Open Research Projects, Research

Senescent cells in progression of IBD to CRC

Principle Investigator

Scientific interest within the context of the graduate college:

Our group “Signal Transduction in Health and Disease” (Department of Hepatology and Gastroenterology, Charité Campus Mitte and Campus Virchow) aims to understand the molecular mechanisms involved in tissue homeostasis, inflammation, and resolution of inflammation. Our main focus is on the transcription factor NF-κB and its role in the intestinal epithelium. Our current projects range from determining the role of the transcription factor in epithelial regeneration in colitis and in inflammatory bowel diseases (Re-Thinking Health, 2022), to refining analgesia (3R funded project), to investigating the role of NF-κB in cellular senescence in the gut (DFG) or its role in metabolism.

Project description:

Introduction: Senescent cells are characterized by terminal cell cycle arrest, epigenetic changes, and by the senescence associated secretory phenotype (SASP). SASP is comprised of scores of cytokines, chemokines, and growth factors, which regulate cells and tissues in a paracrine manner. Therefore, even a small number of senescent cells can have a dramatic impact on distant tissues and were shown to sustain inflammation, fuel carcinogenesis, and shorten lifespan. Most of the genes that code for SASP factors are transcriptionally regulated by NF-κB8.1,2 Under physiological conditions SASP promotes wound healing and recruitment of immune cells, which help clear senescent cells.

Figure 1. Multiplex immunofluorescence staining of senescence. Mouse colon (colitis model) was stained with markers for senescence. Simultaneous staining with numerous markers (multiplex) is required to rule out other cell states (proliferation, apoptosis, quiescence). Zoom-in on select fully senescent cells is shown on the right.

We are interested in investigating what kind of senescent populations arise in inflammatory bowel diseases (IBD) versus those that progressed to colorectal cancer (CRC). We are especially interested in the role that SASP plays in disease progression and whether distinct forms of SASP can be exploited therapeutically.

As part of our preliminary data, we have already identified distinct populations dependent on stage of inflammation and importantly, we show that no single type of senescence exists, but rather cells display different proficiencies for SASP and thus for communication with their environment. It is not known how these differences skew progression of IBD.

Aim 1: Characterize senescent cells in IBD and CRC and in murine colitis and CRC models. As part of this work package you will perform multiplex stainings (as in Figure 1) using already available samples from IBD and CRC patient samples and from murine mouse models. You will also receive training in basic analysis of single-cell RNA sequencing and will therefore quantify cells that have SASP versus those that do not. You will then isolate these cells using FACS and determine how different types of SASP alter immune cell recruitment.

Aim 2: Reprogram senescent cells to transform immunosuppressive “cold” tumor microenvironment environment into “hot”. Here you will use available senolytics and senomorphics (drugs that kill senescent cells or suppress their SASP), and those identified via our collaborators through deep learning, to reprogram senescent cells in 2D culture and in human and mouse intestinal organoids. Successful senolytics will be used in pre-clinical trials in CRC mouse models to determine if these expose tumors to immunosurveillance.

Figure 2. Immunofluorescence staining of mouse fluorescent organoid. All our projects combine work with mouse models. patient samples (including organoids) and bioinformatics.

Methods you will learn as part of this project: multiplex immunofluorescent staining, single-cell data analysis, immunohistochemistry, human and mouse organoid cultures (Figure 2), qPCR.


  1. Kolesnichenko M, Mikuda N, Höpken UE, Kärgel E, Uyar B, Tufan AB, […], Schmidt-Ullrich R, Schmitt CA, Scheidereit C. Transcriptional repression of NFKBIA triggers constitutive IKK- and proteasome-independent p65/RelA activation in senescence. EMBO J. 2021; 40(6):e104296.
  2. Mikuda N, Schmidt-Ullrich R, Kärgel E, Golusda L, Wolf J, Höpken UE, Scheidereit C, Kühl AA, Kolesnichenko M. Deficiency in IκBα in the intestinal epithelium leads to spontaneous inflammation and mediates apoptosis in the gut. J Pathol. 2020; 251(2):160-174.