Biology subjects

Liu, Y.

Publications and source records attributed to Liu, Y..

At least 595 records · Page 33Linked to original sources

bioRxiv2025

Spalt-related is an integrated stress response-activated inhibitor of mTORC1-mediated growth

Anabolic and catabolic processes are coordinated by a conserved regulatory network, which includes the nutrient sensing protein kinase mTOR complex 1 (mTORC1) and the insulin- and stress-responsive transcription factor FoxO. In physiological setting these regulators align growth, storage, reproduction, and aging with nutrient availability. Here, we identify transcription factor Spalt-related (Salr), previously implicated in organogenesis, as a negative regulator of growth and lipid storage. In the Drosophila fat body Salr activates catabolic gene expression and restricts mTORC1-mediated cell growth. The genomic binding of Salr overlaps extensively with that of FoxO and similar convergence is observed between their mammalian homologs SALL1 and FOXO1. Both Salr and FoxO are activated upon fasting but respond to distinct cues: while FoxO displays transient activation and is responsive to AKT inhibition, Salr is activated in a slow and sustained manner through the integrated stress response. Once activated, Salr counters nuclear localization of FoxO. Together, Salr and FoxO are converging transcriptional activators of catabolism during nutrient stress.

cell biology↗

bioRxiv2025

Designing smart spatial omics experiments with S2Omics

Spatial omics technologies have transformed biomedical research by enabling high-resolution molecular profiling while preserving the native tissue architecture. These advances provide unprecedented insights into tissue structure and function. However, the high cost and time-intensive nature of spatial omics experiments necessitate careful experimental design, particularly in selecting regions of interest (ROIs) from large tissue sections. Currently, ROI selection is performed manually, which introduces subjectivity, inconsistency, and a lack of reproducibility. Previous studies have shown strong correlations between spatial molecular patterns and histological features, suggesting that readily available and cost-effective histology images can be leveraged to guide spatial omics experiments. Here, we present S2Omics, an end-to-end workflow that automatically selects ROIs from histology images with the goal of maximizing molecular information content in the ROIs. Through comprehensive evaluations across multiple spatial omics platforms and tissue types, we demonstrate that S2Omics enables systematic and reproducible ROI selection and enhances the robustness and impact of downstream biological discovery.

genomics↗

bioRxiv2025

Evolutionary patterns and repeated adaptive strategies of deep-sea anemones

Sea anemones occupy the full depth of the oceans, yet their evolutionary patterns and adaptive strategies to the enigmatic deep sea have remained contentious and poorly resolved. Here, we assemble genomes (n = 13) and transcriptomes for 15 species collected between 432 and 6,000 m and integrate them with all publicly available actiniarian data. Phylogenomic analyses reveal a mosaic topology among deep-sea and shallow-water clades. Using a novel framework that contrasts convergent gene-loss patterns, we show that a large number of light-associated gene families-- including the complete circadian toolkit--were independently deleted after lineages entered the aphotic realm, whereas comparable loss in shallow taxa is negligible, providing decisive support for a shallow-water origin followed by multiple descents. Intriguingly, some deep-sea lineages further streamline energy budgets by recurrent loss or pseudogenisation of key meiotic genes (e.g., Meiosin, Ythdc2, Spo11, Rad21, Mlh3), indicating a shift towards asexual reproduction. Despite this extensive genomic erosion, deep-sea anemones exhibit sophisticated molecular tuning: specific amino-acid substitutions enhance protein stability and activity under deep-sea conditions, while selective expansions of gene families related to neural excitability, membrane systems, etc., likely mitigate the suppressive environmental effects on vital physiological processes. Enzyme activity assays in the yeast system confirm that the deep-sea variants exhibit superior activity and enhanced growth at 4{degrees}C. These results define a "loss-optimization-innovation" triad that underlies bathymetric adaptations and may apply to other deep-sea fauna worldwide.

evolutionary biology↗

bioRxiv2025

Protection and deprotection of the Rec8 cohesin complex during meiosis

In the first meiotic division, the cohesin Rec8 is cleaved by separase along the chromosome arms but is protected at the centromere by shugoshin (Sgo1), maintaining centromeric cohesion throughout meiosis I. Another meiotic regulator, meikin (Moa1), supports the protective function of Sgo1 primarily by phosphorylating S450 of Rec8. Both Sgo1 and Moa1 are meiosis I-specific proteins. Unlike fission yeast Sgo1, mammalian shugoshin (SGO2) persists at centromeres throughout meiosis I and II, but REC8 cohesin is protected only during meiosis I. Here, we show that fission yeast Moa1 and Sgo1 appear at kinetochores/centromeres from prophase I to metaphase I and are degraded during anaphase I by the APC/C-Slp1 pathway. We expressed non-degradable versions of Moa1 and Sgo1 in meiosis II and investigated how these proteins protect the cohesin Rec8 during meiosis II. Our analyses suggest that the localization of Sgo1 and the phosphorylation of Rec8 at S449 and S450 are necessary and sufficient events for protecting Rec8 cohesin during meiosis II. The absence of either event leads to deprotection at meiosis II.

cell biology↗

bioRxiv2025

LieOTMap: A Differentiable Approach to Cryo-EM Fitting via Lie-Theoretic Optimal Transport

MotivationThe integration of high-resolution atomic models with lower-resolution cryo-electron microscopy (cryo-EM) maps is a fundamental task in structural biology. However, this rigid-body fitting problem is challenged by complex scoring landscapes and the non-differentiable nature of standard structural similarity metrics like TM-score, precluding their direct use in modern gradient-based optimization pipelines. MethodWe present LieOTMap, a novel, fully differentiable framework for cryo-EM fitting. Our approach introduces two key innovations. First, we parameterize rigid-body transformations on the Lie algebra se(3), which provides a minimal, singularity-free representation of the motion. Second, we formulate a loss function based on the Sinkhorn divergence, a differentiable proxy for the Optimal Transport (Wasserstein) distance. This loss function serves as a robust, geometrically meaningful surrogate for non-differentiable scores, allowing us to leverage powerful gradient descent optimizers to navigate the search space. ResultsWe demonstrate the effectiveness of LieOTMap by fitting the apo-state structure of E. coli GroEL (PDB: 1aon) into the ATP-bound state cryo-EM map (EMD-1046). Our method successfully navigates a large-scale conformational change, achieving a highly accurate final RMSD of 3.08 [A] with respect to the ground-truth structure (PDB: 1GRU). This result showcases the power of combining Lie-theoretic representations with differentiable geometric loss functions for complex structural alignment tasks. AvailabilityThe source code is available at https://github.com/YueHuLab/LieOTMap.

bioinformatics↗

bioRxiv2025

LieMap: A Fast and Transparent Gradient-Based Method for Cryo-EM Structure Fitting

Fitting high-resolution atomic models into lower-resolution cryo-electron microscopy (cryo-EM) maps is a critical yet challenging step in structural biology. We present LieMap, a straightforward, fast, and transparent gradient-based fitting protocol designed for practical applications. Our method parameterizes rigid-body motion on the Lie algebra se(3) to provide a minimal and singularity-free representation. The optimization objective is to directly maximize a real-space cross-correlation score, calculated as the mean density value sampled from the map at the atomic coordinates. This score is computed differentiably using trilinear interpolation and optimized with the Adam optimizer in a multi-stage fashion. We demonstrate the effectiveness of LieMap by fitting the apo-state structure of E. coli GroEL (PDB: 1aon) into its ATP-bound state cryo-EM map (EMD-1046). The protocol successfully navigates the large conformational change, achieving a final RMSD of 3.23 [A]. LieMaps simplicity, computational efficiency, and transparent optimization process make it a valuable and practical tool for structural biologists.

bioinformatics↗

bioRxiv2025

Comparing Neuroprotective Drug Efficacy in Rodent Neonatal Brain Injury Models

BackgroundA challenge in preclinical neonatal neuroprotection research is implementation of study designs that enable direct comparison of multiple potentially effective drugs. We used adaptive design to test four FDA approved drugs (azithromycin, erythropoietin, caffeine, melatonin) concurrently and determine which best combined safety and efficacy. MethodsSeven-day-old (P7) rats underwent hypoxia-ischemia (HI; right carotid ligation + timed 8% O2 exposure); some experiments included pre-treatment with agents that induced inflammation, and some included post-HI brief moderate hypothermia. Sensorimotor and neuropathology measures were incorporated into a Composite Score that also accounted for deaths. Outcome was initially evaluated at P21 and in confirmatory studies at P35. A pre-specified Bayesian algorithm with futility and efficacy stopping rules was devised to analyze emerging data and adjust subsequent animal allocation among drug groups. ResultsIn all models either azithromycin or erythropoietin (EPO) offered superior neuroprotection at P21 and the other was "runner-up". Caffeine and melatonin conferred modest neuroprotection in pure HI but were quickly eliminated in hypothermia-treated HI. At P35 azithromycin and EPO outcomes were generally similar. ConclusionThese results support azithromycin or erythropoietin as candidate neuroprotective agents and warrant future studies in large animal neonatal cerebral hypoxia-ischemia models. ImpactO_LIOur preclinical comparative efficacy strategy using adaptive design tested four clinically available drugs (azithromycin, caffeine, erythropoietin and melatonin) in multiple preclinical rodent brain injury models and consistently identified differences in efficacy among drugs. C_LIO_LIThree key factors differentiating our approach from existing reports were direct within-litter comparisons, evaluation in multiple injury models and inclusion of both function and neuropathology outcomes. C_LIO_LIEither azithromycin or erythropoietin, even with a 2-hour initiation delay, was the most neuroprotective drug in all models, with the other a close "runner-up". C_LIO_LILess effective drugs were recognized and eliminated early by the prespecified Bayesian algorithm. C_LIO_LIThese results support azithromycin or erythropoietin as candidate neuroprotective agents and support future studies in large animal neonatal cerebral hypoxia-ischemia models. C_LI

neuroscience↗

bioRxiv2025

Dual EZH1/2 inhibition enhances DNMT inhibitor efficacy in colon cancer through targeting H3K27me1

Abnormal DNA methylation patterning is a defining epigenetic hallmark of human cancer and is therapeutically targetable with DNA methyltransferase inhibitors (DNMTis). However, DNMTi-induced DNA hypomethylation promotes adaptive chromatin remodeling that limits molecular and therapeutic responses to these drugs. Here, we identify EZH1-dependent H3K27 mono-methylation (H3K27me1) as a previously unrecognized adaptive barrier to DNMTi response in colorectal cancer. While EZH2-selective inhibitors deplete H3K27me2 and H3K27me3, they preserve EZH1-dependent H3K27me1 at Polycomb-enriched genomic regions. In contrast, dual EZH1/2 inhibition eliminates all H3K27 methylation states and robustly synergizes with DNMTi to enhance transcriptional activation and growth suppression. Mechanistically, dual EZH1/2 inhibition induces a redistribution of p300/CBP-dependent H3K27 acetylation (H3K27ac), generating a therapy-associated bivalent chromatin state characterized by coexisting DNA methylation and H3K27ac. DNMT inhibition resolves this induced bivalency, enabling activation of tumor-suppressive transcriptional programs. At the same time, coordinated loss of H3K27me1 and gene-body DNA methylation, together with depletion of promoter-associated H3K27ac, suppresses MYC- and E2F-driven oncogenic transcription networks that define the cancer cell-intrinsic therapeutic response. Collectively, these findings establish EZH1-dependent H3K27me1 as a key mediator of adaptive epigenetic plasticity and provide mechanistic rationale for combining DNMT inhibitors with dual EZH1/2i inhibitors to reprogram chromatin and suppress oncogenic transcription in solid tumors. HighlightsO_LIEZH1-dependent H3K27me1 sustains an adaptive barrier to DNMT inhibitor response in colorectal cancer. C_LIO_LIDual EZH1/2 inhibition eliminates all H3K27 methylation states and remodels chromatin architecture. C_LIO_LIEZH inhibition induces a DNA methylation-H3K27ac bivalent chromatin state. C_LIO_LIDNMT and EZH1/2 co-inhibition reprograms enhancers and promoters to activate tumor-suppressive pathways. C_LIO_LICombination therapy suppresses MYC/E2F-driven oncogenic transcription, defining its cancer cell-intrinsic therapeutic efficacy. C_LI

cancer biology↗

bioRxiv2025

PIEZO channels link mechanical forces to uterine contractions in parturition

AbstractMechanical forces are extensively involved in pregnancy and parturition, but their precise roles and mechanisms remain poorly understood. Here, we identify mechanically activated ion channels PIEZO1 and PIEZO2 as key mechanotransducers required for labor progression. Genetic deletion of Piezo1 and Piezo2 in mice resulted in weakened uterine contractions and severe parturition defects. Tissue-specific knockouts revealed that deletion in either the uterus or sensory neurons alone caused modest defects, whereas combined loss significantly impaired labor, demonstrating additive effects. Single-nuclei sequencing showed that loss of PIEZO reduced expression of connexin43 (Gja1), a gap junction protein in uterine smooth muscle cells, suggesting a mechanistic link to impaired contraction. These findings highlight the critical role of PIEZO channels in mechanotransduction during parturition and suggest therapeutic targets for labor dysfunction.

physiology↗

bioRxiv2025

Telomere-to-telomere gap-free genome assembly of a male donkey and the identification of novel SVs associated with functional genes

Previous assemblies of the donkey genome remain with gaps and structural errors, and a complete donkey genome will greatly facilitate genetic research related to donkeys. In the present study, a 2.78-Gb telomere-to-telomere gap-free donkey genome (CAU_T2T_donkey) was assembled, including a 29.78-Mb Y chromosome, aided by ONT and trio-binning approach. CAU_T2T_donkey corrected the structural errors of previous assemblies and added a total of 153.8-Mb previously unresolved regions and 354 genes to the reference genome EquAss-T2T_v2. We identified a 1.9-Mb PAR on CAU_T2T_donkey-chromosome Y, and added 17.1Mb regions and 75 new genes to the chromosome Y of the previous reference genome ASM1607732v2. Multi-copy genes, such as TSPY, L1RE, ETY, HSFY, and ETSTY were also identified in CAU_T2T_donkey-chromosome Y. Totally 6 types of repetitive sequences in centromeric regions were identified, and the features of the centromeric regions were revealed, and satellite-free centromeres were identified. We aligned HiFi long-read sequences of donkeys from six breeds against CAU_T2T_donkey and identified SVs in previously unresolved regions, and some of the novel SVs were located in functional genes, such as AOX1 (Chr4:DEL61), ASIC2 (Chr13:INS954), and Twist2 (Chr19:DEL98).

genomics↗

bioRxiv2025

A ratio-based framework using Quartet reference materials for integrating long- and short-read RNA-seq

Long-read RNA sequencing (lrRNA-seq) enables full-length transcript profiling but is confounded by technical batch effects that compromise quantification and prevent data integration across platforms, protocols, and laboratories. The lack of a transcriptome-wide biological ground truth has hindered objective benchmarking. To address these dual challenges, we leveraged certified Quartet reference materials to generate one of the largest multi-center lrRNA-seq resources to date: over one billion long reads from 144 libraries across four PacBio and Nanopore protocols in four independent laboratories. We first establish that ratio-based quantification against built-in reference samples effectively removes technical noise, revealing underlying biological signals. We then constructed the first ratio-based reference datasets for full-length transcripts-- comprising 10,218 isoforms and 6,032 alternative splicing (AS) events--and orthogonally validated them with RT-qPCR. Finally, a comprehensive benchmark using these ground truths reveals that a hybrid strategy integrating long- and short-read data (hybrid-seq) achieves the highest quantification accuracy for both isoforms and AS events. Our work provides a foundational framework and resource for evaluating lrRNA-seq technologies and accelerating the standardization of full-length transcriptomics for research and clinical applications.

genomics↗

bioRxiv2025

Single-nucleus transcriptomics reveal disrupted pathways in the prefrontal cortex of Scn2a-deficient mice

Truncating variants in SCN2A, which encodes the NaV1.2 sodium channel critical for action potential initiation and propagation, are associated with autism spectrum disorder (ASD) and epilepsy. To investigate SCN2A deficiency-related phenotypes, we developed a preclinical mouse model with under 50% NaV1.2 expression, exhibiting neuronal hyperexcitability and social deficits. However, the neuronal populations and molecular alterations underlying these phenotypes at single-cell resolution have not been investigated. In this study, we conducted single-nucleus RNA sequencing (snRNA-seq) of wild-type (WT), homozygous Scn2a-deficient (HOM) mice, and HOM mice with Scn2a restoration (HOM-FlpO) to examine the effects of Scn2a level on gene expression in the medial prefrontal cortex (mPFC), a critical brain region related to ASD development. Differential expression analysis in GABAergic and glutamatergic neurons between genotypes revealed gene expression enriched in neurotransmitter activity regulation and synapse organization. Lastly, snRNA-seq results in HOM-FlpO identified genes that were rescued after Scn2a restoration. These results reveal that reduced Scn2a expression disrupts RNA transcriptomes in multiple neuronal subtypes, providing insight into cell type-specific mechanisms underlying SCN2A-related disorders.

neuroscience↗

bioRxiv2025

RhoV Promotes Proliferation, Migration, and MAPK Activation in Pancreatic Ductal Adenocarcinoma

Background and AimsPancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy characterized by diagnosis at advanced stages, limited therapeutic options, and frequent resistance to therapies. Although oncogenic KRAS mutations are central drivers of PDAC, alternative pathways indisputably contribute to its tumorigenesis and progression. RhoV, a member of the Rho family of small GTPases, has been implicated in tumor development in other cancer types, such as breast cancer and lung adenocarcinoma; however, its role in PDAC remains unclear. MethodsIn this study, we investigated the expression and functional impact of RhoV on PDAC. Analysis of publicly available datasets and immunohistochemical profiling of 114 PDAC patient specimens were used to evaluate the expression of RhoV in PDAC and its prognostic impact. Overexpression and CRISPR-Cas9-mediated knockout of RhoV were established in three pancreatic cancer cell lines. Functional analyses, such as cell proliferation, migration, invasion, colony formation, spheroid growth, and mouse xenograft, were used to evaluate the role of RhoV in PDAC cells. ResultsRhoV overexpression was associated with reduced overall and recurrence-free survival in public datasets and our own patient cohort. Functional assays demonstrated that RhoV overexpression promoted PDAC cell proliferation, colony formation, and spheroid growth, whereas knockout of RhoV suppressed these changes. Moreover, RhoV enhanced PDAC cell migration and invasion in vitro, accompanied by downregulation of E-cadherin and upregulation of N-cadherin and vimentin, indicating induction of epithelial-mesenchymal transition. Mechanistically, RhoV overexpression activated key MAPK pathway components, including phosphorylation of ERK, JNK, and p38. In vivo, xenograft models confirmed that RhoV drives tumor growth and increases tumor burden. ConclusionThese results establish RhoV as a novel oncogenic factor in PDAC progression and highlight its potential as a biomarker and therapeutic target, warranting further investigation into combinatorial targeting strategies to overcome KRAS inhibitor resistance.

cancer biology↗

bioRxiv2025

Allosteric Disordering of eIF2B Regulates the Integrated Stress Response

The ternary complex (TC), composed of translation initiation factor eIF2, GTP, and initiator methionyl tRNA, delivers the first amino acid to the ribosome to initiate protein synthesis. The activity of the decameric eukaryotic initiation factor 2B complex (eIF2B) initiates TC assembly by catalyzing GDP to GTP exchange on eIF2, thereby setting the TC levels in the cell. Stress-induced phosphorylation converts eIF2 from the substrate of the GDP/GTP exchange reaction into an inhibitor (eIF2-P) of eIF2B. This conversion reduces the cells TC levels and induces the widespread reprogramming of translation known as the Integrated Stress Response (ISR). Here, we chart an allosteric axis running through eIF2B, revealing the importance of a protrusive -helix in its {beta}-subunit, the latch-helix, that locks onto the -subunit to induce eIF2B activity. eIF2-P binding unhooks the latch-helix, opening eIF2B, which inhibits its GDP/GTP exchange activity. Distinct viral proteins have convergently evolved to bind to eIF2B and stabilize the latch-helix-bound active state. Using these insights, we generated ISR-ACTivating compounds, ISRACTs, that stabilize eIF2B in its inhibited, unlatched state. Our study thus highlights how state-transitions in eIF2B are regulated via long-range allostery.

biochemistry↗

bioRxiv2025

Epigenomic Heterogeneity of Non-Functional Pancreatic Neuroendocrine Tumors Uncovered by Single nucleus and Spatial ATAC Profiling

Non-functional pancreatic neuroendocrine tumors (NF-PanNETs) account for the majority of neuroendocrine neoplasms arising in the pancreas and exhibit substantial clinical and biological heterogeneity, yet their epigenetic regulation and spatial architecture remain poorly understood. Here, we present an integrative study of NF-PanNETs across multiple tumor grades using single-nucleus ATAC-seq (snATAC-seq) and spatial ATAC-seq. snATAC-seq delineates the chromatin accessibility landscapes of distinct tumor subtypes, immune cells, and cancer-associated fibroblasts (CAFs), revealing key transcription factor (TF) programs that drive tumor progression and shape microenvironmental interactions. Spatial ATAC-seq further identifies two distinct tumor-stroma ecological niches: a proliferative niche marked by MYC and FOX family, and an invasive niche enriched for Snail family TFs and KRAS pathway activity. These findings demonstrate that cellular behavior in NF-PanNETs is governed not only by intrinsic epigenetic states but also by spatial context. Together, our study provides a spatially resolved epigenomic framework for dissecting NF-PanNET heterogeneity and evolution, offering new biomarkers and regulatory axes for molecular stratification and precision therapy.

cancer biology↗

bioRxiv2025

Mistimed surveys lead to underestimated migratory bird impacts from wind farms

Accurately estimating the likelihood of occurrence of threatened species is essential for effective impact assessments at development sites. Current survey guidelines often rely on coarse, static species distribution maps, risking misalignment for migratory birds present only seasonally. We evaluated 70 wind farms in eastern Australia to assess the alignment between survey timing and seasonal occurrence of four migratory species. Using eBird-based relative abundance models we classified recommended and actual survey periods as optimal, suboptimal, or poorly timed. Half of all surveys were not optimal, and one fifth missed the species potential temporal window of presence altogether. Field detections mostly occurred within modelled optimal or suboptimal windows, validating our approach. Likelihood of occurrence was significantly lower in poorly or suboptimally timed surveys, indicating current guidance for surveying migratory birds at Australian windfarms contains critical shortcomings. Evidence-based alignment with seasonal presence is needed to improve biodiversity assessment guidelines for wind energy development.

ecology↗

bioRxiv2025

A morphometric approach to the taxonomic dilemma of Zonozoe drabowiensis Barrande, 1872 and Zonoscutum solum Chlup&aacute&ccaron, 1999 (Upper Ordovician, Czech Republic)

Zonozoe drabowiensis Barrande, 1872 and Zonoscutum solum Chlupa[c], 1999 are rare and incompletely preserved arthropods from the Upper Ordovician of the Czech Republic. Their classification has been a subject of debate for over a century due to the limited number of specimens and the absence of clear diagnostic features. They were previously thought to belong to Aglaspidida, an extinct group of arthropods from the Cambrian and Ordovician, within Vicissicaudata, a branch of the larger arthropod clade Artiopoda that also includes trilobites. Herein, we used analyses of cephalic outline to quantify whether Zonozoe and Zonoscutum are morphologically more similar to vicissicaudates than other early Palaeozoic arthropods. We assembled a dataset of twenty-six cephalic outlines representing twenty-six early Palaeozoic species, including Zonozoe, Zonoscutum, five euchelicerates, six aglaspidids, three cheloniellids, and a selection of other artiopodans. We quantified their shape using elliptical Fourier analysis. Principal component analysis (PCA) and linear discriminant analysis (LDA) place Zonozoe and Zonoscutum within and close to the vicissicaudatan morphospace, clearly distinguishing them from euchelicerates and non-vicissicaudatan artiopodans. These data support the most conservative classification of Zonozoe and Zonoscutum within Artiopoda, while strengthening the case for a more specific affinity with Vicissicaudata, helping to resolve a 150-year-old taxonomic uncertainty. More broadly, this study demonstrates the value of outline-based morphometrics in testing systematic hypotheses when discrete characters are unavailable or scarce, offering a reproducible tool for re-evaluating other problematic fossils.

paleontology↗

bioRxiv2025

Decoder-FFPE-seq enables sensitive, genome-wide spatial transcriptomics of archival tissues at single-cell resolution

Formalin-fixed paraffin-embedded (FFPE) tissue-compatible spatial transcriptomics (ST) is transforming biology and histopathology, but achieving high sensitivity, genome-wide coverage, single-cell resolution and researcher-accessibility remains challenging. Here, we present a dendrimeric DNA coordinate-barcoding design for FFPE-adapted spatial RNA sequencing (Decoder-FFPE-seq), by integrating RNA-to-DNA probe conversion with blotting-assisted barcoding. Decoder-FFPE-seq provides single-cell resolution with a 2.54-4.25-fold sensitivity increase in mouse brain transcriptomic profiling over similar assays with an available protocol, successfully mapping rare genes and sparse cell types. It robustly resolves tumor microenvironments (TMEs) in clinical archives preserved 6-20 years. With expanded probe libraries, Decoder-FFPE-seq captures long non-coding and viral RNAs, revealing spatial co-expression networks with mRNAs in oral squamous cell carcinomas (OSCCs). In an OSCC immunotherapy cohort, it delineates TME heterogeneity across pathology response groups and tracks spatial cellular dynamics pre- and post-immuno-chemotherapy. Decoder-FFPE-seq establishes a robust, high-resolution framework for sensitive ST profiling in fundamental and translational studies of archival tissues.

genomics↗