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Spitz tumours: Current insights and challenges in diagnosis and management.

Spitz tumours are a distinct subtype of melanocytic lesions composed of epithelioid and/or spindled cells. They comprise Spitz naevi (SN), atypical Spitz tumours/Spitz melanocytoma (AST), and Spitz melanoma (SM). According to the 5th WHO Classification, SM is defined by the co-occurrence of spitzoid morphology and a Spitz-defining genomic alteration, typically a kinase fusion or HRAS mutation, making it a molecularly distinct entity. Molecularly confirmed SM is exceedingly rare, usually occurs in younger adults, and appears to demonstrate a more favorable clinical course than spitzoid melanoma driven by BRAF or NRAS mutations, although robust comparative data remain limited. Dermoscopy may raise clinical suspicion based on characteristic patterns and remains an important first-line diagnostic tool; however, it cannot reliably distinguish AST from SM. In addition, Spitz tumours may exhibit overlapping histopathological features, further complicating their differentiation. In particular, the distinction between ASTs and SMs is often challenging. Immunohistochemical and molecular analyses, particularly next-generation sequencing (NGS), play a crucial role in resolving diagnostically challenging Spitz tumours and in differentiating true Spitz tumours from their morphological mimics. Furthermore, NGS contributes to improved risk stratification and has revealed high-risk genomic alterations associated with progression. Increased application of molecular techniques is expected to refine prognostic assessment and support individualized management strategies.

Journal Article↗

Large-scale AI analysis reveals missed opportunities in albuminuria testing and disease-modifying therapy implementation.

AIMS: Albuminuria is a key diagnostic and prognostic biomarker of chronic kidney disease (CKD), associated with adverse cardiovascular and renal outcomes. Despite guideline recommendations, urine albumin-to-creatinine ratio (UACR) testing is infrequently performed in cardiology. This study assessed the uptake of UACR testing, the estimated prevalence of undiagnosed albuminuria, and the use of disease-modifying therapies in patients with cardio-kidney-metabolic (CKM) disease. METHODS AND RESULTS: We conducted a retrospective cohort study of all adults seen at the cardiology department of a tertiary referral centre between 2019 and 2024. Data were extracted using CTcue, an AI-driven platform. Albuminuria was defined as UACR &#x2265;30 mg/g. A weighted logistic regression model estimated albuminuria prevalence in untested patients. Among 77 351 patients (44.8% female, mean age 64.4 years), only 8.9% had a recorded UACR, of whom 46.4% had albuminuria. Testing rates were low across high-risk groups: 29.9% in diabetes, 21.7% in heart failure, and 13.7% in hypertension. In untested patients, the predicted prevalence of albuminuria was 36.6%, and highest in those with eGFR <30 mL/min/1.73m2 (70.0%), heart failure (47.8%), or diabetes (46.8%). Use of disease-modifying therapies was low, even among patients with confirmed albuminuria. In patients with documented vs. predicted albuminuria, 43.0% vs. 39.1% received renin-angiotensin system inhibitors, 12.8% vs. 5.7% received SGLT2 inhibitors, and <1% in both groups received finerenone. CONCLUSION: Albuminuria is substantially underdetected in cardiology practice, possibly contributing to underuse of effective CKM therapies. Systematic UACR screening with structured treatment protocols may help close this gap and improve outcomes for patients with CKM disease.

Humans↗

Genetic testing and reporting: What the endocrinologists should know and can expect (Joint position paper of the ENDO-ERN).

Over the last decade, next generation sequencing (NGS) has become an essential tool for diagnostic DNA testing in human genetics. To improve the understanding of available genetic testing strategies and to facilitate the request of genetic testing in daily endocrine practice, clinical and laboratory experts in the field have summarized the major issues which should be known and considered. In this joint position paper of the ENDO-ERN, the roles and responsibilities of the health care professionals involved in the diagnostic workflow are described, and the major issues concerning genetic testing workflows are overviewed. These issues encompass all relevant steps, including test request and pre-analytical procedures, laboratory and data processing workflows, quality assurance, and reporting. As NGS procedures result in an increasing number of variants of unknown significance and incidental findings, these aspects are addressed as well. Accompanied by illustrations of the genetic diagnostic workflow and of concise reports for a fast orientation about the major aspects of genetic testing, this joint paper should support the health care professionals during a request for genetic testing.

VUS↗

Cardiac remodelling and dysfunction in cancer patients receiving cardiotoxic therapies: proteomic and metabolomic profiling.

BACKGROUND AND AIMS: The objective of this study was to define the relationships between the circulating proteome and metabolome with cardiac structure and function in patients with breast cancer receiving cardiotoxic therapies. METHODS: Proteomics and metabolomics profiling was performed in a longitudinal, prospective cohort study of breast cancer patients receiving anthracyclines and/or trastuzumab, using the Olink Explore 3072 platform and rapid liquid chromatography-mass spectrometry, respectively. Multivariable linear mixed-effect models evaluated the contemporaneous (same visit) and lagged (subsequent visit) associations between repeated measures of individual proteins or metabolites with quantitative echocardiographic measures of cardiac structure [left ventricular (LV) mass and left atrial volume index] and function [LV ejection fraction (LVEF), longitudinal and circumferential strain, E/e', and ventricular-arterial coupling]. Cox regression and pathway enrichment analyses were conducted for biomarkers demonstrating significant associations with cardiac function. RESULTS: Across 547 breast cancer participants (median age 50 years), 203 unique proteins and 16 unique metabolites were significantly associated with measures of cardiac structure and function in contemporaneous and lagged analyses. Notably, cathepsin C was associated with LVEF [false discovery rate (FDR), P = .017], longitudinal strain (FDR, P = .046), left atrial volume index (FDR, P = .035), and incident cardiac dysfunction, defined by an LVEF decline &#x2265;10% to <50% (hazard ratio .61, 95% confidence interval .41, .90). The 147 proteins associated with cardiac function were enriched in biological processes reflective of protein deubiquitination, protein modification by small protein removal, macromolecule catabolic processes, and global metabolic pathways. Individual metabolites significantly associated with cardiac function (LVEF, longitudinal strain) included n-acetylglutamine, aspartic acid, acetylasparagine, alanyl-alanine, and prolyl-glycine (FDR, P-value < .001), and belonged to amino acids and derivatives and peptides. CONCLUSIONS: These findings provide translational insights into cancer therapy-related cardiac dysfunction and remodelling and identify potential new biomarkers of cardiotoxicity. There is an important need for validation of these findings and a deeper understanding of the biology of these biomarkers.

Humans↗

Comparison of Performance of Publicly Available Polygenic Risk Scores to Predict Clinically Actionable Coronary Artery Calcium Scores: The BioHEART-CT Cohort.

AIM: Coronary artery disease (CAD) remains the leading cause of morbidity and mortality globally. Polygenic Risk Scores (PRS) have been trained against major adverse cardiovascular outcomes (MACE) in large cohorts. Few studies have examined the effectiveness of these CAD MACE PRS tools in detecting individuals with subclinical coronary calcification. An association would provide an opportunity for clinical translation and targeting of CT imaging to new patients at risk for subclinical disease. METHODS: An analysis of 53 publicly available CAD PRS tools was completed in participants of the BioHEART-CT Discovery 1000 cohort presenting for clinically referred CT coronary angiography (CCTA). Associations between PRS and two binary CACS outcomes reflecting clinically significant coronary calcification were assessed: a) Absolute CACS (CACS &#x2265;100 Agatston units [AU]; and b) Percentile CACS (CACS &#x2265;75th age-/sex-adjusted percentile). Models were adjusted for genetic principal components, modifiable cardiovascular risk factors, and age/sex (in Absolute CACS). A subgroup analysis was performed using Framingham Risk Score (FRS) at baseline. RESULTS: Among 803 BioHEART-CT Discovery 1000 participants, 487 (60.6%) had any detectable coronary calcium. Most PRS tools demonstrated significant association with CACS outcomes, particularly evident when PRS was modelled as a continuous predictor. For Percentile CACS, 94.3% of PRS tools were significantly associated after full adjustment (median OR per PRS SD 1.41 (IQR 1.23-1.60). Quintile-based analysis revealed that individuals in the Top Quintile PRS had up to 7.99-fold increased odds of Percentile CACS &#x2265;75th compared to those in the Bottom Quintile. Analysis by FRS group revealed positive performance, especially in individuals of Low FRS wherein incorporating a PRS increased pre-test probability from 14% to 26%. CONCLUSION: Whilst most CAD PRS tools have been developed against clinical events, we show their ability to predict clinically relevant coronary calcification. Utility appears strongest in individuals traditionally considered lower risk, presenting an opportunity for clinical translation for improved diagnosis in the primary prevention setting, with the potential to triage individuals into a CACS screening pathway.

coronary artery disease↗

Biological Parts in Yeast Synthetic Biology: From Regulatory Elements to Predictive Design Platforms.

Yeasts, particularly Saccharomyces cerevisiae, are important eukaryotic chassis for synthetic biology because of their tractable genetics, versatile toolkits, and broad utility in metabolic engineering and functional genomics. Progress in this field has been driven by biological parts that enable programmable control of gene expression and cellular behavior. Early efforts focused mainly on promoters, terminators, and other regulatory elements for tuning individual genes. However, as engineering expanded to multigene pathways, genetic circuits, and dynamic regulatory systems, the limits of part-centric design became clear. Part performance is often shaped by genomic context, chromatin state, host physiology, and interactions with other components, which restricts modularity and predictability. In response, yeast synthetic biology is shifting toward integrated design frameworks combining multilayer regulation, standardized assembly, automated experimentation, and computational modeling. This review provides an integrated perspective on the evolution of biological parts across DNA-, RNA-, and protein-level regulation, connecting these advances with assembly frameworks, biofoundries, and machine learning to trace the trajectory from part-centric engineering toward predictive, system-level design in yeast synthetic biology.

Biofoundry↗

Draft genome assembly of the green-bronze dung beetle, Onthophagus orpheus.

Dung beetles (Coleoptera: Scarabaeinae) are ecologically important insects, yet genomic resources for this diverse lineage remain limited. Here, we present a high-quality genome assembly for Onthophagus orpheus, an understudied species that is abundant in urban forests in the eastern United States. The assembled genome is a scaffold-level assembly, with a high degree of genic completeness as assessed by Benchmarking Universal Single-Copy Ortholog (BUSCO) analyses, indicating robust representation of conserved protein-coding genes. Structural and functional annotation recovered a comprehensive gene set consistent with expectations for coleopteran genomes. This genome assembly provides an important resource for future work on the behavioral ecology and population genetics of Onthophagus orpheus, specifically, and Scarabaeidae more broadly.

Onthophagus↗

Identification of novel inhibitors of Mycobacterium smegmatis growth through genome-wide overexpression of Cluster P3 mycobacteriophage Xavia genes.

Bacteriophages encode numerous genes with no known function, many of which can affect essential cellular processes when expressed in the bacterial host. For mycobacteriophages, genome-wide overexpression in Mycobacterium smegmatis can be used to identify proteins that impair growth. To evaluate the cytotoxic potential of the Cluster P3 phage Xavia, we constructed a plasmid library containing 71 predicted Xavia genes under the anhydrotetracycline inducible promoter pTet and screened this library in a plate-based cytotoxicity assay to measure impacts on M. smegmatis growth. Two genes prevented transformants recovery, consistent with toxicity under basal promoter leakiness, and inducible expression of 18 additional genes impaired growth. These inhibitory proteins include structural components; factors involved in DNA metabolism, lysogeny, and lysis; and several proteins with no known function. These results extend functional screening into a lineage of actinobacteriophages that has not previously been characterized, and identify new proteins that warrant further mechanistic analysis.

Mycobacterium smegmatis↗

A high-quality draft genome assembly of Johnsongrass illuminates relationships between polyploidization, crop-wild hybridization, and reproductive biology.

Johnsongrass [Sorghum halepense (L.) Pers.] is an allopolyploid, rhizomatous, perennial grass species and one of the most troublesome weeds in global agriculture. We assembled the first Johnsongrass genome to clarify poorly understood genetic factors influencing variable rates of crop-wild hybridization with cultivated sorghum [S. bicolor (L.) Moench]. The draft genome assembly has a total size of 3.26 Gb and BUSCO completeness of 95.3%. We also report the first evolutionary analysis of INHIBITION OF ALIEN POLLEN (IAP), the only known cross-(in)compatibility locus in the genus. Our results reveal an evolutionary history of genome instability, including the loss of distinct parental subgenomes, and suggest that Nebraska accession 'J-37,' the genome donor, is a segmental allotetraploid that may function as a diploid or aneuploid during meiosis. Genome instability could explain observations of variable ploidies in Johnsongrass and facilitate ongoing hybridization with sorghum where gamete ploidies and IAP alleles match. Given this information, we provide a suggested research framework for studying evolution and gene expression in the Sorghum genus where crop-wild hybridization occurs and for predicting the potential for hybridization between specific crossing partners. Collectively, this work will bolster efforts to study and manage reproductive biology in other crop-wild polyploid complexes.

Sorghum↗

Screening for dual sgRNAs with comparable indel efficiencies enhances CRISPR-mediated large-fragment deletion.

CRISPR-mediated large-fragment deletion provides a powerful approach for gene clusters, noncoding regions and structural variants, but its broader application is limited by low and variable deletion efficiency. Here, we systematically designed and evaluated 78 sgRNAs targeting nine representative gene clusters (ttn.1-ttn.2 cluster, 7 hox clusters and nppb-nppa cluster), containing 31 large fragments (5 kb-340 kb) to investigate the determinants of deletion efficiency. We found two key rules for achieving high deletion efficiency: (i) using dual sgRNAs with similar indel efficiencies, and (ii) applying a single sgRNA pair rather than multiple sgRNAs. Based on those rules, a 340 kb deletion is detected in the progenies of 95% of founders. Whereas the deletion size showed no significant linear correlation with deletion efficiency within the tested range. Implementing these rules resulted in an average of 70% of founders transmitting deletions across all tested sgRNA pairs. Therefore, screening sgRNAs can effectively enhance CRISPR utility in deletions, thereby facilitating the application of genomic manipulation in vertebrates and other species.

CRISPR↗

MACS3: A Peak-calling Platform for Bulk and Single-cell Regulatory Genomics.

Since the original publication of Model-based Analysis for ChIP-Seq (MACS), the software has been widely used to identify enriched genomic regions in ChIP-seq, ATAC-seq, CUT&RUN, DNase-seq, and related regulatory genomics assays. Over the years, MACS has evolved substantially, with MACS version 3 (MACS3) now serving as the actively maintained implementation. MACS3 preserves the core MACS framework for fragment pileup, dynamic local background noise, statistical enrichment testing, and peak refinement, while adding functionality needed for contemporary bulk and single-cell workflows. It supports conventional bulk peak calling, paired-end and fragment-based file formats, modular signal processing, direct analysis of single-cell ATAC-seq fragment files, barcode-restricted pseudobulk and cluster-level peak calling, specialized ATAC-seq and variant-calling modules, as well as command-line and programmatic interfaces. MACS3 is distributed through standard software channels and supported by continuous testing across operating systems, Python versions, and CPU architectures. Here we describe the architecture, current capabilities, and recommended use of MACS3, providing an updated reference for applying the MACS framework in contemporary bulk and single-cell regulatory genomics workflows. MACS3 is open-source software available at https://github.com/macs3-project/MACS.

Bioinformatics software↗

Cross-domain cooperation drives nutrient acquisition and metabolism in the bark beetle holobiont.

Microbial symbiosis underpins host adaptation, yet mechanisms of metabolic integration in holobionts remain unclear. Using metatranscriptomics, genomics, and metabolic assays, we investigated gut microbiome interactions in the European spruce bark beetle (Ips typographus). We observed metabolic complementarity among symbionts and host, forming cross-domain networks that support nutrient acquisition. Nitrogen recycling revealed strong interdependence: no single partner possessed a complete uric acid degradation pathway, but combined evidence supports a distributed pathway spanning beetle, Bacteria, and fungi. Additionally, bacterial nitrate reduction to ammonia indicates a potential nitrogen influx, making otherwise inaccessible inorganic nitrogen available to the host. Shaped by microbial interactions, symbionts also likely supply specific amino acids, while vitamin metabolism showed cross-domain co-metabolism, with Bacteria as main producers of B vitamins, while host and fungi modulated interconversion. Carbohydrate degradation was highly partitioned; bacteria target xylan and pectin, while fungi contribute to glucan breakdown. Crucially, our data provide indirect evidence that the beetle may contribute to complete cellulose degradation, highlighting an underappreciated host role in lignocellulose processing. In terms of enzymatic functional diversity, the bacteriome emerged as the most important microbiome component-an observation that contrasts with the traditional focus on fungi and underscores the need to consider bacterial contributions in insect symbioses. Despite life-stage variation, core metabolic functions remained stable. Overall, metabolic interdependence, rather than microbial composition alone, structures holobiont function. These results highlight functional redundancy and ecological resilience, emphasizing the importance of microbial cooperation and host-microbe metabolic evolution.

Bark beetle↗

Outer membrane changes enable evolutionary escape from bacterial predation.

Antimicrobial resistance (AMR) is a threat to modern medicine. To combat AMR pathogens, natural predators like bacteriophages and predatory bacteria have gained interest recently. Predatory bacterium Bdellovibrio bacteriovorus is ubiquitous and has a broad prey range. It is particularly potent at killing many AMR Gram-negative bacterial pathogens featured on the WHO priority list. However, it is currently unclear whether prey bacteria can evolve genetically-determined resistance against predation by B. bacteriovorus. Here, we show that the model bacterium Escherichia coli K-12 consistently evolves resistance against B. bacteriovorus during experimental evolution. Selection for resistance scaled positively with predation pressure and was widespread after two cycles of predator exposure. Similar to antibiotics, predation resistance was costly, manifesting in a trade-off between predation resistance and fitness in the absence of predators. Genetic analysis combined with proteomics identified mutations that lead to the down-regulation of the outer membrane porin OmpF as a common resistance mechanism. In addition, a rarer mutation in cell envelope lipopolysaccharide-modifying enzyme WaaF also conferred predation resistance, likely by a pleiotropic effect, which included OmpF down regulation. While our study uncovers evolutionary and mechanistic aspects of prey escape from predation, it also highlights that the high cost of resistance reflects a handicap for the pathogen and can thus be exploited to increase treatment sustainability. Altogether, our work generates essential knowledge in ecologically important predator-prey interactions and can advance predatory bacteria as "living antibiotics" to combat AMR.

Bdellovibrio bacteriovorus↗

Environmental Gradients as a Dominant Force in the Macroevolution of a Host-Associated Marine Bacterium.

Natural selection is imposed by both abiotic environmental filtering and biotic interactions, yet their relative roles in shaping the deep phylogeny of widespread, generalist host-associated bacteria remain unclear. Here, we integrate large-scale phylogenomics, environmental sequencing, functional genomics, and global metagenomic analysis to demonstrate that tidal zonation overrides host association as the dominant macroevolutionary force structuring the marine bacterial genus Ruegeria. Analysis of 533 genomes and 74 global coastal metagenomes reveals that the intertidal-subtidal boundary structures the deepest phylogenetic splits, driving the repeated evolution of distinct ecotypes through independent zonation transitions across global coastlines. These ecotypes possess divergent genomic toolkits: intertidal strains are enriched for genes coding for stress resistance and anaerobic metabolism, whereas subtidal strains specialize in high-affinity nutrient scavenging. Our findings establish that predictable physicochemical gradients act as filters that generate foundational diversity from which specialized host symbionts subsequently emerge, reframing how environmental gradients shape microbial evolution at the eco-evolutionary interface.

Journal Article↗

Target-Site Selection by Transcription Factors: Roles of DNA, Chromatin, and Cofactor-Mediated Regulation.

Transcription factors (TFs) are sequence-specific DNA-binding proteins that regulate gene-expression programs and cell fate. The ability of a defined combination of four TFs to reprogram differentiated cells into induced pluripotent stem cells illustrates the powerful role of TFs in determining cellular identity. However, TFs usually recognize short and degenerate DNA motifs of approximately 6-12 base pairs, generating thousands to millions of potential motif matches in mammalian genomes. In living cells, TFs occupy only a restricted subset of these sites, indicating that motif presence alone is insufficient for functional target selection. Several layers of regulation contribute to this selective occupancy, including DNA methylation, nucleosome organization, histone modifications, chromatin remodeling, TF oligomerization, TF availability and localization, and cofactors that regulate DNA-binding domains. This review outlines how DNA/chromatin features and TF-centered mechanisms contribute to target-site selection. The principal aim is to highlight DNA-binding domain-directed cofactor regulation as an underappreciated mechanism that modulates TF-DNA binding and may help explain selective genomic occupancy.

Target-site selection↗

Back on the ground: genome analysis of convergent flight loss in rails.

Similar phenotypic traits can evolve independently in response to comparable environmental challenges. A striking example of this process is the repeated and irreversible loss of flight in birds, particularly on islands. The rail family (Rallidae) provides an exceptional model for studying this phenomenon, as nearly a quarter of the 130 extant species have independently become flightless. Here, we present the first genome-wide comparative analysis of multiple independent flightless rail lineages to identify the molecular basis of flight loss. We compared coding regions from 7 rail species (4 flightless and 3 volant) using more than 11,000 alignments and multiple phylogeny-based tests, including branch-site models of selection, relative evolutionary rate analyses, and assessments of function-altering amino acid substitutions. Across all analyses, 116 genes showed significant associations with flightlessness, of which 37 were linked to biological functions related to flight capacity-such as muscle, bone, limb, and heart development-or to traits reflecting ecological consequences of flight loss, including immune response, renal function, lipid metabolism, cognition, and sensory perception. Many genes under selection in flightless species were also involved in gene regulation and post-translational modification. These findings suggest that convergent loss of flight in rails arises not from major mutations in a few key loci but from numerous small, repeated genetic changes affecting both developmental pathways and regulatory mechanisms.

Animals↗

The twofold cost of sex reconsidered: meiotic mechanisms protect anisogamous populations from invasion by thelytoky.

Most multicellular animals practice anisogamy (fertilization between eggs and sperm). When mothers produce sons and daughters at a 1:1 ratio, the "twofold cost of males" arises because males do not directly contribute to population growth. If thelytokous parthenogens producing only daughters invade a population, they should spread rapidly. Although thelytoky has repeatedly evolved across invertebrate and vertebrate taxa, it remains a minority. Why? The evolutionary transition from anisogamy to thelytoky requires eggs to initiate embryonic development without fertilization. However, in metazoan animals, meiotic metaphase (MM) arrest halts oogenesis midway and normally resumes only after stimulation by sperm penetration. Empirical and experimental evidences indicate that release of MM arrest without fertilization is extremely difficult, providing a strong mechanistic barrier against parthenogenesis. Even if MM arrest were released, oogenesis would proceed to produce either a haploid embryo or a diploid embryo through refusion with the second polar body (terminal fusion automixis). Outbred species typically accumulate more than one lethal equivalent of recessive deleterious alleles per genome as heterozygotes. Upon transition to haploid or automictic development, these recessive lethals normally masked in outbred diploids would be exposed simultaneously, causing embryonic death and creating the next barrier. Thus, thelytoky cannot be achieved simply by modification of the existing meiotic system; instead, other mechanisms, such as apomixis, that bypass meiosis are required. Mathematical models and simulations support this "meiotic constraint" hypothesis. Combined with recently proposed immediate benefits of anisogamy and traditional genetic benefits (e.g., Red Queen), it may largely explain the maintenance of costly anisogamy.

Animals↗

The evolutionary origins of the parthenogenetic lizard Aspidoscelis tesselatus.

Most vertebrate species reproduce sexually. The whiptail lizards (Aspidoscelis) are a notable exception; at least 11 of the 45 recognized species are parthenogenetic. Here, we focus on one such species (Aspidoscelis tesselatus) as a case study to understand how parthenogenetic species originate and evolve. Using genome-wide sequence data and ecological niche modelling, we find that A. tesselatus likely arose from a single hybrid speciation event between A. scalaris and A. marmoratus less than 500,000 years ago. The geographic ranges of A. tesselatus and its parental species overlap currently, and niche modelling shows this zone of sympatry was even broader during the period when A. tesselatus likely formed. We additionally show evidence that A. tesselatus has a dynamic genome post-formation, with de novo mutations, introgression, and double-strand break associated events all contributing to variation within the species. These results show that asexual lineages can continue to be shaped by ongoing genomic and ecological dynamics, illuminating the processes that influence transitions in reproductive mode.

asexuality↗