STAR Protoc. 2025 Jun 20;6(3):103914. doi: 10.1016/j.xpro.2025.103914. Online ahead of print.

ABSTRACT

Here, we present a protocol for quantifying the expression of genes detected by fluorescence insitu hybridization at single-cell spatial resolution using an imaging analysis pipeline developed based on CellProfiler software. We describe steps for comparing gene expression between cancer samples with and without metastasis. We detail procedures for detecting target transcripts using RNAscope multiplex fluorescent assays and visualization using Vectra Polaris Automated Quantitative Pathology Imaging. This protocol also provides an alternative option to analyze signal interactions across adjacent tissue sections. For complete details on the use and execution of this protocol, please refer to Sari et al.1.

PMID:40544447 | DOI:10.1016/j.xpro.2025.103914

J Mol Evol. 2025 Jun 21. doi: 10.1007/s00239-025-10256-6. Online ahead of print.

ABSTRACT

Vpu, an accessory protein of human immunodeficiency virus-1 (HIV-1), plays a crucial role in viral particle production and significantly contributes to HIV virulence. However, the evolution of the vpu gene remains poorly understood. We conducted a computational analysis of approximately 39,000 simian immunodeficiency virus (SIV) and HIV sequences, focusing on 141 representative Vpu proteins. Phylogenetic analysis classified the SIV and HIV strains into four major types based on their Vpu proteins: Vpu-type 1 (ancestral, found in SIVs such as SIVmon and SIVgsn), Vpu-type 2 (SIVgor and HIV-1 group O), Vpu-type 3 (SIVcpz), and Vpu-type 4 (HIV-1 group M and N). Notably, Vpu-type 1 exhibited variability in gene length, genome length, and the overlap between vpu and env compared with other Vpu-types. A phylogenetic tree was constructed using 426 nucleotide sequences from HIV-1, HIV-2, and SIVs focusing on the region between the pol and env genes. Vpu-type 1 was closely clustered with SIVasc and SIVsyk, lacking both vpu and vpx. The similarities observed between vpu and genes such as vpr and env suggest that vpu originated within the SIV genome. In addition, a phylogenetic tree constructed from 252 Vpu-type 4a sequences from the HIV pandemic strain and 135 sequences of circulating recombinant forms of HIV-1 revealed 18 distinct protein subtypes, exceeding the number of previously recognized subtypes. The systematic analysis of the sequences from large datasets has enabled a detailed characterization of the transition states of vpu, enhancing our understanding of the processes driving viral diversity.

PMID:40544231 | DOI:10.1007/s00239-025-10256-6

Prog Mol Biol Transl Sci. 2025;214:81-100. doi: 10.1016/bs.pmbts.2025.01.001. Epub 2025 Mar 19.

ABSTRACT

This chapter x-rays the pivotal roles of non-coding RNAs (ncRNAs) in gene regulation and cellular processes with emphasis on their diverse functions and mechanisms. The ncRNA types, which include miRNAs, siRNAs, and lncRNAs were highlighted stating their significance in gene regulation and disease. Then, the biogenesis and functional roles of these ncRNAs were explained with a focus on their transcription, processing, and mechanisms of action such as RNA interference and gene silencing. Furthermore, the chapter delves into the pathways of miRNAs, siRNAs, and lncRNAs to elucidate their regulatory roles in chromatin remodeling, transcription, and post-transcriptional processes. Omics technologies, including genomics, transcriptomics, proteomics, and epigenomics were piqued for their transformative impact on ncRNA research towards enabling comprehensive analysis and discovery of novel ncRNA functions. Consistently, the integration of multi-omics data, showcasing bioinformatics tools, and exemplified studies that reveal ncRNA networks and systems biology approaches were highlighted. These led to the suggestion that addressing technical and computational challenges, such as data quality, reproducibility, and integration is pivotal to future advancements in applications of lncRNA. Therefore, dissecting ncRNA Pathways and Omics Integration shows the potential applications of ncRNA research in personalized medicine and therapeutics which has culminated in its growing significance in biomedical research and its promise for innovative treatment strategies.

PMID:40543918 | DOI:10.1016/bs.pmbts.2025.01.001

Autoimmun Rev. 2025 Jun 19:103855. doi: 10.1016/j.autrev.2025.103855. Online ahead of print.

ABSTRACT

The 5th International Symposium on Regulatory Autoantibodies Targeting GPCR (RAB-GPCRs) advanced the understanding of the significant role played by autoantibodies targeting G-protein-coupled receptors (GPCRs) in various human diseases. Once considered passive markers, RAB-GPCRs are now recognized as active modulators of cellular signaling, immune regulation, and inflammation. The symposium highlighted their involvement in multiple prominent pathologies, including autoimmune diseases, cardio- and cerebrovascular diseases, and neuroimmunologic disorders such as myalgic encephalomyelitis/chronic fatigue syndrome and post-COVID-19 syndrome (ME/CFS/PCS), as well as solid organ and hematopoietic stem cell transplantation (SOT/HSCT). Experts from rheumatology, immunology, and neurology presented interdisciplinary discussions on the potential of RAB-GPCRs as biomarkers and therapeutic targets. Advances in screening methods, biomarker identification, and therapeutic strategies were shared, emphasizing their diagnostic potential and application in novel therapeutic interventions. This report summarizes key insights from the symposium, particularly focusing on the modulatory properties of RAB-GPCRs and their relevance in both immune-mediated diseases and other pathologies (e.g., vascular, degenerative) that are traditionally not considered primarily immune-mediated. Ongoing research is expected to further establish these autoantibodies as crucial components in disease modulation and systems biology contexts, offering new opportunities for precision medicine and improved clinical outcomes in immune-related disorders.

PMID:40543860 | DOI:10.1016/j.autrev.2025.103855

Microb Pathog. 2025 Jun 19:107825. doi: 10.1016/j.micpath.2025.107825. Online ahead of print.

ABSTRACT

Leptospirosis, a global health concern caused by Leptospira sp. is largely unknown due to its elusive phylogeographic distribution and flow. Therefore, this study aimed to understand the geographical distribution and evolutionary changes of pathogenic, non-pathogenic, and opportunistic strains of Leptospira. This study used genome-scale data, 16S rDNA gene sequences, and virulence proteins to construct precise phylogenetic trees using robust bootstrapping techniques. Phylogenomic studies indicated that pathogenic Leptospira strains constituted a distinct cluster from opportunistic and non-pathogenic variants. The pathogenic strains coalesced, creating a central group in the phylogenetic tree based on the 16S rDNA gene. Pathogenic strains had a close evolutionary relationship with non-pathogenic and opportunistic strains, since they shared the outer membrane protein L. The opportunistic strains formed a clearly defined clade, suggesting that there were no evolutionary transitions between them. Nevertheless, we found potential transitions between the pathogenic and non-pathogenic strains. Additionally, this study unveiled the participation of prominent countries in the dissemination of Leptospira strains to various geographical areas, such as Thailand, the USA, Peru, Italy, Turkey, Malaysia, New Caledonia, Brazil, and Iran. This work provides novel perspectives on the evolutionary shift, geographical dissemination, and emergence of highly pathogenic Leptospira strains.

PMID:40543632 | DOI:10.1016/j.micpath.2025.107825

Am J Hum Genet. 2025 Jun 17:S0002-9297(25)00212-5. doi: 10.1016/j.ajhg.2025.05.014. Online ahead of print.

ABSTRACT

Laterality defects are defined by perturbations in the usual left-right asymmetry of organs. The genetic etiology that underlies congenital heart disease (CHD) is often unknown (less than 40%), so we used a digenic model approach for the identification of contributing variants in known laterality-defect-associated genes (n = 115) in the exome/genome sequencing (ES/GS) data from individuals with clinically diagnosed laterality defects. The unsolved ES/GS data were analyzed from three CHD cohorts: Baylor College of Medicine-Genomics Research to Elucidate the Genetics of Rare Diseases (BCM-GREGoR; n= 251 proband ES), Gabriella Miller Kids First Pediatric Research Program (Kids First; n = 158 trio GS), and Pediatric Cardiac Genomics Consortium (PCGC; n = 163 trio ES). trans-heterozygous digenic variants were identified in 2.8% (inherited digenic variants in 0.4%), 8.2%, and 13.5% of individuals, respectively; this was significantly higher than in 602 control trios provided by the 1000 Genomes Project (p = 0.001, 1.4e-07, and 8.9e-13, respectively). trans-heterozygous digenic variants were also identified in 0.4% and 1.4% of individuals with non-laterality CHD in Kids First and PCGC datasets, respectively, which was not statistically significant as compared to control trios (p = 1 and 0.059, respectively). Altogether, in laterality cohorts, 23% of digenic pairs were in the same structural complex of motile cilia. Out of 39 unique digenic pairs in laterality CHD, 29 are more likely to be potential digenic hits as predicted by the DiGePred tool. These findings provide further evidence that digenic epistatic interactions can contribute to the complex genetics of laterality defects.

PMID:40543504 | DOI:10.1016/j.ajhg.2025.05.014

Cell. 2025 Jun 19:S0092-8674(25)00624-5. doi: 10.1016/j.cell.2025.05.037. Online ahead of print.

ABSTRACT

Next-generation sequencing is pivotal for diagnosing inborn errors of immunity (IEI) but predominantly yields variants of uncertain significance (VUS), creating clinical ambiguity. Activated PI3Kδ syndrome (APDS) is caused by gain-of-function (GOF) variants in PIK3CD or PIK3R1, which encode the PI3Kδ heterodimer. We performed massively parallel base editing of PIK3CD/PIK3R1 in human T cells and mapped thousands of variants to a clinically important readout (phospho-AKT/S6), nominating >100 VUS and unannotated variants for functional classification and validating 27 hits. Leniolisib, an FDA-approved PI3Kδ inhibitor, rescued aberrant signaling and dysfunction in GOF-harboring T cells and revealed partially drug-resistant PIK3R1 hotspots that responded to novel combination therapies of leniolisib with mTORC1/2 inhibition. We confirmed these findings in T cells from APDS patients spanning the functional spectrum discovered in the screen. Integrating our screens with population-level genomic studies revealed that APDS may be more prevalent than previously estimated. This work exemplifies a broadly applicable framework for removing ambiguity from sequencing in IEI.

PMID:40543502 | DOI:10.1016/j.cell.2025.05.037

Cell Rep Methods. 2025 Jun 18:101086. doi: 10.1016/j.crmeth.2025.101086. Online ahead of print.

ABSTRACT

Single-cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex biological systems. However, most sequencing studies overlook the contribution of transposable element (TE) expression to the transcriptome. The quantification of locus-specific TE expression in scRNA-seq experiments is challenging due to their repetitive sequence content and poorly characterized annotations. Here, we developed a computational tool for single-cell transposable element locus-level analysis of scRNA sequencing (Stellarscope) that reassigns multimapped reads to specific genomic loci using an expectation maximization algorithm. Using Stellarscope, we built an atlas of TE expression in human PBMCs. We found that locus-specific TEs delineate cell types and define cell subsets not identified by standard mRNA expression profiles. Altogether, this study provides comprehensive insights into the influence of TEs in human biology at the single-cell level.

PMID:40543500 | DOI:10.1016/j.crmeth.2025.101086

Food Chem. 2025 Jun 16;491:145151. doi: 10.1016/j.foodchem.2025.145151. Online ahead of print.

ABSTRACT

While CO2 production during yeasted dough fermentation is essential for a desirable bread loaf volume, the fastest volume increase occurs during baking, known as oven rise. The significance of CO2 production during this phase of bread-making remains unexplored. This study hypothesised that stress-resistant yeast strains could remain active longer during baking, supporting oven rise. The oven rise obtained with standard baker's yeast was compared to 15 Saccharomyces cerevisiae strains selected for high-stress resistance on plate. During electrical resistance oven baking, dough height increases between 18.6 and 31.5 % were obtained. The increase was strongly and positively correlated with cell viability and, hence, thermotolerance. The best-performing strain showed a 42.2 % cell viability at a dough temperature of 77 °C compared to 11.8 % for the reference baker's yeast. This study provides the first insights into the correlation between yeast viability during baking and loaf volume, opening new avenues for selecting superior yeasts.

PMID:40543122 | DOI:10.1016/j.foodchem.2025.145151

G3 (Bethesda). 2025 Jun 21:jkaf134. doi: 10.1093/g3journal/jkaf134. Online ahead of print.

ABSTRACT

Given the interest in the biogeography and diversity of the Caenorhabditis genus, we established a collection of these nematodes from field surveys on four Indonesian islands. We isolated over 60 Caenorhabditis strains belonging to ten species. Five species were previously known from other locations: C. briggsae, which was predominant, C. tropicalis, C. nigoni, C. brenneri and C. elegans. The five other species are new discoveries for science, and we describe them here as Caenorhabditis indonesiana, Caenorhabditis malinoi, Caenorhabditis ceno, Caenorhabditis brawijaya and Caenorhabditis ubi. RNA sequence analysis of 1,861 orthologous genes placed all species from Indonesia in the Elegans group of Caenorhabditis species. Four of the new species belong to a Sinica subclade of species so far only found in an East Asia-Indo-Pacific world region. The fifth new species, C. indonesiana, appears as the sister of the C. tropicalis-C. wallacei pair, both also found in Indonesia. The present findings are thus consistent with diversification in the Elegans group having occurred in this world region. Crosses between closely related species showed counterexamples to Haldane's "rule": for several pairs of species, in one cross direction we only found hybrid males. In addition, we found a pair of species that could partially interbreed: Caenorhabditis ubi (East Java) with C. sp. 41 (Solomon islands), with the hybrid males in one cross direction being fertile. Such closely related species pairs are good models for genetic studies of incompatibilities arising during speciation.

PMID:40542721 | DOI:10.1093/g3journal/jkaf134

Biophys J. 2025 Jun 19:S0006-3495(25)00382-0. doi: 10.1016/j.bpj.2025.06.022. Online ahead of print.

ABSTRACT

Lamin proteins are essential structural elements of the nuclear envelope, critically involved in maintaining nuclear shape and mechanical stability. Lamin A/C, specifically, acts as a mechanotransducer that senses extracellular mechanical cues and transmits them into intracellular biochemical signals, thereby influencing cell adhesion, motility, and differentiation. Although microRNAs (miRNAs) have emerged as key regulators of cellular mechanotransduction pathways, the precise roles of miRNAs in modulating lamin A/C at the single-cell level have remained poorly understood. Here, we utilized advanced fluorescence resonance energy transfer (FRET)-based biosensors and traction force microscopy to elucidate the impact of miRNA-548t-3p-induced lamin A/C downregulation on nuclear mechanical properties in single cells. Our findings demonstrate that miRNA-548t-3p specifically reduces lamin A/C levels, resulting in decreased nuclear tension and compromised focal adhesion dynamics. Furthermore, miRNA-548t-3p significantly diminishes the ability of cells to sense and respond to variations in extracellular matrix stiffness, leading to reduced cellular traction forces. These results underscore the pivotal role of lamin A/C in cellular mechanosensitivity and highlight miRNA-548t-3p as a critical modulator of nuclear mechanotransduction and mechanical homeostasis at the single-cell scale. This study provides new insights into the complex interplay between miRNAs, nuclear mechanics, and cell-environment interactions, suggesting potential avenues for therapeutic intervention in diseases associated with disrupted mechanotransduction.

PMID:40542505 | DOI:10.1016/j.bpj.2025.06.022

Genome Biol. 2025 Jun 20;26(1):175. doi: 10.1186/s13059-025-03615-5.

ABSTRACT

HiChIP enables cost-effective and high-resolution profiling of chromatin loops. To leverage the increasing number of HiChIP datasets, we develop Loop Catalog ( https://loopcatalog.lji.org ), a web-based database featuring loop calls from over 1000 distinct human and mouse HiChIP samples from 152 studies plus 44 high-resolution Hi-C samples. We demonstrate its utility for interpreting GWAS and eQTL variants through SNP-to-gene linking, identifying enriched sequence motifs and motif pairs, and generating regulatory networks and 2D representations of chromatin structure. Our catalog spans more than 4.19M unique loops, and with embedded analysis modules, constitutes an important resource for the field.

PMID:40542429 | DOI:10.1186/s13059-025-03615-5

Hum Genomics. 2025 Jun 21;19(1):70. doi: 10.1186/s40246-025-00778-x.

ABSTRACT

BACKGROUND: High-throughput sequencing has revolutionized genetic disorder diagnosis, but variant pathogenicity interpretation is still challenging. Even though the human genome variation society (HGVS) provides recommendations for variant nomenclature, discrepancies in annotation remain a significant hurdle.

RESULTS: In this study, we evaluated the annotation concordance between three tools-ANNOVAR, SnpEff, and variant effect predictor (VEP)-using 164,549 two-star variants from ClinVar. The analysis used HGVS nomenclature string-match comparisons to assess annotation consistency from each tool, corresponding coding impacts, and associated ACMG criteria inferred from the annotations. The analysis revealed variable concordance rates, with 58.52% agreement for HGVSc, 84.04% for HGVSp, and 85.58% for the coding impact. SnpEff showed the highest match for HGVSc (0.988), while VEP bettered for HGVSp (0.977). The substantial discrepancies were noted in the loss-of-function (LoF) category. Incorrect PVS1 interpretations affected the final pathogenicity and downgraded PLP variants (ANNOVAR 55.9%, SnpEff 66.5%, VEP 67.3%), risking false negatives of clinically relevant variants in reports.

CONCLUSIONS: These findings highlight the critical challenges in accurately interpreting variant pathogenicity due to discrepancies in annotations. To enhance the reliability of genetic variant interpretation in clinical practice, standardizing transcript sets and systematically cross-validating results across multiple annotation tools is essential.

PMID:40542397 | DOI:10.1186/s40246-025-00778-x

Nat Microbiol. 2025 Jun 20. doi: 10.1038/s41564-025-02035-2. Online ahead of print.

ABSTRACT

Numerous important environments harbour low levels of microbial biomass, including certain human tissues, the atmosphere, plant seeds, treated drinking water, hyper-arid soils and the deep subsurface, with some environments lacking resident microbes altogether. These low microbial biomass environments pose unique challenges for standard DNA-based sequencing approaches, as the inevitability of contamination from external sources becomes a critical concern when working near the limits of detection. Likewise, lower-biomass samples can be disproportionately impacted by cross-contamination and practices suitable for handling higher-biomass samples may produce misleading results when applied to lower microbial biomass samples. This Consensus Statement outlines strategies to reduce contamination and cross-contamination, focusing on marker gene and metagenomic analyses. We also provide minimal standards for reporting contamination information and removal workflows. Considerations must be made at every study stage, from sample collection and handling through data analysis and reporting to reduce and identify contaminants. We urge researchers to adopt these recommendations when designing, implementing and reporting microbiome studies, especially those conducted in low-biomass systems.

PMID:40542287 | DOI:10.1038/s41564-025-02035-2

Nature. 2025 Jun 20. doi: 10.1038/s41586-025-09134-4. Online ahead of print.

NO ABSTRACT

PMID:40542162 | DOI:10.1038/s41586-025-09134-4

Sci Rep. 2025 Jun 20;15(1):20208. doi: 10.1038/s41598-025-06427-6.

ABSTRACT

Praying mantises (Mantodea, Insecta) are capable of capturing larger invertebrates and also smaller vertebrates with their raptorial forelegs. Forelegs may exhibit morphological adaptations based on the type of prey they prefer (e.g., softer or harder invertebrates). Since the functionality of a structure is also influenced by its material composition, it could be tailored to match the prey as well. To pave the way for deeper studies on trophic adaptations in insects, this study investigates the morphology, material composition and mechanical properties of the raptorial forelegs of two species of praying mantises with different prey preferences. Sphodromantis lineola favours harder and larger invertebrates, such as cockroaches (Blattaria), whereas Gongylus gongylodes feeds on softer and smaller invertebrates like flies (Diptera). Both males and females were examined in both species to assess potential sexual dimorphism. The results suggest that the morphology of the raptorial forelegs, the arrangement and tiltability of the spines, and the material mechanical properties of the leg cuticle could potentially be related to the preferred prey type. Autofluorescence documentations reflected the presence of micro gradients in the spines, which are related to their mechanical properties. However, pigmentation in the structures of G. gongylodes seemed to corrupt the autofluorescence, complicating comparisons between the species. Elemental analysis confirmed the presence of traces of transition and alkaline earth metals in the raptorial forelegs, though no significant species-specific differences and no correlations to the mechanical properties were detected.

PMID:40542085 | DOI:10.1038/s41598-025-06427-6

Sci Data. 2025 Jun 20;12(1):1044. doi: 10.1038/s41597-025-05372-3.

ABSTRACT

Cultivar Désirée is an important model for potato functional genomics studies to assist breeding strategies. Here, we present a haplotype-resolved genome assembly of Désirée, achieved by assembling PacBio HiFi reads and Hi-C scaffolding, resulting in a high-contiguity chromosome-level assembly. We implemented a comprehensive annotation pipeline incorporating gene models and functional annotations from the Solanum tuberosum Phureja DM reference genome alongside RNA-seq reads to provide high-quality gene and transcript annotations. Additionally, we provide a genome-wide DNA methylation profile using Oxford Nanopore reads, enabling insights into potato epigenetics. The assembled genome, annotations, methylation and expression data are visualised in a publicly accessible genome browser, providing a valuable resource for the potato research community.

PMID:40541992 | DOI:10.1038/s41597-025-05372-3

Sci Data. 2025 Jun 20;12(1):1047. doi: 10.1038/s41597-025-05295-z.

ABSTRACT

Physical samples and their associated data and metadata underpin scientific discoveries across disciplines and can enable new science when appropriately archived. However, there are significant gaps in current practices and infrastructure that prevent accurate provenance tracking, reproducibility, and attribution. For most samples, descriptive metadata are often sparse, inaccessible, or absent. Samples and associated data and metadata may also be scattered across numerous physical collections, data repositories, laboratories, data files, and papers with no clear linkage or provenance tracking as new information is generated over time. The Earth Science Information Partners (ESIP) Physical Samples Curation Cluster has therefore developed guidance for scientific authors on 'Publishing Open Research Using Physical Samples.' This involved synthesizing existing practices, gathering community feedback, and assessing real-world examples. We identified improvements needed to enable authors to efficiently cite and link Earth science samples and related data, and track their use. Our goal is to help improve discoverability, interoperability, and reuse of physical samples, and associated data and metadata. Though primarily focused on the needs of Earth and environmental sciences, these guidelines are broadly applicable.

PMID:40541980 | DOI:10.1038/s41597-025-05295-z

Cell Syst. 2025 Jun 13:101321. doi: 10.1016/j.cels.2025.101321. Online ahead of print.

ABSTRACT

Responses of endothelial cells to elevated levels of vascular endothelial growth factor (VEGF), frequently accompanying local decrease in oxygen supply, include loosening of cell contacts, rearrangement of cells in vessel remodeling, and ultimately, angiogenic growth. How these complex processes, occurring on diverse time scales, are coordinated and how they are guided by a single key signaling input is still incompletely understood. Here, we show that the various phenotypic responses associated with VEGF signaling are controlled at different steps of a pathway involving sequential activation of Src, tumor endothelial marker 4 (TEM4), YAP, and components of pro-angiogenic Notch signaling. Notably, due to feedback regulation at different pathway levels, the functional outcomes are controlled by oscillations of the pathway components occurring on distinct time scales. Deeper pathway layers integrate faster upstream responses and control progressively slower phenotypic outcomes. This signal-decoding pathway organization can ensure a high degree of complexity in a vital physiological process. A record of this paper's transparent peer review process is included in the supplemental information.

PMID:40541183 | DOI:10.1016/j.cels.2025.101321

Mod Pathol. 2025 Jun 19;38(8):100819. doi: 10.1016/j.modpat.2025.100819. Online ahead of print.

NO ABSTRACT

PMID:40541156 | DOI:10.1016/j.modpat.2025.100819