Genome Biol. 2025 Apr 24;26(1):105. doi: 10.1186/s13059-025-03554-1.

ABSTRACT

In spatial transcriptomics data, spatially correlated genes promise to reveal high-interest phenomena like cell-cell interactions and latent variables. But in practice, most spatial correlations arise from the spatial arrangement of cell types, obscuring the more interesting relationships we hope to discover. We introduce InSituCor, a toolkit for discovering modules of spatially correlated genes. InSituCor returns only correlations not explainable by already-known factors like the cell type landscape; this spares precious analyst effort. InSituCor supports both unbiased discovery of whole-dataset correlations and knowledge-driven exploration of genes of interest. As a special case, it evaluates ligand-receptor pairs for spatial co-regulation.

PMID:40275395 | DOI:10.1186/s13059-025-03554-1

BMC Microbiol. 2025 Apr 24;25(1):243. doi: 10.1186/s12866-025-03933-5.

ABSTRACT

BACKGROUND: Inflammatory events followed by bacterial infections are related to the progression of the atherosclerosis process. The study investigated the signaling and metabolic pathways of endothelial cells (ECs), macrophages (MQs), vascular smooth muscle cells (VSMCs), and dendritic cells (DCs) after exposure to Gram-negative bacterial infections. Moreover, it aimed at cross-talking and enriching the pathways on the cellular and plaque networks.

METHODS AND MATERIALS: High-throughput expression data series (n = 9) were selected through GEO and MAT data repositories. Upregulated differential expression genes (DEGs) were determined using R software and applied to identify the cellular signaling pathways using Enricher/Reactome tools. Then, the cell networks were visualized using the Cytoscape software and enriched by the pathways of secretory proteins identified using Gene ontology (GO).

RESULTS: The important pathways of the Cytokines (Degree 4, p < 6 × 10-26), and INF (Degree 4, p < 8.6 × 10-31) in ECs, Cytokines (Degree 4, p < 9.35 × 10-8), and GPCR (Degree 3, p < 1.45 × 10-4) in MQs, NOTCH (Degree 6, p < 0.027) in VSMCs, and Cytokines (Degree 4, p < 1.45 × 10-17) in DCs were found to be activated and enriched after exposure to Gram-negative bacterial infections on the cell networks. Furthermore, the Netrin- 1 (Degree 6, p < 0.028), and EGFR (Degree 5, p < 0.036) pathways were activated in the intimal thick/xanthoma plaque network while the innate (Degree 9, p < 8.9 × 10-20) and adaptive (Degree 7, p < 4.1 × 10-12) immune systems pathways were activated in the fibrous cap atheroma plaque network.

CONCLUSION: The study revealed the signaling pathways after exposure to Gram-negative bacterial infections on the cell networks in the vessel microenvironment. Furthermore, the cell cross-talks exacerbated these pathways in cells and unstable plaques.

CLINICAL TRIAL NUMBER: Not applicable.

PMID:40275124 | DOI:10.1186/s12866-025-03933-5

BJC Rep. 2025 Apr 24;3(1):27. doi: 10.1038/s44276-025-00134-5.

ABSTRACT

BACKGROUND: Glioblastoma (GB), an aggressive brain malignancy with a poor prognosis of 1.5-2 years, rarely exhibits extracranial metastasis (ECM). However, metabolic reprogramming has emerged as a key driver of GB progression and invasiveness. This study presents a rare case of recurrent GB with scalp metastasis, exploring how metabolic shifts enable GB cells to evade treatment and adapt to hostile environments, offering insights for developing innovative therapies.

METHODS: Tandem mass spectrometry (MS/MS) was employed to analyze amino acid profiles in both the recurrent and metastatic stages of GB. Systems biology approaches were used to uncover genetic alterations and metabolic reprogramming associated with the progression from recurrence to metastasis.

RESULTS: Our analysis revealed distinct amino acid utilization patterns in a patient with a molecular phenotype of wild-type IDH-1&2, TERT mutation, non-mutated BRAF and EGFR, and non-methylated MGMT. During recurrence and metastasis, significant differences in amino acid profiles were observed between blood and cerebrospinal fluid (CSF) samples. Additionally, protein-protein interaction (PPI) analysis identified key genomic drivers potentially responsible for the transition from recurrent to metastatic GB.

CONCLUSIONS: Beyond established risk factors such as craniotomy, biopsies, ventricular shunting, and radiation therapy, our findings suggest that metabolic reprogramming plays a crucial role in the transition from recurrent to metastatic GB. Targeting these metabolic shifts could provide new avenues for managing and preventing extracranial metastasis in GB, making this an important focus for future research.

PMID:40274950 | DOI:10.1038/s44276-025-00134-5

Anal Chim Acta. 2025 Jun 15;1355:343999. doi: 10.1016/j.aca.2025.343999. Epub 2025 Apr 1.

ABSTRACT

BACKGROUND: Quantitative bioimaging of trace elements at the single-cell level is crucial for understanding cellular processes, including metal uptake and distribution. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) has emerged as a gold standard for elemental bioimaging due to its high sensitivity and spatial resolution. However, calibration remains challenging due to the lack of homogeneous biological standards. This study addresses these challenges by introducing a gelatin-based calibration strategy optimized for Zn mapping in human parietal cells. By minimizing heterogeneity in gelatin standards and optimizing laser ablation conditions, the approach ensures accurate and reproducible results for cellular bioimaging.

RESULTS: A gelatin-based calibration strategy for LA-ICP-MS was developed to quantify intracellular Zn at a single-cell level in human parietal cells. Preparation conditions for gelatin standards were optimized to minimize heterogeneity, eliminating the need for entire droplet ablation and significantly reducing analysis time. Atomic force microscopy (AFM) was employed to optimize laser ablation conditions and determine ablated volumes, ensuring quantitative Zn detection. The method demonstrated high linearity (R2 > 0.99) and reproducibility. Application of the calibration strategy to ZnCl2-treated parietal cells revealed Zn distribution at a cellular level, visualized using a 5 μm laser beam. Integration with bright field imaging enabled the exclusion of apoptotic cells and debris, ensuring robust analysis. Validation with bulk ICP-MS showed excellent agreement, confirming the method's reliability and potential for high-resolution bioimaging.

SIGNIFICANCE: This work introduces a robust and reproducible calibration strategy for quantitative elemental bioimaging using LA-ICP-MS. It details the preparation of a gelatin matrix with a homogeneous element distribution, serving as an alternative to using biological material and significantly reducing analysis time. Laser ablation parameters were optimized using AFM to ensure quantitative ablation, which is necessary for calibration through LA-ICP-MS imaging. This approach provides a powerful tool for studying trace element dynamics in single cells and holds potential for diverse biological and biomedical applications.

PMID:40274329 | DOI:10.1016/j.aca.2025.343999

Lupus Sci Med. 2025 Apr 23;12(1):e001446. doi: 10.1136/lupus-2024-001446.

ABSTRACT

OBJECTIVES: This study aimed to identify novel, non-invasive biomarkers for lupus nephritis (LN) through serum proteomics.

METHODS: Serum proteins were detected in patients with LN and healthy control (HC) groups through liquid chromatography-tandem mass spectrometry. The key networks associated with LN were screened out using Cytoscape software, followed by pathway enrichment analysis. The best candidate biomarkers were selected by machine learning models, further validated in a larger independent cohort. Finally, the expression of these candidate markers was verified in kidney tissue samples, and the mechanism was explored by knocking down the expression of intercellular adhesion molecule 2 (ICAM2) through in vitro cell transfection with siRNA.

RESULTS: Following the serum proteomic screening of LN, a key network of 20 proteins was identified. Machine learning models were used to select ICAM2 (CD102), metalloproteinase inhibitor 1 (TIMP1) and thrombospondin 1 (THSB1) for validation in independent cohorts. ICAM2 exhibited the highest area under the curve (AUC) value in distinguishing LN from HC (AUC=0.92) and was significantly correlated with activity index, proteinuria, albumin and anti-dsDNA antibody levels. Particularly, ICAM2 was significantly elevated in proliferative LN and was associated with specific pathological attributes, outperforming conventional parameters in distinguishing proliferative LN from non-proliferative LN. ICAM2 expression was also elevated in renal tissue samples from patients with proliferative LN. In vitro, knockdown of ICAM2 expression can inhibit the activation of the PI3K/Akt pathway and alleviate the injury of glomerular endothelial cells.

CONCLUSION: ICAM2 (CD102) may serve as a potential serum biomarker for proliferative LN that reflects renal pathology activity, potentially contributing to the progression of LN through the PI3K/Akt pathway.

PMID:40274316 | DOI:10.1136/lupus-2024-001446

Pract Radiat Oncol. 2025 Apr 22:S1879-8500(25)00097-9. doi: 10.1016/j.prro.2025.03.010. Online ahead of print.

ABSTRACT

177Lu-PSMA-617 (LuPSMA) is an effective radiopharmaceutical therapy for patients with metastatic castration-resistant prostate cancer (mCRPC). While LuPSMA can treat disseminated disease, additional localized control of metastatic disease may be required. Metastasis-targeted external beam radiation therapy (M-EBRT) can be an effective adjunct. However, the indications, efficacy, and safety/toxicity of combining M-EBRT with LuPSMA are unclear. Here, we report our experience with M-EBRT in patients receiving LuPSMA and assess M-EBRT's ability for local disease control and palliation.

METHODS: This retrospective IRB-exempted study reviewed patients treated with LuPSMA at a multi-institutional academic cancer center within the first two years post-FDA approval receiving contemporaneous M-EBRT. Clinical factors driving the use of M-EBRT were analyzed.

RESULTS: Treatment courses of 261 patients receiving LuPSMA were reviewed; 52 patients received M-EBRT contemporaneously. M-EBRT was administered for intracranial/epidural disease (n=22/52; 42%), bone pain palliation (n=17/52; 33%), prevention of pathological fractures (n=12/52; 23%), 12% (n=6/52) for various other indications. M-EBRT timing varied among patients, with 54% (n=28/52) receiving M-EBRT before, 27% (n=14/52) after, and 13% (n=7/52) during LuPSMA therapy. EBRT was mostly well-tolerated, although lymphopenia was commonly experienced. Most patients (n=32/52, 62%) had symptom relief following M-EBRT. Symptom relief post-M-EBRT was 68%, 85% vs. 50%, and mortality rates were 32%, 29% vs. 57% for patients receiving EBRT before, during, and after LuPSMA treatment, respectively, albeit not statistically significant (p>0.23). PSA50 (decrease in prostate-specific antigen by 50% during treatment) response in this patient population was 41% compared to 50% in the general LuPSMA population, but the magnitude of PSA response was heterogeneous (p=0.27).

CONCLUSION: In our experience, M-EBRT was used effectively with LuPSMA therapy for local tumor control and symptom management, especially for localized osseous and central nervous system lesions, and with good tolerability. M-EBRT may be an important adjunct treatment modality that facilitates the initiation and/or continuation of LuPSMA.

PMID:40274261 | DOI:10.1016/j.prro.2025.03.010

Life Sci. 2025 Apr 22:123635. doi: 10.1016/j.lfs.2025.123635. Online ahead of print.

ABSTRACT

AIMS: Aralia continentalis Kitag roots (ACKRs) have been regarded as a nutritional natural resource for treating different diseases, including type 2 diabetes mellitus (T2DM), and its complications (heart attack; HA, diabetic nephropathy; DN). Nonetheless, an extensive investigation of T2DM-derived complications has yet to be performed.

MAIN METHODS: Accordingly, we adopted gas chromatography-mass spectrometry (GC-MS) to identify the molecules of ACKRs, followed by the use of cheminformatics (Similarity Ensemble Approach; SEA, SwissTargetPrediction; STP), bioinformatics (STRING, DisGeNET, and OMIM), and computer screening tools to investigate its corresponding targets, in T2DM diseases and its complications.

KEY FINDINGS: The primary targets (PPARG, and IL6) were confirmed via a protein-protein interaction (PPI) network, suggesting that IL6- Andrographolide, PPARA-Germacrene D, PPARD- Kaurenoic acid, PPARG- Kaurenoic acid, NR1H3- 1-Naphthalenepropanol, α-ethenyldecahydro-5-(hydroxymethyl)-α,2,5,5,8a-pentamethyl-, and FABP4- Kaurenoic acid conformers on PPAR signaling pathway might exert agonistic mode.

SIGNIFICANCE: These findings underline that ACKRs' bioactives filtered by the devised platform could prevent T2DM-derived complications through multiple-target.

PMID:40274257 | DOI:10.1016/j.lfs.2025.123635

Cell. 2025 Apr 21:S0092-8674(25)00398-8. doi: 10.1016/j.cell.2025.03.046. Online ahead of print.

ABSTRACT

In humans, selective and promiscuous interactions between 46 secreted chemokine ligands and 23 cell surface chemokine receptors of the G-protein-coupled receptor (GPCR) family form a complex network to coordinate cell migration. While chemokines and their GPCRs each share common structural scaffolds, the molecular principles driving selectivity and promiscuity remain elusive. Here, we identify conserved, semi-conserved, and variable determinants (i.e., recognition elements) that are encoded and decoded by chemokines and their receptors to mediate interactions. Selectivity and promiscuity emerge from an ensemble of generalized ("public/conserved") and specific ("private/variable") determinants distributed among structured and unstructured protein regions, with ligands and receptors recognizing these determinants combinatorially. We employ these principles to engineer a viral chemokine with altered GPCR coupling preferences and provide a web resource to facilitate sequence-structure-function studies and protein design efforts for developing immuno-therapeutics and cell therapies.

PMID:40273912 | DOI:10.1016/j.cell.2025.03.046

Cell. 2025 Apr 17:S0092-8674(25)00397-6. doi: 10.1016/j.cell.2025.03.045. Online ahead of print.

ABSTRACT

Virtually all individuals aged 65 or older develop at least early pathology of Alzheimer's disease (AD), yet most lack disease-causing mutations in APP, PSEN, or MAPT, and many do not carry the APOE4 risk allele. This raises questions about AD development in the general population. Although transcriptional dysregulation has not traditionally been a hallmark of AD, recent studies reveal significant epigenomic changes in late-onset AD (LOAD) patients. We show that altered expression of the LOAD biomarker phosphoglycerate dehydrogenase (PHGDH) modulates AD pathology in mice and human brain organoids independent of its enzymatic activity. PHGDH has an uncharacterized role in transcriptional regulation, promoting the transcription of inhibitor of nuclear factor kappa-B kinase subunit alpha (IKKa) and high-mobility group box 1 (HMGB1) in astrocytes, which suppress autophagy and accelerate amyloid pathology. A blood-brain-barrier-permeable small-molecule inhibitor targeting PHGDH's transcriptional function reduces amyloid pathology and improves AD-related behavioral deficits. These findings highlight transcriptional regulation in LOAD and suggest therapeutic strategies beyond targeting familial mutations.

PMID:40273909 | DOI:10.1016/j.cell.2025.03.045

J Hazard Mater. 2025 Apr 22;493:138383. doi: 10.1016/j.jhazmat.2025.138383. Online ahead of print.

ABSTRACT

Uranium (U) can impact microbially driven soil phosphorus (P) and carbon (C) cycling. However, the response of microbial P and C turnover to U in different soils is not well understood. Through the quantitative assay of P pools and soil organic C (SOC) quantitative assay and sequencing of 16S rRNA gene amplicons and metagenomes, we investigated the effect of U on P and C biotransformation in grassland (GL), paddy soil (PY), forest soil (FT). U (60 mg kg-1) impacted the diversity, interaction and stability of soil bacterial communities, leading to a decrease in available P (AP). Under U stress, organophosphate mineralization substantially contributed to the AP in GL and FT, whereas intracellular P metabolism dominated the AP in PY. Also, the reductive citrate cycle (rTCA cycle) promoted the content of SOC in GL, while the rTCA cycle and complex organic C degradation pathways enhanced the SOC in PY and FT, respectively. Notably, functional bacteria carrying organic C degradation genes could decompose SOC to enhance soil AP. Bacteria developed various resistance strategies to cope with U stress. This study reveals soil-dependent response of microbial P and C cycling and its ecological functions under the influence of radioactive contaminants in different soil systems.

PMID:40273857 | DOI:10.1016/j.jhazmat.2025.138383

Neurology. 2025 May 27;104(10):e213592. doi: 10.1212/WNL.0000000000213592. Epub 2025 Apr 24.

ABSTRACT

BACKGROUND AND OBJECTIVES: Coffee intake is linked to a reduced risk of Parkinson disease (PD), but whether this effect is mediated by gut microbiota and metabolomic changes remains unclear. This study examines PD-associated metabolomic shifts, caffeine metabolism, and their connection to gut microbiome alterations in a multicenter study.

METHODS: We conducted an untargeted serum metabolomic assay using liquid chromatography with high-resolution mass spectrometry on an exploratory cohort recruited from National Taiwan University Hospital (NTUH). A targeted metabolomic assay focusing on caffeine and its 12 downstream metabolites was conducted and validated in an independent cohort from University Malaya Medical Centre (UMMC). In the exploratory cohort, the association of each caffeine metabolite with gut microbiota changes was investigated by metagenomic shotgun sequencing. A clustering-based approach was used to correlate microbiome changes with plasma caffeine metabolite level and clinical severity. Body mass index, antiparkinsonism medication use, and dietary habits (including coffee and tea intake) were recorded.

RESULTS: Sixty-three patients with PD and 54 controls from NTUH formed the exploratory cohort while 36 patients with PD and 20 controls from UMMC served as an validation cohort to replicate the plasma caffeine findings. A total of 5,158 metabolites were detected from untargeted metabolomic analysis, with 3,131 having high confidence for analysis. Compared with controls, the abundance of 56 metabolites was significantly higher and that of 7 metabolites was significantly lower (adjusted p < 0.05 and log2 fold change >1) in patients with PD. Caffeine metabolism was significantly lower in patients with PD (p = 0.0013), and serum levels of caffeine and its metabolites negatively correlated with motor severity (p < 0.01). Targeted metabolomic analysis confirmed reduced levels of caffeine and its metabolites, including theophylline, paraxanthine, 1,7-dimethyluric acid, and 5-acetylamino-6-amino-3-methyluracil, in patients with PD; these findings were replicated in the validation cohort (p < 0.05). A clustering approach found that 56 microbiome species enriched in patients with PD negatively correlated with caffeine and its metabolites paraxanthine and theophylline (both p < 0.05), notably Clostridium sp000435655, Acetatifactor sp900066565, Oliverpabstia intestinalis, and Ruminiclostridium siraeum.

DISCUSSION: This study identifies PD-related changes in microbial-caffeine metabolism compared with controls. Our findings offer insights for future functional research on caffeine-microbiome interactions in PD.

PMID:40273394 | DOI:10.1212/WNL.0000000000213592

ACS Appl Bio Mater. 2025 Apr 24. doi: 10.1021/acsabm.5c00307. Online ahead of print.

ABSTRACT

In public health emergencies or in resource-constrained settings, laboratory-based diagnostic methods, such as RT-qPCR, need to be complemented with accurate, rapid, and accessible approaches to increase testing capacity, as this will translate into better outcomes in disease prevention and management. Here, we develop an original nucleic acid detection platform by leveraging CRISPR-Cas9 and lateral flow immunochromatography technologies. In combination with an isothermal amplification that runs with a biotinylated primer, the system exploits the interaction between the CRISPR-Cas9 R-loop formed upon targeting a specific nucleic acid and a fluorescein-labeled probe to generate a visual readout on a lateral flow device. Our method enables rapid, sensitive detection of nucleic acids, achieving a limit of 1-10 copies/μL in 1 h at a low temperature. We validated the efficacy of the method by using clinical samples of patients infected with SARS-CoV-2. Compared with other assays, it operates with more accessible molecular elements and showcases a robust signal-to-noise ratio. Moreover, multiplexed detection was demonstrated using primers labeled with biotin and digoxigenin, achieving the simultaneous identification of target genes on lateral flow devices with two test lines. We successfully detected SARS-CoV-2 and Influenza A (H1N1) in spiked samples, highlighting the potential of the method for multiplexed diagnostics of respiratory viruses. All in all, this represents a versatile and manageable platform for point-of-care testing, thereby supporting better patient outcomes and enhanced pandemic preparedness.

PMID:40273314 | DOI:10.1021/acsabm.5c00307

Gigascience. 2025 Jan 6;14:giaf028. doi: 10.1093/gigascience/giaf028.

ABSTRACT

We introduce RWRtoolkit, a multiplex generation, exploration, and statistical package built for R and command-line users. RWRtoolkit enables the efficient exploration of large and highly complex biological networks generated from custom experimental data and/or from publicly available datasets, and is species agnostic. A range of functions can be used to find topological distances between biological entities, determine relationships within sets of interest, search for topological context around sets of interest, and statistically evaluate the strength of relationships within and between sets. The command-line interface is designed for parallelization on high-performance cluster systems, which enables high-throughput analysis such as permutation testing. Several tools in the package have also been made available for use in reproducible workflows via the KBase web application.

PMID:40272882 | DOI:10.1093/gigascience/giaf028

Probiotics Antimicrob Proteins. 2025 Apr 24. doi: 10.1007/s12602-025-10549-8. Online ahead of print.

ABSTRACT

The rise of antimicrobial-resistant infections highlights the need for novel therapeutic strategies. Class IIb microcins, a subclass of ribosomally synthesized bacteriocins, play a significant role in modulating bacterial communities by targeting iron acquisition systems in competitive environments, such as the gastrointestinal tract. In this study, we describe and characterize Ec W, a novel class IIb microcin from Escherichia coli strain NCTC10444. This strain is the first known to harbor two homologs of the class IIb microcin biosynthesis cluster and to encode four class IIb microcins in its genome. Sequence analysis revealed that Ec W shows similarity to class IIb microcin Gq W, extending the known repertoire of this microcin class to 18. Heterologous expression and inhibition assays demonstrated potent antimicrobial activity of Ec W against numerous enteric pathogens from the Enterobacteriaceae family, including drug-resistant and hypervirulent strains of E. coli and Klebsiella pneumoniae. These findings suggest that Ec W holds substantial promise as an antimicrobial agent, providing a potential alternative to traditional antibiotics for combating multidrug-resistant pathogens. This study emphasizes the importance of exploring microcins as a novel strategy to tackle the growing threat of infections caused by multidrug-resistant bacteria.

PMID:40272760 | DOI:10.1007/s12602-025-10549-8

Inflamm Res. 2025 Apr 24;74(1):69. doi: 10.1007/s00011-025-02036-1.

ABSTRACT

BACKGROUND: Due to the possible influence of inflammation and gut microbiota in cancers.

METHODS: Fc gamma receptor IIb deficient (FcGRIIb-/-) and cyclic GMP-AMP synthase deficient (cGAS-/-) mice, the model with hyperinflammation and hypo-inflammation, respectively, were subcutaneously injected with MC38 cells (a murine colon cancer cell line).

RESULTS: As such, the tumor burdens were most prominent in cGAS-/- mice, while FcGRIIb-/- mice demonstrated the least tumor sizes compared with wild-type (WT). Intra-tumoral mononuclear cells of FcGRIIb-/- (hematoxylin and eosin staining) were more prominent than other groups with the most dominant CD86-positive cells (mostly M1 proinflammatory macrophages) and the least CD206-positive cells (mostly M2 anti-inflammatory macrophages). While fecal microbiome analysis demonstrated a subtle difference among mouse strains with tumors at 24 days post-cancer injection, serum cytokines (TNF-α, IL-6, IL-1α, IFN-β, IFN-γ, IL-23, IL-12p70, GM-CSF, IL-27, and IL-17A) (fluorescence-encoded bead multiplex assay) and the expansion of immune cells in the spleens of FcGRIIb-/- mice (flow cytometry) were more prominent than others. With bone marrow-derived macrophages, prominent M1 (LPS) and M2 polarization (IL4 and cancer supernatant) in FcGRIIb-/- and cGAS-/- macrophages, respectively, were demonstrated using polymerase chain reaction and flow cytometry. The most prominent tumoricidal activity (percentage of F4/80-negative flexible780 viable dye-positive cells using flow cytometry) of LPS-stimulated FcGRIIb-/- macrophages compared with other groups supported dominant pro-inflammatory characteristics of FcGRIIb-/- macrophages.

CONCLUSIONS: In conclusion, the protective and promoting effects of FcGRIIb-/- and cGAS-/- mice, respectively, against cancers are partly related to macrophage functions with a subtle correlation to fecal microbiota, and FcGRIIb inhibitors and cGAS enhancers might be helpful for cancer adjuvant treatment.

PMID:40272597 | DOI:10.1007/s00011-025-02036-1

Clin Chem. 2025 Apr 24:hvaf043. doi: 10.1093/clinchem/hvaf043. Online ahead of print.

ABSTRACT

BACKGROUND: In 2009, the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines established standards for the design, execution, and reporting of quantitative PCR (qPCR) in research. The expansion of qPCR into numerous new domains has driven the development of new reagents, methods, consumables, and instruments, requiring revisions to best practices that are tailored to the evolving complexities of contemporary qPCR applications.

CONTENT: Transparent, clear, and comprehensive description and reporting of all experimental details are necessary to ensure the repeatability and reproducibility of qPCR results. These revised MIQE guidelines reflect recent advances in qPCR technology, offering clear recommendations for sample handling, assay design, and validation, along with guidance on qPCR data analysis. Instrument manufacturers are encouraged to enable the export of raw data to facilitate thorough analyses and re-evaluation by manuscript reviewers and interested researchers. The guidelines emphasize that quantification cycle (Cq) values should be converted into efficiency-corrected target quantities and reported with prediction intervals, along with detection limits and dynamic ranges for each target, based on the chosen quantification method. Additionally, best practices for normalization and quality control are outlined and reporting requirements have been clarified and streamlined. The aim is to encourage researchers to provide all necessary information without undue burden, thereby promoting more rigorous and reproducible qPCR research.

SUMMARY: Building on the collaborative efforts of an international team of researchers, we present updates, simplifications, and new recommendations to the original MIQE guidelines, designed to maintain their relevance and applicability in the context of emerging technologies and evolving qPCR applications.

PMID:40272429 | DOI:10.1093/clinchem/hvaf043

Nucleic Acids Res. 2025 Apr 22;53(8):gkaf329. doi: 10.1093/nar/gkaf329.

ABSTRACT

Inverted repeats are repetitive elements that can form hairpin and cruciform structures. They are linked to genomic instability; however, they also have various biological functions. Their distribution differs markedly across taxonomic groups in the tree of life, and they exhibit high polymorphism due to their inherent genomic instability. Advances in sequencing technologies and declined costs have enabled the generation of an ever-growing number of complete genomes for organisms across taxonomic groups in the tree of life. However, a comprehensive database encompassing inverted repeats across diverse organismal genomes has been lacking. We present invertiaDB, the first comprehensive database of inverted repeats spanning multiple taxa, featuring repeats identified in the genomes of 118 101 organisms across all major taxonomic groups. For each organism, we derived inverted repeats with arm lengths of at least 10 bp, spacer lengths up to 8 bp, and no mismatches in the arms. The database currently hosts 34 330 450 inverted repeat sequences, serving as a centralized, user-friendly repository to perform searches and interactive visualizations, and download existing inverted repeat data for independent analysis. invertiaDB is implemented as a web portal for browsing, analyzing, and downloading inverted repeat data. invertiaDB is publicly available at https://invertiadb.netlify.app/homepage.html.

PMID:40272360 | DOI:10.1093/nar/gkaf329

Microscopy (Oxf). 2025 Apr 24:dfaf020. doi: 10.1093/jmicro/dfaf020. Online ahead of print.

ABSTRACT

Genome-wide profiling of gene expression levels in cells, such as transcriptomics and proteomics, is a powerful experimental approach in modern biology, allowing not only efficient exploration of the genetic elements responsible for biological phenomena of interest, but also characterization of the global constraints behind plastic phenotypic changes of cells that accompany large-scale remodeling of omics profiles. To understand how individual cells change their molecular profiles to achieve specific phenotypic changes in phenomena such as differentiation, cancer metastasis and adaptation, it is crucial to characterize the dynamics of cellular phenotypes and omics profiles simultaneously at the single-cell level. Especially in the last decade, significant technical progress has been made in the in situ identification of omics profiles of cells on the microscope. However, most approaches still remain destructive and cannot unravel the post-measurement dynamics. In recent years, Raman spectroscopy-based methods for omics inference have emerged, allowing the characterization of genome-wide molecular profile dynamics in living cells. In this review, we give a brief overview of the recent development of imaging-based omics profiling methods. We then present the approach to infer omics profiles from single-cell Raman spectra. Since Raman spectra can be obtained from living cells in a non-destructive and non-staining manner, this method may open the door to live-cell omics.

PMID:40271815 | DOI:10.1093/jmicro/dfaf020

Nucleic Acids Res. 2025 Apr 24:gkaf335. doi: 10.1093/nar/gkaf335. Online ahead of print.

ABSTRACT

The Bakta command line application is widely used and one of the most established tools for bacterial genome annotation. It balances comprehensive annotation with computational efficiency via alignment-free sequence identifications. However, the usage of command line software tools and the interpretation of result files in various formats might be challenging and pose technical barriers. Here, we present the recent updates on the Bakta web server, a user-friendly web interface for conducting and visualizing annotations using Bakta without requiring command line expertise or local computing resources. Key features include interactive visualizations through circular genome plots, linear genome browsers, and searchable data tables facilitating the interpretation of complex annotation results. The web server generates standard bioinformatics outputs (GFF3, GenBank, EMBL) and annotates diverse genomic features, including coding sequences, non-coding RNAs, small open reading frames (sORFs), and many more. The development of an auto-scaling cloud-native architecture and improved database integration led to substantially faster processing times and higher throughputs. The system supports FAIR principles via extensive cross-reference links to external databases, including RefSeq, UniRef, and Gene Ontology. Also, novel features have been implemented to foster sharing and collaborative interpretation of results. The web server is freely available at https://bakta.computational.bio.

PMID:40271661 | DOI:10.1093/nar/gkaf335

iScience. 2025 Mar 26;28(5):112167. doi: 10.1016/j.isci.2025.112167. eCollection 2025 May 16.

ABSTRACT

Dormant lung adenocarcinoma (LUAD) cells in the bone microenvironment can re-emerge as metastatic disease through osteoclast interactions. Using a 3D dormancy model and a mouse bone metastasis model, this study reveals that arachidonic acid (AA) is the initiating molecule transferred from osteoclasts to dormant LUAD cells, triggering their activation. Dormant LUAD cells uptake AA through CD36, which activates the PPARγ-ANGPTL4 pathway and activates tumor cells. There is a dose-response relationship in the activation effect of AA, and inhibiting AA metabolism prevents this reactivation. The study also finds that the serum levels of AA and ANGPTL4 are significantly elevated in patients with clinical bone metastases compared to those without. This research confirms that osteoclasts transmit AA via the CD36-PPARγ-ANGPTL4 axis to activate dormant LUAD cells, suggesting that AA and ANGPTL4 may serve as valuable biomarkers and potential clinical applications in treatment and prediction of LUAD bone metastasis.

PMID:40271019 | PMC:PMC12018030 | DOI:10.1016/j.isci.2025.112167