Biology subjects

Li, Y.

Publications and source records attributed to Li, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Decision benchmarking reveals when protein foundation models add experimental value

Protein engineering is shifting from model-based variant scoring to deciding what to measure next. This exposes a limitation of fixed-dataset benchmarks, which rank predictors without showing when their advantage survives as evidence accumulates. We therefore introduce decision benchmarking across 217 ProteinGym assays, 2.47 million variants and 95 predictors to evaluate whether models and measurements improve decisions at matched cost. Zero-shot accuracy explained less than one-fifth of the variation in discovery after calibration. Calibrated priors exceeded budget-matched additivity at 20-100 measurements, but the advantage narrowed as component measurements accumulated. Measured additivity then overtook zero-shot models after 50-100 measurements for top-variant discovery and around 500 for global ranking. The same principle showed that double-mutant measurements improved prediction in models using mutation identity, whereas prediction-guided acquisition improved discovery. Evidence-based routing improved strategy selection. Decision benchmarking thus identifies which strategy adds value given the information already available and the decision that follows.

bioengineering↗

bioRxiv2026

Pharmacologic inhibition of OLIG2 by CT-179 disrupts mitotic progression and enhances standard-of-care chemoradiotherapy in glioblastoma

Background: Glioblastoma (GBM) remains uniformly fatal. The basic helix-loop-helix transcription factor OLIG2 is universally expressed in diffuse glioma, sustains the tumor-propagating stem-like fraction, and opposes p53-mediated genotoxic responses, but has historically been considered undruggable. We characterized CT-179, a brain-penetrant small-molecule OLIG2 inhibitor, as a candidate therapeutic for GBM. Methods: Target engagement was assessed by cellular thermal shift assay, differential scanning fluorimetry, crosslinking, and electrophoretic mobility shift assay. Anti-tumor activity was evaluated across eleven patient-derived GBM cell lines, in zebrafish oligodendrocyte precursor cell (OPC)-derived tumors, and orthotopic and subcutaneous GBM models, including combinations with radiotherapy plus temozolomide and with selective Bcl-2 family inhibitors. Results: CT-179 engaged OLIG2 and altered the conformation of dimerized OLIG2 on chromatin without preventing dimerization or fully displacing OLIG2 from DNA. CT-179 reduced OLIG2-positive OPCs and OPC-derived tumors in zebrafish and inhibited proliferation across all eleven GBM lines (IC50 < 360 nM), depleting the stem-like fraction and inducing apoptosis through mitotic catastrophe, mitotic slippage, or a hybrid response. RNA-seq across three patient-derived glioma stem cell lines identified {beta}-tubulin gene isoforms as the most strongly CT-179-down-regulated transcripts at the early time point and showed correlated {beta}-tubulin and OLIG2 expression in TCGA glioblastoma specimens. Combination with the Mcl-1 inhibitor S63845 or the Bcl-2/Bcl-xL/Bcl-w inhibitor ABT-737 produced greater-than-additive cytotoxicity. Oral CT-179 crossed the blood-brain barrier and extended median survival as a single agent across two independent adult orthotopic patient-derived backgrounds (GBM8 and G06); intraperitoneal CT-179 was associated with reduced intratumoral OLIG2 and Ki-67 staining in GBM8 orthotopic xenografts. Combination of CT-179 with radiotherapy and temozolomide eliminated all GBM8 and 7 of 8 GBM4 subcutaneous xenografts without weight loss and significantly extended survival when combined with radiotherapy in MGMT-unmethylated GBM6 orthotopic xenografts (CT-179 administered intraperitoneally). Conclusions: CT-179 is a brain-penetrant inhibitor of an established GBM driver with single-agent and combination activity across several orthotopic models, supporting clinical development for GBM and translational evaluation in other OLIG2-dependent CNS malignancies.

cancer biology↗

bioRxiv2026

Single-nucleus chromatin accessibility time course of excisional wound repair in rat skin

We present a time-series single-nucleus ATAC-seq dataset from full-thickness excisional wounds in Sprague-Dawley rats. Samples were taken from unwounded skin (normal control) and at 1, 2, 5, 10, and 19 days post-wounding, spanning the inflammatory, proliferative, and remodeling phases of skin repair. We extracted nuclei with a two-step tissue dissociation protocol and prepared libraries using the DNBelab C Series Single-Nucleus ATAC Kit, then sequenced on the MGI DNBSEQ-T1 platform. After stringent quality filtering, 37,555 nuclei passed quality control; the resulting chromatin accessibility profiles cover 23 cell types: fibroblast subpopulations, keratinocytes, vascular endothelial cells, immune cells, and skin appendage cell types. This genome-wide chromatin accessibility dataset is a resource for studying regulatory dynamics during excisional wound repair and for comparing results with other wound healing systems.

bioinformatics↗

bioRxiv2026

BNIP3L/NIX-mediated mitophagy limits Alzheimer disease pathology and preserves neuronal function

Defective mitophagy is emerging as a key contributor to Alzheimer disease (AD), but the neuronal pathways governing mitochondrial clearance and their contribution to disease progression remain poorly understood. Here, we identify BNIP3L/NIX-dependent mitophagy as a conserved neuronal quality control pathway that maintains mitochondrial fitness and constrains AD-associated proteotoxicity. Loss of BNIP3L/NIX or its C. elegans orthologue DCT-1 impaired basal and stressed-induced mitophagy, disrupted mitochondrial homeostasis, enhanced Tau and Amyloid-beta pathology and compromised neuronal network, synaptic and behavioral function across human neuronal and in vivo models. Conversely, restoring BNIP3L/NIX and DCT-1 activity improved neuronal function under proteotoxic stress in vivo, reduced disease-associated Tau phosphorylation in human neurons and markedly suppressed seeded Tau aggregation in primary mouse neurons. Together, these findings identify BNIP3L/NIX-mediated mitophagy as a mechanistic link between mitochondrial quality control, proteostasis and neuronal function, and establish its restoration as a potential strategy for counteracting AD-associated pathology.

cell biology↗

bioRxiv2026

Evolution-Guided Engineering of Non-conserved N-Glycosylation Sites Improves Heterologous Production of Sulfotransferases

Escherichia coli features low cost, mature fermentation technology and high recombinant protein output, but the expression of glycosylation-dependent eukaryotic proteins therein is severely limited. Many glycosylated proteins are key tool enzymes for the biosynthesis of various pharmaceutical molecules, such as glycosaminoglycan-related synthases, but there is a lack of universal protein engineering methods to enable the adaptive evolution of these enzymes in E. coli. We established an evolution-guided optimization strategy that targets non-conserved N-glycosylation sites (EGO-NGly). The core of this strategy lies in the phylogeny-guided selective reversion of evolutionarily acquired N-glycosylation sequons to naturally occurring non-glycosylated residues from early-divergent orthologs, thereby improving heterologous production and residual activity stability for selected sulfotransferases in E. coli. Using heparin 3-O-sulfotransferase 1 (3OST-1) as a model enzyme apparatus in eukaryotic organisms, EGO-NGly extended the residual activity half-life by 4.5-fold. Structural analysis and molecular dynamics simulations indicate that greater surface rigidity and remodeling of intramolecular interaction networks contribute to the improved conformational stability of M7 in an aglycosylated host. EGO-NGly was further applied to a panel of 3OST and 6OST homologs, demonstrating its applicability to a subset of the tested enzymes. Furthermore, EGO-NGly can be orthogonally integrated with other complementary protein engineering strategies, as exemplified by its combination with the machine learning-aided Protein Repair One-Stop Service, generating variants with 8-fold and 17-fold extensions in residual activity half-life. Collectively, these results establish EGO-NGly as a practical and potentially cost-effective engineering strategy for improving the prokaryotic expression and functional performance of selected glycosylation-dependent eukaryotic sulfotransferases.

biochemistry↗

bioRxiv2026

NEIL2 regulates RNA polymerase II dynamics to suppress transcription replication conflicts in pancreatic cancer

Transcription replication conflicts (TRCs) arise from spatiotemporal interference between replication and transcription machinery and contribute to genome instability in cancer cells. In pancreatic ductal adenocarcinoma (PDAC) cells, oncogenic KRAS drives TRC formation, and base excision repair (BER) contributes to TRC resolution as an adaptive response. Here, we show that TRCs are enriched in pancreatic tumor sections from patients and are associated with malignant progression. We identify NEIL2, a bifunctional DNA glycosylase in the BER pathway, as a critical regulator of TRCs in PDAC cells. Mechanistically, NEIL2 loss causes aberrant RNA polymerase II (RNAPII) occupancy at transcription start sites and downstream of transcription end sites. Dysregulated RNAPII dynamics promote R-loop-dependent and -independent TRCs contributing to replication stress, DNA damage, and impaired cancer cell proliferation. Notably, the DNA-binding motif of NEIL2 necessary for canonical BER function is dispensable for TRC regulation. Together, these findings reveal an unrecognized role for NEIL2 in regulating RNAPII dynamics and mitigating TRCs in pancreatic cancer cells.

molecular biology↗

bioRxiv2026

DCAF: Unifying Data Validity, Evaluation Validity and Predictive Modeling for Single-cell Perturbation Simulation

Single-cell perturbation profiling is limited by cost and throughput, while computational methods remain constrained by inconsistent evaluation and underperformance relative to simple baselines. Here we present DCAF, a unified framework for single-cell perturbation simulation that that jointly addresses data validity, evaluation validity and predictive modeling. Among its three components, DCAF-data addresses the single-measurement limitation by reconstructing pre- and post-perturbation status using entropy-regularized optimal transport, and is demonstrated on both cell line and multi-cell type datasets. DCAF-criterion evaluates log fold changes in non-silenced genes to improve sensitivity to model error and robustness to zero inflation noise, validated on synthetic datasets. DCAF-model combines JEPA with explicit modeling for regulatory-dynamics modeling for interpretable prediction. Across benchmarks, DCAF outperforms state-of-the-art deep-learning methods, as well as mean and linear baselines in cross-gene, cross-cell-type and cross-region generalization. In adult Mouse brain, DCAF recapitulates known cell-type-specific regulatory heterogeneity of Dgcr8 knockdown at both cell type and gene levels. DCAF thus provides a rigorous and biologically grounded foundation for reliable perturbation simulation across development, disease and therapeutic discovery.

bioinformatics↗

bioRxiv2026

DCSMAP: A Hybrid Linear-Pangenome Framework for Accurate and Efficient Read Alignment

Background: Linear-reference read alignment is computationally efficient but is susceptible to reference bias, whereas pangenome graph alignment better represents genetic diversity at substantially greater computational cost. Findings: We developed DCSMAP, a hybrid workflow that combines linear alignment with machine-learning-based selection of reads for remapping to a personalized pangenome graph, followed by local indel realignment. An XGBoost classifier trained on linear-alignment features achieved an area under the receiver operating characteristic curve of 0.9831 on held-out test data. Across 17 runs covering seven Genome in a Bottle samples, two sequencing platforms, and two read lengths, it selected a mean of 14.80% of read pairs for graph remapping. The optimized hybrid workflows reduced variant-calling errors by 46.66% relative to BWA-MEM2 and 8.39% relative to vg personalized-pangenome alignment. Heterozygous allelic balance indicated that the hybrid workflows substantially reduced reference bias relative to BWA-MEM2 linear alignment, yielding reference bias comparable to that of the pangenome alignment. On HG003 DNBSEQ PE150 data, DCSMAP achieved a 2 to 2.5 times speedup over the personalized-pangenome workflow; both workflows used 32 threads. Efficiency gains arose from both the hybrid architecture and tool-level optimizations, which accelerated personalized-graph construction by 2.5 times, graph alignment by 1.2 times, and indel realignment by 2.5 times. Conclusions: Selectively applying graph alignment to reads with potentially unreliable linear placements retains the accuracy benefits of personalized pangenomes while substantially reducing computation. DCSMAP provides an accurate and resource-efficient approach to short-read mapping on a standard CPU server.

bioinformatics↗

bioRxiv2026

Pan-cancer nucleosome landscapes reveal tumor heterogeneity and inform cell-free DNA-based detection

Background: Nucleosome positioning and occupancy are fundamental features of chromatin organization, yet their variation across human cancers and potential utility for noninvasive cancer detection remain poorly characterized. Methods: We systematically characterized nucleosome organization across 410 primary tumors spanning 23 cancer types using ATAC-seq, establishing a high-confidence pan-cancer nucleosome atlas validated by independent MNase-seq data. We characterized shared and cancer-type-enriched nucleosome patterns, investigated their associations with tumor heterogeneity and regulatory alterations, and evaluated tissue-derived nucleosome signatures for cancer classification and detection using circulating cell-free DNA (cfDNA). Results: The atlas identified shared and cancer-type-enriched nucleosomes associated with distinct regulatory programs. Notably, nucleosome occupancy provided information complementary to chromatin accessibility for tumor stratification and revealed molecular heterogeneity within individual cancers, including subgroups associated with Basal-like breast cancer. In hepatocellular carcinoma, differential nucleosome analysis revealed cancer-associated chromatin remodeling involving regulatory pathways, transcription factor motifs, and candidate genes. Importantly, tissue-derived nucleosome signatures were detectable in cfDNA, enabling classification among three cancer types (AUROC = 0.877) and colorectal cancer detection (AUROC = 0.930), with an AUROC of 0.773 in an independent validation cohort. We also developed OncoNucAtlas, a publicly accessible database facilitating exploration of these nucleosome landscapes. Conclusions: Our study cancer-associated nucleosome organization as a complementary source of epigenomic information and demonstrates the potential of tissue-derived nucleosome signatures for cfDNA-based cancer detection. The pan-cancer atlas provides a resource for investigating tumor heterogeneity and developing noninvasive cancer detection approaches.

bioinformatics↗

bioRxiv2026

LIF is a pro-algesic mediator in human and mouse models of arthritis-related pain

Purpose: Emerging clinical and experimental data suggest that JAK inhibitors (JAKi) are effective in reducing pain in Rheumatoid Arthritis (RA). We recently showed that JAK/STAT signalling cytokines, specifically IL-6, LIF and IL-11, are present in the RA joint and can act directly on human induced pluripotent stem cell (iPSC) derived sensory neurons by increasing their STAT3 phosphorylation (pSTAT3) levels and expression of select pain-relevant genes. In this study, we determined that LIF is the most consequential cytokine out of the three, altering neuronal signalling, outgrowth and pain-like behaviours in in vitro and in vivo models of arthritis. Methods: Human iPSC-derived sensory neurons were stimulated with RA synovial fluid (SF) or with cytokine-treated RA synovial fibroblast conditioned media (CM) in the absence or presence of anti-cytokine antibodies. pSTAT3 and pSTAT1 levels, and gene expression patterns, were assessed by Western blot and RNA-sequencing (RNA-seq). The immortalised dorsal root ganglion (DRG)-derived cell line (HD 10.6) was assessed for LIF-induced JAK/STAT signalling in addition to neurite outgrowth assays as a functional readout of the sensory neurons. Lastly, mouse models were used to assess pain-related behaviours in vivo. Results: LIF was found to be consistently present in the SF from painful joints from individuals with inflammatory arthritis. Western blotting revealed that the addition of RA SF to iPSC-derived sensory neurons led to LIF-dependent induction of pSTAT3 and pSTAT1, while RNA-seq demonstrated that LIF alters the transcriptome of sensory neurons more prominently than IL-6 and IL-11, up-regulating signature genes related to peripheral neuron sensitization, such as TRPV1, NTRK1, BDNF, HRH1 and SCN10A. Similarly, cytokine-treated fibroblast conditioned media was shown to induce neuronal pSTAT3 and pSTAT1 and upregulate expression of BDNF, HRH1 and VGF in a LIF-dependent manner. Additionally, the immortalised dorsal root ganglion (DRG)-derived cell line (HD 10.6), which also exhibited LIF-induced pSTAT1 and pSTAT3, showed increased neurite outgrowth after axotomy when treated with LIF. Finally, in a mouse model of inflammatory arthritis, LIF was shown to be significantly increased in the affected joint. Furthermore, intraarticular injection of LIF into a healthy mouse knee resulted in increased responsiveness to painful pressure stimuli in that joint. Conclusions: Our data indicate that LIF may be a pro-algesic mediator and a possible therapeutic target to improve pain management in individuals living with inflammatory arthritis.

neuroscience↗

bioRxiv2026

A Compact Regulatory Logic Governs Fibroblast Cell State Plasticity in Fibrosis

Fibroblast activation drives organ failure across human diseases, yet its regulatory basis remains largely undefined. Here, we repressed 280 conserved disease-activated enhancers using CRISPR droplet sequencing (CROP-seq) in ~550,000 fibroblasts, constructing a regulome of 15 gene programs governing the profibrotic state. Systematic TF perturbation converged on MEOX1 as a central regulator, and fibroblast-specific Meox1 deletion in mice improved cardiac function, reduced fibrosis, and rewired profibrotic fibroblasts toward quiescence in heart failure. Effector gene perturbation in human cardiac fibroblasts revealed distinct regulators of contractility, migration, and inflammatory signaling, and these programs were conserved across profibrotic states in human lung, liver, and skin. Simultaneous repression of just six enhancers using a multiplexed dCas12a-KRAB system collapsed the profibrotic network, suppressed migration and contraction, and rewired fibroblast paracrine signaling to attenuate macrophage inflammation. These findings define the regulatory logic of fibroblast plasticity and establish a new framework for reprogramming profibrotic cell states in disease.

genomics↗

bioRxiv2026

A conservative moving-boundary multiphysics framework reveals nonlinear coupling between osmotic flow and actin-driven cell migration

Cell migration couples membrane transport, intracellular fluid motion, and actin remodeling on a boundary that deforms with the cell. Quantitative interpretation of this coupling requires accurate one-sided membrane solute transport and conservative transfer between the G-actin and F-actin pools, because these fields determine the osmotic pressure and polymerization flux that enter the force balance. We develop an implicit immersed-boundary Stokes--Brinkman solver coupled to a sharp interface Cartesian grid advection--diffusion solver that enforces Robin conditions on the evolving membrane and advances F-actin/G-actin exchange through paired interface fluxes on the same accepted geometry. The framework resolves membrane mechanics, osmotic water permeation, solute transport, actin turnover, substrate drag, and intracellular advection in one calculation. Long-duration tests show excellent conservation of total actin and total solute under sustained interface motion and transport. The actin calculations recover biphasic dependencies on both depolymerization and substrate coupling, while pump-induced migration generates a rearward cell-relative cytosolic flow. In the fully coupled system, this flow redistributes G-actin more strongly than F-actin, reorganizes membrane polymerization and F-actin stress, and changes cell migration. Matched controls show that the coupled actin--osmotic system travels farther than the baseline-corrected sum of the isolated actin- and pump-driven responses. The calculations identify cytosolic convection as a physical route through which polarized membrane transport reorganizes the force-generating actin system and produces a nonlinear migration response.

biophysics↗

bioRxiv2026

Self-extending DNA recording with stochastic and programmed writing

Recording cellular histories requires new information to accumulate without erasing earlier records. Here we introduce Infinite Printer, a CRISPR recording architecture that couples self-extension to regeneration of a writable terminal context. A self-targeting prime-editing guide RNA (stpegRNA) directs repeat extension, while base editing generates diversity in situ without a separate insertion template for each character state. Earlier sequence remains upstream of the renewed terminus, linking substrate growth with record retention. Auxiliary pegRNAs specify payloads within a write-renew-write architecture. After three rounds of payload input, 4,436 distinct complete CCA-based records contained identities from all three pools. Longer AC/AT records retained shared upstream marks, and full-length sequence analysis resolved additional endpoint distinctions. Joint single-cell readout recovered 1,549 distinct records and 7,669 combinations across 12,302 transcriptome-linked cell labels from a single stpegRNA design. Spatial-transcriptomic readout recovered spacer records at 11,330 capture spots, linking record content to tissue coordinates and gene-expression profiles. Infinite Printer unites substrate renewal, sequence diversification and programmed writing with cell- and tissue-linked readout, providing a foundation for future lineage recording across large cell populations during mammalian development.

synthetic biology↗

bioRxiv2026

PatientPheX: A Full-Text Biomedical Corpus for Patient-Specific Phenotype Information Extraction

Patient-specific phenotype information extraction identifiers and normalizes phenotype entities and links them with individual patients, supporting rare disease research and genotype-phenotype analysis. However, existing datasets rarely combine full-text biomedical content with detailed annotations of patients, phenotypes, related entities, and their associations. In this work, we present PatientPheX, a corpus for patient-specific phenotype information extraction comprising 200 full-text articles, primarily case reports and case series. The corpus provides mention annotations and normalization for seven biomedical entity types, together with explicit associations between patients and entities across sentences, paragraphs, and sections. Negated findings and composite phenotype mentions are also annotated. Corpus construction combines automated pre-annotation, large language model (LLM)-assisted verification, and manual review and adjudication. Benchmarks cover entity recognition and normalization and patient-phenotype association extraction using gold-standard and predicted entities. The overall document-level entity F1 was 86.95%, while phenotype F1 was 79.33%. The best relation extraction macro-F1 decreased from 84.14% with gold-standard entities to 54.98% with predicted entities, highlighting the combined challenges of phenotype extraction and patient attribution. PatientPheX provides a resource for developing and evaluating patient-centered information extraction methods and supports the construction of structured patient-level knowledge resources for phenotype-driven biomedical research.

bioinformatics↗

bioRxiv2026

SMARTFlexDB: a paired apo-holo RNA structure database and analysis platform for RNA conformational flexibility and small-molecule recognition

RNA structures can undergo substantial conformational changes upon small-molecule binding, yet existing structural resources provide only static RNA-ligand snapshots without connecting ligand-bound (holo) RNA structures to corresponding ligand-free (apo) conformations. SMARTFlexDB is a curated database and analysis platform that uses paired apo-holo RNA structures to characterize conformational differences and RNA-small-molecule recognition. Candidate pairs were identified from the Protein Data Bank by matching RNA chains with at least 90% sequence identity and coverage, and fully conserved binding pocket nucleotides. The current release contains 434 binding pockets from 266 holo structures, linked to 186 apo structures to yield 1,187 pocket-level apo-holo pairs organized into 734 database entries, spanning 150 small molecules and 23 RNA functional classes. Each entry integrates RNA sequence and secondary-structure annotations, apo and holo three-dimensional structures, RNA-ligand atomic interactions, and quantitative descriptors of global and local conformational changes. An interactive web interface enables users to explore sequence alignments and structural overlays, compare secondary structures and RNA motifs, and upload paired apo-holo structures for customized analysis. By linking ligand-bound and ligand-free RNA structures, SMARTFlexDB provides a robust foundation for investigating RNA structural flexibility and supporting RNA-targeted small-molecule drug discovery. The database and analysis platform are available at https://aidd.rc.ufl.edu/app/smartflexdb/.

bioinformatics↗

bioRxiv2026

AMPK-dependent brain-wide norepinephrine release promotes recovery from metabolic coma in mice

Coma is a pathological brain state characterized by loss of consciousness. How the brain recovers from coma remains largely unknown. Using mouse models of metabolic coma, we identified an endogenous neuromodulatory pathway that actively promotes coma recovery. In mice subjected to hypoglycemic coma, hypoglycemia triggered AMPK-dependent excitation of nucleus tractus solitarius (NTS) neurons, which activated locus coeruleus (LC) norepinephrine neurons through a glutamatergic NTS-LC circuit. LC activation drives widespread norepinephrine release across cortical and subcortical regions, thereby promoting post-coma arousal. Notably, coma-associated brain-wide norepinephrine release was unconventional in both scale and duration, with a magnitude approximately 10-fold higher than physiological norepinephrine release during sleep-wake cycles. This neuromodulatory process also operated during hypercapnic coma. Vagus nerve stimulation accelerated coma recovery by engaging this endogenous anti-coma mechanism. Our findings uncover an AMPK-dependent brainstem circuit that actively restores arousal from metabolic coma, revealing a neural defense strategy against profound metabolic stress.

neuroscience↗

bioRxiv2026

Pan-cancer estimation of prognostic immune biomarkers from histopathology using artificial intelligence

Multiplex immunofluorescence (mIF) assays such as ImmunoProfile provide standardized quantification of prognostic immune markers but are costly and not routinely used in clinical settings. We developed a weakly-supervised AI model, HistoProfile, to estimate intratumoral cell densities of key immune biomarkers (CD8, FOXP3, PD-1, and PD-L1) and the PD-L1 tumor proportion score from routine H&E-stained whole-slide images. Trained on a large pan-cancer cohort with paired H&E and mIF data, HistoProfile discriminated biomarker-high from biomarker-low tumors in held-out samples and tumor-specific subgroups (AUROCs of 0.78-0.89 across biomarkers). Critically, the estimated biomarkers preserved prognostic stratification in downstream survival analyses, and showed cancer-specific survival associations across TCGA cohorts where mIF is unavailable. These findings support scalable H&E-based estimation of key immune biomarker measurements for large-scale immune profiling and risk stratification.

bioinformatics↗

bioRxiv2026

A telomere-to-telomere genome of Holstein cattle resolves chromosome-end architecture and the genetic basis of telomere length

Telomeres safeguard chromosome-end integrity, yet population-scale dissection of telomere-length genetics has been largely restricted to humans. Here, we report a 3.01-Gb telomere-to-telomere (T2T) genome of Holstein cattle that resolves repeat-rich chromosome ends and centromeres and enables telomere-length quantification at single-chromosome-end resolution. Holstein chromosome ends show marked telomere-length asymmetry and end-specific variation in telomere variant repeats, subtelomeric tandem repeats, GC/CpG composition, and DNA methylation. Using sequencing-depth-corrected telomere-length phenotypes from 9,591 cows, teloGWAS identifies major loci encompassing RTEL1, CTC1, and TERT, while multi-tissue eQTL, sQTL, TWAS, and co-expression analyses prioritize CTC1 and implicate DNA replication, DNA repair, and stress-response networks. Together, these findings extend population-scale telomere genetics beyond humans and establish a sequence-resolved framework for chromosome-end biology and telomere-informed livestock genomics.

genomics↗