Research Team — Detailed Description

Structure and expertise of the research team.

The NUMIEP consortium integrates a multidisciplinary team whose combined expertise spans plant biofortification, microbiome science, intestinal physiology, nutriepigenomics and multi-omics data integration. The structure of the team directly reflects the work-package organisation, ensuring full methodological coverage of WP1–WP7.

Polish Team (PL) – Lead Unit (WP1, WP2, WP5, WP6, WP7). The Polish group provides host-centric expertise in functional-food development, in vivo nutritional models, transcriptomics, epigenomics and multi-omics integration. PL is responsible for lettuce biofortification, the complete mouse feeding study, biobanking, and the generation of host omics datasets.

Project Leader – Prof. Aneta Koronowicz (ORCID: 0000-0002-1653-2867). Specialist in biofortification, nutrigenomics and dietary epigenetics; developed validated iodine-lettuce protocols and analytical workflows (qPCR, Bio-Plex, ELISA, PyroMark, NGS microbiome profiling). Provides the methodological basis for WP1-WP2 and WP5–WP7.

Prof. Iwona Kowalska (ORCID: 0000-0002-0012-6143) – WP1. Expert in plant mineral nutrition, hydroponics and I/Se biofortification; responsible for cultivation and mineral profiling of lettuce.

Prof. Sylwester Smoleń (ORCID: 0000-0001-8093-3801) – WP1. Leader of the mass-spectrometry laboratory; specialist in iodine/selenium speciation (ICP-MS/HPLC-ICP-MS), plant metabolomics and mineral analysis.

DVM Anna Gałuszka (ORCID: 0000-0003-2690-1459) – WP2. Veterinarian experienced in SPF rodent experiments, necropsy, histopathology and endocrine profiling; ensures compliance and methodological accuracy of the in vivo study. 

Dr Piotr Pawlicki (ORCID: 0000-0002-3945-8639) – WP2. Expert in endocrinology, Ca²⁺ signalling and dietary interventions; supports physiological and molecular analyses.

Prof. Artur Gurgul (ORCID: 0000-0001-5979-144X) – WP5–WP7. Bioinformatician specialising in multi-omics integration, metagenomics, statistical genomics and workflow development.

Dr n. med. Adam Master (ORCID: 0000-0001-9391-8846) – WP5–WP7 (PL/USA). Expert in transcriptomics, epigenomics, THRB/THRA regulation and multi-omics pipelines; contributes mechanistic modelling and interpretation of epigenomic and transcriptomic outcomes.

Czech Team (CZ) – Co-Leading Unit (WP3, WP4, WP6, WP7). The Czech group provides microbiome-centric expertise including anaerobic fermentation, epithelial models and metabolomics.

Dr Ivo Doskočil (ORCID: 0000-0002-7373-1360) – WP3–WP4. Specialist in diet–microbiota interactions, microbial metabolites and epithelial signalling; leads anaerobic fermentations, SCFA/metabolomics workflows and epithelial assays.

Dr Petr Šmíd (ORCID: 0009-0004-0442-7084) – WP3–WP4. Expert in in-vitro digestion, epithelial barrier assays, imaging,  chemical analyses,  metabolomics and functional readouts essential for mechanistic validation.

5.2. International Partners (Canada & USA) – Unfunded Experts

Prof. Barbara Stefańska (CA; ORCID: 0000-0001-5421-3165). Internationally recognised leader in nutriepigenomics, specialising in DNA methylation, chromatin accessibility and diet-responsive epigenetic regulation. Her lab contributes expertise in genome-wide methylation profiling, enhancer mapping and interpretation of epigenetic responses to dietary compounds. She co-authored the first mechanistic studies on iodine-biofortified lettuce, providing a fully aligned baseline for NUMIEP WP4–WP6. 

Dr Adam Master (US; dual role described above). Provides thyroid signalling expertise, mechanistic modelling and bioinformatic interpretation of epigenomic/transcriptomic outcomes.

Team Complementarity and Added Value. The consortium integrates complementary strengths essential to reconstructing the full mechanistic axis: biofortified functional food → microbiome → metabolome → epithelial signalling → host epigenome. PL contributes in vivo models, plant biofortification, molecular phenotyping, methylation/ATAC-seq profiling and multi-omics integration. CZ contributes microbiome fermentation systems, SCFA/metabolomics workflows, microbiology and advanced epithelial models. CA adds world-leading nutriepigenomics and interpretation of methylome/chromatin responses. US adds mechanistic expertise in thyroid-hormone signalling and RNA-mediated regulation. Together, the teams provide full methodological feasibility for WP1–WP7, high reproducibility and access to complementary expertise necessary to deliver an integrated, multi-omics understanding of diet–microbiome–epigenome interactions.

Dr. Aneta Koronowicz, PhD, MSc, Eng.  (PL)

Aneta Koronowicz’s preliminary work relevant to the NUMIEP project includes: development of iodine lettuce biofortification protocols (WP1), mechanistic cellular studies using biofortified lettuce extracts (supporting WP4–WP6), NGS-based control microbiome genotyping, baseline epigenomic profiling using PyroMark Q48 (WP5), as well as the elaboration and optimisation of multiple analytical and molecular workflows underpinning WP1, WP2, WP5 and WP6, as detailed below.

Aneta Koronowicz has generated a substantial body of preliminary results directly supporting the NUMIEP project. She has developed and validated a complete protocol for iodine biofortification of lettuce, including nutrient application, uptake efficiency, biochemical stability, and quality control. Her published studies demonstrate that iodine-enriched lettuce is a safe and bioavailable functional food, providing a fully operational platform for WP1. In parallel, Koronowicz conducted mechanistic in vitro experiments using extracts from iodine-biofortified lettuce in human epithelial cell lines (Caco-2, HT-29). These studies revealed modulation of inflammatory, metabolic, antioxidant and thyroid-axis markers, forming a baseline dataset against which NUMIEP will compare the effects of microbiome-conditioned media in WP4–WP6.

Koronowicz has optimized and routinely uses key analytical platforms—Bio-Plex 200, ChemiDoc, Bio-Rad CFX96 qPCR system, ELISA and spectrophotometric assays—generating high-quality preliminary protein, gene-expression and metabolic profiles. These validated molecular readouts will be reused within WP4–WP6. She has also performed mouse nutritional intervention experiments, generating baseline endocrine, metabolic and tissue-level data, and established dosing and sampling procedures compatible with WP2. The Millipore mouse metabolic system available at URK has been previously used in these studies.

Koronowicz has produced preliminary microbiome sequencing datasets using the in-house Illumina MiSeq system, including baseline microbial profiles of control mice and optimized protocols for library preparation and taxonomic assignment. These datasets form the methodological and biological foundation for WP3 and WP5. Furthermore, using the PyroMark Q48 platform, she has optimized bisulfite conversion and promoter methylation assays in mouse tissues and human epithelial cells, generating reproducible methylation baselines for genes relevant to thyroid signaling, metabolism and epigenetic regulation. These findings provide essential epigenetic reference points for WP5 multi-omics integration and WP6 mechanistic validation.

Collectively, these preliminary results demonstrate full methodological readiness, access to optimized workflows, validated analytical pipelines, and biologically relevant baseline datasets covering plant biofortification, microbial profiling, cellular phenotyping, in vivo nutrition models and targeted epigenetics. They ensure the feasibility of the project and directly support the execution of WP1–WP7. See References.

dr. n. med. ADAM MASTER (US, PL)

1. Dr. Adam Master has generated extensive preliminary results directly supporting NUMIEP, providing a validated mechanistic and multi‑omics foundation for WP2, WP5, WP6 and WP7. His long‑term research on thyroid hormone receptor beta (THRB) and epigenetic regulation (Master et al. 2010; Wojcicka et al. 2014; Master & Nauman 2014) establishes mechanistic groundwork for NUMIEP’s focus on THRB/THRA-dependent pathways and thyroid-epigenetics feedback loops.

2. Validated mechanistic baseline (THRB/THRA axis). Across multiple peer‑reviewed studies, Dr. Master identified and experimentally characterised novel THRB 5′/3′ UTR isoforms (Biochim Biophys Acta 2010), discovered RNA structural elements modulating translation, and demonstrated epigenetic dysregulation of THRB in renal cancer (PLoS One 2014). His invited THRB gene entry for the Atlas of Genetics and Cytogenetics in Oncology and Haematology (2014) and award‑winning mechanistic review (Postępy Biochemii, 2014) provide a strong mechanistic baseline for NUMIEP’s thyroid‑axis analyses in WP5–WP6.

3. In the 2014 study Epigenetic Regulation of Thyroid Hormone Receptor Beta in Renal Cancer (Wojcicka et al., 2014), Master and co-authors demonstrated that down-regulation of THRB in clear-cell renal cell carcinoma (ccRCC) is regulated not only by promoter CpG hypermethylation, but also microRNA-mediated post-transcriptional silencing. These findings provide a concrete mechanistic link between non-coding RNA regulation and modulation of thyroid hormone receptor signalling — validating the concept that epigenetic and post-transcriptional mechanisms can control THRB expression and its epigenetic loop and thereby supporting the main concept of the project. This work thus constitutes a strong empirical foundation for NUMIEP’s focus on metabolite- and epigenome-driven regulation of THRB/THRA pathways (planned in WP5–WP6), and supports the feasibility of using epigenetic/translational regulation analyses in the project.

4. Preliminary datasets for NUMIEP (pilot work at PL). PL has already optimised extraction and QC workflows for mouse epithelial DNA, RNA and chromatin (24-years experience in genetic laboratory), producing high‑integrity material (RIN >8) transposition profiles, confirming feasibility of bulk RNA‑seq, targeted bisulfite assays and single‑nucleus multiome analyses. Pilot data reveal diet‑responsive changes in THRB/THRA, DNMTs, TETs and HDACs, supporting the mechanistic hypotheses of WP5–WP6. ATAC-seq however needs to be optimized (with (...).

5. Validated omics pipelines (RNA‑seq, methylation, multiome). Dr. Master developed reproducible Nextflow/Snakemake pipelines integrating transcriptomics, methylation, and metabolomics using DESeq2, MixOmics, mediation modelling and pathway tools. Some of these pipelines were tested on published datasets including: Paclitaxel neuropathy DRG/SN transcriptomes (GSE249643), Rabbit conjunctiva RNA‑seq (GSE171043), Nutrigenomic datasets involving CLA‑modulated transcriptomes (Genes Nutr 2016; Nutr Cancer 2020), THRB/DIO1 variant discovery (multiple GenBank accessions: GQ869478.1, KF669869.1, FJ002243–FJ002249). This demonstrates full readiness to execute WP5 multi‑omics tasks and integrate microbiome/metabolite → epigenome → transcriptome regulatory chains.

6. Epigenetic and translational regulatory technologies. A major achievement is the development of dGoligo‑mediated translation enhancement (PL237080B1; PLoS One 2016), a technology directly relevant to planned mechanistic validation in WP6. His work encompasses gene‑specific enhancement of selected genes, RNA structure engineering, antisense‑mediated regulation and variant‑specific expression analysis (gain- and loss-of-function assays for THRB and other related genes are elaborated, as shown in this paper).

7. Nutritional omics and diet‑responsive transcriptomes. Dr. Master co‑authored nutrigenomic studies involving iodine‑biofortified lettuce extract (Koronowicz et al., PLoS One 2016) and CLA‑driven metabolic reprogramming (Nutr Cancer 2020). These serve as methodological baselines for NUMIEP’s diet–epigenome interaction studies.

8. Summary (PL contribution). Dr. Master’s preliminary work provides: validated THRB/THRA mechanistic pathways for WP6, optimised nucleic‑acid and chromatin workflows enabling immediate execution of WP2/WP5, pilot epigenetic/transcriptomic datasets confirming responsiveness to dietary/metabolite cues, fully functional and tested multi‑omics computational pipelines for WP5–WP7,proven experience in variant discovery, methylation profiling, ATAC‑seq and RNA regulatory biology. These results ensure that NUMIEP begins with an exceptionally strong mechanistic and analytical foundation.

Experience: https://sites.google.com/view/adammaster/home/experience?authuser=0

Research: https://sites.google.com/view/adammaster/home/research?authuser=0 

Publikactions: https://sites.google.com/view/adammaster/home/publications?authuser=0

Patents: https://sites.google.com/view/adammaster/home?authuser=0

Inventions: https://sites.google.com/view/adammaster/home?authuser=0 

Dr Ivo Doskočil (CZ)

Dr. Doskočil’s team already possesses validated gastrointestinal models, extensive experience in microbiota–nutrient interactions, established analytical pipelines, and dataset-level evidence that directly supports the technical feasibility of WP3 (microbiota interactions), WP4 (diet–microbiota modulation), WP6 (metabolite–epigenome mediation) and WP7 (data curation, integration and harmonisation).

Dr. Ivo Doskočil and his CZ team have already generated a substantial body of peer-reviewed empirical evidence directly supporting the aims of WP3–WP4 and contributing to WP6–WP7. His preliminary results stem from validated experimental systems modelling gut epithelial function, diet-microbiota interactions, bacterial adherence, microbial metabolite production, and nutrient-dependent immunomodulation. Collectively, these studies confirm the feasibility of the methodological approaches proposed for NUMIEP and demonstrate that the team possesses both the biological models and analytical pipelines necessary for immediate execution of WP3 and WP4.

First, Doskočil has established and validated multiple in vitro intestinal models (Caco-2, HT29-MTX, colon fermentation models) enabling mechanistic testing of dietary components, microbial metabolites, probiotics, and pathogenic strains. These systems were used to quantify epithelial responses, mucin expression, adherence patterns, cytotoxicity, transcriptomic changes and metabolic conversions of plant-derived compounds (e.g., resveratrol, 2-arylbenzofurans), documented in several publications (Jarosova et al., 2020; Vesely et al., 2021). Such validated epithelial–microbial platforms directly support the execution of WP3 (microbiota–diet interactions) and provide immediate assay-ready methodology for NUMIEP.

Second, Doskočil generated high-quality datasets on microbial adherence and competitive colonisation, including the influence of human milk oligosaccharides (HMOs) on bifidobacteria/clostridia adherence (Musilova et al., 2017), the effects of prebiotic saccharides on Listeria adherence (Kodesova et al., 2025), and quantification of bacterial colonisation patterns in diverse microbial systems. These datasets demonstrate reproducible microbial–host interaction phenotyping, which is central to WP3 and WP4.

Third, he contributed to the development of defined microbiota models. A key publication showed that a defined pig microbiota confers protective effects against Salmonella Typhimurium infection (Horvathova et al., 2023), establishing the feasibility of microbiota engineering and pathogen-resilience studies. This directly supports WP3 (diet–microbiota–host pathways) and WP6 (microbiome signals interacting with host epigenetic networks).

Fourth, Doskočil has produced experimental evidence linking dietary components and microbial co-factors with immune modulation, including studies on n-3 PUFAs in antiviral immunity (Lampova et al., 2022), coffee polyphenols, chlorogenic acid, and epicatechin gallate influencing mucin secretion (Volstatova et al., 2019). These results validate nutrient-dependent immunometabolic readouts essential for WP4.

Fifth, his work on selenium-enriched probiotics (Mrvikova et al., 2024; Mrvikova et al., 2025) provides direct mechanistic relevance to NUMIEP because selenium and selenium-containing microbial metabolites are known modulators of methyl-donor metabolism, antioxidant pathways and epigenetic regulation. The team has validated selenium uptake, bioavailability, digestion kinetics and epithelial permeability — all crucial for metabolite→epigenome mediation studies in WP6.

Sixth, Doskočil has co-developed several analytical pipelines for assessing antimicrobial, cytotoxic and metabolic effects of dietary and plant compounds. This includes a validated broth macrodilution volatilization assay for volatile agents (Chaure et al., 2023; Houdkova et al., 2021) and high-throughput cytotoxicity profiling of complex extracts (e.g., Cannabis sativa; Malik et al., 2024). These datasets demonstrate that the group routinely generates high-throughput, standardised, statistically robust datasets, facilitating cross-study integration required in WP7.

Finally, his publications on honey bee gut microbiota diversity (Hroncova et al., 2015) and microbial community dynamics confirm expertise in microbiome profiling, microbial ecology and data analysis, providing an additional foundation for integrating NUMIEP microbiome and metabolome datasets across species.

mgr Petr Šmíd (CZ)

Preliminary work performed by Dr. Petr Šmíd provides experimentally validated foundations for WP3 and WP4, particularly in nutrient digestion, metabolite release and epithelial functional assays. His studies on protein digestibility and intestinal responses, including cricket vs. whey protein digestion (PMID: 39125003) and sardine/sprat digestion models (PMID: 40565705), confirm that his laboratory has fully optimised in-vitro digestion workflows, epithelial barrier readouts and metabolite-dependent immune activation assays. Additional work on intestinal integrity and macrophage activation (PMID: 41227723) provides a direct functional baseline highly relevant to NUMIEP’s WP4 and WP6.

Dr. Šmíd also brings specialised expertise in quantitative optical measurement and image-based analysis, supported by peer-reviewed publications in speckle-correlation techniques and real-time biological motion analysis (PMID: 16946768; PMID: 17538666; PMID: 22673438). These methods strengthen WP4 and WP6 by enabling precise quantification of epithelial morphology, spheroid dynamics and barrier changes in response to microbial metabolites.

His research on bioactive compounds and epithelial modulation, including flaxseed-derived bioactives (PMID: 41228480) and mucin secretion in intestinal models (PMID: 30847127), provides additional preliminary evidence for metabolite-responsive epithelial pathways relevant to WP6. Collectively, these results demonstrate that Dr. Šmíd’s laboratory already possesses optimised digestion, epithelial, functional and analytical workflows essential for NUMIEP and will directly support multi-omics integration in WP7.

Prof. Barbara Stefańska (CA)

Barbara Stefańska provides strong preliminary epigenomic evidence directly supporting WP4–WP6. Her laboratory has experimentally demonstrated that dietary bioactive molecules—including phytoestrogens, resveratrol and pterostilbene—induce locus-specific DNA methylation changes, DNMT3A/DNMT3B-dependent gene silencing and enhancer remodelling in epithelial cells, establishing mechanistic frameworks highly relevant for diet-responsive epigenetic regulation in the intestine (Ma et al., 2025; Harandi-Zadeh et al., 2021; Beetch et al., 2019; Boycott et al., 2025). Stefańska’s work revealed that stilbenoids and other dietary antioxidants can reshape global and promoter-specific methylation patterns, modulate chromatin accessibility, and regulate transcriptional programs involved in metabolism, ageing and oncogenesis (Beetch et al., 2018; Tello-Palencia et al., 2024; Boycott et al., 2022). These studies provide validated pipelines for genome-wide methylation profiling, enhancer-level epigenetic mapping and integrated methylation–transcriptome analysis that will be directly implemented in NUMIEP. Importantly, Stefańska co-authored the first mechanistic studies on iodine-biofortified lettuce, showing mitochondrial and epigenetically mediated responses in gastrointestinal epithelial cells (Sularz et al., 2022; Sularz et al., 2023), providing NUMIEP with a unique, fully aligned baseline model for biofortification-driven epigenetic effects. Her earlier work also defined promoter hypomethylation landscapes in liver cancer and identified methylation biomarkers across tissues (Stefanska et al., 2011; Stefanska et al., 2013; Stefanska et al., 2014), establishing analytical and conceptual foundations for interpreting locus-specific methylation changes in complex tissues. Collectively, these preliminary results demonstrate that Stefańska’s group already possesses the mechanistic, methodological and interpretative framework required to analyse microbiota- and metabolite-driven epigenomic regulation in WP4–WP6.
Prof. Barbara Stefańska’s laboratory (University of British Columbia, Stefanska Lab) is internationally recognised for its contribution to nutriepigenomics, with expertise spanning DNA methylation biology, chromatin regulation, and the epigenetic effects of dietary bioactive molecules. This aligns directly with the project’s aim of characterising how iodine/selenium biofortification and microbiota-derived metabolites modulate the intestinal epigenome. The collaboration with UBC will provide critical added value in several areas: a) Design of epigenomic strategies Prof. Stefańska will advise on the optimal selection of DNA methylation markers, gene targets and analytical platforms (targeted panels vs. genome-wide approaches), ensuring that the project employs modern, internationally validated methodologies.  b) Interpretation of epigenetic data
The Stefanska Lab brings in specialised expertise in distinguishing global vs. locus-specific methylation changes, understanding diet-related chromatin dynamics, and interpreting the “epigenetic paradox” relevant to micronutrient and SCFA-driven gene regulation. This expertise is not available in Poland and markedly increases scientific reliability. c) Training and capacity building UBC will offer short-term training stays for PhD students and postdocs, providing experience in epigenomic analysis pipelines, QC standards, and data interpretation frameworks. This supports the long-term scientific development of the Polish team. d) Co-authorship of high-impact publications. UBC’s nutriepigenomic perspective will increase the translational relevance of the findings, facilitating publication in journals focused on nutrition, epigenetics, and preventive medicine. Prof. Stefańska’s team already investigates epigenetic responses to polyphenols and other dietary compounds, enabling direct comparison with the biofortified-lettuce model and strengthening mechanistic conclusions. The project leader previously completed a 3-month research fellowship in Prof. Stefańska’s laboratory, ensuring pre-established communication channels, mutual methodological familiarity, and a high likelihood of effective collaboration.