Junior Group 'Intestinal Stem Cells in Inflammation and Vascular Niches'

Dr. Natalia Soshnikova

Intestinal stem cells (ISCs) ensure lifelong regeneration of the gut epithelium and play central roles in inflammatory bowel disease and colorectal cancer. Our research aims to understand how stem cell identity is established during development and how it determines regenerative capacity and disease susceptibility in adult tissues.

We investigate how embryonic signalling environments shape long-term stem cell programs that persist into adulthood. A central focus of our work is the interplay between signalling pathways, transcriptional regulators and epigenetic states that define stem cell fate decisions. These intrinsic programs are tightly controlled by the surrounding microenvironment, including endothelial cells, immune components and extracellular matrix signals. Using genetic lineage tracing, organoid-based models, single-cell transcriptomic and chromatin accessibility approaches, we dissect how these molecular programs control lineage specification, plasticity and tumour initiation.

A major goal of our group is to define how vascular-derived cues and inflammatory signals regulate intestinal stem cell maintenance, lineage commitment and plasticity. By studying endothelial–epithelial cross-talk during homeostasis and inflammation, we connect epithelial regeneration to vascular biology and haemostatic processes.

To model these interactions under controlled conditions, we develop advanced organoid systems and defined extracellular matrix platforms that allow us to dissect niche-specific regulation in healthy, inflamed and early neoplastic tissue states.

By integrating developmental biology, stem cell research and vascular niche biology, we aim to uncover mechanisms that drive inflammation-associated tumorigenesis and to identify stem cell populations that shape disease progression.

If you are interested in joining our group or collaborating, you are welcome to contact us.

Research Interests

• Developmental programming of intestinal stem cell identity
• Stem cell maintenance, lineage commitment and plasticity
• Endothelial–epithelial cross-talk in the intestinal niche
• Inflammation-driven epithelial reprogramming in IBD
• Mechanisms of intestinal tumor initiation and inflammation-associated cancer

Research Funding

• German Research Foundation (DFG), SO 1738/3-3 (2026–2028) “Functional heterogeneity of intestinal stem cells: molecular mechanisms and relevance in disease”.
• Associate Member, Collaborative Research Centre 1551 “Polymer Concepts in Cellular Function”

Partners of Collaboration

Partners at the University Medical Center Mainz

• Prof. Dr. Christoph Reinhardt (CTH)
• Dr. Madhusudhan Thati (CTH)
• Prof. Dr. Tobias Bopp (Institute of Immunology)
• Prof. Dr. Michael Delacher (Institute of Immunology)
• Prof. Dr. Hans-Jörg Schild (Institute of Immunology)
• Prof. Dr. Dr. Detlev Schuppan (Institute for Translational Immunology)
• Prof. Dr. Beate Straub (Institute of Pathology)
• Prof. Dr. Stefan Tenzer (Institute of Immunology)
• Prof. Ari Waisman (Institute for Molecular Medicine)

National Partners

• Dr. Sudhanshu Bhushan (University of Giessen)
• Prof. Dr. Andreas Diefenbach (Charité, Universitätsmedizin Berlin)

Biography – Natalia Soshnikova

Positions:
Since 2025 – Group Leader, Centre for Thrombosis and Haemostasis (CTH), University Medical Center of the Johannes Gutenberg University Mainz
2019–2024 – Group Leader, Heisenberg Programme, Institute of Molecular Medicine, University of Mainz
2012–2018 – Group Leader, Institute of Molecular Biology (IMB), Mainz

Research Career:
2007–2011 – Senior Scientist, University of Geneva, Switzerland
2004–2006 – EMBO Postdoctoral Fellow, University of Geneva, Switzerland

Professional Education:
2004 – Dr. rer. nat. (summa cum laude), Humboldt University Berlin, Germany
1993–1998 – Diploma in Molecular Biology (with honours), Novosibirsk State University, Russia

Team - Juniorgruppe 'Darmstammzellen bei Entzündungen und in vaskulären Nischen'

• Contact

Dr Natalia Soshnikova

Group Leader

06131 17-8364

Original Articles (Selection)

• Leite JA, Menezes L, Martins E, Rodrigues TS, Tavares L, Ebering A, Schelmbauer C, Martelossi Cebinelli GC, Zinina V, Golden A, Soshnikova N, Zamboni DS, Cunha FQ, Huber M, Silva JS, Waisman A, Carlos D, Saraiva Câmara NO. AIM2 promotes TH17 cells differentiation by regulating RORγt transcription activity. iScience. 2023 Oct 4;26(11):108134.
• Pontarollo G, Kollar B, Mann A, Khuu MP, Kiouptsi K, Bayer F, Brandão I, Zinina VV, Hahlbrock J, Malinarich F, Mimmler M, Bhushan S, Marini F, Ruf W, Belheouane M, Baines JF, Endres K, Reba SM, Raker VK, Deppermann C, Welsch C, Bosmann M, Soshnikova N, Chassaing B, Bergentall M, Sommer F, Bäckhed F, Reinhardt C. Commensal bacteria weaken the intestinal barrier by suppressing epithelial neuropilin-1 and Hedgehog signaling. Nat Metab. 2023 Jul;5(7):1174-1187.
• Zinina VV, Sauer M, Nigmatullina L, Kreim N, Soshnikova N. TCF7L1 Controls the Differentiation of Tuft Cells in Mouse Small Intestine. Cells. 2023 May 23;12(11):1452.
• Zinina VV, Ruehle F, Winkler P, Rebmann L, Lukas H, Möckel S, Diefenbach A, Mendez-Lago M, Soshnikova N. ID2 controls differentiation of enteroendocrine cells in mouse small intestine. Acta Physiol (Oxf). 2022 Feb;234(2):e13773.
• Sayols S, Klassek J, Werner C, Möckel S, Ritz S, Mendez-Lago M, Soshnikova N. Signalling codes for the maintenance and lineage commitment of embryonic gastric epithelial progenitors. Development. 2020 Sep 15;147(18):dev188839.
• Szenker-Ravi E, Altunoglu U, Leushacke M, Bosso-Lefèvre C, Khatoo M, Thi Tran H, Naert T, Noelanders R, Hajamohideen A, Beneteau C, de Sousa SB, Karaman B, Latypova X, Başaran S, Yücel EB, Tan TT, Vlaminck L, Nayak SS, Shukla A, Girisha KM, Le Caignec C, Soshnikova N, Uyguner ZO, Vleminckx K, Barker N, Kayserili H, Reversade B. RSPO2 inhibition of RNF43 and ZNRF3 governs limb development independently of LGR4/5/6. Nature. 2018 May;557(7706):564-569.
• Dzama MM, Nigmatullina L, Sayols S, Kreim N, Soshnikova N. Distinct populations of embryonic epithelial progenitors generate Lgr5+ intestinal stem cells. Dev Biol. 2017 Dec 15;432(2):258-264.
• Kazakevych J, Sayols S, Messner B, Krienke C, Soshnikova N. Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells. Nucleic Acids Res. 2017 Jun 2;45(10):5770-5784.
• Nigmatullina L, Norkin M, Dzama MM, Messner B, Sayols S, Soshnikova N. Id2 controls specification of Lgr5+ intestinal stem cell progenitors during gut development. EMBO J. 2017 Apr 3;36(7):869-885.

Reviews (Selection)

• Soshnikova N. KDM6A/B Demethylases in Gut Homeostasis. Cell Mol Gastroenterol Hepatol. 2023;15(4):1016-1017.
• Bayer F, Dremova O, Khuu MP, Mammadova K, Pontarollo G, Kiouptsi K, Soshnikova N, May-Simera HL, Endres K, Reinhardt C. The Interplay between Nutrition, Innate Immunity, and the Commensal Microbiota in Adaptive Intestinal Morphogenesis. Nutrients. 2021 Jun 26;13(7):2198.
• Soshnikova N. Functions of SETD7 during development, homeostasis and cancer. Stem Cell Investig. 2019 Sep 2;6:26.