OR Imunologie
Vypsané doktorské práce pro akademický rok 2025/2026
Transcriptional control of chronic inflammation
Alberich Jorda Meritxell, doc., Ph.D.
278916
Chronic inflammation is a constant state of alert that keeps the immune system active for long periods of time and is characterized by a long-term overproduction of cytokines and chemokines. It is a hallmark of autoimmune and autoinflammatory disorders including rheumatoid arthritis, chronic recurrent multifocal osteomyelitis, and systemic lupus erythematosus. In addition, it has been reported that chronic inflammation can contribute to the development of other diseases, such as type 2 diabetes, cardiovascular conditions, cancer, and dementia. Recently, we demonstrated that chronic inflammation has a negative impact on hematopoiesis and exerts a detrimental effect on the hematopoietic stem and progenitor cells. Using murine models, we have demonstrated that chronic inflammation accelerates leukemia progression. In this thesis, we aim to explore the molecular mechanisms driving chronic inflammation with the ultimate goal to design strategies to control chronic inflammation. Animal models of chronic inflammation will be utilized, as well as transcriptomics and proteomic approaches. The results of this project will provide a deep understanding of the transcriptional machinery that drives and sustains chronic inflammation.
Characterization of Mouse Breast Milk and Maternal-Fetal Microchimerism Established During Lactation and Its Impact on Offspring's Immune System
Černý Jan, prof. RNDr., Ph.D.
279861
Maternal-fetal microchimerism (MMc) is a widely accepted physiological phenomenon during which maternal cells migrate into the tissues of the offspring. This occurs both during pregnancy and through breast milk. While MMc established during pregnancy has long been recognized, the migration of maternal cells via breast milk has only come into focus in recent years. The aim of this project is to characterize mouse breast milk, including its hormone content and cellular populations, with an emphasis on immune cells. Furthermore, the project will investigate the transfer of these maternal cells to the offspring, specifically their migration pathways, target organs, and their quantities and frequencies within specific tissues. Special attention will be paid to the phenotypes of these cells and their potential to influence the development of the offspring's immune system, with implications for possible transgenerational transfer of immune memory. The project will also include the characterization of differences between two mouse strains – C57Bl6 and Ly5.1. Recent data from our laboratory have highlighted differences in development, breast milk composition, and the establishment of MMc between these strains. Therefore, the project will also focus on the differences between these two mouse strains and their impact on offspring development and immune system function, highlighting a contribution from MMc. As an important model, the MHCII–EGFP knock-in mouse will be utilized, which is an exceptional tool for systemic and quantitative immunology. The project also includes characterization of the lymphatic system/gastrointestinal tract in the context of early postnatal development, breastfeeding, and microbiota.
The function of a new interacting partner of ORMDL3, LAIR-1, in mast cell physiology
Dráber Petr, RNDr., DrSc.
277476
The human and mouse ORMDL3 genes encode proteins comprised of 153 amino acids. Genetic studies have linked ORMDL3 with asthma and inflammatory diseases [1]. Asthma and associated allergies stem from the coordinated release of cytokines, chemokines, lipid mediators, proteolytic enzymes, and vasoactive mediators originating from activated tissue mast cells during degranulation [2]. Our recent studies found that various antigen-mediated signaling pathways are affected by the activity of the serine-palmitoyl transferase (SPT), the activity of which is inhibited by interaction with ORMDL3 [3-6]. Our unpublished immunoprecipitation and mass spectrometry data showed that ORMDL3 binds several proteins, including LAIR-1 (CD305), and that this binding affects the inhibitory activity of ORMDL3.
In this project, we will investigate the effect of ORMDL3 interacting partner LAIR-1 in mast cell signaling and asthma-related inflammatory diseases. We will cross ORMDL3 knockout (KO) mice, generated in our laboratory and maintained on the C57BL/6 genetic background, with LAIR-1 KO mice to generate ORMDL3/LAIR-1 double KO mice and determine airway hyperresponsiveness to ovalbumin-induced inflammation and antigen-induced allergies in vivo. Based on previous findings that collagen binds to LAIR-1 [7], we will prepare new bispecific tools formed by TNP-modified collagen. We propose that the TNP-modified collagen will bind to both LAIR-1 (via collagen) and TNP-specific-IgE-receptor complexes to inhibit the FcεRI signaling. We aim to prepare constructs that will inhibit FcεRI signaling by crosslinkíng LAIR 1 with FcεRI complexes under in vivo and in vitro conditions. The project will use various methods, including high-resolution microscopy, lentiviral transduction, mass spectrometry, immunochemistry, and transcriptomics. At least three publications in high-impact journals will be published based on the data from this project.
Mechanism of autoantigen egress from seminiferous tubules and establishment of immune tolerance in testes
Filipp Dominik, RNDr., CSc.
280198
Sertoli cell (SCs) are the main building blocks of the testicular seminiferous tubules where they facilitate the process of spermatogenesis. In adition to hormonal, nutritional and physical support, SCs aid developing spermatocytes by engulfing their cytoplasmic waste which is full of unique antigens which can be targetted by immune system and cause autoimmunity. To prevent that, SCs form a protected endoluminal compartment which is sealed off by the blood-testis barrier (BTB). Despite the fact that the transport of even the smallest molecules and ions can be effectivelly blocked by BTB, recent reports documented that many germ-cell-specific autoantigens can egress outside of BTB, into interstitial space which is seeded with immune cells. Many relevant questions need to be answered to understand processes which underpin the role of BTB in establishment of testicular immune tolerance. The main goal of this project is to investigate (i) the egress mechanism of germ-derived autoantigens outside of BTB, (ii) whether these autoantigens are acquired and presented by the antigen presenting cells in the interstitial space, and (iii) whether recessive or dominant tolerance, or both, play a role in tolerization of germ-specific selfreactive T-cells. The project will utilize already generated new reporter mouse models expressing a fluorescent protein tdTomato with an OVA peptide in the developing germ cells. These models will be instrumental in tracking the pathway of neo-self-antigens from the germ cells to the outside of BTB. We will use microscopy, flow cytometry and several antigen-presenting assays to identify this APC subset and to assess its tolerization potential.
Modulation of antigen presentation to assess its effect on the establishment of central tolerance
Filipp Dominik, RNDr., CSc.
280195
Thymic antigen-presenting cells (APCs) are critical cellular component of the mechanism of central tolerance which generates both functional and self-tolerant T cells which then eggres the thymus and protect the host. Critical to this mechanism is the presentation of thousands of self-antigens on major histocompatibility complex molecules type I and II (MHC I and II), the recognition of which by developing T cells with distinct affinity and avidity has a major impact on their fate, i.e., either they die by neglect in thymic cortex (antigen presentation by cortical thymic epithelial cell), or undergo apoptosis, or survive and fully develop into a conventional or regulatory T cell (antigen presentation by medullary thymic epithelial cells (mTECs), dendritic cell (DCs) or B cells).
Recently, it has been shown that thymic APCs are highly heterogeneous and that central tolerance establishment depends on the cooperation and preferential pairing between specific subsets of thymic APCs. In this PhD project, we would like to follow up on our previous results regarding this preferential pairing in cooperative antigen transfer (CAT) (Vobořil, Březina et.al. 2022; eLife), specifically, an unidirectional self-antigen transfer from mTEC to DC subsets. Additionally, we will compare the antigen presentation requirements for T cell selection processes in the thymic cortex vs. thymic medulla in regards of both helper (CD4+) as well as cytotoxic (CD8+) T cells. To this end, we will use mouse models that simulate the expression of either ubiquitous or tissue-restricted self-antigens using the model of neo-self-antigens, the ovalbumin fragments OVAI for CD8+ and OVAII for CD4+. By combining OVA-expressing models with models that allow specific depletion of MHCII on mTEC or DC subsets, we will investigate the relevance of antigen presentation in individual thymic APC subsets. By modulating the number of mTECs with the highest tissue-restricted antigen expression and DCs with the highest antigen presentation capacity, we will modulate the avidity/affinity of OVA recognition, the essential parameter of antigen presentation process. These experiments will contribute to deeper understanding the decision-making process between clonal deletion of self-reactive T cells (apoptosis commitment) or agonist regulatory T cell selection. Finally, we will use several techniques routinely used in our laboratory to analyze the impact of modulating thymic antigen presentation under different circumstances on the development of autoimmunity.
Effect of gluten-free diet (GFD) on immune parameters, microbiome and metabolome in inflammatory bowel disease and primary sclerosing cholangitis
Funda David, MUDr., Ph.D.
246642
Idiopathic inflammatory bowel diseases (IBD) are chronic, relapsing, immune-mediated inflammatory disorders of the gastrointestinal tract. Primary sclerosing cholangitis (PSC) is a progressive disease of the bile ducts, which in advanced stages of the disease represents one of the most common indications for orthotopic liver transplantation in developed countries. While genetic factors contribute to the development of these diseases, environmental factors (such as diets) and subsequent changes in the microbiome likely have a significant impact on the etiopathogenesis of these diseases. PSC is associated with IBD in approximately 70% of patients. Recently, independent evidence has emerged regarding the role of chronic intestinal inflammation in a wide range of immune-mediated diseases. Gluten and its components have a pro-inflammatory effect similar to lipopolysaccharide. Beneficial effects of a gluten-free diet (GFD) have already been demonstrated in several autoimmune diseases (type 1 diabetes, certain neurological disorders).
The aim of this project is to elucidate the mechanisms of interaction between a gluten-free diet, the microbiome, and the metabolome, and to study the impact of GFD on mucosal and innate immunity in IBD and PSC. The project is based on both human randomized clinical trials (the effect of a gluten-free diet on clinical symptoms of PSC and IBD; ClinicalTrials.gov Identifier: NCT06026449) and on mouse-induced models of IBD (DSS-induced colitis model in BALB/c mice) and PSC ( PSC model in Mdr2-/- KO mice, possibly also in combination with DSS-induced colitis).
Mechanistic studies include the analysis of immune parameters, changes in metabolomes, and changes in bacteriomes in relation to a gluten-free diet. Methods used in this project include isolation of peripheral blood leukocytes from patients and cells from lymphoid tissues in mice, flow cytometry, histology, immunohistochemistry, tissue culture, ELISA, metabolome characterization (in collaboration with the Laboratory for Molecular Structure Characterization), sample preparation for bacteriome sequencing, data analysis, and eventually also single cell transcriptomics. The project involves international collaborations.
The role of dietary factors (e.g. gluten-free diet) on development and immune parameters in Parkinson's disease or other alfa-synucleinopathies e.g. Multiple System Atrophy (MSA)
Funda David, MUDr., Ph.D.
280086
Recent data suggest that the brain-gut axis, chronic intestinal inflammation, diets and/or gut microbiota contribute to the pathogenesis of neurodegenerative diseases with alfa-synucleinopathy, which include above all Parkinson`s disease (PD) and Multiple system atrophy (MSA). The interplay of environmental factors e.g. diets, gut microbiota, metabolites and immune mechanisms seems to play important role in pathogenesis of these diseases but also represents a safe approach for intervention preventive or symptomatic, clinical course-improving strategies. No prevention or other efficient symptomatic therapy substantially ameliorating these diseases exists at present.
The aim of this project is to partly dissect the complex interplay of environmental factors such as diet, microbiomes, metabolites and their immune influences in PD, or alfa-synucleinopathies in general, by studying anti-inflammatory dietary interventions, e.g. gluten-free diet but also other dietary interventions, on the course and clinical signs of the diseases in both in appropriate animal models (e.g. MPTP chronic mouse model of PD), but also using material from human prospective clinical trial (ClinicalTrials.gov Identifier: NCT05238545). More specifically, this project will address dietary effects in the development of PD or other alfa-synucleinopathies (MSA) in animal model using array of methods such as monitoring changes in the striatal content of dopamin and its metabolites in mouse brain, immunohistochemistry, histology, spatial brain histology, behavioral tests (e.g. open field test and others), and most importantly immune parameters assessed from mouse lymphoid organs or patients PBMCs or cerebrospinal fluid (CSF) cells by flow cytometry, cell cultures, ELISA`s and/or by other omic-based methods. In addition, metabolomic analyses (in collaboration with the Laboratory of Molecular Structure Characterization, IMIC) and preparation of samples for bacteriome sequencing may be part of this project. Last but not least, by having access to the human material such as plasma, urine and CFS, this project may also include studying possible novel biomarkers in alfa-synucleinopathies e.g. the role of ferrum and its storage/ distribution in relation to the disease onset and progression.
This project will also comprise of study of relevant literature, participation in immunological and/or other methodological courses, and it will include international collaborations (e.g. Denmark, USA). This project is at present supported by the grant NU21-04-00443, “The effect of gluten-free diet on clinical symptoms, immune parameters and metabolome in neurodegenerative diseases with alfa-synucleinopathy“; ClinicalTrials.gov Identifier: NCT05238545, fom the Ministry of Health of the Czech Republic. Applications for other support have already been or are about to be submitted to Czech as well as international grant agencies.
Mechanobiology of lymphocytes
Hons Miroslav, Mgr., Ph.D.
280057
An efficient immune response requires cells of the immune system to be at the right place at the right time and depends on their migration and correct positioning in tissues. We work at the interface between cell biology and immunology and study how leukocytes establish motility, distinguish various environmental cues and interpret them in their behavior. Our primary focus are mechanical aspects – we want to understand how leukocytes recognize physical stress, adapt to obstacles and integrate mechanical and chemical signals from the environment. We concentrate on the role of cytoskeleton and signaling pathways that trigger cytoskeletal rearrangement. To this end, we use combination of artificial environments, pharmacologic/genetic interventions and various types of imaging.
To expose cells to mechanical stress or defined obstacles in their migratory paths we use silicon devices with custom-made imprinted patterns. This way we apply on cells defined deformations or force them to migrate through channels with a given diameter. The basis of our work lies in broad spectrum of imaging methods. We benefit from exceptional core resources and equipment in BIOCEV and we use many modalities of live cell imaging (FLIM, FRET, TIRF) and electron microscopy.
About the lab:
https://hons-lab.lf1.cuni.cz/
We are looking for dedicated candidates interested in cell biology, cell migration, cytoskeleton, immunology and microscopy. We offer part-time employment and an opportunity to work in a newly established research group within the BIOCEV with its exceptional equipment.
Applicants are encouraged to provide a brief CV with summary of recent work to Miroslav Hons, PhD (miroslav.hons@lf1.cuni.cz)
Vliv časného postnatálního podávání probiotického kmene Escherichia coli O83:K24:H31 na vývoj novorozeneckého imunitního systému se speciálním zaměřením vývoj přirozených lymfoidních buněk a regulačních populací
Hrdý Jiří, prof. RNDr., Ph.D.
279580
The dissertation thesis will study the effect of early postnatal administration of the probiotic strain Escherichia coli O83:K24:H31 (EcO83) on the development of the immune system of newborn mice with a special focus on the induction of innate lymphoid cells type 3 (NCR+ and NCR- ILC3 including Lti - lymphoid tissue inducers) and regulatory subpopulations with a special focus on regulatory T lymphocytes (Treg). To achieve the outlined goal, the student will learn the methods of cell isolation from tissues and their characterization using flow cytometry. Both the probiotic strain included in the Colinfant Newborn probiotic vaccine and the modified strain of EcO83 carrying plasmids encoding genes for fluorescent proteins or luciferase will be used for better visualization and detection of EcO83 in the gastrointestinal tract of mice. The student will also focus on the ability of EcO83 to impact the activation of innate immune mechanisms with a special focus on molecules playing a role in antitumor immunity (e.g. cGAS).
Intestinal barrier disruption as a consequence of modulation of Th17 pathway in obese psoriatic patients:mechanisms of action and microbiota involvement
Jirásková Zákostelská Zuzana, RNDr., Ph.D.
279741
Goals: Our aim is to determine whether the specific composition of the intestinal microbiota of psoriasis patients can influence the intestinal mucosal immune system and the Th17 immune response in the pathogenesis of psoriasis.
Intensive efforts are being made to determine what triggers intestinal barrier dysfunction in patients with psoriasis and whether the composition of the gut microbiota plays a role in this process. Another unknown is how the gut-skin axis influences the pathogenesis of the disease. In addition, we do not know why some patients with psoriasis do not respond appropriately to therapy or in whom the adverse effects are seen. It could be connected to the role of IL-17 in maintenance of intestinal barrier integrity on one hand and its role in intestinal inflammation during pathogenesis of psoriasis on the other. For all these reasons, we would like to try to achieve our proposed goals using unique gnotobiological techniques, genetically modified mice, high-throughput sequencing and transcriptomics.
1) To elucidate the impact of patients’ microbiota in mouse models of psoriasis and by colonization of mice with samples collected from patients with or without an attenuated Th17 immune response (using gnotobiotic models).
2) To determine the consequences of Th17 pathway attenuation on immune system regulation and intestinal barrier integrity in experimental mouse models of psoriasis using knockout mice or IL-17 inhibitors.
3) To characterize cellular pathways triggered by specific bacterial consortia isolated from the patients with psoriasis prior and during anti Th17 treatment by in vitro experiments in human primary cells and cell lines
To evaluate the role of obesity in disease pathogenesis using spatial transcriptomics and unique gnotobiotic techniques.
Sdílené a unikátní rysy T lymfocytární imunity u pacientů s poruchou funkce thymu a se syndromy poruchy opravy DNA
Klocperk Adam, doc. MUDr., Ph.D.
280000
The thesis will focus on the development, differentiation, and (dys)function of T lymphocytes in patients with inborn errors of immunity, specifically those with defects of thymic (DTD) and with DNA repair syndromes (DRS). Based on our clinical and research experience, patients suffering from 22q11.2 deletion syndrome, ataxia-telangiectasia, Nijmegen breakage syndrome, and Schimke immuno-osseous dysplasia share numerous characteristics of gross immunophenotype, such as reduced numbers of T lymphocytes and their skewing towards memory effector stages. However, these two groups of diseases arise from fundamentally distinct pathophysiological mechanisms — DTDs result from dysfunction of the thymic stroma, whereas DRSs stem from intrinsic defects in DNA repair during T lymphocyte development. It is therefore hypothesized that the immune system of these patients differs at the levels of gene transcription, epigenetics, clonality, and function, which cannot be detected by routinely employed diagnostic methods.
The core aim of the thesis will be to establish a robust cohort of DTD and DRS patients and annotate it clinically in collaboration with the supervisor and other physicians at the University Hospital in Motol. Subsequently, the candidate will employ modern methods to analyze the function of patients’ immune cells, with a particular focus on T lymphocytes, thymopoiesis, and T-lymphocyte-mediated responses. This will include the use of flow cytometry, including spectral cytometry, mass cytometry (in collaboration with partnering institutions), and omics-based approaches such as single-cell RNA sequencing and proteomics, both ex vivo and in cell cultures, including artificial thymic organoids (ATO) and preclinical testing of available drugs to modulate and support the cellular immunity of patients. Through domestic and international collaboration, expertise from foreign centers will be leveraged to expand methodologies and facilitate research stays.
The outcome of this work will be one or more first-author publications in international journals.
Funkční analýza imunitních odpovědí proti akutní myelodní leukémii
Musil Jan, RNDr., Ph.D.
279222
Acute myeloid leukemia (AML) represents a bone marrow malignancy characterized by expanding myeloid precursor cells. If left untreated or after treatment failure, this expansion ultimately leads to bone marrow failure.
Despite intensive research into novel chemotherapeutic combinations and improvements in medical care following transplantation of hematopoietic stem cells (HSCT), the prognosis of older patients has not improved substantially. Still, HSCT following induction chemotherapy remains the most effective treatment available today. However, about 30 – 40% of patients experience AML relapse. The effectiveness of HSCT is based on the graft versus leukemia (GvL) immune response, during which immune cells such as NK cells and T cells recognize surviving leukemic cells and eliminate them.
Significant efforts are being made to improve patients’ survival by including immunotherapy in AML treatment. Various approaches are being researched in clinical trials, such as killer immunoglobulin-like receptor (KIR) miss-matched NK cells or T cells genetically modified to express chimeric antigen receptors (CAR). However, all these therapies are hampered by two major factors. Firstly, AML develops in close proximity to the immune system in the bone marrow and, therefore, possesses immune evasive capabilities. Secondly, AML cells do not express unique markers that can be easily targeted by CAR T cells. Furthermore, AML cells have a relatively low mutational burden, which causes the lack of suitable antigens for classical T cell therapies.
In recent years, research into immune responses identified various immune subsets capable of recognizing AML cells. These include NK cell subsets, gdT cell subsets, NKT cells, abT cells, and even M1 macrophages. Most results on the recognition of AML by these cell types come from in vitro experiments utilizing cell lines or mouse experiments. Therefore, it is unclear what the importance of these cells is in vivo and how precisely they interact with AML cells. In this thesis, we will combine recent advantages in the field of multiparametric flow cytometry, imaging-based cell sorting, functional assays, and proteomics to characterize the functional interaction between immune and AML cells using our ex vivo AML PBMC system.
Horizontálni mitochondriální přenos a jeho regulace
Neužil Jiří, prof. Ing., CSc.
280160
Horizontal mitochondrial transfer (HMT) has emerged recently as a novel phenomenon of cancer and other pathologies, and of tissue homeostasis. HMT allows for trafficking of mitochondrial from donor to acceptor cells, which makes the latter fitter. In cancer, for example, it appears that this makes cancer cells more resistant to therapy. One mechanism of mitochondrial trafficking is their intercellular transfer via tunnelling nanotubes (TNTs), intercellular bridges spanning two cells, with tubulin fibers as conduits for the process. However, how TNTs are formed and how exactly mitochondria move across is not known.
The Project will focus on formation of TNTs and the mechanism allowing mitochondria movement between cells. This includes tubulin polymerization and energy supply to drive the kinesin/dynein based mobility system, assuming that the process can be bi-directional. The student will use methods of modern cell biology, including high-end microscopic approaches, with the research constructed on three levels: a reconstituted system, co-culture of cells (including the use of microfluidics) as well as mouse cancer models (using multi-photon intravital microscopy and cryo-EM).
The result of this research will be conducted in a leading laboratory in the field of HMT (see e.g. PMID: 39792553, 36795453, 30449682). It will further our understanding of a process that seems to be part of basic cell biology and that is involved in tumour growth and cancer resistance to therapy.
Dynamika změn nádorového mikroprostředí jako důsledek protinádorové léčby: Vliv na prognózu pacientů
Ozaniak Střížová Zuzana, doc. MUDr., Ph.D.
279540
Anticancer immunotherapy represents one of the cornerstone approaches in the treatment of oncology patients, particularly in metastatic stages of cancer. However, the effectiveness of this therapy is fundamentally influenced by the characteristics of the tumor microenvironment, which undergoes dynamic changes over time and can be affected by various systemic treatments such as chemotherapy, radiotherapy, or proton therapy.
Patients who respond positively to treatment with so-called checkpoint inhibitors typically exhibit a high mutational burden, the presence of tertiary lymphoid structures, and increased T-lymphocyte infiltration. The proposed project aims to conduct a detailed investigation of the dynamic changes in the tumor microenvironment induced by these therapies and to analyze their impact on patients' clinical prognosis.
The primary focus of the project lies in the phenotypic and functional analysis of T-lymphocytes isolated from tumor tissue. To achieve these objectives, the study will employ culture assays, flow cytometry, and advanced statistical and analytical methods for working with clinical data. The project is funded by the Agency for Medical Research (AZV).
Spojení střevního mikrobiomu a synukleinopatie
Procházková Petra, RNDr. Mgr., Ph.D.
279977
Synucleinopathies - Parkinson's disease (PD), dementia with Lewy bodies (DLB) and multisystem atrophy - are so far untreatable neurodegenerative diseases characterized by inclusions of pathological synuclein in the nervous tissue. The manifestation of PN and DLB is preceded by a prodromal stage with isolated REM sleep behavior disorder (iRBD). One of the two pathways of synuclein distribution in the body begins in the enteric autonomic nerves. Alteration of the gut microbiome has been reported in both PD and RBD, but the mechanism of this alteration and its development during the course of the disease is unknown. In the proposed project, we plan to document the changes in the human microbiome, its metabolites and neuroimmunological parameters, their evolution in the iRBD phase and the status at the onset of Parkinson's disease before starting treatment. A mouse model based on rotenone application will also be established to understand in detail the pathogenesis and the relationship between the changes in the gut microbiota and nervous system function. In addition, we want to determine whether the transfer of the microbiota from PD or iRBD patients to mice can lead to the spread of pathogenic synuclein species or whether this microbiota can contribute to synuclein aggregation in the cells of the murine recipient.
Work description:
Analysis of the fecal microbiome in patients with iRBD and healthy volunteers (control group). Analysis of changes in intestinal barrier function in diseased individuals. Metabolomic analysis. Work with a mouse model of PD. Collection of mouse blood and organs. Determination of immunological markers in serum. Fecal transplantation of the human microbiota into mice. Analysis of gene expression. Flow cytometer analysis of immune cells. Immunohistochemical preparation of skin, intestinal and brain samples. Correlation of changes in the composition of the microbiome with clinical parameters in patients. Presentation of the results at scientific conferences (posters/presentations) and their publication in renowned international journals.
Mikrobiom a regulace příjmu potravy
Roubalová Radka, RNDr., Ph.D.
280005
In recent years, research has increasingly shown a link between the gut microbiome and various civilization diseases, including obesity and eating disorders.
In the doctoral thesis, the student will investigate the influence of the microbiome on the regulation of food intake on the gut-brain-axis (GBA). Antibiotic-treated or germ-free mice will be transplanted with microbiota from previously obtained samples from lean or obese humans according to an established protocol. In addition to changes in the composition and function of the gut microbiome, the mice will be monitored for parameters such as weight, activity, body fat percentage and other basic metabolic parameters detected in serum.
With regard to appetite regulation, peripheral orexigenic and anorexigenic neuropeptides (leptin, ghrelin, PYY, GLP-1) will be detected by multiplex analysis. The production of these neuropeptides is directly influenced by microbial metabolites such as short-chain fatty acids. In the hypothalamus, we will detect the expression of central appetite regulators (orexigenic – AgRP, NPY, MCH, TRH, GABA, Orexin and anorexigenic – POMC, CART, CRH) using RNA-seq and qPCR methods.
The immune system is an essential component of GBA and inflammatory changes influence a number of physiological processes and behaviors. Therefore, we will monitor immune system settings at the level of cellular immunity (flow cytometry) and inflammation-regulating cytokines (multiplex analysis, ELISA).
Komunikace střevních bakterií s mladým rostoucím hostitelem za podmínek chronické podvýživy a při normální dietě
Schwarzer Martin, Mgr., Ph.D.
279259
Previously, we have shown that microbiota is necessary to sustain optimal weight gain and linear growth of infant mice when fed a standard diet or a nutritionally depleted isocaloric diet (Schwarzer et al., Science 2016). Using monocolonized mouse model we showed that lactobacilli previously selected in Drosophila model of chronic undernutrition for their growth promoting capabilities were sufficient to increase linear growth of mice in a strain-dependent manner and recapitulated the whole microbiota's effect on growth. The same bacterial strain sustained the postnatal growth of malnourished conventional animals and supports both insulin-like growth factor–1 (IGF-1) and insulin production and activity. We have identified cell walls isolated from LpWJL, as well as muramyl dipeptide and mifamurtide, as sufficient cues to stimulate animal growth despite undernutrition. Further, we found that NOD2 is necessary in intestinal epithelial cells for LpWJL-mediated IGF-1 production and for postnatal growth promotion in malnourished conventional animals (Schwarzer et al., Science 2023). We are further dissecting the molecular mechanism behind the bacteria driven host growth promotion with the ultimate goal to improve the current treatment of undernutrition in human population. Further reading (Schwarzer et al., Calcif Tissue Int 2018; Brabec et al., J Exp Med 2023). Methods: Within the framework of the Ph.D. study you will master the handling of germ-free and conventional mice and piglets and exploit the capabilities of our state-of-the-art gnotobiotic unit. You will use classical and molecular-biological methods for bacterial detection and cultivation. You will master different methods such as ELISA, Western-blot, PCR and real-time PCR, flow cytometry, in vitro cell and cell line cultivation, histology and immunohistochemistry. Location: Martin Schwarzer’s group at Laboratory of Gnotobiology (http://gnotobio.mbu.cas.cz/), Institute of Microbiology of the Czech Academy of Sciences, Doly 183, Nový Hrádek, 54922 (Doctoral studies of Immunology at Charles University in Prague) Interested applicants feel free to contact schwarzer@biomed.cas.cz for further details.
In-Depth Analysis of Phenotypic Acute Leukemia MRD Dynamics Using Single-Cell Data
Stuchlý Jan, Mgr., Ph.D.
280047
The heterogeneity and dynamic behavior of leukemic blasts present significant challenges for minimal residual disease (MRD) monitoring and the assessment of treatment responses. This project focuses on characterizing the dynamic processes driving acute leukemia cell evolution, including phenotypic drift and lineage switching, by integrating multimodal single-cell data with additional topological and kinetic measures (e.g., RNA velocity).
The aim of this thesis is to employ advanced computational and mathematical methods—such as computational topology, stochastic modeling, or deep learning—to dissect state transitions and fate-determining processes in leukemic cells.
Key Responsibilities:
Conduct mathematical and computational research to design novel algorithms and tools for single-cell data analysis.
Develop and implement methods for modeling phenotypic dynamics of MRD in leukemia using spectral and mass cytometry and single-cell RNA sequencing data.
Validate computational tools in collaboration with experimental and clinical researchers.
Publish results in high-impact journals and present findings at international conferences.
Candidate Profile:
A Master’s degree in computational biology, bioinformatics, mathematics, biomedical sciences, or related disciplines. Strong programming skills (e.g., Python, R); familiarity with machine learning or AI techniques is an advantage.
A keen interest in interdisciplinary research and the ability to integrate computational and biological perspectives.
Excellent communication skills in English, both written and verbal.
Enthusiasm for teamwork in a collaborative, international research environment.
MSCA Mobility Rules: To qualify, applicants must not have resided or carried out their main activity (work, studies, etc.) in the Czech Republic for more than 12 months in the three years immediately preceding the recruitment date.
Mikrobiální osídlení gastrointestinálního traktu a jeho vliv na hostitele
Šplíchal Igor, doc. Ing. Bc., CSc.
279043
The gastrointestinal tract (GIT) of multicellular hosts is colonized with microbial settlers called microbiota. The microbiota's main part is located in the lower GIT and influences hosts directly on the epithelial cell interface and indirectly through metabolites. The first microbial colonization by the mother microbiota of naturally-born infants occurs during birth. In contrast, Cesarean section-born infants can spontaneously be colonized by microbes from hospital surroundings. Surgically derived germ-free piglets can serve as animal models of immunocompromised infants to study the development of host-microbiota cross-talk and the influence of microbiota on the host immune system and metabolic profile.
During the doctoral study, the student will work with mini pigs reared in gnotobiotic (microbiologically controlled) conditions to study the impact of microbiota on its host. Histology of the intestinal barrier and production of mucin, pattern recognition receptors (TLR and NLR) signaling, and systemic and local appearance of inflammatory/sepsis markers, e.g., cytokines, HMGB1, presepsin, procalcitonin, and sites of their production will be analyzed
The doctoral study will occur at the Institute of Microbiology of the Czech Academy of Sciences in Nový Hrádek (Kralovehradecký region), where the student will work on a grant project. The student will use Real-Time PCR (RNA isolation, cDNA synthesis, qPCR), Western blot, histology, immunohistochemistry, xMAP technology (Luminex), hemocytometry, and flow cytometry.
Kinázy rodiny SRC v biologii T-lymfocytů
Štěpánek Ondřej, Mgr., Ph.D.
278922
The project will investigate the role of SRC-family kinases LCK and FYN in T-cell antigen receptor signaling, which is crucial for proper T-cell development and immune response. It is known for decades that LCK, and to lesser extent FYN, catalyze the first biochemical step in TCR signaling, i.e., tyrosine phosphorylation of activation motifs in the TCR/CD3 complex. However, the role of these kinases in particular biological context is still incompletely understood. This project is a follow-up to our previous studies (Stepanek et al. 2014, Cell Horkova et al. 2020 Cell Reports, Horkova et al. 2023 Nature Immunology) and focuses mostly on the role LCK and FYN in the peripheral responses and in particular cells types. We have generated a genetically modified mouse model that enables cell specific and/or time-induced deletion of LCK. We will use this novel model together with other established models (whole body LCK, FYN knock-outs, LCK CA knock-in mouse unable to bind to CD4 and CD8 co-receptors, TCR transgenic mice) to address:
- The role of LCK and FYN in the differentiation of helper CD4 T cells into particular subtypes during infection.
- The role of LCK and FYN in the function of regulatory T cells in autoimmunity and cancer.
The main methods will include (but will not be limited to) in vivo experiments with mice, flow cytometry, single-cell RNA sequencing.
Cancer Immunotherapy Based on Drug Delivery Systems for IDO Inhibitors in Combination with Chemotherapy
Větvička David, Mgr., Ph.D.
280092
The aim of this dissertation is to explore the potential and benefits of using targeted drug delivery systems for the administration of IDO inhibitors in combination with chemotherapy, with a focus on enhancing the efficacy of immunotherapy in the treatment of cancer. The work will focus on the development and optimization of IDO inhibitor delivery using modern technologies, such as nanoparticles and other carriers, and will assess their effectiveness in combination with conventional anticancer therapies, particularly chemotherapy and immune checkpoint blockade.
Imunoterapie nádorů a systémy doručování léčiv: Využití siRNA a aktivace RIG-I a STING v cílené terapii nádorů
Větvička David, Mgr., Ph.D.
280093
This dissertation focuses on developing innovative approaches in tumor immunotherapy utilizing small interfering RNA (siRNA) and targeted drug delivery systems. Key siRNA targets include PD-L1, IDO, STAT3, and TGF-β, which play critical roles in creating an immunosuppressive microenvironment, suppressing antitumor immunity, and promoting tumor cell survival. Strategies activating innate immune pathways through RIG-I and STING are combined with advanced nanocarriers to enhance siRNA delivery and therapeutic efficacy.
From an immunological perspective, the student will evaluate changes in the tumor microenvironment, including immune cell infiltration (e.g., cytotoxic T lymphocytes, regulatory T cells, macrophages) and cytokine and chemokine expression profiles. Systemic changes, such as blood cell counts, levels of inflammatory markers, and serum cytokines, will also be analyzed to assess the therapy’s impact on immune responses and the overall health status of the organism. The research aims to validate these approaches in preclinical models, overcoming tumor resistance to treatment and reactivating antitumor immunity.
The role of myeloid cells in thymic T cell tolerance in health and disease
Vobořil Matouš, Mgr., Ph.D.
279650
The incidence of autoimmune diseases has been increasing in recent decades, often manifesting in association with or following infections. Our primary focus revolves around central immune tolerance, the pivotal process occurring in the thymus that is fundamental for the formation of a functional and safe T cell repertoire. The previous findings indicate that the thymus harbors various subtypes of myeloid cells crucial for presenting self-antigens to developing T cell to delete self-reactive T cell clones or convert them to regulatory T cells. However, the effect of peripheral inflammation on thymic myeloid cell function and its subsequent role in T cell selection remains unexplored.
The proposed doctoral project aims to characterize the role of systemic as well as tissue-specific bacterial and viral infections on the heterogeneity and function of thymic myeloid cells, as well as the mechanism of thymic T cell tolerance. The project will utilize various mice infection models, including bacterial Listeria monocytogenes or viral Lymphocytic choriomeningitis virus infections. The changes in thymic myeloid cells induced by different types of infections will be elucidated by single-cell RNA sequencing, which will be complemented by multiparametric flow cytometric analysis, as well as microscopic analysis of thymic architecture and myeloid cells localization. The changes in T cell selection associated with infection will be assessed by measuring numbers and phenotype of developing T cells, as well as by RNA sequencing of T cell repertoire. The project also aims to implement the “dirty” co-house mouse technology to assess the potential changes in T sell selection in more physiological conditions. Addressing this project will provide valuable insight into how inflammation affects T cell tolerance processes and enhance our understanding of autoimmune disease development.
Project duration: 3-4 years
Methodological advances: work with mouse models, immune cell isolation, flow cytometry, scRNA sequencing, T cell repertoire sequencing.
Grant support: PRIMUS Research Programme (2025–2029), GACR Junior Star (2025–2029)
Transitional dendritic cells as new players in T cell tolerance
Vobořil Matouš, Mgr., Ph.D.
279651
Myeloid cells, including dendritic cells and macrophages, are essential for establishing central tolerance in the thymus by promoting T cell clonal deletion and regulatory T cell generation. Previous studies suggest that the thymic dendritic cell (DC) pool comprises plasmacytoid DC, XCR1+ DC1 and SIRPa+ DC2. Yet the precise origin, development, and homeostasis, particularly of DC2, remain unresolved. Our preliminary data indicate that the thymus harbors a novel thymic population of transitional DC (tDC) amongst DC2 that possess thymus-immigrating capacity.
The proposed doctoral project aims to elucidate the origin and characteristics of tDC in the thymus and uncover their specific role in the mechanism of T cell tolerance in steady-state and during inflammation. Specifically, the project will employ various lineage-tracing and lineage-defining mouse models to determine the origin of thymic tDCs. Using photoconvertible mouse models and mouse-to-mouse cell transfer experiments, the project will characterize the immigrational potential of tDC under steady-state and during peripheral inflammation. To assess the importance of tDC in T cells selection, the project will utilize tDC-depleted mouse models and test the impact of tDC deficiency on T cell clonal deletion, regulatory T cells generation, and subsequent development of autoimmunity under both steady-state conditions and during tissue-specific inflammation. Methodologically, the project will rely on flow cytometry analysis of transgenic mouse models, complemented by RNA sequencing of T cell repertoire, T cell receptors cloning, and the generation of T cell hybridomas. The research will be conducted in close collaboration with the Juliana Idoyaga Laboratory at the University of California, San Diego, USA.
Project duration: 3-4 years
Methodological advances: work with transgenic mouse models, dendritic cells isolation, immune cell adoptive transfers, flow cytometry, T cell repertoire sequencing and cloning, and generation of T cell hybridomas.
Grant support: PRIMUS Research Programme (2025–2029), GACR Junior Star (2025–2029)