iiinova — where your digital self keeps evolving

Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 25/10/2026

new paper: "Enhancing Interpretation of Functional Enrichment Analysis Results with Advanced Network Visualizations" doi.org/10.1002/cpz1.70472 "By revealing shared gene content, expression patterns, and network topology, this approach helps […] [Original post on social.edu.nl]

Figure 3 Pie chart network visualization of WikiPathways enrichment results using cyemapplot. WikiPathways enrichment identified 76 terms from IBM differential expression data (6154 DEGs; |log2FC| > 1 and p‐value < 0.05). Pie charts show query genes (purple) versus other genes in the pathway (white). Edges represent gene overlap (Jaccard ≥ 0.2). The highlighted nodes and edges (pink) show the top cluster in the main network with pathway related to immune regulation.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 25/10/2026

new paper: "User-driven development and evaluation of an agentic framework for analysis of large pathway diagrams" doi.org/10.1093/bioadv/vbag277 "By involving domain experts from the very first prototyping in the form of a hackathon and collecting […] [Original post on social.edu.nl]

Figure 1The workflow of Llemy. Users provide their prompt and select a map they want to process. Then, the prompt is enriched with instructions for the content of the answer (see full system prompt in Supplementary P1), and, in parallel, map data is fetched from the corresponding MINERVA Platform. Both enriched prompt and processed map data are combined and used as the LLM prompt. The answer is provided to the user for evaluation, and system performance logs are collected. Green: process, blue: data.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 25/10/2026

new paper: "Stem cells redirect the neuroinflammatory trajectory of primed microglia in an ovine chorioamnionitis model" doi.org/10.1016/j.bbih.2026.101359 "Antenatal inflammation resulted in an increased efferocytotic capacity following in vitro LPS […] [Original post on social.edu.nl]

Fig. 2. Brain regions of interest analyzed through immunohistochemistry. Nissl staining of the selected regions of interest for immunohistochemical staining of the paraffin-embedded coronal brain sections. Coronal sections are analyzed at the plane of the frontal cortex, striatum and mid-thalamic region, which includes the hippocampus and lateral ventricles. In all three regions of interest, blood vessels of the blood-brain barrier (BBB) were selected.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 25/10/2026

new paper: "Polyunsaturated fatty acids and psychotic disorders: integrating mechanistic, genetic, and clinical evidence" doi.org/10.3389/fnut.2026.1929742 "Finally, we evaluate clinical trials of n-3 PUFA supplementation, considering both its […] [Original post on social.edu.nl]

Figure 1: Overview of polyunsaturated fatty acid (PUFA) metabolic pathways. Dietary omega-6 (n-6) and omega-3 (n-3) essential fatty acids are metabolized through a shared series of desaturation and elongation reactions catalyzed by Δ 6-desaturase (FADS2), elongases (ELOVL family), and Δ 5-desaturase (FADS1). Linoleic acid (LA; n-6) and α -linolenic acid (ALA; n-3) compete for these enzymes, resulting in the production of arachidonic acid (ARA; n-6) and eicosapentaenoic acid (EPA; n-3), respectively. EPA is further elongated and desaturated to generate docosapentaenoic acid (DPA; n-3; not shown) and ultimately docosahexaenoic acid (DHA; n-3). Long-chain PUFAs may be esterified into membrane phospholipids, where they contribute to membrane structure and serve as reservoirs for bioactive lipids. Upon cellular activation, phospholipase-mediated release of these fatty acids enables their conversion into lipid mediators via cyclooxygenase (COX) and lipoxygenase (LOX) pathways. These mediators, including eicosanoids derived primarily from AA and resolvins derived from EPA and DHA, exert diverse and often opposing effects on inflammation and its resolution.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 25/10/2026

new paper: "Functional perturbation reveals context-dependent contributions of nuclear receptors to drug-induced hepatic steatosis" doi.org/10.1016/j.toxlet.2026.113202 "In differentiated HepaRG cells, nuclear receptor depletion influenced basal lipid […] [Original post on social.edu.nl]

Fig. 2. Concentration–response analysis of representative steatogenic drugs in HepG2 and differentiated HepaRG cells. Concentration–response curves for valproic acid (VPA), tamoxifen, amiodarone, and rifampicin in (A) HepG2 cells and (B) differentiated HepaRG cells following 24 h exposure. Cell viability was determined using the Alamar Blue assay, and IC₅₀ values were calculated by nonlinear regression analysis. Data are presented as mean ± SD from three independent biological experiments.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 25/10/2026

new paper: "CACNA1C Genetic Variants Differentially Affect Neuronal Networks Through Divergent Pathways" doi.org/10.1016/j.bpsgos.2026.100792 "Neurons carrying CACNA1C variants displayed opposing alterations in network dynamics, depending on variant […] [Original post on social.edu.nl]

Figure 5. Differential gene expression of CACNA1C LoF cell line on day 30 compared with isogenic control cell line. (A) RNA sequencing volcano plots of DEGs in a CACNA1C LoF mutant compared with wild type, determined by the DESeq2 method with a 0.5-FC threshold and an FDR-adjusted p < .01. (B) Ranked enrichment analysis of CACNA1C LoF gene expression signatures using the GOBP database by the fgsea multilevel enrichment test and genes ranked by minimum significant difference (signed msd) (fgsea). (C) Network of enriched GOBP terms, clustered by shared ID and colored by p value, for upregulated DEGs. Enriched GOBP terms were clustered based on semantic similarity using GOSemSim (R package), and clusters were manually summarized. Node size indicates the number of genes. (D) Brain cell-type enrichment analysis using gene expression per tissue based on brain tissue single-cell data. Significant cell types (p < .05) are in blue. (E) Disease-gene enrichment analysis performed for all DEGs and disease associations from DisGeNET, with significance determined as p < .001. Bar plot color indicates the number of enriched genes within a given disease gene-set. Ast, astrocytes; DEG, differentially expressed gene; End, endothelial cell; FC, fold change; FDR, false discovery rate; GOBP, Gene Ontology biological process; LoF, loss-of-function; Mic, microglia; Oli, oligodendrocytes; OPC, oligodendrocyte precursor cells; Per, pericytes.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 25/10/2026

new paper: "Polyaromatic hydrocarbon driven developmental toxicity is dependent on the aryl hydrocarbon receptor: A case study with benzo(a)pyrene" doi.org/10.1016/j.yrtph.2026.106219 "Transcriptomic profiling of blood, kidney, liver, and thymus […] [Original post on social.edu.nl]

Fig. 2. Impact of BaP on AhR-KO type rats on four selected tissues. a. Venn diagram of the DEG between the WT (in blue) and the AhR-KO (yellow) rat DEG for the liver (top) and kidney (bottom). b-e. Barplots of the expression of Cyp2b1 (b), Cyp2b2 (c), Cyp3a23-3a1 (d) and Slc51a (e). The y-axis represents normalized read counts, except for Cyp2b1 which is expressed in Log2 (of these normalized read counts). All four tissues are represented in this order: blood, kidney, liver and thymus. Group 1 stands for WT control, Group2 for WT exposed to 300 mg/kg/d of BaP, Group 3 for AhR-KO control, Group 4 for AhR-KO exposed to 300 mg/kg/d BaP and Group 5 for AhR-KO exposed to 550 mg/kg/d BaP.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 25/10/2026

new paper: "Impact of a pristine versus gastric acid-treated low-density polyethylene in a human epithelial colorectal adenocarcinoma (Caco-2) cell line" doi.org/10.1016/j.ecoenv.2026.120532 "We focused on Low-Density Polyethylene due to its widespread […] [Original post on social.edu.nl]

ToC graphics showing various aspects of the work: leached metals after weathering (Al, Mn, Zn, Fe, Pb), metals in LDPE plastics (Al, Cu, Ni, Fe, Mn, Zn, Ti, Zn), size distribution histogram, and in vitor study aspects.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 25/10/2026

new paper: "Endogenous fructose production in patients and mice with aldolase B deficiency" doi.org/10.1016/j.ymgme.2026.110219 "Although endogenous fructose production contributes to circulating and hepatic fructose levels in Aldob-/-, inhibition of […] [Original post on social.edu.nl]

Fig. 1. Hepatic endogenous fructose production. In the hepatocyte, the polyol pathway is a two-step metabolic pathway that converts glucose into fructose, which could contribute to higher intrahepatic F1P levels in aldolase B deficiency. Dashed lines indicate simplified pathways. Abbreviations: ALDOB (aldolase B), AR (aldose reductase), F1P (fructose 1-phosphate), KHK (ketohexokinase), SDH, sorbitol dehydrogenase. Figure created in BioRender.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 25/10/2026

new paper: "Right ventricular function, exercise capacity and quality of life in adults with congenital heart disease and the effect of a home-based exercise program" doi.org/10.1016/j.ijcchd.2026.100694 "Right ventricular function correlates with […] [Original post on social.edu.nl]

Fig. 1 Multiplane imaging of the RV Views acquired by electronic plane rotation from a single RV focused apical echocardiographic position: the RV focused apical four chamber view visualising the RV lateral wall (0° rotation), the coronary sinus view visualising the RV anterior wall (±+40° rotation), the aortic view visualising the RV inferior wall (±−40° rotation) and the coronal view (±−90° rotation) visualising the RV outflow tract and inferior wall of the RV. • Abbreviations: 4C = four chamber view, Ao = aortic view, CS = coronary sinus view, CV = coronal view, RV = right ventricle.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 25/10/2026

new paper: "The dual role of mTOR in multiple sclerosis pathophysiology: a systematic review" doi.org/10.1007/s00415-026-13970-3 "Studies using in vitro and in vivo (mainly rodent models, both sexes) models of MS, as well as MS patient tissue or data […] [Original post on social.edu.nl]

Fig.1: The mammalian target of rapamycin (mTOR) signaling pathway. This schematic illustrates the PI3K/AKT/mTOR pathway and its role in regulating cell growth and cytoskeletal organization through the two mTOR complexes mTORC1 and mTORC2. Abbreviations: 4EBP1: eukaryotic translation initiation factor 4E-binding protein 1, AKT: protein kinase B, Deptor: DEP domain-containing mTOR-interacting protein, mLST8: mammalian lethal with Sec13 protein 8, mSIN1: mammalian stress-activated protein kinase-interacting protein 1, mTORC1: mechanistic target of rapamycin complex 1, mTORC2: mechanistic target of rapamycin complex 2, PDK1: 3-phosphoinositide-dependent protein kinase-1, PI3K: phosphoinositide 3-kinase, PKCα: protein kinase C alpha, PRAS40: proline-rich AKT substrate of 40 kDa, Protor: protein observed with rictor, Raptor: regulatory-associated protein of mTOR, Rheb: Ras homolog enriched in brain, Rictor: rapamycin-insensitive companion of mTOR, S6K: ribosomal protein S6 kinase, TSC1/2: tuberous sclerosis complex 1 and 2. Figure created using Biorender.com

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 25/10/2026

new paper: "Transcriptomic responses to repeated exposure of human C3A liver spheroids to polystyrene nanoplastics" doi.org/10.1007/s00204-026-04473-1 "PS NPs accumulated within the human liver spheroids in a concentration-dependent and spatially […] [Original post on social.edu.nl]

Fig. 2: Accumulation of polystyrene nanoplastics in human liver spheroids. Human liver spheroids were exposed to low (0.0068 µg/mL), mid (0.068 µg/mL), and high (1.6 µg/mL) concentrations of fluorescently labeled polystyrene nanoplastics for 3, 12, and 21 days. a Representative fluorescence images, showing polystyrene nanoplastic-associated fluorescence signal (green). Yellow contours delineate spheroid boundaries. Imaging parameters were kept constant within each time point but adjusted between time points to avoid signal saturation and preserve detection sensitivity. Vehicle control spheroids were included at each time point for background subtraction. b Quantification of polystyrene nanoplastic-associated fluorescence signal. Data are expressed as percentage of spheroid area. Statistical comparisons were performed within individual time points. N = 3, n = 3–6 spheroids; *** p-value < 0.001, ** p-value < 0.01. All data are presented as mean ± SD

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 25/10/2026

new paper: "Neural peer pressure: intercellular dynamics and emergent phenotypes in the mosaic Rett syndrome brain" doi.org/10.1186/s12964-026-02987-w "During female embryogenesis, each cell randomly inactivates either the maternal or paternal X […] [Original post on social.edu.nl]

Fig. 3 Schematic overview of “disease” signals produced by mutant MECP2-expressing neural cells. These “disease” signals include EV-derived and free-floating proteins, miRNAs, and other biomolecules, as well as extracellular matrix components and contact-dependent signals. In vitro and in vivo studies demonstrated that these “disease” signals can negatively affect morphology and function neighboring wildtype cells within a mosaic cellular environment. Image created with BioRender.com

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 25/10/2026

new paper: "GSEA and the coexpression network approach identify novel pathway connections of molecular processes affected in Porto-sinusoidal vascular disease" doi.org/10.1371/journal.pone.0347338 "a novel coordinated dysregulation in PSVD was […] [Original post on social.edu.nl]

Fig 2. Gene set enrichment analysis (GSEA) results. A node represents each enriched gene set of the Gene Ontology class Biological Process and canonical pathways with a false discovery rate cut-off of < 0.05. The node border color indicates normalized enrichment scores of the terms. The pie chart displayed within the node indicates the number of significantly up-regulated and down-regulated (red and blue, respectively) out of the total genes in a gene set. The node size is assigned based on the setSize (number of genes in a term). The edge weight representing the overlap coefficient (similarity index between two terms) has filtered with a cut-off value of 0.4.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 25/10/2026

new paper: "Cord-blood black carbon burden is associated with coordinated inflammatory and heme-metabolic transcriptional programs at birth in Bradford, United Kingdom" doi.org/10.1016/j.scitotenv.2026.18… "Of 109 mother-infant pairs with exposure […] [Original post on social.edu.nl]

ToC graphics with a colorful display showing upregulation of inflammation, downregulation of metabolism, and the "Conclusion: Molecular footprint linking the prenatal pollution to altered neonatal immune & metabolic development"

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 07/10/2026

News: "TGX in Brno: second half of the ELIXIR exchange with RECETOX" www.maastrichtuniversity.nl/news/tg… #elixirEurope @elixir-nl.bsky.social "From 24 to 28 August, Egon, Denise, Javier and Marvin drove to […] [Original post on social.edu.nl]

Photo of the TGX and RECETOX researchers in front of an entrance of Masarykova Univerzita.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 04/09/2026

Dr Susan Coort was keynote at the NuGOweek 2026 this week: "Connecting the dots: pathways and networks in nutrition research" nugo2026.pan.olsztyn.pl #nutrigenomics #NuGOweek #wikipathways Find more about her research here […] [Original post on social.edu.nl]

Coort on stage in front of one of her slides, showing information about the WikIpathways project.

Photo: All rights reserved, Meike Bünger, Health-RI / ELIXIR-NL.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 29/08/2026

"Network-based stratification of allele-specific expression reveals patient subgroups in Huntington’s disease" doi.org/10.1093/bioinformatics/btag… "Intersection of differentially imbalanced and expressed genes identified FAM181B as a candidate gene […] [Original post on social.edu.nl]

Figure 1Patient clusters identified by network-based stratification of allele-specific expression profiles. (left; A) The heatmap shows the co-cluster frequency for each patient pair over 1000 iterations. Patients are grouped by cluster assignment, indicated by coloured bars (red: cluster 1, green: cluster 2, cyan: cluster 3). (right; B) Network representation of patient clusters. Nodes represent individual patients, coloured by cluster assignments. Edges connect patients with a co-cluster frequency 0.63, with edge width scaling linearly with co-cluster frequency.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 17/08/2026

new paper: "Genome-Wide Association of Genetic Variants with Intestinal Cholesterol Absorption Markers in a European Population" doi.org/10.3390/nu18162679 "A total of 16 SNPs were identified. Eight SNPs overlapped with both campesterol/TC and […] [Original post on social.edu.nl]

Table of Contents graphics, showing a visualization of the intestinal lumen, along with dietary cholesterol. With 398 data points, this genome-wide association analysis found several SNPs of interest, including rs439976, rs6544713, rs4245791, rs260769, rs5011112, rs4962526, rs2033254, and rs12708980. These are found on chromosomes 2-4, 10, and 16, with nearby genes being ABCG8, ADAM12, and CETP.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 12/08/2026

new paper: "Integrating transcriptomics and molecular AOPs to identify T3-dependent regulation of neuronal development in the human neural progenitor test" doi.org/10.1016/j.tox.2026.154542 "This study illustrates the utility of integrating […] [Original post on social.edu.nl]

Table of Contents graphics showing three sections ("Experiment setup", "Transcriptomics response", and "Molecular AOP interpretation"). The first shows the three T3 doses, the middle a Venn diagrem of differential expressed genes, and the last a network with key events and molecular pathways.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 12/08/2026

new paper: "Colonoid-Based Transcriptomics Reveals Conserved and Model-Specific Mechanisms of Doxorubicin-Induced Intestinal Toxicity" doi.org/10.3390/ijms27167072 "Using a parallelogram approach, differential expression, co-expression, pathway mapping […] [Original post on social.edu.nl]

Table of Contents graphics showing two rows, the top one showing depictions of the methods (RNA-seq, DE Seq2, WGCNA, pathway enrichment, ad CTD benchmark(-ing)), and the second (larger) row with the three used models (in vitro human and mouse colonoids and in vivo mouse colon), the core responses (dna damage response, cell-cycle arrest, and intrinsic apoptosis), and the translation/implications to human colon (in vivo). At the bottom the text "gut-relevant candidate markers highlighting CTD gaps across models" is given.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 03/07/2026

new paper: "The Secretome of a Cachexia-Inducing Lung Tumor Impairs Mitochondrial Function and Skeletal Muscle Differentiation" doi.org/10.3390/cancers18132130 "344P tumor-conditioned medium did not induce myotube atrophy, or activation of […] [Original post on social.edu.nl]

Figure 1. Differential expression analysis of genes involved in processes related to proteolysis (A) and myogenesis (B) in gastrocnemius muscles of OLCC mice compared to sham control mice. Upregulated genes are depicted in red; downregulated DEGs are depicted in blue. Directional bias was assessed by Fisher’s exact test (two-tailed) with FDR correction. A literature-based approach for atrophy-related genes yielded 82 genes. A literature-based search for genes related to myogenic processes yielded 56 genes, shown in a regulatory network with interconnecting nodes. Node size indicates the number of log 2-fold changes; green node border indicates DEGs. Edges represent TF–target interactions from TFLink, supported by small-scale evidence or by high-throughput ChIP-seq (C). Edges with at least one small-scale record are drawn thicker (higher confidence). Edges supported only by ChIP-seq are drawn thinner. ** FDR ≤ 0.005, *** FDR ≤ 0.001

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 03/07/2026

new paper: "Genetic variants associated with triglyceride metabolism and fasting triglyceride concentrations: a systematic review and a meta-analysis" doi.org/10.1016/j.jacl.2026.06.019 "Five of those (rs58542926, rs738409, rs320, rs328, and rs1801282) […] [Original post on social.edu.nl]

Table of Contents graphcis, showing the research question at the top, and a flow diagram of the used approached (CC-BY).

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 30/04/2026

new paper: "Multi-omics characterization of developing forebrain organoids unravels the dynamic molecular events of Rett syndrome pathogenesis" doi.org/10.1186/s11689-026-09699-9 "The spatiotemporal transcriptomic analysis revealed alterations in […] [Original post on social.edu.nl]

Table of Contents graphical abstract showing various aspects of the biology, experimental design, and analysis: dorsal brain organoids, iPSC, regulatory networks, validation, and spatiotemporal alterations.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 30/04/2026

new paper: "A dataset of rare copy number variants associated with neurodevelopmental and neuropsychiatric disorders" doi.org/10.1038/s41597-026-07345-6 "We present a curated machine readable dataset, CNVPathwayAtlas, that integrates 38 pathogenic CNVs […] [Original post on social.edu.nl]

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 07/04/2026

new paper: "Reduced NR2F6 expression reshapes the VPA-induced transcriptome in human hepatocytes and increases lipid accumulation" doi.org/10.1016/j.tox.2026.154457 "Functional validation in HepG2 and HepaRG models demonstrated that NR2F6 knockdown […] [Original post on social.edu.nl]

Fig. 6. Mechanistic model of NR2F6 modulation of VPA-induced lipid accumulation. Reduced NR2F6 expression alters hepatocellular responses to VPA by decreasing CPT1A, increasing CPT2, upregulating PLIN2, reducing PLIN4, lowering FASN, and increasing CYP2B6 expression. These coordinated changes shift lipid-droplet composition, modify fatty-acid handling, and enhance susceptibility to VPA-induced steatosis.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 07/04/2026

new paper: "Effects of acute fluctuations of extracellular Zinc on network activity of human iPSC-derived neurons; impact of NMDA Receptor and L-Type Calcium Channel Activation" doi.org/10.1016/j.neuropharm.2026.1… "Addition of nMolar […] [Original post on social.edu.nl]

Fig. 6. Expression analysis of genes encoding various neuronal markers. Analysis of a panel of a–f: MAP2, GRIN1, GRIN2A, GRIN2B, VGLUT1, and CACNA1C in control neurons in the absence and presence of added 200 nM or 5 μM ZnCl2 in the absence or presence of ZX1. Data are presented as fold change relative to the control, which is indicated by the horizontal line. Data are represented as means ± SEM. *p < 0.05, ***p < 0.001 following One-way ANOVA with post hoc comparisons using Dunnett's multiple comparisons test. N = 6 for MAP2 and VGLUT1 and CACNA1C, and 3 for GRIN1, GRIN2A and GRIN2B.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 07/04/2026

new paper: "ToxTempAssistant: using large language models to standardise cell-based toxicological test method descriptions" doi.org/10.1080/2833373X.2026.26380… "This study quantifies the tool’s baseline performance under controlled conditions […] [Original post on social.edu.nl]

Figure 1. Schematic overview of the ToxTempAssistant workflow. The ToxTempAssistant enables automated drafting of ToxTemp templates using a large language model (LLM). Users upload contextual documents along with the assay name and short assay description. For each of the 77 ToxTemp questions across 11 sections (Krebs et al. Citation2020), targeted prompts extract relevant information via the LLM. Deviating from the graphic, the current software implementation allows sending requests to the LLM in parallel. Users validate and edit the draft before exporting the completed template.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 14/03/2026

new paper: "Black carbon is detectable in association with small extracellular vesicles in fetal circulation" doi.org/10.1016/j.envint.2026.110186 "Here we show that black carbon (BC) is detectable in association with small extracellular vesicles […] [Original post on social.edu.nl]

ToC graphics, showing three papels explaining the paper: "Maternal exposure", "Placental interface exchange", and "Fetal circulation & BC-Brain accomodation".

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 14/03/2026

new paper: "Outcomes and future activities of the ‘Pan-European network in Lipidomics and EpiLipidomics – EpiLipidNET’" doi.org/10.1007/s11306-026-02396-7 #lipidomics #metabolism

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 01/03/2026

new paper: "pyBiodatafuse: extending interoperability of data using modular queries across biomedical resources" doi.org/10.1093/bioinformatics/btag… "Additionally, the tool offers plugins for widely used platforms such as Cytoscape, Neo4j, and […] [Original post on social.edu.nl]

Figure 2The property graph data model of the biomedical knowledge graph was generated by pyBiodatafuse.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 12/02/2026

Our team organized in December the 7th @vhp4safety hackathon in Maastricht. The photo is the hackathon in action. A report is available here: www.sciencrew.com/c/9347/a/33561849… More about the VHP4Safety […] [Original post on social.edu.nl]

Photo of a room of 16 people sitting around tables, laptops open, sideways looking at a presentation given on a large TV screen on the far side of the room.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 12/02/2026

new paper: "Food Additive Titanium Dioxide (E171) Alters Gut Microbial Metabolic Activity and Butyrate Production in the TIM-2 In Vitro Colon Model" doi.org/10.1093/jambio/lxag042 "E171 undergoes distinct physicochemical transformations depending on […] [Original post on social.edu.nl]

Figure 3: Cumulative production (mmol) of SCFAs (acetate, propionate, butyrate) at 24 h, 48 h, D and 72 h for Ctrl-aq, E171-aq, Ctrl-yog, and E171-yog within SIEM. The addition of E171 Edrastically increases butyrate production T in E171-aq and E171-yog settings, with an overall increase in total SCFA production.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 18/01/2026

new paper: "Short-term high-dose nicotinamide treatment across glaucoma subtypes reveals increased mtDNA content and minimal metabolomic change in blood" doi.org/10.1016/j.exer.2025.110807 "All groups showed a similar metabolome response to treatment […] [Original post on social.edu.nl]

Fig. 1. Control and glaucoma subtypes have similar plasma metabolomes following oral NAM treatment. A) Analysis by construction of a linear model with covariate adjustment (age, sex) demonstrated that baseline (pre-NAM) plasma metabolomes were similar across all subtypes compared to normal controls, with only ethylmalonic acid demonstrating a small yet significant relative increase in glaucoma. B) Unsupervised hierarchical clustering demonstrated that individual plasma samples clustered into pre- and post-NAM groups based on the metabolome alone, which appears to be largely driven by 4 NAM species metabolites. C) Individual comparisons of responses to NAM treatment (pre vs. post) demonstrated that all conditions respond similarly to high dose NAM treatment. NAM was significantly elevated across all conditions, and methylated NAM species were also detected suggesting active metabolism in the liver. In support of this, betaine (a methyl donor produced predominantly in the liver) was significantly reduced. D) Comparison of these responses by construction of a linear model with covariate adjustment (age, sex) demonstrated that sarcosine was the only metabolite that was significantly different across conditions. Sarcosine was significantly reduced in HTG and NTG patients but not in controls and PEXG. HTG: high tension glaucoma; NAM: nicotinamide; NTG: normal tension glaucoma; PEXG: pseudoexfoliative glaucoma.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 18/01/2026

new preprint: "Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe's life science Communities" doi.org/10.12688/f1000research.1682… "The ELIXIR Communities framework is made up of a suite of tools and processes that ensure […] [Original post on social.edu.nl]

"Figure 1. Stages in the development of ELIXIR Communities.

Timeline to show the progression of each ELIXIR Community through the stages of Community maturity, following the processes outlined along the top row. Once a community has reached the phase of Heads of Nodes approval (i.e. approval by the country-level bioinformatics leads), it becomes an official ELIXIR Community and can begin work on an internal project funded through ELIXIR’s core funds. The most mature Communities are shown in the top right (these were the four ELIXIR-EXCELERATE Use Cases), with the newest Communities shown in the bottom left (Communities portfolio as of December 2023)."

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 18/01/2026

new paper: 'Beyond Single Variants: A Pathway-Based Approach to Explore the Genetic Basis of Memory" doi.org/10.1007/s12035-025-05582-1 "We present three independent genome-wide association studies within the Human Connectome Project on a (i) Penn-Word […] [Original post on social.edu.nl]

Figure 1: Manhattan plots for each of the performed GWASs. Orange dots highlight the SNPs with p-value < 1E−5.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 15/01/2026

new paper: "Single-cell transcriptomics of acetaminophen-induced responses in human 2D and 3D liver microtissues" doi.org/10.1007/s00204-025-04296-6 "Here, we applied single cell RNA sequencing to characterize cellular responses to acetaminophen […] [Original post on social.edu.nl]

Figure 1: Baseline transcriptional and pathway-level differences between 2 and 3D liver cell cultures identified by scRNA-seq.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 30/11/2025

new paper: "Small extracellular vesicles: connecting early life exposure outcomes to air pollution during pregnancy to early childhood health" doi.org/10.1186/s12940-025-01238-8 "In this review, we explore mechanisms involving sEVs in transplacental […] [Original post on social.edu.nl]

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 30/11/2025

new paper: "Molecular pathways of kidney development and their applications to clinical research" doi.org/10.1016/j.kint.2025.09.032 "Here, we develop and describe fully machine-readable, well annotated pathways to visualize and analyze key events […] [Original post on social.edu.nl]

Figure 3. Subnetworks derived from kidney development pathways, extended with chemical compound information and annotated with the compounds’ usages in humans. a) Subnetwork showing interactions of known nephrotoxic compounds with kidney development pathway proteins. b) Herbicidal compounds interacting with kidney development pathway proteins. c) Chemical compounds binding to or affecting expression of GDNF.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 09/11/2025

new paper: "Placental gene expression of the AMPK signaling pathway in association with gestational exposure to ambient air pollution" doi.org/10.1016/j.envres.2025.123280 "Higher prenatal levels of BC, NO2, and PM2.5 were associated with downregulated […] [Original post on social.edu.nl]

Fig. 1. Overview of the AMPK signaling pathway, divided into clusters of sub-pathways based on the KEGG database pathway (hsa04152). The green clusters are the upstream cascades, the blue cluster is the central AMPK cluster, and the orange clusters are the downstream cascades. The genes CAMKK2 and CCND1, used in the RT-qPCR validation, are linked to their respective gene clusters. The generally known triggers of this pathway are nutrient deficiency (mostly glucose), hypoxia, and the hormones leptin and adiponectin. The drug metformin is a well-known AMPK activator.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 01/11/2025

new paper: "Dimethyl Sulfoxide Conditions Induced Pluripotent Stem Cells for more Efficient Nephron Progenitor and Kidney Organoid Differentiation" doi.org/10.1007/s12015-025-10971-z "We found that treating hiPSCs with 1–2% DMSO affects gene expression […] [Original post on social.edu.nl]

Figure 6: Characteristic LUMC hiPSC-derived kidney organoid protein expression images and differentiation efficiency quantification on day 21 of the differentiation protocol. (a) Schematic of the final 12 days of differentiation from emergence of nephron progenitors on day 9 to kidney organoids on day 21. b-d) Percentage of wells (n=60) with successfully differentiated kidney organoid colonies developing; (b) no treatment, (c) 1% DMSO, (d) – 2% DMSO. (e) Total fluorescent signal measured in each well (n = 5), and used to calculate normalised signal of characteristic proteins found in different sections of the developing nephron; (f) podocalyxin – glomerulus, (g) megalin - proximal tubule, (h) and GATA3 - distal tubule/collecting duct. Representative immunofluorescence images of day 21 kidney organoids showing a general overview of each well with characteristic proteins found in different sections of the developing nephron: (i) nephrin – glomerulus (yellow), megalin - proximal tubule (red), and GATA3 - distal tubule and collecting duct (green). (j) podocalyxin – glomerulus (yellow), lotus tetragonolobus lectin (LTL) – proximal tubule (green), and E-cadherin – distal tubule (red). Scalebar of 100 μm valid for all images

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 01/11/2025

new paper: "A bioinformatics pipeline for identifying homoplasmic and heteroplasmic mitochondrial DNA SNVs in single-cell RNA-Seq datasets" doi.org/10.1016/j.ygeno.2025.111122 "Development of a bioinformatics pipeline for reliable identification of […] [Original post on social.edu.nl]

Fig. 5. Coverage plots of the mitochondrial genome in scRNA-Seq data with and without removing of duplicates. The mean read depth (Y axis) is in log2 scale.

(a) Coverage of dataset with UMIs before (black line) and after (blue line) technical duplicates have been removed.
(b) Coverage depth in dataset without UMIs before (black line) and after (blue line) all duplicates have been removed.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 01/11/2025

new paper: "Alterations in the transcriptome of human primary bronchial epithelial cells exposed to emissions from a heated tobacco product" doi.org/10.1016/j.bbagen.2025.130869 "IQOS is a Heated Tobacco Product marketed as reduced-risk alternative to […] [Original post on social.edu.nl]

ToC graphics showing the experimental design of measuring the extracts of IQOS smoke and the impact on primary bronchial epithelial cells after 24 hours using differential expressed genes.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 01/11/2025

new paper: "Quantitative systems toxicology: modelling to mechanistically understand and predict drug safety" doi.org/10.1038/s41573-025-01308-z "Here, we highlight recent developments in the burgeoning field of quantitative systems toxicology (QST) […] [Original post on social.edu.nl]

Fig. 3: Overview of the virtual assay platform for in silico drug trials to predict drug-induced pro-arrhythmic cardiotoxicity. In vitro data on drug activity against ion channels are generally used as inputs50. The Virtual Assay simulation software allows the use of both built-in or newly generated populations (that is, disease phenotypes) of virtual human cardiac cell models for the detection of potential cardiotoxicity and the identification of biomarkers of drug action across the entire population. Potential cardiotoxicity is informed by the simulations combined with experimental data from in vivo and in vitro models. The findings can be further validated using pre-existing clinical trial data in public repositories, if available. IC50, half-maximal inhibitory concentration; MP, membrane potential.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 11/09/2025

e.g. @Marvin will present his e-poster, titled "Making the AOP-Wiki knowledge graph usable across disciplines in toxicological assessment" #aopwiki #toxicology #openscience #vhp4safety #EUROTOX2025

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 07/09/2025

new paper: "Unveiling Cell-Type-Specific Immune Reactions in Human Blood Following Varied Fruit and Vegetable Blends Interventions" doi.org/10.1002/mnfr.70238 "DEGs and pathway analyses showed that some blends affected DNA repair in B cells, NF-kappa B […] [Original post on social.edu.nl]

Figure 5: Altered pathways in T cells after different fruit and vegetable (F&V) blend interventions. Pie charts show the grouped terms of the enriched KEGG pathways in T cell after intervention of Blends 1, 3, and 5 (** adjusted group p < 0.01, * adjusted group p < 0.05).

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 30/08/2025

new paper: "Employing human intestinal organoids as advanced in vitro models for mechanistic studies on dietary ingredients" doi.org/10.1080/10408398.2025.25505… 'This review provides a framework for utilizing intestinal organoids to study dietary […] [Original post on social.edu.nl]

Table of content graphs showing the 5 steps in the approach: Step 1: Choose organoids or not, Step 2: Construction strategies, Step 3: Quality Assessment, Step 4: Exposure methods, Step 5: Measurement and analysis. Each step is associated with graphics of several organoid systems, experimental details, samples, etc.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 23/08/2025

new paper: "The role of DNA repair deficiency in lipid accumulation: A proof-of-concept study" doi.org/10.1016/j.dnarep.2025.103880 "Upon exposure to a mixture of oleic and palmitic acid, DNA damage and mitochondrial copy number were only altered in […] [Original post on social.edu.nl]

Graphical abstract, showing the idea of the proof-of-concept study presented in the article, with on the left the experimental settings, and on the right the main finding, depicted as a bar plot comparing various situations.

In white-on-orange at the bottom: "Conclusion: Impaired DNA repair (BER) activity leads to enhanced lipid accumulation via mitochondrial dysfunction"

Details are described in detail in the article.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 23/08/2025

new paper: "The MiBlend Randomized Trial: Investigating Genetic Polymorphisms in Personalized Responses to Fruit and Vegetable Interventions for Chronic Disease Prevention" doi.org/10.3390/antiox14070828 "XRCC1 wildtype carriers were more protected […] [Original post on social.edu.nl]

Figure 3 "Effect of genotype on changes in % Tail DNA after consuming different combinations of fruits and vegetables for two weeks. The polyphenol-rich blends are a combination of Blends 1, 2, and 5, and the carotenoid-rich blends are a combination of Blends 3 and 6. Data are presented as the change in mean values ± SEM. Absent bars signify an n = 0 for that group, and absent error bars signify an n = 1 for that group. Gray * = the change in the outcome is significantly different for the indicated genotypes within a gene (p < 0.05); colored * = the change in the outcome is significantly different for the indicated genotypes within a gene after multiple-testing correction by false discovery rate (q < 0.05). * = p < 0.05, *** = p < 0.001."

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 25/07/2025

new paper: "The FAIR AOP roadmap for 2025: Advancing findability, accessibility, interoperability, and re-usability of adverse outcome pathways" doi.org/10.1016/j.comtox.2025.100368 "Herein current efforts in addressing the FAIRification of AOP […] [Original post on social.edu.nl]

Fig. 2. Network of data domains represented by each AOP tool.

It shows a (math) graph network with "FAIR enbling tools" in the middle and (linked) nodes around it, in various colors and sizes (info, see the article text), in various sections, like Gene, Chemical, Species-Taxa, and Misc.

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