Associated PhD students

Description

Inflammatory Bowel Disease (IBD) is a chronic, idiopathic disease that affects the gastrointestinal tract. IBD is highly associated with irregular immune response, microbiota dysbiosis and abnormal gastrointestinal function. All of these factors are controlled by the circadian system or at least show diurnal fluctuation.  The circadian system represents the internal body mechanisms in preparing and adapting to external recurring environmental factors. The circadian system is composed of transcription-translation feedback loop oscillate in a ~24 hrs. rhythm – so-called circadian rhythm.  This endogenous system regulates the transcription of thousands of clock-controlled genes. As a result, various physiological functions fluctuate between day and night.

Shift work or frequent jet lag impair the internal clock ability to entrain with external environmental cues, and this misalignment results in disruption of the circadian system. Shift worker and people frequently exposed to jet lag appeared to be at higher risk to develop various physiological diseases, such as metabolic abnormalities, cancer and gastrointestinal diseases including IBD. A likely explanation why the risk to develop gastrointestinal diseases is increased in shift worker is the disruption of the circadian system, which is known to result in disruption of gastrointestinal functions, impairment of the immune response and causes microbiota dysbiosis.

In the current project, we are aiming to analyze different aspects of the circadian system controlling microbiota composition, which may be involved in IBD development. In addition we aim to understand whether the disruption in the circadian system increase the disease progression through changes in microbiota composition and finally, to assess the possibility of manipulating the microbiota fluctuations to attenuate the IBD symptoms.

Publications

• Altaha, B., Wadi, J. and Shehabi, A. (2018). Detection Probiotic's DNA of Lactobacillus paracasei in Healthy Human Faeces. Journal of Pharmaceutical Research International, 23(6), pp.1-9.

• Altaha, B., Wadi, J. and Shehabi, A. (2018). Probiotics: Past, Present and Future Challenges. The International Arabic Journal of Antimicrobial Agents, 8(1).

Description of Thesis 
coming soon

Description of Thesis 

A potentially curative treatment for patients suffering from hematological malignancies consists of cytotoxic therapy regimens followed by allogeneic hematopoietic stem cell transplantation (allo-HSCT). However, the broader applicability of this treatment is limited by several adverse affects which immensely increase morbidity and transplant-related mortality. Still the most common life-threatening complication is the gastrointestinal graft-versus-host-disease (GvHD) caused by donor T-cells attacking healthy recipient tissues. Recent research has highlighted strong correlations between intestinal bacterial microbiome alterations, their influence on GvHD pathophysiology and the clinical outcomes after transplantation. The intestinal microbiome in allo-HSCT recipients is altered by loss of bacterial diversity and single-taxon domination. Previous studies described a change in bacteria-derived metabolites during allo-HSCT and classified metabolite-producing bacterial consortia as either protective or deleterious according to their association with GvHD severity and mortality. Most studies have focused on microbiota compositions during transplantation period whereas clinical studies about the post-transplantation microbiome are still lacking. Thus, we aim to investigate the extent of microbiome recovery and its modulating factors and to identify potential metabolite-producing bacterial consortia in the post-transplantation microbiome, that may correlate with clinical outcomes. In order to establish a comprehensive longitudinal profiling of bacterial compositions and bacteria-derived metabolites in allo-HSCT patients, we perform translational analysis based on an ongoing prospective, observational clinical study. We longitudinally obtain human stool samples. We compare metabolite profiles (analyzed by mass spectrometry) and microbiome compositions (analyzed by 16S rRNA sequencing) of stool samples obtained after allo-HSCT with those profiles of samples obtained shortly before transplantation. Stool samples are referenced with extensive clinical metadata (occurrence of intestinal GvHD, survival data) and potential confounding factors (diet, antibiotic and immunosuppressive therapy).

Description

Our bodies carry more bacterial than human cells. Massive efforts have been made to understand which changes bacterial communities undergo between health and disease. A particular challenge is not only to quantify these changes, but to explain the causes triggering population shifts, such as the exposure to drugs. The microbiome is key to many physiological reactions of the host, yet our poor understanding of its mechanisms gives an urgent need for unravelling their molecular basis.

My PhD proposal unites the highest-performance techniques of modern microbiology and chemical biology to explain how drugs affect the gut microbiome. I will characterize anaerobic Desulfovibrio gut bacteria and will establish strategies to genetically modify them to study their stress adaptation and sensory systems. I will also directly investigate host-microbiome interactions using in vivo disease-models of mice, allowing us to bridge the gap between Molecular and Systems Biology.

Altogether, the strategies I will develop will be key to advance the fields of microbiome research to immunology and personalized medicine. By uniting classic characterisation approaches with in vivo models of disease they will help unravel how hormones and drugs affect the gut microbiome to regulate essential host-microbiome interactions.

Description of Thesis 

Colon cancer is one of the most common types of cancer worldwide, the number of new cases is rising. Despite improvement in prevention and treatment, half of the patients dies within 5 years after diagnosis. It has been shown that a high number of tumor infiltrating immune cells (eg CD8+ cytotoxic effector T-cells) favour the survival of the patients. For the recruitment, these T-cells need specific chemokines, which were shown to be expressed by tumour cells on exposure to gut bacteria. However, it is unclear which bacterial signatures and taxa are correlated with specific adaptive and innate immune infiltrates. Further, subgroups of colon cancer have been shown to have significantly worse prognosis, especially signet ring cell cancer, whereas the involvement of gut microbiota is unclear.Therefore, we want to investigate if there are specific bacterial taxa, or a specific composition of the gut microbiome, that leads to a higher TH1-type lymphocyte infiltration and therefore to a putative tumor suppression. Therefore, we are collecting stool and matched tissue samples from patients with colon cancer from different types (Adenocarcinoma, mucinous and signet ring cell carcinoma). The Immuno infiltrate is quantified on tissue by ChipCytometry (Zellkraftwerk). Microbome data are evaluated by 16S rRNA amplicon sequencing. As complementary in vitro model, organoids are established from tumors and normal mucosa from tumors of all subtypes. Statistical evaluation is done  by correlating the results of the immuno-infiltrate with the output of the microbiome sequencing, including clinical relevant data of the patients.  We aim to gather prognostic information  about the course of disease, and, in the long term, to modify the tumor-influencing milieu, with the goal of a better clinical outcome and overall survival. 

Description

Colorectal cancer (CRC) ist the third most common cancer worldwide, with colorectal polyps serving as a main precursor. Several studies identified various lifestyle and epidemiological factors that may influence the risk of developing CRC. Moreover, evidence suggests that these factors contribute to the development of CRC through changes in gut microbiome. In this study we investigate different epidemiological, dietary, lifestyle, clinical, laboratory and microbial factors in patients with colorectal polyps. Defining risk and protector factors at the stage of precursor lesion could lead to important changes in prevention strategies.

Description
Analysis of changes to microbial diversity and richness in adult patients suffering from IBD.

Description of Thesis 

Genetically engineered mouse models (GEMMs) are the most frequently employed animal models for human colorectal cancer (CRC) research. However, there are tumor characteristics which are different in mice and humans, whereas spontaneous tumors of companion animals (e.g., cats) resemble the human phenotype more closely. This project addresses the need for a standardized and comparative histological classification and grading system for animal models of human CRC. Following this comparative approach, we aim at further deciphering the role of different mast cell subtypes and the microbiome within the intestinal tumor microenvironment during adenoma-carcinoma progression by comparing diverse GEMMs for intestinal cancer, spontaneous feline, and human colorectal neoplasia.

Description of Thesis 

Description

Atopic dermatitis (AD) is a chronic inflammatory skin disease typically characterized by skin barrier defects and microbial dysbiosis. Clinical trials and patient data demonstrated the causal role of type 2 cytokines in AD. Therapeutically targeting type 2 cytokines re-established barrier function and normalized cutaneous microbial composition in AD patients. However, it is not yet understood whether targeting barrier disruption or dysbiosis in AD is effective with regard to type 2 immune inflammation. To disclose the impact of barrier impairment and microbial dysbiosis on type 2 inflammation in AD, we set up a new model mimicking the initial phase of AD. To monitor the kinetics and to identify cellular contributors of type 2 immune responses, we use IL-4 and IL-13 reporter mice. On the long term, this project will contribute to the development of treatment strategies towards personalized AD therapy.

Description of Thesis 

We are investigating the impact intestinal dysbiosis has on infection complications of patients during stem cell transplantation. Translocation of bacteria from the gut into the vascular system, if the mucous barrier is disrupted, is the center of my research. We want to evaluate if it is possible to detect the pathogen in the gut and other mucous membranes before a blood stream infection occurs

Description

Allergic diseases are highly prevalent in industrial countries. This risen prevalence has been attributed to a change in lifestyle factors that also affects intestinal microbiota composition. Such a microbial dysbiosis - particularly early in life - has been associated with atopic diseases later in life. In murine models, we amongst others have shown that mice housed under germ-free conditions show an impaired immune system in the gut. In particular, these mice have drastically reduced frequencies of peripherally-induced regulatory T Cells in the intestine. Re-colonization of germ-free mice re-establishes such inducible Treg populations, which are defined by the co-expression of the transcription factors Foxp3 and ROR(γt). We hypothesize therefore that these cells are key regulators in intestinal immune tolerance. The microbial factors driving this Treg induction remain still poorly understood.

In this project we will make use of a set of mice with reduced microbial complexities: ASF (Altered Schaedler flora, eight strains), Oligo-MM (Oligo-Mouse Microbiota, twelve strains) and SPF (specific pathogen free, complex microbiota) in collaboration with members of this consortium (AG Bleich and AG Stecher-Letsch). In order to identify causative host-microbiome relationships these gnotobiotic mouse models are used to identify microbial-derived parameters (using metatranscriptomics/metagenomics and metabolomics approaches) that enforce or break intestinal immune tolerance. Murine food allergy models to known allergens including a model of red meat allergy (in cooperation with the AG Biedermann) will be used to determine how differential microbial compositions affect disease outcomes.

Description of Thesis 

Highly diverse viral communities inhabit the human body, including eukaryotic viruses and bacteriophages. Phages residing in the human gut outnumber tenfold gut bacteria. The numerical dominance enables gut phages to encounter and interact with the host bacteria. They can shape bacteriome by directly lytic infecting host bacteria, alternatively, by integrating into bacterial chromosomes to supply them with virulence associated-auxiliary metabolic genes (AMGs). Specific environmental stimuli can induce the phages with latter capacity turning into lytic cycle and transferring these genes to adjacent susceptible hosts, eventually increasing the pathogenicity of the opportunistic pathogens to trigger the diseases. Hence, further understanding of the alterations of the gut phage community, and their interactions with host bacteria, could help to elucidate the molecular mechanisms underlying disease pathogenesis.

Helicobacter pylori is the main risk factor for gastric cancer development and also elicits systemic consequences on extragastric diseases, especially colorectal cancer (CRC), which is the second most commonly diagnosed cancer. We established cooperation with AG Gerhard, whose study suggests a possible link between H. pylori infection and intestinal/colonic pathologies through alterations in the gut microbiota and host immunity. However, the study directly describing the role of gut virome in H. pylori derived-CRC is still missing.

In this project, we postulate that the gut viral community is associated with H. pylori derived-CRC tumorigenesis via its interaction with the bacterial community. In addition, given that H. pylori is typically treated with a combination of antibiotics plus a proton pump inhibitor, we would further study the impacts on virome bought by H. pylori eradication treatment.

Description

Proteomics based on mass spectrometry is a powerful tool for analysing proteome-wide changes within cells in response to external stimuli. We apply this technique to discover protein targets of gut metabolites with unknown function produced by the gut microbiota. Our chemical proteomics approach consists of two complementary techniques: (1) Activity-Based Protein Profiling (ABPP), which uses chemically modified probes, and (2) Thermal Proteome Profiling (TPP), which does not require modification of compounds. Taken together, the discovery of gut metabolite targets will help improve our understanding of the interactions between the gut microbiota and its host and shed light on the role of those metabolites in disease pathways.

Description

BRAF-mutant colorectal cancers form a large tumour subset with distinctive morphologic, genetic and clinical characteristic. The molecular evolution of these cancers is however poorly understood. In order to identify genes and pathways that cooperate with Braf in the setting and progression of CRC we developed a PiggyBac transposon-based cancer gene discover tool-kit in mice, which enables unbiased genetic screening in vivo. Using this approach relevant pathways or pathway branches are “hit” by transposons at multiple levels and the transposon integration pattern predicts the gene’s function as oncogenic or tumour suppressive. For the validation of these “hits” we developed an orthotopic transplantation model based on colonoscopy-guided injections of intestinal organoids into the submucosa of the rectum/distal colon. This technology allows the control of tumour development in an efficient spatio-temporal manner without the need for extensive intercrossing of mice. Intestinal organoids derived from the normal and tumour mouse tissue recapitulate key morphological and histological features of the organ architecture of the mouse. Additionally we are currently using CRISPR/Cas9 genetic editing tool in order to inactivate tumour suppressor genes in WT or Braf-mutant organoids. Upon injection of the edited organoids into recipient mice, tumour formation will be assessed and the tumours characterized. Furthermore, the combination of these technologies enables the characterization of the microbiota signatures both at the site of primary tumour (colon) and at metastatic sites (liver and lung) as tumours injected with organois have the ability to progress to advanced stages of disease.

Description
Project description: Analysis of changes to microbial diversity and richness in adult patients suffering from IBD.

Description of Thesis 

The entirety of all genomes of microbes in an ecosystem is defined as microbiome and the human body is colonized by microbes with at least as many cells as number of human cells. The individual composition of the intestinal microbiome is influenced by many different factors such as diet, medication, the hosts genes, infections and many others. The microbiome itself has an immense impact on the human metabolism, immune maturation, the regulation of intestine endocrine functions and the progression of certain diseases. These include obesity, colon cancer or chronic inflammatory bowel disease and autoimmune diseases.

Recent findings also suggest a connection between certain microbial compositions and the carcinogenesis of different malignancies. Ways in which microbes and according metabolites effect malignancies include DNA damage or an alteration of gene expression through certain metabolites.

In our working group we are focusing on hematological malignancies and their correlation with the intestinal microbiome. Our latest project takes a closer look at patients with Multiple Myeloma (MM) and the pre-stage “monoclonal gammopathy of unclear significance” (MGUS). MM belongs to the B-cell Non-Hodgkin-Lymphomas, is a hematological plasma cell malignancy, and is characterized by an increased proliferation of plasma cells infiltrating the bone marrow. Previous mouse studies suggest a cytokine mediated migration of different immune cell populations and metabolites from the gut into the bone marrow. We investigate the influence certain bacterial compositions and according metabolites may have on the progression of MM and the efficacy of myeloma specific therapies.

Therefore, I analyze bone marrow samples of myeloma patients using intracellular cytokine staining and flow cytometry. With statistical analyses we will correlate these findings with 16s-rRNA microbiome data including information about composition, diversity and metabolites of the intestinal microbiome.