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PubMed2026

Insights into phylogenetic relationships of Veronica species (Plantaginaceae) based on comparative chloroplast genomics.

INTRODUCTION: Veronica L. is one of the most species-rich genera in Plantaginaceae and several species have medicinal, horticultural, or ecological value. METHODS: In this study, the complete chloroplast genomes of three Veronica species were assembled and annotated using Illumina sequencing data. RESULTS: The plastomes exhibited a typical quadripartite structures, with total lengths of 150,202 bp for Veronica biloba L., 151,159 bp for Veronica ciliata Fisch. and 151,098 bp for Veronica vandellioides Maxim. Each genome contained 130-132 unique genes, including 86-87 protein-coding genes, 36-37 tRNA genes, and 8 rRNA genes. Comparative analyses of 24 Veronica plastomes indicated that the IR/SC junctions were largely conserved, although slight boundary shifts occurred around rps19, ndhF, and ycf1. Forward, palindromic, complement, and reverse repeats were detected, and A/T mononucleotide repeats were the dominant SSR type. Nucleotide diversity analysis identified rpl32-trnL, trnK-rps16, rpl32, ycf1, ndhF, accD, matK, and rpoB as highly variable regions. Phylogenetic analyses recovered Veronica as a well-supported monophyletic lineage and clarified the plastid positions of the three newly sequenced species. Divergence time estimation suggested that the estimation suggested of Veronica was around 14.9 Ma, with V. biloba, V. ciliata and V. vandellioides diverging approximately 3.9 Ma, 0.6 Ma, and 6.9 Ma, respectively. DISCUSSION: Because the analyses were based on plastid genomes, the inferred topology should be interpreted as chloroplast phylogenetic evidence rather than a complete species-history reconstruction. These results provide plastome resources and molecular evidence for taxonomy, species identification, and future evolutionary studies of Veronica.

Plantaginaceae↗

PubMed2026

The genome sequence of Veronica verna L., 1753 (Lamiales: Plantaginaceae).

We present a genome assembly of Veronica verna (Spring Speedwell; Streptophyta; Magnoliopsida; Lamiales; Plantaginaceae). The genome sequence has a total length of 463.88 megabases. Most of the assembly (98.85%) is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial sequence has a length of 311.81 kilobases and the plastid genome assembly has a length of 149.82 kilobases. Gene annotation of this assembly on Ensembl identified 22 903 protein-coding genes. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.

Asterales↗

PubMed2026

Cognitive Behavior vs Bright Light Therapy for Insomnia in Women Undergoing Chemotherapy for Breast Cancer: A Randomized Clinical Trial.

IMPORTANCE: Women receiving chemotherapy for breast cancer experience insomnia and fatigue, which impair quality of life. To date, no randomized clinical trial (RCT) has evaluated the use of cognitive behavior therapy for insomnia (CBT-I) and bright light therapy (BLT) both alone and in combination, and few have evaluated the use of either during chemotherapy. OBJECTIVE: To determine the main effects of CBT-I and BLT on insomnia and fatigue symptoms in women undergoing chemotherapy for breast cancer. DESIGN, SETTING, AND PARTICIPANTS: Sleep, Cancer, Rest (SleepCARE) was a 6-week, 2 × 2 factorial, superiority, parallel RCT conducted at 5 metropolitan and regional hospitals in Australia from January 22, 2021, to August 21, 2024. Participants were women (aged ≥18 years) receiving chemotherapy for early or metastatic breast cancer. INTERVENTIONS: Two brief interventions were administered: CBT-I and BLT alone (using light glasses at 1500 lux) and in combination, creating 4 groups (CBT-I alone, BLT alone, CBT-I plus BLT, and sleep hygiene education [SHE]). All interventions included SHE. The interventions lasted 6 weeks and included a 1:1 consultation session, emails sent once or twice per week, and a midpoint call for all groups, as well as light glasses for the BLT groups. MAIN OUTCOMES AND MEASURES: Dual primary outcomes were Insomnia Severity Index (ISI) scores and Patient-Reported Outcomes Measurement Information System (PROMIS)-Fatigue T scores. Both are patient-reported outcome measures and measure insomnia and fatigue symptoms, respectively. Assessments occurred via surveys administered at baseline and at the midpoint (3 weeks), postintervention (6 weeks), and follow-up (3 months and 6 months) periods. Modified intention-to-treat analyses used latent growth models. RESULTS: Of the 219 women enrolled (mean [SD] age, 50.7 [10.8] years; 54 [26.9%] with metastatic cancer), 55 were randomized to CBT-I, 55 to BLT, 52 to CBT-I plus BLT, and 57 to SHE. A total of 208 women (95.0%) with any data at any time point were analyzed. Insomnia symptoms (ISI score mean difference [MD], -2.19 [95% CI, -3.33 to -1.05] points; P = .002) but not fatigue symptoms (PROMIS-Fatigue score MD, -0.90 [95% CI, -3.08 to 1.28] points; P = .52) improved more in the CBT-I groups compared with the non-CBT-I groups. The BLT groups (compared with the non-BLT groups) did not differ in insomnia symptoms (ISI score MD, -0.88 [95% CI, -2.02 to 0.26] points; P = .26) or fatigue symptoms (PROMIS-Fatigue score MD, -0.71 [95% CI, -2.89 to 1.47] points; P = .52). Comparable results emerged in the high-adherence subgroup and in the subgroups with high initial insomnia and fatigue symptoms. However, exploratory subgroup analyses in women with metastatic breast cancer showed that BLT (vs non-BLT) improved insomnia symptoms (ISI score MD, -2.87 [95% CI, -5.06 to -0.67] points; P = .01) and fatigue symptoms (PROMIS-Fatigue score MD, -5.16 [95% CI, -9.57 to -0.76] points; P = .02). CONCLUSIONS AND RELEVANCE: In the SleepCARE RCT of CBT-I and BLT administered for 6 weeks to women receiving chemotherapy for breast cancer, CBT-I improved insomnia but not fatigue compared with SHE or BLT. BLT did not produce greater improvements in fatigue or insomnia symptoms compared with non-BLT treatment. The study findings indicate that brief CBT-I, but not BLT, may reduce insomnia symptoms among women receiving chemotherapy for breast cancer. TRIAL REGISTRATION: ANZCTR Identifier: ACTRN12620001133921.

Humans↗

PubMed2026

Regulation of the lncRNA NEAT1 by p53-ΔNp63 crosstalk modulates the DNA damage response and therapeutic efficacy in HNSCC.

Head and neck squamous cell carcinomas (HNSCCs) are characterized by recurrent genetic alterations, including the inactivation of the tumor suppressor TP53 gene and dysregulation of the TP63 gene. The TP63 gene encodes multiple isoforms, among which the N-terminal truncated isoform ΔNp63 is fundamental for the integrity of stratified epithelial tissues. We previously demonstrated that ΔNp63 represses the expression of the lncRNA NEAT1. Here, we investigated the functional crosstalk between p53 and ΔNp63 in modulating NEAT1 expression following genotoxic stress. We found that upon genotoxic insults, p53 activation and the concomitant downregulation of ΔNp63 promote NEAT1 transcription. In p53-proficient HNSCC cells, NEAT1 targeting leads to increased DNA damage, highlighting its potential role in maintaining genomic stability and facilitating efficient DNA repair. Importantly, we showed that histone deacetylase inhibitors (HDACis) upregulate NEAT1 expression independently of p53, and NEAT1 silencing enhances HDACis-induced DNA damage. Overall, our findings establish NEAT1 as an early regulator of the DNA damage response in HNSCCs and suggest that combining NEAT1 targeting with HDAC inhibition may potentiate therapeutic efficacy, particularly in TP53-mutant HNSCCs.

DNA damage↗

PubMed2018

High-Throughput Metabolomics by 1D NMR.

Metabolomics deals with the whole ensemble of metabolites (the metabolome). As one of the -omic sciences, it relates to biology, physiology, pathology and medicine; but metabolites are chemical entities, small organic molecules or inorganic ions. Therefore, their proper identification and quantitation in complex biological matrices requires a solid chemical ground. With respect to for example, DNA, metabolites are much more prone to oxidation or enzymatic degradation: we can reconstruct large parts of a mammoth's genome from a small specimen, but we are unable to do the same with its metabolome, which was probably largely degraded a few hours after the animal's death. Thus, we need standard operating procedures, good chemical skills in sample preparation for storage and subsequent analysis, accurate analytical procedures, a broad knowledge of chemometrics and advanced statistical tools, and a good knowledge of at least one of the two metabolomic techniques, MS or NMR. All these skills are traditionally cultivated by chemists. Here we focus on metabolomics from the chemical standpoint and restrict ourselves to NMR. From the analytical point of view, NMR has pros and cons but does provide a peculiar holistic perspective that may speak for its future adoption as a population-wide health screening technique.

Animals↗

PubMed2025

Methylation patterns associated with TTV load in geriatric hospitalized patients: an exploratory functional analysis.

Torque Teno Virus (TTV) is a widespread commensal virus within the human virome, characterized by a high prevalence in human population and an unclear pathogenic role. Over the past three decades, TTV has garnered increasing attention due to its ability to establish lifelong chronic viremia, which intriguingly fluctuates among individuals in relation to immune competence status, with a typical peak after an organ transplantation, followed by a plateau and a slow decrease. The regulatory mechanisms underlying TTV infection remain elusive, and factors influencing its interactions with the immune system have yet to be identified. To explore this complex interplay, we analyzed DNA methylation patterns associated with TTV load in older adult hospitalized patients (mean age: 83.15 ± 7.49) from the PROMOTERA cohort. In this study, we present for the first time the identification of differentially methylated probes (DMPs) correlated to TTV load in our cohort. The statistically significant DMPs were located in genes involved in immune regulation and lipid metabolism. To further characterize these findings, we performed an exploratory enrichment analysis by applying several p-value thresholds, which yielded multiple gene lists derived from the sets of significant probes. Genes associated with this epigenetic signature were found to enrich functional pathways related to immune activation, leukocyte differentiation, and cytokine production, while additional significantly enriched gene sets were involved in cell-cell adhesion and cell migration processes. Since our analysis followed an exploratory approach, these results should be interpreted as hypothesis-generating and warrant further investigation.

Humans↗

PubMed2026

Evaluation of Indigenous Bacillus Strains from Asian Fermented Foods for Probiotic Properties.

Bacillus species hold particular importance due to their versatile enzymatic repertoire and ability to synthesize diverse bioactive metabolites. In this study, two fermented food-derived strains, Bacillus siamensis BB3 (from douchi) and Bacillus velezensis TMA10 (from tapai) were evaluated for their probiotic, anti-microbial and functional potentials. Both strains exhibited desirable probiotic characteristics, including desirable tolerance to simulated gastric and intestinal conditions, with BB3 showing greater acid tolerance than TMA10. Safety assessments confirmed the absence of hemolytic activity, virulence factors and antibiotic resistance genes. Whole genome sequencing showed that the strains harbored genomic sequences for a wide range of metabolites, including non-ribosomal peptides and polyketides. Ethyl acetate (EtOAc) extracts from both strains demonstrated broad-spectrum anti-microbial activity against several indicator microorganisms, including Listeria grayi, Bacillus cereus, Serratia marcescens, Escherichia coli, and Pseudomonas aeruginosa, with TMA10 additionally inhibiting MRSA and Streptococcus mutans. Liquid Chromatography-Mass Spectrometry profiling identified key anti-microbial compounds, namely surfactins, macrolactins, bacillaene from BB3 and TMA10. In addition, difficidins were also detected from TMA10. Genomic analysis further indicated diverse carbohydrate utilization capacities; both strains encoded pathways for sucrose, raffinose-family oligosaccharides and lactose metabolism, while TMA10 possessed pathways for trehalose, glucomannan and arabinoxylan degradation. Both strains also showed anti-oxidant activity, with enhanced effects observed in their cell-free supernatants and heat-killed preparations. Overall, these findings highlight BB3 and TMA10 as promising candidates for the development of fermented food-derived Bacillus probiotics and functional cultures with anti-microbial, anti-oxidant, and broad carbohydrate-utilization capabilities.

Bacillus↗

PubMed2024

Conservation of antiviral systems across domains of life reveals immune genes in humans.

Deciphering the immune organization of eukaryotes is important for human health and for understanding ecosystems. The recent discovery of antiphage systems revealed that various eukaryotic immune proteins originate from prokaryotic antiphage systems. However, whether bacterial antiphage proteins can illuminate immune organization in eukaryotes remains unexplored. Here, we use a phylogeny-driven approach to uncover eukaryotic immune proteins by searching for homologs of bacterial antiphage systems. We demonstrate that proteins displaying sequence similarity with recently discovered antiphage systems are widespread in eukaryotes and maintain a role in human immunity. Two eukaryotic proteins of the anti-transposon piRNA pathway are evolutionarily linked to the antiphage system Mokosh. Additionally, human GTPases of immunity-associated proteins (GIMAPs) as well as two genes encoded in microsynteny, FHAD1 and CTRC, are respectively related to the Eleos and Lamassu prokaryotic systems and exhibit antiviral activity. Our work illustrates how comparative genomics of immune mechanisms can uncover defense genes in eukaryotes.

Humans↗

PubMed2024

Payer perspectives on genomic testing in the United States: A systematic literature review.

PURPOSE: Health care stakeholders' perspectives on the value of genomic testing vary widely and directly affect the access and practice of genomic medicine. To our knowledge, a review of US health care payers' perspectives on genomic testing has not been performed. METHODS: We conducted a systematic literature review of US payers' perspectives on genomic testing in the MEDLINE, PubMed, and Cumulative Index to Nursing and Allied Health Literature (CINAHL) databases. Of the 161 nonduplicate records screened, we summarized findings from 20 included records, and using the framework method, common domains were recorded. RESULTS: Domains included clinical utility, coverage decision frameworks, potential harms, costs, paying for research, demand/pressure, the flexibility of outcomes considered, and personal utility. There was consensus on the definition of clinical utility as improved health outcomes, and the nuances of genomic testing were reported as challenging to fit within existing coverage decision frameworks. Perspectives varied on accepting broader outcomes or uses of genomic testing and whether costs influence coverage decisions. Study methodologies were heterogeneous. CONCLUSION: A deeper understanding of how payers approach genomic testing may allow comparison with other stakeholders' perspectives and may identify challenges, opportunities, and solutions to align a conceptual and evidentiary framework better to demonstrate the value of genomic testing.

Humans↗

PubMed2026

Deletion of the MALAT1 RNA 3' end promotes transcript decay and inhibits proliferation in gastric and breast cancer cells.

The long non-coding RNA MALAT1 is a conserved oncogenic driver whose function relies on a 3' triple-helix motif. While its biochemistry is well-characterized in vitro, the endogenous requirement for this motif in regulating the stability of the transcript and other genes residing in its locus remains unclear. In this study, we employed a dual-sgRNA CRISPR-Cas9 approach to systematically excise triple-helix-forming sequences from the native MALAT1 locus in gastric (AGS) and breast (MCF7) cancer cells. Our findings demonstrate that the 3' end strongly contributes to MALAT1 stability. Perturbations ranging from genomic deletions to a single-base changes trigger transcript collapse and rapid exonucleolytic decay, while the biogenesis of the small RNA mascRNA (a byproduct of MALAT1, also involved in cancer) remains decoupled and unaffected. In cellulo, DMS probing reveals that edited transcripts retain structural complexity in the 3' region. Phenotypically, structural disruption of the 3' end significantly impairs proliferation of both cancer cellular models. These results identify the 3' triple-helix as a determinant of MALAT1 stability and provide endogenous validation for its role in the analyzed AGS and MCF7 cells.

Cancer↗

PubMed2026

p62/SQSTM1-KEAP1 complex prevents clearance of ubiquitinated Z alpha-1 antitrypsin and aggravates liver proteotoxicity.

Liver disease in Alpha-1 antitrypsin deficiency (AATD) is caused by the toxic accumulation of mutant Z alpha-1 antitrypsin (Z-AAT) within the endoplasmic reticulum (ER) of hepatocytes. Livers from PiZ transgenic mice expressing the human Z-AAT and AATD patients who are homozygotes for the allele expressing Z-AAT were found to have increased p62/SQSTM1, a multifunctional protein involved in protein homeostasis. The goal of this study was to elucidate the involvement of p62/SQSTM1 in the formation of Z-AAT globules that are responsible for liver injury in AATD. In the present study, we found that p62/SQSTM1 decorated ubiquitin-positive, Periodic-Acid Shiff-diastase-resistant Z-AAT globules and interacted with Z-AAT at the ER-cytosol interface. Genetic ablation of p62/SQSTM1 in PiZ mice (PiZ;p62-/-) led to marked reduction in hepatic Z-AAT globules and polymers, and decreased serum Z-AAT, highlighting a central role for p62/SQSTM1 in disease pathogenesis. Moreover, hepatocyte-specific somatic deletion of the ubiquitin-association (UBA) domain of p62/SQSTM1 reduced Z-AAT aggregation. Furthermore, KEAP1 was identified as a binding partner of p62/SQSTM1-Z-AAT complex, leading to nuclear translocation and activation of NRF2. Inhibition of KEAP1-p62/SQSTM1 interaction reduced the abundance of p62 and phosphorylated p62, decreased intracellular Z-AAT, and redistributed NRF2 to the cytoplasm. In conclusion, this study identifies p62/SQSTM1 as a regulator of Z-AAT proteostasis and link Z-AAT/p62 accumulation to KEAP1 sequestration and NRF2 pathway activation in liver disease due to Z-AAT.

AATD↗

PubMed2026

Predicting bloodstream infection by plasma cell-free metagenomic sequencing: a prospective cohort study.

BACKGROUND: Patients receiving myelosuppressive chemotherapy or haematopoietic cell transplantation are at high risk for life-threatening bloodstream infections. A novel pre-emptive treatment paradigm guided by pathogen detection before symptoms appear might reduce this risk, but no validated screening test is available. This study evaluated the sensitivity and specificity of plasma microbial cell-free DNA metagenomic sequencing (mcfDNA-Seq) for predicting bloodstream infections in children and adolescents receiving therapy for high-risk leukaemia. METHODS: In this prospective cohort study, between Aug 9, 2017, and Feb 28, 2022, leftover clinical plasma samples were prospectively collected up to once per day from patients who were younger than 25 years, receiving care for leukaemia at St Jude Children's Research Hospital (Memphis, TN, USA), and at high risk for life-threatening bloodstream infections. mcfDNA-Seq was used to identify pathogen DNA in blood samples obtained during the 7 days before to 1 day after bloodstream infection onset, and in control samples from the same population in the absence of fever or infection. The testing laboratory was masked to sample status. Primary outcomes were predictive sensitivity of mcfDNA-Seq for detecting the expected bloodstream infection pathogen during the 3 days preceding the day of bloodstream infection onset, with a prespecified favourable sensitivity of 50%, and predictive specificity of mcfDNA-Seq in control samples. Exploratory analyses comprised assessing sensitivity and specificity restricted to bacteria or common bloodstream infection pathogens, and after applying a data-derived DNA fragment concentration cutoff; estimating the predictive sensitivity on each of the 7 days before bloodstream infection onset; identifying clinical characteristics that affected predictive sensitivity or specificity; and examining the clinical relevance of additional organisms identified by mcfDNA-Seq during bloodstream infection episodes. Diagnostic sensitivity was also assessed on samples collected on the day of, or day after, diagnosis of bloodstream infection. This study is registered with ClinicalTrials.gov, NCT03226158. FINDINGS: 94 evaluable bloodstream infections occurred in 60 (38%) of 158 enrolled participants; 19 episodes were previously described in the pilot phase of this study. The predictive sensitivity of mcfDNA-Seq was 51·9% (95% CI 40·5-63·1) for all bloodstream infection episodes, 53·8% (42·2-65·2) for bacterial infection only, and 51·9% (40·5-63·1) when applying a DNA fragment concentration cutoff of 140 molecules per μL. Sensitivity was lowest at day -7 and increased daily until the day of diagnosis. Diagnostic sensitivity was 81·3% (95% CI 71·0-89·1) for all bloodstream infection episodes and 83·1% (72·9-90·7) for bacterial infections only. Predictive specificity was 82·7% (95% CI 76·0-88·2), but improved to 88·9% (83·0-93·3) for common bloodstream infection pathogens, and to 93·8% (88·9-97·0) when also applying the DNA fragment concentration cutoff. Predictive sensitivity was higher in participants with acute lymphoblastic leukaemia (adjusted odds ratio [aOR] 11·1 [1·7-74·2] vs those with acute myeloid leukaemia), and it was lower in polymicrobial infections (aOR 0·0 [0·0-0·2] vs monomicrobial Gram-positive infections). Clinical false-positive results were positively associated with gastrointestinal disturbance alone (p=0·037) or combined with recent administration of high-dose cytarabine (p=0·012). Additional organisms identified by mcfDNA-Seq that were not identified by blood culture were less likely than expected organisms to have an increasing DNA concentration during the days preceding bloodstream infection diagnosis. INTERPRETATION: mcfDNA-Seq can detect causative pathogens before the onset of some bloodstream infection episodes in profoundly immunocompromised patients. Predictive specificity might be improved by restricting results to a subgroup of relevant organisms, excluding patients with high risk of false-positive results, or applying a higher concentration cutoff. Clinical trials are needed to evaluate mcfDNA-Seq-guided pre-emptive therapy for preventing life-threatening bloodstream infections in patients with high risk. FUNDING: The National Cancer Institute, American Lebanese Syrian Associated Charities, St Jude Children's Research Hospital, and Karius.

Adolescent↗

PubMed2026

Urine Proteomics as a Source of Biological Information and Outcome Predictor in Living Kidney Transplantation.

Kidney transplantation (KTx) is the preferred treatment for kidney failure. However, post-transplant management is challenging due to the limited lifespan of transplanted organs. Current methods for monitoring post-transplant complications are invasive and have limitations. Therefore, there is an urgent need for novel non-invasive biomarkers. This study investigates the proteomic composition of urine to understand renal biology during the process of transplantation and to identify potential markers for outcome prediction. Urine samples were collected from donors before transplantation and from recipients 4 weeks and 1 year after transplantation. Proteomic analysis was performed using mass spectrometry and label-free quantification. Statistical analyses included principal component analysis (PCA) and enrichment analysis. The resulting key findings were confirmed in an independent validation cohort. In addition, correlative regression models to evaluate the relationship between protein abundance and clinical outcomes in the further course after transplantation were performed. 106 urine samples in the setting of 70 kidney transplantations were analyzed. PCA revealed distinct clustering of donor and recipient samples, indicating significant proteomic changes after transplantation. Hierarchical clustering and gene ontology analysis identified molecular changes as a response to transplantation and showed an over-representation of relevant pathways related to inflammation, cell immune response and coagulation in both the original and validation cohorts. Multivariate regression analysis, including linear and logistic regression, identified 11 potential protein biomarkers, including ORM2, IL1RAP, APP, and FABP4 as predictors of eGFR 12 months after transplantation and 1 HP as a predictor of infections within the first year after transplantation, respectively. This study underscores the potential of non-invasive urine proteomics for identifying biological processes involved in kidney transplantation and for enhancing post-transplant monitoring and outcome prediction. We identified 12 potential biomarkers with added value to standard clinical parameters linked to transplant outcomes, which will be promising candidates for future outcome monitoring after KTx.

Humans↗

PubMed2026

In genomes we trust: Assessing genomic reliability within the family Nectriaceae.

Reliable evolutionary inference increasingly depends on public genome resources, and the effects of uneven assembly quality, incomplete metadata, and biased taxonomic sampling remain poorly quantified. Using the species-rich fungal lineage Nectriaceae as a model system, we analysed 1530 genome sequence assemblies to assess metadata completeness, sampling representation, and genome quality. One-third of the assemblies lacked essential metadata, sequencing was heavily skewed toward a few agriculturally important lineages, and sampling of many genera was limited or nonexistent. BUSCO and QUAST metrics revealed substantial heterogeneity in assembly quality, with widespread fragmentation and numerous assemblies falling outside expected quality thresholds. From 763 single-copy orthologs identified in 576 higher-quality genomes, we reconstructed a phylogenomic backbone and quantified gene- and site-level concordance across the tree. Although major clades were broadly recovered, extensive gene-tree discordance and a polyphyletic Fusarium nisikadoi species complex revealed unresolved boundaries and conflict among loci. These results show how data quality, incomplete sampling, and discordant genomic histories can constrain phylogenomic resolution, and provide a general framework for improving comparative genomic resources and large-scale evolutionary inference.

Gene-tree discordance↗

PubMed2026

Effects of dietary interventions on gut microbiota and related cardiometabolic changes in pediatric obesity: a systematic review and meta-analysis.

BACKGROUND: Gut microbiota imbalances may contribute to obesity, yet whether dietary interventions can modulate the microbiota and improve metabolic health in pediatrics has not been thoroughly reviewed. This systematic review and meta-analysis explores the impact of dietary interventions on the gut microbiota of children and adolescents with overweight or obesity, and its association with cardiometabolic improvements. METHODS: A systematic search of clinical trials in Pubmed, Cochrane and EMBASE was conducted following PRISMA guidelines (PROSPERO n°CRD42024505494). Risk of bias was assessed with RoB2 and ROBINS, for randomized and non-randomized intervention studies. RESULTS: Overall, 60 articles were assessed for full-text eligibility, 8 were included, and 4 provided alpha-diversity data for meta-analysis. A total of 200 participants were included (6-16 years). Six studies implemented calorie-restricted diets, one a low free-sugar diet, and one CHILD-1 diet. The meta-analysis revealed a significant increase in Chao1 (48.76 [95%CI 1.81; 95.70]; I2 = 86.8%, p < 0.001) following a balanced calorie-restricted dietary intervention. Although there was heterogeneity in taxa-level changes, several butyrate-producing genera (Clostridium XVIa, Coprococcus, Roseburia, Faecalibacterium, Blautia, Butyricimonas) increased following dietary intervention. CONCLUSIONS: Balanced dietary interventions with calorie-restriction adequate for pediatric age could increase gut microbiota richness and butyrate-producing bacteria abundance. Future trials should clarify diet-driven gut microbiota changes in childhood obesity and related metabolic changes. IMPACT: Balanced calorie restriction diet may increase gut microbiota richness in childhood obesity Butyrate-producer expansion needs long-term dietary intervention Gaps in linking microbiota-metabolism interplay in pediatric obesity.

Journal Article↗

PubMed2024

Exploring the transcriptional cooperation between RUNX2 and its associated elncRNA RAIN.

Recent insights into the mechanisms controlling gene expression identified enhancer-associated long non-coding RNAs (elncRNAs) as master players of transcription in cancers. RUNX2, a mammalian RUNT-related transcription factor, is increasingly recognized in cancer biology for its role in supporting survival and progression also in thyroid cancer (TC). We recently identified, within the RUNX2 locus, a novel elncRNA that we named RAIN (RUNX2 associated intergenic lncRNA). We showed that RAIN and RUNX2 expression correlate in TC, both in vitro and in vivo, and that RAIN promotes RUNX2 expression by interacting with and affecting the activity of the RUNX2 P2 promoter through two distinct mechanisms. Here, we took forward these observations to explore the genome-wide transcriptional function of RAIN and its contribution to the RUNX2-dependent gene expression program in TC. By combining multiple omics data, we demonstrated that RAIN functionally cooperates with RUNX2 to the regulation of a subset of functionally related genes involved in promoting matrix remodeling, migration, and loss of differentiation. We showed that RAIN interacts with RUNX2 and its expression is required for the efficient recruitment of this TF to its target regulatory regions. In addition, our data revealed that besides RUNX2, RAIN governs a hierarchically organized complex transcriptional program by controlling a core of cancer-associated TFs that, in turn, orchestrate the expression of downstream genes. This evidence indicates that the functional cooperation observed between RAIN and RUNX2 can be a diffuse work mechanism for this elncRNA.

Core Binding Factor Alpha 1 Subunit↗

PubMed2025

Modulating the PPARγ pathway upregulates NECTIN4 and enhances chimeric antigen receptor (CAR) T cell therapy in bladder cancer.

With the approval of the antibody-drug conjugate enfortumab vedotin (EV), NECTIN4 has emerged as a bona fide therapeutic target in urothelial carcinoma (UC). Here, we report the development of a NECTIN4-directed chimeric antigen receptor (CAR) T cell, which exhibits reactivity across cells expressing a range of endogenous NECTIN4, with enhanced activity in high expressors. We demonstrate that the PPARγ pathway, critical for luminal differentiation, transcriptionally controls NECTIN4, and that the PPARγ agonist rosiglitazone primes and augments NECTIN4 expression, thereby increasing sensitivity to NECTIN4-CAR T cell-mediated killing. NECTIN4-CAR T cells have potent anti-tumor activity even against EV resistant cells, which largely retain NECTIN4 expression, including in a post-EV biopsy cohort. Our results elucidate a therapeutically actionable mechanism that UC cells use to control NECTIN4 expression and suggest therapeutic approaches that leverage PPARγ agonists for rational combinations with NECTIN4-targeting agents in UC, as well as future potential treatment options for EV-refractory patients.

Humans↗

PubMed2025

Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem.

Emerging spatial multiomics technologies provide an increasingly large amount of information content at multiple scales. However, it remains challenging to efficiently represent and harmonize diverse spatial datasets. Here we present Giotto Suite, a suite of modular packages that provides scalable and extensible end-to-end solutions for multiscale and multiomic data analysis, integration and visualization. At its core, Giotto Suite is centered around an innovative data framework, allowing the representation and integration of spatial omics data in a technology-agnostic manner. Giotto Suite integrates molecular, morphology, spatial and annotated feature information to create a responsive and flexible workflow, as demonstrated by applications to several state-of-the-art spatial technologies. Furthermore, Giotto Suite builds upon interoperable interfaces and data structures that bridge the established fields of genomics and spatial data science in R, thereby enabling independent developers to create custom-engineered pipelines. As such, Giotto Suite creates an immersive and multiscale ecosystem for spatial multiomic data analysis.

Genomics↗