Dept of Translational Genomics
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tgx-um.social.edu.nl.ap.brid.gy
Dept of Translational Genomics
@tgx-um.social.edu.nl.ap.brid.gy
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We are the Department of Translational Genomics of Maastricht University, a multidisciplinary team of (cell) biologists, chemists, geneticists, toxicologists and […]

🌉 bridged from https://social.edu.nl/@tgx_um on the fediverse by https://fed.brid.gy/
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tgx-um.social.edu.nl.ap.brid.gy
new paper: "Short-term high-dose nicotinamide treatment across glaucoma subtypes reveals increased mtDNA content and minimal metabolomic change in blood" https://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.
January 18, 2026 at 11:37 AM
tgx-um.social.edu.nl.ap.brid.gy
new preprint: "Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe's life science Communities" https://doi.org/10.12688/f1000research.168288.1

"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)."
January 18, 2026 at 11:35 AM
tgx-um.social.edu.nl.ap.brid.gy
new paper: "Quantitative Adverse Outcome Pathway Modeling of Cisplatin-Induced Nephrotoxicity: Developing In Vitro and In Vivo Models for Predictive Extrapolation" https://doi.org/10.1093/toxsci/kfaf177

"Here, we focus on the development of ordinary differential equation (ODE)-based qAOPs for […]
Original post on social.edu.nl
social.edu.nl
January 18, 2026 at 11:24 AM
tgx-um.social.edu.nl.ap.brid.gy
new paper: 'Beyond Single Variants: A Pathway-Based Approach to Explore the Genetic Basis of Memory" https://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.
January 18, 2026 at 11:17 AM
tgx-um.social.edu.nl.ap.brid.gy
new paper: "Single-cell transcriptomics of acetaminophen-induced responses in human 2D and 3D liver microtissues" https://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.
January 15, 2026 at 5:30 PM
tgx-um.social.edu.nl.ap.brid.gy
RE: https://fediscience.org/@biohackrxiv/115739166395967179

with our Javier Millán Acosta
biohackrxiv.fediscience.org.ap.brid.gy BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · Dec 18
"MCP server tools with RDF shapes" https://doi.org/10.37044/osf.io/8qeh5_v1

"In this paper, we present the work we have done during the Japan Biohackathon 2025 about implementing MCP servers supported by RDF data shapes to improve natural language interactions with large RDF datasets using […]
Original post on fediscience.org
fediscience.org
December 18, 2025 at 6:33 AM
Reposted by Dept of Translational Genomics
elixir-nl.bsky.social
Last month, ELIXIR-Netherlands joined the ELIXIR-Europe BioHackathon, collaborating with hundreds of researchers, developers and infrastructure experts from across Europe.

Read the full overview, project highlights and participant reflections on our website: www.health-ri.nl/en/news/elix...
ELIXIR BioHackathon 2025 | Health-RI
The ELIXIR BioHackathon brings together experts from across Europe to develop practical solutions for data driven life sciences. This year the event took place from 3 to 7 November in Berlin and gathe...
www.health-ri.nl
December 17, 2025 at 12:45 PM
tgx-um.social.edu.nl.ap.brid.gy
🚀 BioSB course "Knowledge Graphs in the Life Sciences” 🚀
Don't miss this exciting opportunity for Life Sciences researchers and data enthusiasts. In just 9 weeks, BioSB will host this course: https://www.dtls.nl/courses/knowledge-graphs-in-the-life-sciences-2026/
📅 January 5–9, 2025
🗺️ […]
Original post on social.edu.nl
social.edu.nl
December 1, 2025 at 3:32 PM
tgx-um.social.edu.nl.ap.brid.gy
new paper: "Small extracellular vesicles: connecting early life exposure outcomes to air pollution during pregnancy to early childhood health" https://doi.org/10.1186/s12940-025-01238-8

"In this review, we explore mechanisms involving sEVs in transplacental […]

[Original post on social.edu.nl]
Figure 1: Trophoblast cells exposure to air pollutants (PM 2.5) and effects on sEVs biogenesis. Small extracellular vesicle (sEV) formation begins with the inward budding of early endosomes, generating intraluminal vesicles (ILVs) within multivesicular bodies (MVBs). PM2.5 accumulates in trophoblast cells and induces histone modifications, such as ubiquitination, phosphorylation, methylation, and acetylation, which alter gene expression and amplify cellular stress through cytokines like TNF-α, IL-6, and heat shock proteins (HSPs). Lipophilic air pollutants can modify sEV stability by directly attaching to the sEV surface, thereby changing the lipid profile of the sEV membrane and altering the redox balance of sEV cargo. Direct interactions with pollutants can also affect proteins like hnRNPA2B1, which influences selective miRNA loading and promotes cytoskeletal aggregation. Additionally, PM2.5 causes mitochondrial damage, oxidative stress, and inflammation. Air pollutants can also cause deformation and swelling of mitochondria, further disrupting cellular function. Pollutants, including heavy metals and organic compounds, also impact hormonal balance and immune responses by altering levels of hCG, progesterone, and IL-6
November 30, 2025 at 12:15 PM
tgx-um.social.edu.nl.ap.brid.gy
new paper: "Molecular pathways of kidney development and their applications to clinical research" https://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.
November 30, 2025 at 12:09 PM
tgx-um.social.edu.nl.ap.brid.gy
new paper: "Liver Involvement in POLG Disease—a Multicentre Cohort Study of 202 Patients" https://doi.org/10.1002/jimd.70112

"Our findings emphasize the need for early vigilance in monitoring liver involvement in all patients with confirmed POLG disease, particularly those with early-onset […]
Original post on social.edu.nl
social.edu.nl
November 30, 2025 at 12:00 PM
tgx-um.social.edu.nl.ap.brid.gy
new paper: "Repurposing immunomodulatory drugs targeting microglia for amyotrophic lateral sclerosis" https://doi.org/10.1016/j.brainres.2025.150032

"This literature review provides an overview of existing drugs under investigation for ALS, including those that have failed, and highlights […]
Original post on social.edu.nl
social.edu.nl
November 16, 2025 at 6:45 AM
tgx-um.social.edu.nl.ap.brid.gy
new paper: "Placental gene expression of the AMPK signaling pathway in association with gestational exposure to ambient air pollution" https://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.
November 9, 2025 at 12:37 PM
Reposted by Dept of Translational Genomics
bridgedb.fosstodon.org.ap.brid.gy
@bioconductor 3.22 is out, including BridgeDbR 2.22: https://bioconductor.org/packages/release/bioc/html/BridgeDbR.html

This release improves handling of ChEBI compact identifiers from @bioregistry, improves the vignette, and adds a second vignette, and explains more about rJava installation […]
Original post on fosstodon.org
fosstodon.org
November 9, 2025 at 10:53 AM
tgx-um.social.edu.nl.ap.brid.gy
Javier and Denise are attending the @elixir_europe BioHackathon Europe in Berlin. One of them here working with @deNBI colleagues: https://mstdn.science/@deNBI/115491384531573114

#bh25de
November 4, 2025 at 2:23 PM
tgx-um.social.edu.nl.ap.brid.gy
new paper: "Dimethyl Sulfoxide Conditions Induced Pluripotent Stem Cells for more Efficient Nephron Progenitor and Kidney Organoid Differentiation" https://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
November 1, 2025 at 5:37 PM
tgx-um.social.edu.nl.ap.brid.gy
new paper: "A bioinformatics pipeline for identifying homoplasmic and heteroplasmic mitochondrial DNA SNVs in single-cell RNA-Seq datasets" https://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.
November 1, 2025 at 5:32 PM
tgx-um.social.edu.nl.ap.brid.gy
new paper: "Alterations in the transcriptome of human primary bronchial epithelial cells exposed to emissions from a heated tobacco product" https://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.
November 1, 2025 at 5:29 PM
tgx-um.social.edu.nl.ap.brid.gy
new paper: "Quantitative systems toxicology: modelling to mechanistically understand and predict drug safety" https://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.
November 1, 2025 at 5:02 PM
Reposted by Dept of Translational Genomics
elixir-nl.bsky.social
Yesterday, we met at HEALTH-RI with ELIXIR-NL co-leads & representatives to strengthen our life science data community.

📅 Mark your calendars: ELIXIR-NL Symposium on Dec 9, 2025 @ VU Amsterdam. Registration opens next week!

#ELIXIRNL #LifeSciences #ResearchInfrastructure
October 2, 2025 at 7:27 AM
tgx-um.social.edu.nl.ap.brid.gy
multiple group members are already in Athens for the #elixireurope INTOXICOM workshop and will join the EUROTOX (https://www.eurotox2025.com/) meeting next week

#eurotox2025 #elixirtoxicology
Welcome - EUROTOX Congress 2025
● Submission of late abstracts now possible ●● List of Industry Partners published ●● Industry Partner Manual / FAQs available ● Dear Colleagues, It is with a great pleasure and enthusiasm that we warmly invite you to the 59th Congress of the European Societies of Toxicology. The EUROTOX 2025 Congress will take place on 14-17 […]
www.eurotox2025.com
September 11, 2025 at 7:47 AM
tgx-um.social.edu.nl.ap.brid.gy
On Thursday January 15th 2026 at 16:00 CET, Toni Vallbona Garcia will defend his thesis with the title: “Exploring Mitochondrial Dysfunction in Glaucoma Using Blood Biomarkers” (more details later)

#mitochondria #glaucoma
September 9, 2025 at 7:23 AM
Reposted by Dept of Translational Genomics
tgx-um.social.edu.nl.ap.brid.gy
We are the Department of Translational Genomics of Maastricht University, a multidisciplinary team of (cell) biologists, chemists, geneticists, toxicologists and bioinformaticians is working in close collaboration to establish the biological impact of exposures to potentially toxic compounds and […]
Original post on social.edu.nl
social.edu.nl
July 20, 2025 at 5:29 AM
tgx-um.social.edu.nl.ap.brid.gy
#introduction #maastricht

We are the new Maastricht University Department of Translational Genomics (just turned 1 years old!), and we also have a #bluesky account

You can follow us at https://bsky.app/profile/tgx-um.social.edu.nl.ap.brid.gy to get updates, such as new journal articles
September 7, 2025 at 7:58 AM
tgx-um.social.edu.nl.ap.brid.gy
new paper: "Unveiling Cell-Type-Specific Immune Reactions in Human
Blood Following Varied Fruit and Vegetable Blends
Interventions" https://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).
September 7, 2025 at 7:35 AM