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PubMed2025

HallmarkGraph: a cancer hallmark informed graph neural network for classifying hierarchical tumor subtypes.

MOTIVATION: Accurate tumor subtype diagnosis is crucial for precision oncology, yet current methodologies face significant challenges. These include balancing model accuracy with interpretability and the high costs of generating multi-omics data in clinical settings. Moreover, there is a lack of validated models capable of classifying hierarchical tumor subtypes across a comprehensive pan-cancer cohort. RESULTS: We present a graph neural network, HallmarkGraph, the first biologically informed model developed to classify hierarchical tumor subtypes in human cancer. Inspired by cancer hallmarks, the model's architecture integrates transcriptome profiles and gene regulatory interactions to perform multi-label classification. We evaluate the model on a comprehensive pan-cancer cohort comprising 11 476 samples from 26 primary cancers with 405 subtypes up to eight levels. The model demonstrates exceptional performance, achieving 5-fold cross-validation accuracy between 85% and 99% for tumor subtypes labeled with increasing details of genomic information. It also shows good generalizability on a validation dataset of 887 samples, assessed using three metrics that consider tumor subtypes at individual, combined, and sample levels. Benchmarking and ablation experiments show that hallmark-based embeddings slightly influence model performance, while the integrated multilayer perceptron plays a significant role in determining classifier accuracy. Additionally, we use the SHAP method to link cancer hallmarks with genes, identifying key features that influence model decisions. Our findings present a biologically informed machine learning framework capable of tracking tumor transcriptomic trajectories and distinguishing inter- and intra-tumor heterogeneity in pan-cancer. This approach holds promise for enhancing cancer diagnostics. AVAILABILITY AND IMPLEMENTATION: HallmarkGraph is accessible at https://github.com/laixn/HallmarkGraph.

Humans↗

PubMed2026

scSurv: a deep generative model for single-cell survival analysis.

MOTIVATION: Single-cell omics analysis has unveiled the heterogeneity of various cell types within tumors. However, no methodology currently reveals how this heterogeneity influences cancer patient survival at single-cell resolution. Here, we introduce scSurv, combining a Cox proportional hazards model with a deep generative model of single-cell transcriptome, to estimate individual cellular contributions to clinical outcomes. RESULTS: The accuracy of scSurv was validated using both simulated and real datasets. This method identifies cells associated with favorable or adverse prognoses and extracts genes correlated with their contribution levels. In melanoma, scSurv reproduces known prognostic macrophage classifications and facilitates hazard mapping through spatial transcriptomics in renal cell carcinoma. We also identified genes consistently associated with prognosis across multiple cancers and demonstrated the applicability of this method to infectious diseases. scSurv is a novel framework for quantifying the heterogeneity of individual cellular effects on clinical outcomes. AVAILABILITY: The implementation of scSurv is available on GitHub (https://github.com/3254c/scSurv) and Zenodo (https://doi.org/10.5281/zenodo.17793054).

Humans↗

PubMed2026

Amaranth: enhanced single-cell transcript assembly via discriminative modelling of UMI reads and internal reads.

MOTIVATION: Single-cell RNA sequencing (scRNA-seq) has transformed transcriptome profiling at cellular resolution, yet accurate reconstruction of full-length transcripts for individual cells remains a central challenge. Emerging scRNA-seq protocols can produce reads that span entire transcripts, enabling isoform-level expression analysis. For example, Smart-seq protocols combine unique molecular identifier (UMI)-linked reads that index and stitch together multiple reads from the same molecule, with internal reads filling coverage gaps. We demonstrate that these read types exhibit markedly different biological and statistical properties in strandness, 5'/3' coverage bias, and genomic locality. Existing assemblers fail to leverage these distinctions, yielding suboptimal assembly. RESULTS: We developed Amaranth, a novel single-cell assembler that discriminatively models UMI and internal reads. Amaranth implements heuristics specifically designed to address the distinct biases of UMI-linked and internal reads, enabling accurate strandness assignment for internal reads, reliable splicing graph refinement, and precise transcript start site determination. We also developed Amaranth-meta, which integrates information across cells to enhance individual cell assemblies. Benchmarked on Smart-seq3 datasets from human HEK293T and mouse fibroblast cells, Amaranth outperformed other state-of-the-art assemblers in assembling individual cells and in meta-assembly. Amaranth advances isoform-level analysis in single-cell transcriptomics, facilitating detailed studies at cellular resolution. AVAILABILITY AND IMPLEMENTATION: Amaranth is implemented in C++ and is freely available at https://github.com/Shao-Group/amaranth under the BSD-3-Clause license. Scripts, documentation, and data for reproducing experiments in this manuscript are available at https://github.com/Shao-Group/amaranth-test.

Single-Cell Gene Expression Analysis↗

PubMed2026

Pseudomonas aeruginosa adaptation and persistence in the aspergilloma microbiome revealed by integrated multi-omics.

Chronic pulmonary aspergillosis involves the formation of a fungal ball (aspergilloma) in lung cavities. Pseudomonas aeruginosa commonly co-colonizes these lesions; however, the in vivo mechanisms underlying its persistence are unknown. Using a multi-omics approach on resected aspergillomas, we defined the genomic, transcriptional, and metabolic adaptations of P. aeruginosa within this polymicrobial niche. We reconstructed high-quality P. aeruginosa genomes and identified a conserved core genome, along with accessory genes for secondary metabolism, virulence, and antimicrobial resistance. Phylogenomics revealed heterogeneous evolutionary paths among co-colonizing strains. Metatranscriptomics showed stark physiological heterogeneity, from metabolically aggressive to stress-adapted states. High expression of phenazine, quorum-sensing (PQS), siderophore, and secretion-system operons was corroborated by metabolomic detection of phenazine-1-carboxylic acid and 2-heptylquinolin-4(1H)-one, confirming active bacterial antagonism in vivo. Concurrent Aspergillus fumigatus transcriptomics revealed the activation of oxidative stress responses, secondary metabolism (eg fumagillin), and iron scavenging, demonstrating reciprocal competition. Host transcriptomics revealed patient-specific immune signatures that correlated with the metabolic activity of the co-colonizers. This work provides an integrated systems-level analysis of the tri-kingdom aspergilloma ecosystem. P. aeruginosa persistence is driven by genomic plasticity and context-dependent expression of competitive pathways, shaped within a chronic inflammatory environment. These findings redefine aspergillomas as active polymicrobial consortia, establishing a framework for targeting resilient microbial communities in chronic lung disease.

Multiomics↗

PubMed2026

Endozoicomonas acroporae enhances coral thermal resilience through host-microbe coordination.

Probiotics hold promise for enhancing coral resilience under climate-driven thermal stress, yet their mechanisms remain poorly understood. Although the bacterial genus Endozoicomonas has been proposed to benefit corals, in vivo evidence of beneficial effects on the host remains limited. Here, we establish Endozoicomonas acroporae Acr-14T as a coral probiotic and characterize its effects on the reef-building coral Stylophora pistillata. We show that E. acroporae Acr-14T enhances host thermal tolerance, colonizes coral tissues, and forms coral-associated microbial aggregates. Microbial profiling indicates that probiotic treatment is associated with reduced relative abundances of opportunistic microbes and enrichment of putatively beneficial taxa. To support transcriptomic analyses, we assembled a chromosome-level genome of S. pistillata clade 1 (Pacific lineage) and found that E. acroporae Acr-14T treatment mitigates heat-induced protein-folding stress and apoptotic signaling. Single-cell transcriptomics further revealed altered expression of genes involved in S-adenosylmethionine (SAMe) metabolism and pro-survival signaling in gastrodermal cells of probiotic-treated corals. Together, our results provide a cell-type-resolved view of host responses linked to Endozoicomonas-mediated coral thermal resilience and offer insight into molecular mechanisms implicated in host-microbe interactions under environmental stress.

Animals↗

PubMed2026

Stage-specific remodeling of wingless-related integration sites (WNT) signaling during oocyte-to-embryo transition in pigs.

The WNT signaling pathway is a central regulator of cell polarity, adhesion, cytoskeletal dynamics, and lineage specification during early embryonic development. Although its roles have been extensively studied in murine and human models, the temporal regulation and pathway architecture of WNT signaling during early porcine development remain poorly defined. Here, we performed a comprehensive transcriptomic analysis to characterize WNT pathway dynamics across key stages of pig in vitro development, including immature oocytes (IMO), mature oocytes (MO), zygotes (ZY), cleaved embryos (2-4 cells; CL), and blastocysts (BL). Global analyses revealed major transcriptomic transitions (FDR <0.05; |Fold Change| ≥2) during oocyte maturation and blastocyst formation, whereas zygotes and cleaved embryos exhibited highly similar expression profiles. Module-based and gene-level analyses showed that oocyte maturation is associated with increased expression of extracellular WNT antagonists and components of the β-catenin destruction complex, together with selective regulation of Frizzled receptors, consistent with tight control of canonical WNT signaling at the MII stage. Following fertilization, this inhibitory configuration was partially relieved, alongside transient upregulation of specific WNT ligands, transcriptional mediators, and adhesion-related components during zygotic genome activation and early cleavage. At the blastocyst stage, WNT signaling became increasingly associated with planar cell polarity and epithelial organization modules. Together, the data reveal a highly dynamic and stage-specific restructuring of WNT signaling during early porcine development. Our findings indicate that precise temporal modulation-rather than uniform activation-of WNT pathway components accompanies the porcine oocyte-to-embryo transition, providing a molecular framework to better understand early developmental regulation and offering insights relevant to reproductive biotechnology and developmental biology.

Wnt Signaling Pathway↗

PubMed2025

Host-Associated Genetic Differentiation in the Face of Ongoing Gene Flow: Ecological Speciation in a Pathogenic Parasite of Freshwater Fish.

Adaptive evolution in response to varying environments, leading to population divergence, is among the most intriguing processes of speciation. However, the extent to which these adaptive processes effectively drive population divergence amidst ongoing gene flow remains controversial. Our study addresses this by analyzing population genetic structure, gene flow, and genomic divergence between lineages of a tapeworm parasite (Ligula intestinalis) isolated from sympatric fish hosts. This parasite, which must overcome host immunological defenses for successful infection, significantly impacts host health. Utilizing genome-wide Single Nucleotide Polymorphisms (SNPs) and transcriptome data, we investigated whether host species impose distinct selection pressures on parasite populations. Genetic clustering analyses revealed clear divergence, with parasites from bream (Abramis brama) forming a distinct genetic cluster separate from those infecting roach (Rutilus rutilus), rudd (Scardinius erythrophthalmus), and bleak (Alburnus alburnus). Demographic modeling indicated isolation with continuous gene flow as the most plausible scenario for this divergence. Selection analyses identified 896 SNPs under selection, displaying low to moderate nucleotide diversity and genetic divergence compared with neutral loci. Transcriptome profiling supported these findings, revealing distinct gene expression profiles between parasite populations. Examination of selected SNPs and differentially expressed genes identified candidate genes linked to immune evasion mechanisms, potentially driving ecological speciation. This research highlights the interplay of host specificity, population demography, and disruptive selection in ecological speciation. By dissecting genomic factors, our study improves the understanding of mechanisms facilitating population divergence despite ongoing gene flow.

Animals↗

PubMed2025

Rapid Divergence of Visual Systems and Signaling Traits to Contrasting Light Regimes During Early Speciation of African Crater Lake Cichlid Fish.

Sensory adaptation is widely hypothesized to drive ecological speciation, yet empirical evidence from natural populations undergoing early stage divergence remains limited. In Lake Masoko, a young crater lake in East Africa, the haplochromine cichlid Astatotilapia calliptera is undergoing early stage sympatric speciation into shallow-water littoral and deep-water benthic ecotypes that experience contrasting light environments. Here, we integrate retinal transcriptomics, phenotypic analyses, and visual modeling to uncover rapid sensory divergence associated with this ecological transition. We find striking shifts in cone opsin expression, with the benthic ecotype exhibiting a switch from short-wavelength sensitive SWS2B to SWS2A and an overall narrowing of cone sensitivity toward the center of the light spectrum, consistent with changes in deep-water light environment. In contrast, coding sequence variation in opsin genes was limited and no significant differences in allele frequencies were detected across nine polymorphic sites, pointing to expression regulation as the primary axis of early divergence in visual systems. In parallel, we observed divergence in male signaling traits, with benthic males displaying deeper red egg-spots, aligning with predictions from visual modeling of signal efficiency in different light environments. These results demonstrate rapid transcriptomic and phenotypic divergence in associated signaling traits-within ∼1,000 years-supporting a potential role for regulatory evolution in sensory adaptation during early ecological speciation.

Animals↗

PubMed2026

Deep FLASH-seq profiling of purified canine sensory neurons uncovers species-specific signatures relevant to pain and itch.

Naturally occurring pain and itch disorders in the domestic dog represent an important and underexploited opportunity for translational sensory neuroscience. These conditions largely mirror human disease, highlighting the need for detailed comparative understanding of canine somatosensory neurobiology. Here, we present a single-cell transcriptomic characterisation of the canine dorsal root ganglion (DRG), providing molecular insights into sensory neuron diversity in a species of direct veterinary and biomedical relevance. We develop a novel mechanical dissociation and fluorescence-activated cell sorting strategy enabling purification of intact whole neurons from adult canine DRG, followed by deep, full-length RNA sequencing using FLASH-seq. This approach yields high-quality transcriptional profiles with molecular depth analogous to deep neuronal profiling in human DRG, enabling resolution of neuronal identities and subtype-specific gene programs. Using these data, we identify canine sensory neuron clusters conforming to conserved principles of DRG molecular organization observed across species, including peptidergic and noncanonical peptidergic nociceptors, low-threshold mechanoreceptors, proprioceptors, and thermosensory populations. Cross-species comparisons with human and mouse DRG datasets reveal broad conservation of pain- and itch-relevant pathways and therapeutic targets, alongside biologically meaningful divergence. We further identify species-specific differences in subtype-restricted expression of the pharmacologically relevant receptors IL31RA and SSTR2 , which we validate using in situ hybridization and contextualize with human spatial transcriptomic data. Finally, we provide evidence that domestication-associated genes are nonrandomly enriched in specific sensory neurons, suggesting that evolutionary history may have shaped somatosensory function. These data represent a resource for comparative sensory neuroscience and inform translational interpretation of pain and itch therapeutics across species.

Animals↗

PubMed2016

Early leukocyte gene expression associated with age, burn size, and inhalation injury in severely burned adults.

BACKGROUND: In the patient with burn injury, older age, larger percentage of total body surface area (TBS) burned, and inhalation injury are established risk factors for death, which typically results from multisystem organ failure and sepsis, implicating burn-induced immune dysregulation as a contributory mechanism. We sought to identify early transcriptomic changes in circulating leukocytes underlying increased mortality associated with these three risk factors. METHODS: We performed a retrospective analysis of the Glue Grant database. From 2003 to 2010, 324 adults with 20% or greater TBS burned were prospectively enrolled at five US burn centers, and 112 provided blood samples within 1 week after burn. RNA was extracted from pooled leukocytes for hybridization onto Affymetrix HU133 Plus 2.0 GeneChips. A multivariate regression model was constructed to determine risk factors for mortality. Testing for differential gene association associated with age, burn size, and inhalation injury was based on linear models using a fold change threshold of 1.5 and false discovery rate of 0.05. RESULTS: After adjusting for potential confounders, age greater than 60 years (relative risk [RR], 4.53; 95% confidence interval [CI], 2.93-6.99), burn size greater than 40% TBS (RR, 4.24; 95% CI, 2.61-6.91), and inhalation injury (RR, 2.08; 95% CI, 1.35-3.21) were independently associated with mortality. No genes were differentially expressed in association with age greater than 60 years or inhalation injury. Fifty-one probe sets representing 39 unique genes were differentially expressed in leukocytes from patients with burn size greater than 40% TBS; these genes were associated with platelet activation and degranulation/exocytosis, and gene-set enrichment analysis suggested increased cellular proliferation and down-regulation of proinflammatory cytokines. CONCLUSION: Among adults with large burns, older age, increasing burn size, and inhalation injury have a modest effect on the leukocyte transcriptome in the context of the "genomic storm" induced by a 20% or greater than TBS burned. The 39-gene signature we identified may provide novel targets for the development of therapies to reduce morbidity and mortality associated with burns greater than 40% TBS. LEVEL OF EVIDENCE: Epidemiologic study, level III.

Adult↗

PubMed2026

Long-read sequencing reveals widespread novel splicing and neojunction-derived neoantigens in nasopharyngeal carcinoma.

The widespread transcriptomic diversity driven by alternative splicing (AS) contributes to all hallmarks of cancer and represents a critical source of neoantigens for personalized immunotherapy. However, unlike other major malignancies, the full repertoire of AS in nasopharyngeal carcinoma (NPC) remains underexplored. Here, we employ long-read sequencing (LR-seq) to generate a high-resolution, isoform-level transcriptomic atlas from a cohort of 14 NPC tumor samples and four immortalized nasopharyngeal epithelial cell lines. We identify a substantial number of full-length novel transcripts (22,687; ∼44.38%), which reveal diverse splicing patterns and previously unannotated splicing events. By integrating short-read RNA-seq data to quantify isoform expression, we discover a subset of novel transcripts that are differentially expressed between tumor samples and immortalized nasopharyngeal epithelial cell lines. Furthermore, LR-seq enables precise identification of chimeric readthrough fusion transcripts, such as CLDN15-FIS1 and FOXRED2-TXN2 Finally, we develop a computational framework, tumor-specific splicing neoantigen detection (TS-SNAD), to predict neoantigens originating from novel exon-exon junctions (neojunctions) in tumor-specific novel transcripts. Using this framework, we identify neojunction-derived neoantigens and experimentally validate the immunogenicity of selected HLA-B*40:01-restricted neoantigens. These neojunction-derived peptides constitute a new class of noncanonical neoantigens with significant potential for developing personalized cancer vaccines for NPC.

Humans↗

PubMed2026

Integrated Multi-Omics Analysis Reveals the Genetic Basis of Phenotypic Variation in Tibetan Sheep.

Body size is a key economic trait influencing the profitability of farmed animals. This study used genome-wide association studies (GWAS) to identify five single nucleotide polymorphisms (SNPs) significantly associated with body size in the Tibetan sheep population, advancing molecular breeding and providing a basis for genomic selection. These SNPs are located within five candidate genes. SNaPshot validated GWAS results, demonstrating significant correlations between candidate SNPs and body size traits in Tibetan sheep. Concurrently, hematoxylin and eosin staining, alongside muscle fiber analysis, confirmed pronounced morphological differences in muscle tissue between sheep of varying conformation. Therefore, transcriptome and proteomics were performed on the longest dorsi muscle from large and small Tibetan sheep of both sexes. The transcriptome, together with weighted gene co-expression network analysis (WGCNA), identified VEPH1 and PRKG1 as core genes regulating body characteristics in Tibetan sheep through their involvement in the PI3K-Akt signaling pathway and pathways related to fat deposition. The integrative analyses demonstrated significantly different expression of CARNS1 and CRYAB at both transcriptional and protein levels between the muscles of large- and small-sized Tibetan sheep of both sexes, suggesting their importance in body size traits by influencing muscle morphology. This study provides valuable genomic resources that advance sheep genetics research.

GWAS↗

PubMed2026

Mycosis Fungoides-Like Atopic Dermatitis Represents a Th22-Dominant Inflammatory Endotype.

BACKGROUND: Early-stage mycosis fungoides (MF) often presents diagnostic challenges because of its clinical overlap with atopic dermatitis (AD). In clinical practice, we encountered a subset of patients with severe AD who fulfilled the MF diagnostic criteria yet remained clinically indistinguishable from AD and presented refractoriness to advanced therapies. We termed this ambiguous entity "mycosis fungoides-like AD" (mfAD) and sought to determine whether it represents malignant transformation or a distinct inflammatory endotype of AD. METHODS: Skin biopsies were obtained from 7 patients with AD and 11 patients with mfAD. We performed paired single-cell RNA sequencing and single-cell T-cell receptor sequencing analyses. Publicly available MF and AD datasets were integrated for comparative analysis. Spatial transcriptomic profiling was used to contextualize single-cell findings within the tissue architecture. RESULTS: Comparative transcriptomic analysis revealed that T cells in mfAD were aligned with those in AD and lacked genomic instability. High-resolution profiling showed that mfAD was characterized by oligoclonal Th22 expansion rather than a single dominant malignant clone. Notably, all patients with mfAD achieved rapid clinical remission with selective JAK1 inhibition, indicating the therapeutic response characteristics of inflammatory dermatoses. CONCLUSION: Our findings demonstrate that mfAD is not a true malignancy, but rather a Th22-driven inflammatory endotype of AD. These results redefine mfAD as an inflammatory subtype within the AD spectrum, providing a mechanistic explanation for both the "pseudo-monoclonality" that leads to MF misdiagnosis and the failure of dupilumab. This study establishes a rationale for the use of JAK inhibitors in precision medicine for this patient population.

JAK inhibitor↗

PubMed2026

Integrative Multi-Omics Analysis of Stem Growth Habit Divergence in Wild Soybean (Glycine soja).

Stem architecture is a major determinant of lodging resistance, biomass accumulation, and harvest efficiency in soybean. However, the molecular features associated with contrasting stem growth habits in wild soybean remain incompletely characterised. Here, we performed an integrated transcriptomic, metabolomic, and epigenomic analysis of stem growth-habit divergence in wild soybean, comparing the wild-type accession ZYD7068 with contrasting vining and erect mutant lines derived from carbon-ion beam mutagenesis. Pairwise transcriptomic comparisons identified between 20 311 and 28 705 differentially expressed genes per contrast, with a core set of 2672 genes consistently altered across the comparisons. Functional enrichment, gene set variation analysis, and gene set enrichment analysis converged on xylem and phloem pattern formation as a prominent molecular pathway associated with growth-habit divergence. Random forest analysis identified BBR-BPC and ARF transcription factor families as major molecular discriminators, while metabolomic profiling revealed distinct metabolic profiles involving amino-acid-derived and lipid-associated metabolites. Whole-genome bisulfite sequencing revealed context-specific DNA methylation differences, including substantial variation in CHG methylation among erect mutant lines. Integrated network and in silico perturbation analyses prioritised four candidate genes associated with vascular development for future functional validation. Together, these results provide a multi-layer molecular resource for investigating stem growth-habit divergence in G. soja and establish testable candidate pathways and genes for subsequent functional studies and soybean improvement.

glycine soja↗

PubMed2025

The small nucleolar RNA NON-CODING RNA 1 negatively regulates drought tolerance in Arabidopsis thaliana.

Small nucleolar RNAs (snoRNAs) function in ribosome biogenesis, and many ribosome biogenesis-related genes were downregulated by osmotic stress, implying a negative role of snoRNAs in drought tolerance. A snoRNA, namely, the NON-CODING RNA 1 (NCR1) was studied for its roles in drought tolerance in Arabidopsis. In comparison with wild-type (WT) plants, the loss-of-function ncr1 mutant plants showed enhanced drought tolerance, which was restored in the NCR1-complemented plants, whereas the NCR1-overexpressing plants revealed a drought-sensitive phenotype. Physiological analyses revealed that the ncr1 plants had a higher leaf surface temperature, lower water loss rates, and improved cell membrane integrity compared with WT. Comparative leaf transcriptomics and proteomics suggested that wax biosynthesis, anthocyanin metabolism, and leaf senescence processes are regulated by NCR1 under both normal and water-deficit conditions. Under drought, an increase in wax and anthocyanin accumulations and a delay in leaf senescence in ncr1 plants, when compared with WT, supported the transcriptome and proteomics data. Additionally, the ncr1 plants exhibited higher abscisic acid (ABA) sensitivity and longer root hairs than WT. Collectively, our results suggest that NCR1 negatively regulates drought tolerance through modification of wax biosynthesis, anthocyanin accumulation, leaf senescence, cell membrane integrity, ABA responses, and root hair development.

Arabidopsis↗

PubMed2025

Multi-Omics insights into OsZFP252-OsGA20ox5 mediated drought tolerance in rice through stomatal and vascular regulation.

Rice growth is highly dependent on water availability, and drought stress significantly impacts its entire life cycle. However, previous studies lack systematic investigations into drought-responsive candidate genes across the full life cycle of rice. This study integrates transcriptomic and phenotypic data from two rice lines, IR64 (drought-sensitive) and DK151 (drought-tolerant), under varied environmental conditions at distinct growth stages. Using k-means clustering, 13 369 genes were categorized into 17 distinct expression patterns, revealing drought-responsive genes specifically upregulated or downregulated under drought stress. Weighted co-expression network analysis (WGCNA) further identified four gene modules strongly correlated with drought-related phenotypes, co-localizing 2859 drought-responsive genes through both approaches. Proteomics and metabolomics were supplemented at the booting stage, where phenotypic and transcriptomic differences under drought were most pronounced. Integrated omics results demonstrate gibberellin (GA) and abscisic acid (ABA) pathways play a key role during drought tolerance in rice, and 79 high-confidence drought-resistant candidate genes were prioritized from the 2859 drought-responsive genes. Among these, Gibberellin 20-oxidase 5 (OsGA20ox5) was identified as a key negative regulator of drought tolerance. Furthermore, the transcription factor zinc finger protein 252 (OsZFP252) directly binds to the OsGA20ox5 promoter, repressing its expression and enhancing ABA biosynthesis, thereby improving drought tolerance by increasing stomatal closure and expanding vascular bundle water transport capacity. Notably, the drought-tolerant haplotype 2-4 (Hap2-4) of OsGA20ox5 provides valuable insights for drought-resistant breeding.

Oryza↗

PubMed2025

The chromosome-level genome of Stylosanthes guianensis provides insights into genome evolution and environmental adaptation.

Stylosanthes guianensis is a leguminous forage crop of significant economic importance, primarily distributed in tropical and subtropical regions. It exhibits strong adaptability to various stresses, yet the genetic basis underlying this trait remains unclear. In this study, we constructed the first chromosome-scale reference genome of S. guianensis using a combination of Nanopore and Hi-C sequencing technologies. The assembled genome size is 1254 Mb, with 10 pseudochromosomes. Using Nanopore full-length transcriptome data, we generated high-quality transcript-level gene annotations, identifying 36 585 gene models and 110 601 transcripts. The repetitive sequences in S. guianensis account for 79.16% of the genome, with the extensive expansion of Gypsy elements in long terminal repeats contributing to its genome size enlargement. Comparative genomic and transcriptomic analyses revealed that flavonoid metabolism plays a pivotal role in stress adaptation, providing new insights into the genetic basis of stress tolerance. Additionally, we generated whole-genome methylation profiles under cold treatment and control conditions, offering valuable data for future epigenomic research. These findings provide essential molecular resources for understanding stress resilience in S. guianensis and advancing its molecular breeding.

Genome, Plant↗

PubMed2024

Molecular analysis of primary and metastatic sites in patients with renal cell carcinoma.

BACKGROUNDMetastases are the hallmark of lethal cancer, though underlying mechanisms that drive metastatic spread to specific organs remain poorly understood. Renal cell carcinoma (RCC) is known to have distinct sites of metastases, with lung, bone, liver, and lymph nodes being more common than brain, gastrointestinal tract, and endocrine glands. Previous studies have shown varying clinical behavior and prognosis associated with the site of metastatic spread; however, little is known about the molecular underpinnings that contribute to the differential outcomes observed by the site of metastasis.METHODSWe analyzed primary renal tumors and tumors derived from metastatic sites to comprehensively characterize genomic and transcriptomic features of tumor cells as well as to evaluate the tumor microenvironment at both sites.RESULTSWe included a total of 657 tumor samples (340 from the primary site [kidney] and 317 from various sites of metastasis). We show distinct genomic alterations, transcriptomic signatures, and immune and stromal tumor microenvironments across metastatic sites in a large cohort of patients with RCC.CONCLUSIONWe demonstrate significant heterogeneity among primary tumors and metastatic sites and elucidate the complex interplay between tumor cells and the extrinsic tumor microenvironment that is vital for developing effective anticancer therapies.

Humans↗