Immune Regulation

Decoding a New Pathway in T Cell Function: Mechanistic and Therapeutic Exploration in Allergy and Autoimmunity

The central hypothesis is that a undisclosed protein is important in T cell function with implications for their role in immunity and disease.
This PhD project aims to investigate the role of this pathway in T cell biology, focusing on disease models, especially allergic responses, such as asthma, with potential for additional models. Understanding how this pathway affects T cell activity and persistence may offer new therapeutic strategies to modulate immune responses in chronic inflammation.

Objectives:
The overarching goal of this PhD project is to elucidate the role of a new pathway in T cell function, particularly in the context of undesirable activity in disease models such as allergy and autoimmunity.

The specific objectives are:
O1) Characterising the T cell response upon differentiation towards effector function.
O2) Investigating the functional role of the pathway on cell recruitment, activation and function (cytokine production).
O3) Investigating the role of this pathway in models of allergy.
O4) Assessing the role of this pathway in models of autoimmunity or infection.
05) Testing potential therapeutic molecules targeting this pathways to modulate T cell function for improved disease outcomes.

Telomeres & Telomere Transcription in Cancer & Aging / Spinal Cord Regeneration & Tissue Microenvironment

Unraveling the roles of telomere transcription in tissue homeostasis and aging in zebrafish

Telomeres protect chromosome ends and are key to genome stability. Their progressive shortening is linked to aging and disease, including cancer. The telomeric long noncoding RNA TERRA plays a role in telomere regulation and cellular aging, though its function in vertebrates is still not well understood.

We are using zebrafish—a relevant model due to telomere similarities with humans—to investigate TERRA’s expression and potential impact on aging and disease. Our methods include molecular and imaging techniques, as well as long-read sequencing, to study TERRA dynamics in both normal and telomerase-deficient zebrafish. Preliminary data suggest that TERRA levels are influenced by telomere length and may be involved in developmental processes and stress responses, as well as in aging. A new genetic tool developed in our lab allows us to modulate TERRA levels in vivo, providing a platform to explore its functional roles.

This PhD project will focus on generating inducible zebrafish models to study TERRA in the context of aging, regeneration, and disease. The work aims to uncover how TERRA contributes to vertebrate biology and its potential as a target in age-related conditions.

Plasmodium Infection & Anti-malarial Interventions

Molecular, immunological and pathological crosstalk between gammaherpesviruses, Plasmodium and cancer

Background
Endemic Burkitt lymphoma (eBL) is the most common pediatric cancer in sub-Saharan Africa (SSA), peaking between ages 6 and 8. Epstein–Barr virus (EBV), a latent B lymphotropic gammaherpesvirus (gHV), is a recognized oncogenic factor in eBL. SSA is also endemic for the malaria parasite, Plasmodium falciparum (Pf), and intense exposure to Pf is strongly linked to eBL. The interplay between EBV and Pf is believed to drive eBL development, but the precise mechanisms remain elusive. Existing epidemiological studies on EBV-Pf co-infection are limited by an inability to track infection timing or collect relevant tissue samples. To overcome these barriers, controlled studies in animal models are essential.

Objectives
This project aims to investigate how gHV and Plasmodium infections influence each other and contribute to eBL pathogenesis using established rodent models. Specifically, we will:
1. Assess the impact of Plasmodium infection on gHV reactivation: malaria is thought to induce EBV reactivation, but the mechanisms are unknown. We will evaluate the role of Plasmodium liver and blood stages in viral reactivation and identify targets for intervention.
2. Determine the influence of gHV infection on malaria progression: our preliminary data suggest that murine gHV (MHV68, a model for EBV) reduces malaria severity. We will explore immune mechanisms by which gHV alters malaria pathogenesis and identify potential therapeutic targets.
3. Investigate mechanisms of lymphomagenesis in mono- and co-infected hosts: while EBV and Pf are established cofactors in eBL, their combined role in oncogenesis remains unclear. Using our murine co-infection model, we will examine immune and molecular pathways leading to lymphoma and assess the impact of antimalarial and antiviral interventions.

Methodology
We will use C57BL/6 and Balb/c mice infected with MHV68 and P. berghei (a rodent malaria parasite). Controlled infections will allow us to assess pathogen interactions at different stages of infection. We will employ:
Viral and parasitic load quantification to assess the dynamics of co-infection.
Flow cytometry and immunohistochemistry to analyze immune cell populations and cytokine profiles.
Gene expression analysis (RT-qPCR, RNA-seq) to identify pathways involved in viral reactivation and immune modulation.
Histopathological assessment to evaluate lymphoproliferation and lymphoma development.
Antimalarial and antiviral therapeutic interventions to explore potential preventive strategies.
By combining molecular, immunological, and pathological analyses, this approach will provide comprehensive insights into eBL pathogenesis.

Expected Outcomes and Impact
This study will provide critical insights into EBV-Pf interactions in eBL. By identifying key molecular and immune mechanisms, we aim to inform novel prevention and treatment strategies for eBL and severe malaria. Given the burden of both diseases in SSA, our findings could help develop targeted interventions to improve patient outcomes.

Chromatin & Epigenetics

Exploiting RNA-DNA Hybrids for Precision Cancer Therapy

Despite significant advances in cancer immunotherapy, a major challenge remains: only a subset of patients benefit from immune checkpoint blockade (ICB) therapies, while many experience resistance or relapse. Currently, there are no reliable biomarkers to predict ICB response, leading to a trial-and-error approach that exposes patients to unnecessary toxicity and increases healthcare costs. To address this, our research will focus on R-loops—three-stranded nucleic acid structures comprising RNA-DNA hybrids and displaced single-stranded DNA—which have emerged as potential regulators of anti-tumor immunity. However, their clinical relevance remains unclear due to the lack of precise detection tools. We will leverage RHINO, a proprietary high-sensitivity imaging technology, to detect and quantify R-loop levels in tumor samples and investigate their correlation with ICB response. Additionally, we will modulate R-loop levels using genetic and pharmacological approaches to assess their impact on immune activation, potentially uncovering novel therapeutic strategies to enhance the efficacy of immunotherapy. By integrating cutting-edge molecular biology with translational research, this project will pave the way for novel personalized cancer therapies, improving treatment outcomes and expanding the effectiveness of immunotherapy across a broader patient population.

Plant Molecular Biology

Splicing and Plant Immunity: The Role of SR Proteins in Plant-Pathogen Interactions

Plant immunity is a complex, highly adaptable response specifically tailored to oppose a wide range of different pathogens. Alternative splicing, a posttranscriptional mechanism that generates multiple transcripts from a single gene, significantly enhances the flexibility and efficiency of the plant immune response. Pathogen infection, in particular, triggers splicing changes in plant genes involved in the two primary layers of pathogen recognition: pattern-triggered immunity (PTI), in which conserved bacterial molecules (elicitors) are recognized by plant membrane receptors, and effector-triggered immunity (ETI), in which virulence proteins (effectors) are recognized by intracellular receptors. However, the mechanisms governing pathogen-induced alternative splicing remain largely unexplored.
Serine/arginine-rich (SR) proteins are highly conserved RNA-binding proteins and key regulators of pre-mRNA splicing known to modulate alternative splicing in response to abiotic stress. However, their role in regulating alternative splicing during pathogen infection and the underlying molecular mechanisms remain elusive. Recent studies have shown that pathogens can manipulate the splicing of plant defense genes to facilitate infection, often through direct interactions between pathogen effectors and components of the plant splicing machinery, including SR proteins. This suggests an important role for SR proteins in plant immunity, particularly in ETI, though their involvement in PTI remains unexplored.
In this project, the student will use the powerful genetic and molecular tools available for Arabidopsis thaliana and the model plant pathogen Pseudomonas syringae to address key gaps in our understanding of splicing regulation during plant-pathogen interactions. The Paula Duque lab has been characterizing the effects of infection in a collection of Arabidopsis mutants with silenced expression of different SR proteins. The work plan will focus on the following objectives:
1. Identify the splicing targets of SR proteins that play a relevant role during infection by comparing the splicing landscapes of infected and non-infected wild-type and mutant plants using RNA-seq.
2. Pinpoint target genes with potential roles in plant immunity through Gene Ontology (GO) Enrichment analysis, and validate their function by reverse genetics assessing disease symptoms and pathogen growth.
3. Dissect the role of key SR proteins in PTI and ETI by exposing mutant plants to flagellin (a benchmark bacterial elicitor) and a range of Pseudomonas effectors, while also evaluating the effects of infection by Pseudomonas strains lacking key effectors.
4. Confirm SR protein-effector interactions using co-immunoprecipitation and yeast two-hybrid assays.

This PhD project will provide an in-depth understanding of alternative splicing as a crucial component of plant immunity and the role of SR proteins in regulating this process during pathogen infection.

Physical Biochemistry of Drugs & Targets

Towards innovative anticancer drugs using patient-derived biopharmaceuticals from cutting-edge preclinical platforms for drug screening

Biopharmaceuticals are at the forefront of the fight against cancer. Drug discovery is currently at a critical juncture: the costs associated with drug development are rising, the attrition rate of promising compounds entering clinical trials is high, and the approval rate of new molecular entities is stagnating. One reason for this stagnation is that many drug discovery programs rely heavily on traditional biological and chemical concepts, as well as preclinical models. Considering these challenges, we will explore the following questions:

1. How can we design innovative anticancer drugs using patient-derived samples?

2. How can we improve drug development by creating cutting-edge preclinical platforms for drug screening?

Recent findings indicate that the presence of B-cells in tumor stroma, along with the production of anticancer antibodies, is linked to better clinical outcomes. This highlights the potential of investigating antibodies secreted by cancer-activated B-cells as a novel approach to identifying new antibodies that specifically target cancer cells, to use as either diagnostic or therapeutic tools. Our research particularly focuses on cancers with substantial unmet needs, such as brain tumors (both primary and metastatic), which present significant challenges. The blood-brain barrier (BBB) complicates current therapeutic strategies, but we have developed proprietary BBB peptide shuttles (BBBpS) to overcome this obstacle.

This research proposal aims to establish proof of concept that modified anticancer antibodies derived from cancer-activated B-cells can serve as viable therapeutics for brain tumors. To achieve this, the proposal includes three specific objectives:

Objective 1: Develop novel modified anticancer antibodies by utilizing self-circulating antibodies alongside our BBBpS. We will identify the most suitable samples from Care-Biobank’s collection of brain tumors. Collaboration with a biotech company will be crucial for isolating cancer-activated B-cells using advanced techniques and for expressing anticancer antibodies conjugated to BBBpS.

Objective 2: Create patient-derived multicellular tumor spheroids (MTS) for drug screening. We will leverage our expertise to develop these MTS and utilize GIMM facilities to characterize them further. This groundbreaking model enhances existing in vitro preclinical models and facilitates the selection of promising anticancer antibodies for in vivo testing.

Objective 3: Conduct a preclinical evaluation of the self-circulating modified antibodies using an organ-on-chip device that integrates the BBB and MTS. We will build on our expertise with organ-on-a-chip technology, combining our existing platform with patient-derived MTS. This will allow us to perform in vitro preclinical screening of antibodies using a variety of techniques available at GIMM, while also collaborating with international partners to conduct in vivo biodistribution and efficacy studies.

Signaling in Cancer

New fundamental insights into ALL biology and their therapeutic potential

Acute lymphoblastic leukemia (ALL) is an aggressive blood cancer and the most common childhood malignancy. Although current therapies achieve high response rates in children, a considerable fraction (up to 20% of the cases) are refractory to treatment or relapse, and have dismal prognosis. In addition, there are considerable side-effects resulting from conventional chemotherapy. Thus, it is essential to better understand the biology of ALL to more effectively treat patients. In this project, we will explore novel aspects of ALL biology, focusing either on how certain genes can work in opposite ways (in an oncogenic versus a tumor suppressive fashion) depending on particular contexts or on how certain signaling pathways oscillate in a circadian manner and crosstalk with the circadian molecular clock. Exploring these avenues will require the use and integration of patient material, mouse models, and different state-of-the-art in vivo and in vitro strategies to characterize the molecular, cellular and pathophysiological mechanisms involved as well as to explore the therapeutic potential of the molecular targets that we will identify in the process. Our ultimate goal is to use the fundamental knowledge we will generate to devise new therapeutic strategies for ALL treatment.

Advanced Breast Cancer Translational Laboratory

A Translational Approach to Unravel Immune-Stromal-Metabolic Networks in Breast Cancer Progression and Therapy Resistance

Breast cancer is the most prevalent cancer in women worldwide, its incidence and related deaths increasing dramatically particularly amongst young women. Most breast cancer-related deaths occur due to metastatic spreading and subsequent compromise of the target organs.
In breast cancer management, several unmet clinical needs remain, such as: predicting response to current therapies; identifying patients at high risk to develop metastatic disease; discovering novel biomarkers with prognostic and predictive value and developing strategies to target their function and involvement in breast cancer progression. To address these challenges, we are establishing a longitudinal collection of paired samples from breast cancer patients, that include tumor sample at diagnostic, blood and feces, with comprehensive clinical-associated data.
Research and approaches:
The local immune response and tumor-infiltrating lymphocytes are clinically relevant biomarkers for prognosis and treatment response. We are using novel multiplexed imaging to assess over 20 biomarkers on breast cancer human tissues, enabling a comprehensive characterization of the tumour-immune-stromal architecture. The required bioinformatics analysis is developed in-house using open-source software and international collaborations. Furthermore, to add a new layer of insight we are integrating information of in situ metabolomics (soon also transcriptomics). We are seeking metabolite signatures that are associated with specific breast cancer subtypes and overall disease evolution. Additionally, we aim to perform metabolomics from the serum, and analyze the fecal microbiota, of longitudinally BC. This approach aims to generate real-world data and uncover immune-metabolic pathways as potential biomarkers and therapeutic targets.
Our team has extensive expertise in breast cancer mouse models and the functional analysis and manipulation of tumor and immune cells in vivo. We also established in vitro dynamic microfluidic models, of vessel-on-chip and tumor-on-chip, which mimic key aspects of the metastatic cascade in breast cancer (intra- and extravasation).
Leveraging this expertise, we are well positioned to develop gain- and loss-of-function approaches to dissect the role of key metabolic pathways in tumor growth, tumor metastasis and immune regulation. Candidates showing significant effects on tumor proliferation, intra- and extravasation and drug response in vitro will be prioritized for in vivo assessment using syngeneic or xenograft mouse models of breast cancer.
These models will enable us to evaluate the broader impact of metabolic perturbations on tumor growth, metastasis, immune cell recruitment, and therapy sensitivity in a physiologically relevant setting. Taking together, our applied translational research approach aims to bridge critical knowledge gaps of knowledge and tackle unmet clinical needs to improve breast cancer outcome.

Microbiome in Health & Disease Translational Laboratory

PREDICT-AI: Harnessing AI to Uncover Lifestyle and Microbiome Biomarkers in Early-Onset Colorectal Cancer

Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide, with incidence rates steadily increasing. A particularly alarming trend is the rise of early-onset CRC (EoCRC), where one in ten new cases now occurs in adults under 50. Late-stage detection significantly reduces survival rates from 90% to just 10%, underscoring the urgent need for improved early detection methods. Despite the rising incidence of EoCRC, its underlying causes remain largely unknown. Notably, only 25% of cases are linked to a family history of CRC, suggesting that environmental and lifestyle factors play a dominant role. Diets rich in red meat and fat but low in fiber, obesity, alcohol consumption, sedentary behavior, chronic inflammation, and stress are estimated to contribute to 70–90% of CRC risk. The World Cancer Research Fund estimates that nearly 47% of CRC cases could be prevented through lifestyle modifications, particularly in diet and physical activity.
Emerging research has revealed a strong link between lifestyle factors and gut microbiome alterations in CRC patients. The gut microbiome influences tumor progression through metabolic interactions that either enhance immune defenses or create pro-carcinogenic environments. These findings position the gut microbiome as a promising target for early CRC detection and prevention strategies.

The primary goal of this PhD project is to develop machine learning (ML)-based classifiers that integrate microbiome data with clinical, lifestyle, and dietary information to improve early CRC detection. This research will establish a novel, interpretable risk assessment model—akin to BOADICEA, a breast cancer risk prediction model—designed specifically for CRC.

Hypothesis
By integrating microbiome data with clinical and lifestyle factors using ML algorithms, it is possible to develop more accurate and interpretable classifiers that identify individualised CRC risk patterns.

Task 1: Development of a comprehensive CRC database
A robust and representative dataset is essential for effective ML model development. To achieve this, the student will:
Establish a centralised RedCap database integrating microbiome profiles, clinical records, and lifestyle/dietary information from CRC patients.
1.1. Ensure data quality through preprocessing techniques such as feature scaling, normalisation, and categorical variable encoding.
1.2. Prioritise data transparency, accessibility, and fairness while promoting data sharing and reproducibility.

Task 2: Development and Training of ML Classifiers
Using the curated dataset, the student will design and evaluate ML models capable of identifying individualised CRC risk factors. The models will include:
2.1. Interpretable models such as Decision Trees, Random Forests, Gradient Boosting Machines, and Logistic Regression to ensure transparency and clinical relevance.
2.2. Deep learning approaches with explainability techniques to explore their potential in improving CRC prediction.
2.3. Model optimisation through cross-validation, hyperparameter tuning (grid search/randomised search), and evaluation metrics such as accuracy, precision, recall, and AUC-ROC.

Expected Outcomes
The first integrated database combining microbiome, clinical, lifestyle, and dietary data representative of the Portuguese population.
A novel, interpretable ML-based CRC risk prediction model akin to BOADICEA but tailored for CRC, leveraging microbiome data to enhance early detection and personalised risk assessment.

RNA Regulation & Aging

Deciphering the Mechanisms of Transcriptome-Proteome Decoupling in Aging

Aging is associated with a gradual decline of physiologic functions and is the single strongest risk factor for numerous diseases and death. Understanding the molecular mechanisms of aging is thus paramount. Transcriptomic profiling of tissues has revealed age-associated transcriptional changes. Far from being merely a consequence of aging, some of these changes in RNA biogenesis drive the aging process. However, they cannot fully explain the impact of aging on tissue proteomes, as a significant fraction of age-associated changes in protein levels do not correspond to changes in their mRNAs. Indeed, there is a progressive decoupling of RNA and protein expression during aging that has been described in various organs across multiple species, suggesting it is a general phenomenon. While the molecular origins of these alterations remain elusive, they suggest the involvement of posttranscriptional regulators like RNA-binding proteins (RBPs). Consistently, the levels of many RBPs are deregulated with age. Additionally, RBPs are enriched in low complexity, aggregation-prone domains and numerous RBPs form insoluble aggregates during aging. RBPs could also be controlled by age-associated signalling or be sequestered by “sponge” RNA species that accumulate with age, such as circular RNAs.

This proposal aims to address a critical knowledge gap by identifying RBPs that contribute to the progressive decoupling of the transcriptome and proteome with age, using the mouse as a model system. We hypothesize that the dysfunction of specific translation-related RBPs, namely translation factors and regulators, contributes to this decoupling. The overarching goal of this project is to identify these factors and the RNA networks they control. Additionally, it seeks to uncover the principles—such as alterations in expression, solubility, or availability—that drive changes in RBP activity during aging. To this end, we will apply a systems-level multi-omics research program. Initially, we will characterize the effects of selected age-regulated RBPs in mRNA-protein coupling. Then, we will determine the mRNAs and mRNA regions with altered RBP binding in young and old tissues. Finally, using cultured cell systems, we will investigate the mechanisms of action of these RBPs, evaluating their impact on target mRNAs and engineered reporters.

This work will enhance our understanding of posttranscriptional mechanisms driving tissue aging and will provide the basis to target specific RBP activities, potentially leading to the design of innovative therapeutic interventions.

Cell Architecture

Dynamic Regulation of Microtubule-Nucleus Connections in Myofiber Nuclear Positioning

Precise positioning of nuclei within skeletal muscle fibers is essential for muscle development, function, and overall health. Disruption of nuclear placement is a hallmark of several muscle diseases, including muscular dystrophies. However, the mechanisms that regulate nuclear positioning, particularly the role of microtubule (MT)-nucleus connections, remain poorly understood. The student’s project aims to investigate how MT-nucleus connections are dynamically regulated to control nuclear movement and positioning in myofibers.

To address this, the student will employ a combination of advanced techniques, including high-resolution immunofluorescence microscopy to map the localization of key centrosomal proteins at the nuclear envelope, and optogenetic tools to selectively sever microtubules near nuclei and directly assess their role in nuclear movement. Live-cell imaging will be used to compare the dynamics of MT-nucleus connections in central versus peripheral nuclei. The student will also manipulate muscle fiber contraction and nuclear stiffness to explore upstream signals that may trigger changes in MT-nucleus interactions. During muscle growth, newly fused nuclei will be isolated using EdU labeling and FACS sorting, followed by RNA sequencing to profile their gene expression over time.

By integrating these approaches with the laboratory’s primary myofiber organoid system, the student’s project will provide new insights into the molecular machinery controlling nuclear positioning in muscle. This work will also train the student in state-of-the-art experimental techniques and data management skills, which are essential for future research careers in the life sciences. Ultimately, the findings could reveal novel therapeutic targets for muscle diseases characterized by nuclear mispositioning, contributing to improved understanding and treatment of these conditions.

Bacterial Signalling

The role of quorum sensing molecules produced by gut microbes in shaping microbiota functions and host physiology

The gut microbiota plays a crucial role in host health, encompassing nutrition, synthesis of essential compounds (eg. vitamins), immune system maturation, and protection against pathogens. Environmental perturbations that result in dysbiosis, characterized by imbalances in microbiota composition and function with negative consequences for the host, increase susceptibility to both non-communicable (eg. metabolic disorders, chronic inflammation) and communicable diseases (caused by intestinal pathogens). The molecular mechanisms governing microbiota assembly and resilience to perturbations remain largely elusive.

We reason that microbe-microbe interactions, mediated by cell-cell bacterial chemical signals called quorum sensing, play a critical role in coordinating microbiota assembly and response to changes caused by environmental disturbances. This project aims to investigate the role of a novel class of quorum-sensing signals in regulating gut microbiota functions relevant for microbiota assembly and determine how these processes play a role in influencing microbiota resilience in response to diet-induced perturbations. The research plan will include both laboratory bacterial cultures and in vivo mouse models with mono- and multi-species bacterial communities.

The project will focus on the role of quorum sensing in modulating bacterial group behaviors in Bacteroidetes. Bacteroidetes are an abundant group of gut symbionts and pathobionts that play key roles in major gut microbiota functions, namely by its role degrading complex polysaccharide from diet and host-derived glycans, contributing to host metabolism and immune maturation. Here, the focus will be on Phocaeicola vulgatus, a gut pathobiont of major importance for host health, which we know is capable of producing quorum sensing signals and we have expertise in manipulating it.

Specifically the major aims of this project are:

i) Determine the genes and bacterial group behaviors regulated by quorum sensing in P. vulgatus;
ii) Investigate a possible role of P. vulgatus quorum sensing molecules in establishing interactions with other microbiota members and with the host influencing host physiology and behavior;
iii) Elucidate the role of P. vulgatus quorum sensing signaling in diet-induced microbiota perturbations, to evaluate the impact of these mechanisms in host physiology in homeostasis and in response to perturbations.

This project will advance our understanding of molecular mechanisms driving gut microbiota assembly, resilience and consequences of microbiota imbalances. Ultimately, we expect that this knowledge will facilitate the development of strategies leveraging quorum sensing manipulation to promote beneficial microbiota functions, mitigating dysbiosis-related health impacts, such as infections, chronic inflammation, and metabolic imbalances.

Ageing & Tissue Repair

Targeting immune-stem cell interactions in aging to restore organ health

Adult stem cells (SCs) sustain tissue renewal and repair throughout life. The SC niche is fundamental in the regulation of SC function and an important contributor to SC decline in aging. While alterations in the tissue’s immune environment are emerging as important contributors to impairments found in aged organs, their contribution to SC dysfunction in aging is unknown.
The skeletal muscle (SkM) is a paradigmatic model to study age-related loss of repair capacity. Muscle stem cell (MuSC) function during regeneration requires plasticity in transit between states of quiescence, activation and differentiation. MuSC functional impairments in aging result from changes in the extrinsic cues that govern their behavior, but also cell intrinsic alterations, including senescence and defects in lineage commitment. However, we still have a limited understanding of how changes in the environment manifest as SC intrinsic defects.
Our previous work indicates that changes in immune signaling are important drivers of MuSC dysfunction and regenerative decline in aging. We propose to identify the contribution of specific immune populations and signals to changes in regenerative capacity and MuSC activity in aging. We will combine models of accelerated immune aging and genetic mouse models allowing the lineage tracing of MuSCs to understand how age-related alterations in immune signals contribute to MuSC regenerative decline.The knowledge generated on the mechanisms linking immune aging and MuSC dysfunction will be tested for the conservation in human SkM and will be applied to improve the success of MuSC-based therapies in aging.
This project combines expertise, datasets and methodological approaches developed by our team and close collaborators to answer the following fundamental questions in the field of aging and stem cell biology: (i) what is the contribution of immune aging to the regenerative decline of the SkM? (ii) how do immune signals regulate MuSC identity, plasticity and lineage commitment throughout life? (iii) are the mechanisms linking immune aging and MuSC dysfunction conserved in humans, and can they be applied to improve stem cell-based therapies? Answers to these questions will have a major impact on our current thinking on the mechanisms of stem cell aging, with implications beyond our model system of SkM regeneration, and can provide important insights to clinical groups developing stem cell therapies.

Cell Cycle Regulation

Unveiling Homeostatic Regulation of Complex Cytoskeletal Assemblies

Centrioles, which form centrosomes and cilia, have long been considered among the most static cellular organelles, despite their critical roles in cell cycle regulation, signalling, and motility. The mechanisms by which centrioles maintain their integrity through time and multiple cell cycles remain elusive. Our recent work uncovered an intriguing complexity in centriole behaviour: they undergo remodelling and even disassembly during differentiation or disease, in cancer and viral infection. This plasticity is critical for homeostasis, fertility and behaviour. However, the mechanisms that allow centrioles to be both invariable or plastic are not known. Our recent data reveals that key centriole structural components undergo turnover, challenging the long-held view of centrioles as static entities. This project will study turnover mechanisms which protect, repair, and replace centriole components. These explain both centrioles long-term maintenance, through renewal, and their versatility, through remodelling.

Brain Cancer Dynamics & Therapy Translational Laboratory

Liquid Biopsies for Early Detection and Monitoring of Pediatric Brain Tumors (DETECT4Kids)

Standard of care diagnostic and monitoring methods for children with brain tumors include brain and spine MRI (frequently under general anesthesia) and cerebrospinal fluid (CSF) cytology. Unfortunately, these methods have low sensitivity to detect minimal disease leading to late identification of tumor progression and dissemination. Liquid biopsies have emerged as a promising approach to monitor pediatric brain cancer. Although blood and CSF are more commonly used as liquid biopsies, a less invasive tool would be ideal in the context of a pediatric population. Since the retina and the optic nerve extend from the diencephalon and are considered part of the central nervous system (CNS), the detection of brain tumor biomarkers in tears would make a striking difference in the follow-up of children with brain tumors. The other major challenge is the lack of good models to study brain tumors, hampering the preclinical validation of novel drugs or drug repurposing.

Our proposal addresses unmet medical need in Pediatric Neuro-Oncology and has the following specific aims:
1) To develop a non-invasive liquid biopsy tool for early detection of tumor progression and dissemination
Task 1.1 Define a genomic, methylation and proteomic signature of the most common pediatric brain tumors. We will use nanopore sequencing and mass spectrometry-based proteomics to analyze matched tumor tissue and liquid biopsies (plasma or CSF) from the most common pediatric brain tumors (medulloblastoma, ependymoma, pilocytic astrocytoma).
Task 1.2 Perform a clinical prospective study in pediatric brain tumor patients using liquid biopsies to early detect disease progression and monitor response to treatment.
We expect to include 100 children diagnosed with brain tumors over a period of 3 years. Liquid biopsies (plasma, CSF and tears) will be collected at cancer diagnosis, during follow-up (at the time of brain and spine MRI), and at disease progression or dissemination. We aim to investigate if liquid biopsies, particularly tears, can anticipate the diagnosis of disease progression and dissemination, when compared to the conventional MRI.

2) To generate and validate ex vivo patient-derived models of pediatric brain tumors.
Task 2.1 Develop and characterize ex vivo patient-derived tumor fragments (PDTFs).
We will characterize paired primary tumor samples and PDFTs using flow cytometry to assess the cellular composition, including the T cell phenotype, immunohistochemistry and digital pathology to determine tumor architecture, and spatial proteomics.
Task 2.2 Validate the ex vivo patient “avatars” to predict response to therapy.
We will use the PDTFs to create an organotypic 3D testing platform, aiming to predict response to therapy. A library of compounds approved for the treatment of pediatric cancer or currently approved for adult brain tumors will be tested using cell viability as a redout.

Biology of Parasitism

From Transcriptomes to Phenotypes: Unraveling Tissue-Specific Functions in Trypanosoma brucei Using Functional Genomics

Cells must adapt to their environments to survive and thrive—this is true not only for mammalian cells but also for pathogens. The protozoan parasite Trypanosoma brucei, the causative agent of African sleeping sickness and nagana, is an extracellular pathogen that colonizes diverse host tissues, including adipose tissue, skin, and the brain. Using a mouse model, our lab has discovered that T. brucei adapts to the adipose tissue microenvironment, with changes first detected at the transcriptomic level and later confirmed through phenotypic assays. Notably, parasites in adipose tissue proliferate more slowly and are capable of catabolizing fatty acids via β-oxidation. An ongoing RNAi screen in our lab has identified six metabolism-related genes that are more critical for parasite fitness in adipose tissue compared to blood. These findings raise two fundamental and complementary questions that will be addressed during this PhD project:

1. Do T. brucei parasites undergo tissue-specific adaptations—for instance, are brain-resident parasites functionally distinct from those in the adipose tissue or blood?
2. What are the biological consequences of interfering with the parasite’s ability to adapt to different tissue environments?

First, genome-wide RNA-seq will be employed to compare the transcriptomes of T. brucei parasites isolated from multiple mouse tissues (adipose tissue, skin, brain, lung, and kidney). Computational analyses will be used to define tissue-specific expression patterns and test whether adaptation follows a shared program across solid tissues or reflects truly distinct tissue-specific responses. Phenotypic assays will then be used to validate transcriptomic predictions.

Second, the student will investigate the function of candidate metabolism-related parasite genes identified in our RNAi screen. Using reverse genetics, the student will assess the impact of gene knockdown on tissue colonization, characterize underlying cellular mechanisms, and evaluate how disrupted adaptation affects disease progression.

In this project, the student will employ a multidisciplinary toolkit, including computational biology, molecular cloning, in vitro cell culture, phenotypic and cellular assays, as well as in vivo animal experimentation.

RNA & Gene Regulation

Nuclear neighborhoods and their role in gene regulation

Our laboratory studies the biogenesis of mRNA in human cells with the goal of understanding how gene expression is controlled in health and leads to disease when dysregulated. By addressing questions related to transcription and RNA splicing, our long term aim is to contribute new knowledge on gene regulation and provide novel insights into disease mechanisms and therapeutic interventions.
While existing evidence has extensively demonstrated how the dynamic folding of genomic DNA facilitates enhancer-promoter interactions and topological association of sets of co-regulated genes (PMID: 25757416), little is known about RNA folding and its functional consequences in the nucleus. Our previous analysis of intact nascent RNAs using long-read sequencing showed that although many transcripts are immediately spliced, a significant fraction of nascent pre-mRNAs remained unspliced and failed to be cleaved at the polyA site (PMID: 33735606). What happens to these unspliced and uncleaved nascent transcripts? Do they eventually undergo splicing, polyadenylation and export to the cytoplasm, or do they represent dead-end products destined for degradation in the nucleus? Why are some pre-mRNAs rapidly spliced while others remain unspliced? Is delayed splicing functional? We aim to address these questions by tracking in space and time newly synthesized pre-mRNAs and their interactions with the transcription machinery.