splicing modulation. Strikingly, co-administration of CP3 with a Luc7L activator PTC258 significantly lowers PrP levels in the brains of transgenic mice. These results establish splicing modulation as a powerful strategy for PrP reduction and highlight the potential of small-molecule cooperativity for therapeutic RNA targeting.

biochemistry↗

bioRxiv2026

Chromosome-level genome assembly of the Northeast China Brown Frog (Rana dybowskii)

Rana dybowskii is distributed across Northeast Asian and represents a valuable medical resource. A high-quality assembly of the genome has not yet been reproted. This species has 2n=24 chromosomes, but a huge genome size that estimated at 3.5 ~4.6 Gb in the previous studies. The relatively large chromosome size, exceeding hundreds of megabases, may result in difficulties of obtaining a complete chromosome level genome. Here, we constructed a chromosome-level genome assembly of R. dybowskii by integrating PacBio HiFi long-read sequencing for de novo assembly and CiFi (3C coupled with HiFi sequencing) for scaffolding. The final assembly consists of 12 chromosomes with a total of 3.95 Gb and a scaffold N50 length of 455 Mb. BUSCO assessment using the tetrapoda_odb12 database identified 94.2% complete and 0.5% fragmented orthologs, suggesting a high level of completeness of the assembly. Genomic annotation revealed that repetitive sequences comprise over 53% of the assembly, with retroelements and DNA transposons accounting for 22% and 25%, respectively. A total of 43,999 protein-coding genes were predicted with the assistance of RNA-seq reads from four tissues (muscle, eye, testis and skin). This high-quality chromosome-level reference genome provides a valuable genomic resource for advancing genetic studies of the species.

genomics↗

bioRxiv2026

Pseudomonas aeruginosa CRISPR-Cas primes a minimal proline-codon toxin to abort anti-CRISPR phages

Pseudomonas aeruginosa typically carries type I-F CRISPR-Cas systems, which are targeted by diverse (pro)phage-encoded anti-CRISPR (Acr) proteins. Here, we show that [~]26% of P. aeruginosa Cas effectors are reprogrammed by a regulatory RNA guide (CreA) to transcriptionally silence a conserved small RNA toxin (CreT) that arrests cell growth upon Cas inactivation. This toxin unprecedentedly employs two consecutive proline codons, thus termed "proline-codon toxin". Combined phylogenetic and genetic analyses unraveled that CreTA has forced P. aeruginosa to reject prophages whose Acrs disrupt Cas-DNA binding, which is essential for CreT repression. We further show that Acr-armed lytic phages designed to overcome CRISPR adaptive immunity can be instead aborted by CreTA-mediated defense in vitro and in a mouse model. Our findings unravel intra-genomic arms races between CreTAs and anti-CRISPR phages, and underscore the necessity of rational engineering of strain-specific therapeutic phages to penetrate the layered CRISPR and TA barriers of multidrug-resistant P. aeruginosa.

microbiology↗

bioRxiv2026

NFIC-mediated CaSR endocytosis defines a hyperactive TOMM20highCHGAhigh oxyphil cell state as a pathological driver of autonomous secondary hyperparathyroidism

Secondary hyperparathyroidism (SHPT) is a debilitating complication of chronic kidney disease. Its clinical management is frequently compromised by calcimimetic resistance, a refractory state primarily driven by the progressive downregulation of the membrane calcium-sensing receptor (CaSR). Despite the centrality of CaSR as a therapeutic target, the mechanisms governing its aberrant expression and membrane localization remain incompletely elucidated. Here, we generated a single-cell transcriptomic atlas of human parathyroid tissues from SHPT and primary hyperparathyroidism (PHPT) patients, uncovering a unique stromal-immune niche that is specifically induced by uremic stress in SHPT. Our data also observed a striking dissociation between CaSR mRNA and its abundance as a membrane protein in SHPT tissues. Pseudotime trajectory analysis showed a progressive decline in CaSR pathway activity and a concomitant increase in endo-lysosomal activity along the trajectory, terminating in pathological oxyphil cells as the endpoint of chief cell differentiation in SHPT. Mechanistically, Nuclear Factor I C (NFIC) transcriptionally activated clathrin light chain B (CLTB) and Ras-related protein Rab7a (RAB7A) to trigger clathrin-mediated endocytosis and lysosomal degradation of CaSR, thus reducing its membrane abundance. This degradative program was further validated by multiplex immunofluorescence in TOMM20highCHGAhigh pathological oxyphil cells in human SHPT tissues. To translate these mechanistic findings into a clinically actionable strategy, we repurposed the clinically approved lysosomal inhibitor hydroxychloroquine (HCQ) to block this CaSR degradation pathway. In patient-derived xenograft (PDX) mouse models, co-administration of HCQ and cinacalcet acted synergistically to restore membrane CaSR expression, normalize serum PTH and calcium levels and suppress parathyroid tumor growth more effectively than monotherapies. Collectively, our single-cell-guided study identifies an NFIC-driven endo-lysosomal program as a previously unrecognized mechanism underlying CaSR downregulation and calcimimetic resistance in SHPT, and establishes HCQ repurposing as a clinically tractable therapeutic strategy for patients with refractory SHPT.

cell biology↗

bioRxiv2026

A high-resolution atlas of cattle regulatory variants and their cross-species activity in matched human cells

Identifying causal noncoding variants underlying complex traits in cattle remains challenging because high-resolution functional maps of regulatory variation are lacking. Here we combine massively parallel reporter assays with graph genomics to measure autonomous transcriptional activity from >1.5 billion DNA fragments spanning both cattle subspecies. In primary bovine cells, we assay >15 million variants and identify >150,000 expression-modulating variants enriched at cattle eQTL and GWAS loci. This enables the refinement of broad association signals to small sets of candidate functional regulatory variants. Our haplotype-aware framework captures rare, multi-allelic and tightly linked variants poorly resolved by conventional eQTL studies, and quantifies the disproportionate impact of larger variants on transcription. Furthermore, we use these data to train a deep-learning model that successfully predicts bovine promoter activity directly from sequence. Profiling the same cattle DNA in matched primary human cells reveals widespread conservation of promoter and enhancer activity, allelic effects and regulatory grammar, supporting the transfer of annotations and models across species. However, species-dependent effects are enriched in evolutionarily young sequences and p53-family motifs, highlighting the limits to simple cross-species extrapolation. Together, these data provide a high-resolution atlas of cattle regulatory variation and a framework for prioritising causal noncoding variants for cattle trait improvement.

genetics↗

bioRxiv2026

The Structural Code of Breast Cancer Proteoform: Alternative Splicing-driven Protein Isoform Variation and Functional Diversification

Alternative splicing generates extensive transcript diversity, but the extent to which this diversity contributes to the translated proteome and reshapes protein function remains unclear. Here, we develop 3DisoGalaxy, an atlas integrating transcript reconstruction, ribosome profiling, structural modelling and regulatory annotation in breast cancer. We find that 58,292 of 90,929 transcripts are linked to translation-supported ORFs, 71.9% of which arise from non-canonical transcript structures. These products are broadly accommodated within established protein fold space, indicating that alternative isoforms frequently preserve recognizable protein architectures despite substantial sequence variation. Functional divergence is instead concentrated in domains, intrinsically disordered regions, localization determinants and regulatory motifs. Motif remodelling is biased towards gains and is more extensive in cancer-driver genes than in other genes, linking isoform-associated regulatory variation to cancer-relevant proteins. As an example of domain remodelling, we identify an AKT1-{Delta}PH isoform that lacks the N-terminal PH domain while retaining the kinase core, with immunoblotting revealing a lower-molecular-weight AKT1 species consistent with this isoform. Together, our results show that alternative transcript diversity extensively enters translation-supported proteoform space and establish a systematic link between transcript variation and protein functional diversification.

cancer biology↗