Small cell lung cancer (SCLC), an aggressive neuroendocrine malignancy, exhibits high intertumoral heterogeneity and limited treatment options. Immune checkpoint inhibitors (ICIs) provide only modest benefits for SCLC, underscoring the need for clinically actionable phenotypes. Consensus clustering of bulk transcriptomic data identified SCLC molecular phenotypes. Bulk and single-cell RNA sequencing (scRNA-seq) revealed their molecular and immune characteristics, as well as tumor microenvironment interactions. Survival benefits of ICIs were assessed in 41 newly collected extensive-stage SCLC (ES-SCLC) patients treated with chemotherapy plus ICIs, integrated with a public dataset. We identified three distinct SCLC phenotypes, termed proliferative, iNotch, and infiltrated phenotypes, as they were characterized by high proliferation, inhibitory Notch signaling, and immune-rich microenvironments, respectively. These phenotypes were reproducible across three bulk independent datasets. Further intercellular communication analysis of scRNA-seq data revealed a subset with high ANXA1 expression in the infiltrated phenotype suppressed CD8+ T cells via M2 macrophage polarization. Survival analyses showed that only ANXA1Low infiltrated patients derived significant survival benefit from chemotherapy plus ICIs. This study identified three distinct SCLC phenotypes with unique therapeutic vulnerabilities. An ANXA1High subset within the immune-rich infiltrated phenotype showed ICI resistance, offering new strategies to enhance ICI efficacy.

Multi-Parametric Super-Resolution Ultrasound for Evaluating Breast Cancer Characteristics: Improved Diagnostic Performance Over Contrast-Enhanced Ultrasound.

Knowledge graph integration of clustered medicinal plants, molecules, diseases, and targets.

Machine learning reveals sex-biased platelet-associated molecular signatures in systemic lupus erythematosus.

Mechanical loading is essential for the assembly and maintenance of the articular cartilage extracellular matrix (ECM), while alterations in ECM composition profoundly affect cartilage mechanics and function. Type IX collagen is a heterotrimeric fibril-associated collagen with interrupted triple helices (FACIT) that is covalently linked to type II collagen. It restricts lateral fibril growth and mediates interactions with other ECM components. Although type IX collagen expression is mechanosensitive and implicated in cartilage mechanotransduction, its precise functional role is not yet fully understood. This study investigated the combined effects of type IX collagen deficiency and moderate mechanical loading on articular and growth plate cartilage. Twelve-week-old female wild-type (WT) and Col9a1-/- mice were randomly assigned to control (CON) or forced running exercise (EXE) groups (N = 10-12 per group). EXE animals underwent treadmill training for six weeks (20% incline, 18 m/min, 40 min/day, five days/week). Type IX collagen deficiency resulted in an abnormal growth plate architecture and a reduction of all matrilins and cartilage oligomeric matrix protein (COMP) in articular cartilage. Moderate forced running exercise induced a significant increase (p < 0.05) in cartilage thickness at the lateral femoral condyle and altered ECM composition in Col9a1-/- mice, without evidence of cartilage degeneration. WT mice showed no comparable structural changes. In conclusion, moderate mechanical loading elicits localized, non-degenerative structural and molecular adaptations in articular cartilage and only modestly modulates the cartilage phenotype associated with type IX collagen deficiency. These findings suggest a limited, yet context-dependent role of type IX collagen in cartilage mechanoadaptation.

Prostate cancer (PCa) is a hormone-dependent tumor and one of the most prevalent cancers in men worldwide. PCa progression is influenced by its interaction with the surrounding tumor microenvironment, highlighting the role of periprostatic adipose tissue (PPAT), which modulates PCa behavior through the secretion of bioactive molecules (e.g., adipokines). However, the influence of this complex cell communication, particularly under altered metabolic conditions, remains to be fully elucidated. We performed multiomic/bioinformatic approaches integrating transcriptomic, proteomic, and metabolomic data from PPATs and their secretome and circulating/urinary of lipocalin-2 (LCN2) levels using a well-characterized cohort [75 PCa-patients vs. 22 control subjects with benign prostate hyperplasia (BPH)]. Different prostate cell models [normal-like (PNT2) and PCa cells (DU145/LNCaP/22Rv1/PC-3)] were used to test the role of the LCN2/SLC22A17 axis in PCa cell via multiple functional (proliferation/apoptosis/migration/invasion/colony-formation/tumorsphere assays), molecular (transcriptomic/phospho-proteomic/targeted inflammatory proteomics), and preclinical (in vivo xenograft) analyses. External validation was performed using TCGA, Grasso, and Taylor cohorts, alongside longitudinal proteomic data from patient-derived xenograft models. A signature of significantly dysregulated adipokines was identified in PPAT of PCa vs. BPH patients. Unsupervised clustering analyses revealed two distinct molecular phenotypes (T1/T2) with unique adipokine fingerprints associated with differential obesity-related comorbidities (BMI/diabetes/dyslipidemia), being LCN2 the only adipokine showing consistent dysregulation at the transcriptomic/proteomic levels. Functional experiments demonstrated that LCN2 and its receptor SLC22A17 exert context- and transformation state-dependent effects [i.e., in vitro LCN2 and SLC22A17 overexpression promoting migration capacity in normal-like cells, while suppressing aggressive phenotypes (proliferation/invasion/stemness) in malignant models; these findings being also confirmed on in vivo xenograft models]. SLC22A17 expression was progressively lost during PCa progression and associated with significantly poorer survival across multiple independent cohorts. Mechanistically, LCN2 modulated critical oncogenic and inflammatory pathways, including NF-κB, TGF-β, JAK/STAT, and inflammasome-related signaling, and showed obesity-specific associations with arachidonic acid and complement components in the PPAT secretome. These results demonstrate a profound dysregulation of the PPAT-derived adipokine profile in PCa associated with obesity-related comorbidities, and reveal a paradoxical, stage- and context-dependent dual role of the LCN2/SLC22A17 axis as a key modulator of PPAT-PCa microenvironment interactions, with potential implications for inflammation, metabolic signaling, and tumor progression.

Here, we present EMQN Best Practice Guidelines for Genetic Testing and Reporting in RYR1-related disorders. They aim is to aid clinical genetic laboratories in testing, and unequivocal and comprehensive reporting of RYR1 variants for the benefit of patients and their relatives. These guidelines are supported by experts in the field of anaesthesia, (paediatric) neurology, clinical genetics and clinical laboratory genetics. The ryanodine receptor type 1 is a large calcium channel that regulates calcium release from the sarcoplasmic reticulum resulting in muscle contraction. This receptor is encoded by the RYR1 gene and expressed predominantly in skeletal muscle. Pathogenic RYR1 variants are associated with several allelic disorders: malignant hyperthermia, a hypermetabolic reaction to certain anaesthetics in otherwise healthy individuals, exertional rhabdomyolysis and both autosomal dominant and recessive congenital myopathies. In general, RYR1 gain-of-function variants are associated with malignant hyperthermia susceptibility, whereas dominant-negative and loss-of-function variants are associated with dominant and recessive myopathies, respectively. However, a small subset of RYR1 variants is associated with a combination of dominant malignant hyperthermia susceptibility with either a dominant or a recessive myopathy or exertional rhabdomyolysis. The apparent discrepancy between molecular mechanisms and different phenotypes is currently poorly understood. As a consequence, the context-dependent interpretation of RYR1 variants is challenging in diagnostic genetic testing. In particular, it is not trivial to assign a possible associated risk for an allelic disorder for an individual or their relatives, which is especially relevant in family planning.

Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects.

BackgroundThe gut microbiota adapts to and shapes the host’s metabolic state through affecting circulating metabolites and consequent gene regulatory networks, resulting in systemic influences in diverse organs via connections such as the gut–liver axis. Numerous variables such as diet, age, and host genetics modulate the composition of the gut microbiome, but their interactions and specific associative and mechanistic links to host molecular phenotypes remain incompletely unannotated. Integrated multi-omics approaches in genetically diverse populations offer an opportunity to dissect these interactions and identify predictive microbial signatures for host phenotypes, such as body weight and molecular associations with gene expression pathways in gut and liver.ResultsWe sequenced, aligned, and integrated the cecal metagenome, metatranscriptome, and host transcriptome from 232 mice across 175 distinct cohorts according to a low-fat chow diet (CD) or a high-fat diet (HF), four adult ages (between roughly 180 to 730 days of age), and 43 distinct genotypes (inbred BXD strains). Genetics and diet exerted the strongest influence on microbiota abundance and activity, followed by age. HF feeding significantly reduced diversity across all ages and all genotypes, altering > 300 species. Machine learning models based on microbial profiles reliably predicted body weight within dietary group (AUC = 0.84 for CD, 0.79 for HF) and chronological age (AUC = 0.84), with model performance of age prediction rising to 0.95 when integrating top microbial features with liver proteomics. Network analyses of expression data revealed links between genes, pathways, and specific microbes, including a negative association between cecal Ido1 expression and short-chain fatty acid (SCFA)-producing Lachnospiraceae, suggesting dietary fat may modulate host tryptophan metabolism through microbiota shifts.ConclusionsWhole metagenome and metatranscriptome sequencing approaches have massively expanded the landscape of microbiome analysis compared to earlier short-read 16S analyses. The resulting datasets quantify hundreds of uniquely identifiable microbes, which can be used to create sets of highly predictive microbial biomarkers for aging and obesity. When trained on controlled mouse populations, these results demonstrate that microbiome profiling can achieve high predictive capacity (AUC = 0.95 with multi-omics integration) for complex readouts such as age and body weight (AUC = 0.84), even considering genetic and dietary variation, establishing a framework for biomarker development. While at present many bacteria are still functionally unannotated at the species level, multi-omics approaches — including gene expression from the host tissues — provide insights into the functional associations of specific taxa in the microbiome.Video Supplementary InformationThe online version contains supplementary material available at 10.1186/s40168-026-02369-x.

T-cell responses influence recurrence and survival in colorectal cancer. T-cell subset distributions vary by molecular phenotype and anatomic location, shaping cytotoxic or immune-cold tumor immune microenvironments. However, the T-cell contexture and their spatial proximities within preinvasive lesions are not well characterized. We analyzed sessile serrated lesions (SSLs), tubulovillous/villous adenomas (TVs), and tubular adenomas (TAs) from three studies (N=120). Whole-slide multiplex immunofluorescence was used to quantify eight T-cell subsets (CD4⁺, CD8⁺, Th1 (CD4+TBX21+), Th17 (CD4+RORC+), Treg (CD4+FOXP3+), Tc1 (CD8+TBX21+), Tc17 (CD8+RORC+), TcTreg (CD8+FOXP3+). Densities were compared by histology using a generalized linear mixed model with a negative binomial distribution, including an offset for total cell area and adjusting for age, sex, anatomic location, and lesion size. Nearest-neighbor (NN) analyses assessed spatial proximities of T-cell pairs across lesion types. TAs and SSLs had higher CD4⁺ and CD8⁺ T-cell densities than TVs (q<0.05). Compared with TVs, TAs also had higher Th17 cell densities, whereas SSLs showed a trend toward lower Treg densities (q=0.06). NN analysis showed greater Treg clustering in TVs than in SSLs and TAs. In contrast, TA versus SSL comparisons demonstrated predominant CD4⁺ clustering with Th17, Th1, and CD8⁺ subsets. TVs exhibited lower T-cell densities and greater regulatory T-cell clustering, consistent with an immune-cold environment. SSLs and TAs were more immune-infiltrated than TVs, but TAs had higher inflammation and CD4⁺ dominant clustering, suggesting stronger helper coordination. Preinvasive lesions demonstrate immune and spatial heterogeneity which may have implications for primary or secondary prevention.

Immune receptor LAG3 regulates microglia function during Alzheimer's disease.

Serological classification of RhD-negative and weak D is often insufficient in admixed populations, where diverse RHD variants have clinical implications. In Brazil's highly admixed population, RhD interpretation and donor-recipient matching are particularly challenging. We used Duffy phenotyping to support ancestry inference and contextualize Rh variants. Understanding RHD alleles and their associations with RhCE and Duffy is essential for transfusion safety. Here, we characterize RHD variants in Brazilian donors and relate them to RhCE and Duffy phenotypes across regions. We analysed 321 blood donor samples with either weak D expression (n = 295) or a D-negative phenotype with C and/or E antigen positivity (n = 26). RhD, RhCE and Duffy phenotyping was performed, followed by RHD, RHCE and FY genotyping using multiplex polymerase chain reaction with sequence-specific primers (PCR, PCR-SSP) and real-time PCR. Samples unresolved by targeted assays underwent sequencing. Among weak D donors, 88% carried known RHD variants, with weak D types 1, 2 and 3 accounting for 67% of cases. Partial D alleles such as DAR, DAU4 and weak partial 11 were identified, particularly among donors with Fy(a-b-) and Fy(a+b-) phenotypes, often associated with RHCE*733G. In the D-negative group, 50% of samples harboured non-functional or hybrid RHD alleles, including RHD*03N.01/RHD*08N.01 and RHD*08N.01/RHD*01N.01, linked to the r's haplotype and RHCE*ceS allele. This study reveals the wide spectrum of RHD variants in an admixed population and underscores the importance of integrating molecular genotyping and phenotype associations to improve transfusion safety and guide Rh immunoprophylaxis.

Exosomes from joints mediate depressive-like behaviors in MIA arthritis mice.

Chloroplast-to-nucleus retrograde signaling and plastid RNA editing are both essential for chloroplast biogenesis and plant development, but the underlying mechanism linking these 2 processes remains unclear. Here, we identify the mitochondrial transcription termination factor mTERF3/Seedling Lethal 1 (SL1), previously characterized as a plastid-encoded RNA polymerase (PEP)-associated protein, as a key regulator connecting RNA editing to retrograde signaling. SL1 directly interacts with GUN1 and MORF2 and is indispensable for 31 out of 34 plastid RNA editing sites in Arabidopsis. Loss of SL1 function results in a strong genome uncoupled (gun) molecular phenotype under norflurazon (NF) treatment, accompanied by defective RNA editing and complete loss of the NDH complex. Mechanistically, SL1 assembles the editosome by recruiting canonical and atypical PPR-DYW proteins (CRR28, RARE1, DYW1, and DYW2) together with multiple non-PPR editing factors, while its strong affinity to MORF2 ensures appropriate editosome stoichiometry. SL1 also colocalizes with the PEP complex, suggesting a physical coupling between transcription and RNA editing in plastid nucleoids. Furthermore, SL1 modulates RNA editing profiles and regulates GLK1/2 expression during NF-induced retrograde signaling. Our findings expand the functional repertoire of mTERF proteins and uncover a molecular mechanism that connects RNA editing with retrograde signaling through SL1.

Inferring tumor molecular phenotypes from high-dimensional multi-omic data is a fundamental challenge in computational biology. Current methods for estimating tumor cell-specific total mRNA expression (TmS) require matched DNA and RNA sequencing data and rely on computationally intensive deconvolution pipelines. We present TmSNet, a deep learning framework that predicts TmS using mRNA, DNA methylation, miRNA, and immune cell proportions as input features. TmSNet integrates structured feature selection (gradient boosting, LASSO, elastic net) with specialized neural architectures to predict continuous TmS. Across 12 TCGA cancer types, TmSNet achieved cross-validated performance up to concordance correlation coefficient (CCC) = 0.93 and correlation R² = 0.88 and generalized to external cohorts with correlations of 0.54 (SCAN-B) and 0.43 (FUSCC). Predicted TmS values effectively stratify patients by risk and preserve known transcriptional profiles across tumor subtypes. These results demonstrate that TmSNet can infer biologically meaningful phenotypes from multi-omic data and provide a scalable framework for modeling tumor transcriptional activity in heterogeneous cohorts.

Cancer cachexia is a wasting syndrome that remodels the anatomy of the patient. How this remodeling unfolds across tissues, whether it defines distinct disease states, and how these states relate to underlying biology remain unknown. We used longitudinal computed tomography imaging from 4,516 patients to quantify evolution of muscle, adipose, and organs during cachexia. Across two independent institutional cohorts, unsupervised analysis identified three reproducible anatomical subtypes of cachexia, including an inflammatory Type A marked by progressive hepatosplenic enlargement and inferior survival, a Type B dominated by visceral organ atrophy, and a mild Type C. These anatomical subtypes were associated with distinct serological signatures and reflected in molecular phenotypes in tumors and non-cancerous liver tissue, establishing cachexia as discrete anatomical disease states that link whole-body remodeling to systemic and tissue-level biology. This anatomy-first framework for cachexia classification provides a foundation for future patient stratification and development of subtype-specific anti-cachexia therapies.

Transcription and mRNA processing are tightly coupled regulatory layers on gene expression, and their perturbations underly human disorders. X-linked Dystonia-Parkinsonism (XDP) is a unique example of a human disease connecting aberrant mRNA processing and the basal transcription machinery. XDP is a rare, monogenic fatal neurodegenerative disorder, and a limited understanding of the underlying molecular mechanisms hinders the development of effective therapies. In this study, we show that depletion of BRD4, a chromatin reader known for its role in transcriptional pausing, rescues the XDP molecular signature. Unexpectedly, this effect is independent of the canonical coactivator role of BRD4. We demonstrate that the XDP-SVA induces intronic premature cleavage and polyadenylation within the TAF1 locus, and that BRD4 depletion bypasses this premature termination checkpoint. These findings reveal new dimensions of BRD4 activity beyond transcription pause release and suggest modulation of mRNA processing as a therapeutic strategy for XDP.

ABSTRACT Viruses often hijack host developmental programs to promote infection, but the mechanistic links between reproductive regulation and antiviral immunity remain incompletely understood. Here, we identify a virus‐triggered hierarchical degradation cascade that links antiviral immunity and fertility regulation in rice. We show that the rice grassy stunt virus (RGSV) effector P3 transcriptionally activates P3IP1, a RING‐type E3 ubiquitin ligase. P3IP1 ubiquitinates and destabilizes the receptor‐like cytoplasmic kinase RLCK22, which functions as a scaffold to stabilize the floral MADS‐box transcription factors MADS1 and MADS15. The loss of RLCK22 results in decreased MADS1/15 protein levels, accompanied by reduced pollen viability and increased susceptibility to viral infection. Genetic and biochemical analyses support the existence of a regulatory module involving P3IP1, RLCK22, and MADS1/15. Mutants of mads1 , mads15 , or rlck22 exhibit overlapping molecular and antiviral phenotypes, including altered pollen viability and impaired transcriptional responses to RGSV. Our findings uncover a virus‐inducible E3–RLCK–MADS axis linking post‐translational regulation of development and defense, providing new insight into how pathogens manipulate plant fitness through targeted protein degradation.

Exposure to cadmium, a trace metallic element, is a major health concern. Cadmium is associated with a higher risk and predisposition to cardiovascular disease. Identifying molecular targets involved in such an effect is complexified by in utero embryonic and fetal development. To overcome those difficulties, we used the established vertebrate heart model of Xenopus laevis to analyze the neural cell adhesion molecules NCAM and FGF receptors involved in early cardiac development under cadmium treatment. Cadmium exposure is performed from fertilization until the completion of mature heart development at the end of stage 45. Additional molecular modifications occurring within the heart are detected in the expressing signaling system of Xenopus oocytes. Exposure to cadmium results in the absence of heart ventricular myocardial trabeculae and disrupts the regulation of NCAM adhesion molecules and FGF receptor signaling in Xenopus. An increase in polysialylation (PSA) of NCAM is observed, accompanied by the deregulation in the expression of Golgi effectors Rab11 GTPase and Golph3. The sialyltransferases ST8Sia2 and ST8Sia4 are not increased at the transcriptional level but are accumulated in the Golgi apparatus. The highly sialylated NCAM interacts with the FGF receptor, prevents the formation of a complex with Integrin, FAK is O-GlcNAcylated, and the receptor translocation to the nucleus is impaired. Furthermore, the polysialylated-NCAM/FGF receptor signaling recruits higher amounts of Shp2 and leads to Erk2 hyperphosphorylation. Additionally, blocking FAK with a specific antibody in the normal polysialylated-NCAM/FGF receptor signaling causes the deregulated molecular phenotype. These results represent a significant advancement for future studies in environmental toxicology and cardiac developmental dysfunctions resulting from cadmium exposure.

Dravet syndrome (DS) is a rare and severe childhood-onset developmental epileptic encephalopathy caused primarily by mutations in the sodium channel gene SCN1A. Animal models have undeniably advanced our understanding of DS, but they still do not fully capture its clinical heterogeneity, highlighting the need for complementary human invitro systems. Here, we generated induced pluripotent stem cells (iPSCs) from urine epithelial cells of three DS patients carrying distinct SCN1A variants and differentiated them into neural stem cells (NSCs) and early-stage neurospheres. Clinical severity was assessed using the DANCE checklist, and molecular phenotypes were characterized through isobaric quantitative proteomics. Comparative analyses identified differences in protein abundance across patient-derived lines, with distinct molecular patterns associated with clinical severity measures. The patient-derived lines exhibited variability in protein groups related to synaptic organization, mitochondrial processes, and RNA processing, reflecting interindividual molecular differences within the cohort. These findings establish patient-derived neurospheres as a scalable human model for investigating molecular variability in DS. This approach provides a framework to explore disease heterogeneity and provides a foundation for future studies linking molecular profiles to clinical variability in DS.