Spatial and Molecular Organization of Cells in Diseases
A.Y. 2025/2026
Learning objectives
The purpose of this course is the training of the participants in the comprehension of how cells are spatially and hierarchically organized and communicate and the way this organization is altered in diseases.
The course is divided into two distinct modules: "High-content imaging and computational aspects of in vitro and animal model systems" is dedicated to the acquisition, processing and comprehension of data obtained from three popular techniques in the world of bioimaging, i.e., functional MRI, optical microscopy, and mass spectroscopy imaging, "Analytical challenges and opportunities from multi-omics" to the one of numerical analysis and interpretation of data obtained by means of next generation sequencing (NGS) techniques.
The course is divided into two distinct modules: "High-content imaging and computational aspects of in vitro and animal model systems" is dedicated to the acquisition, processing and comprehension of data obtained from three popular techniques in the world of bioimaging, i.e., functional MRI, optical microscopy, and mass spectroscopy imaging, "Analytical challenges and opportunities from multi-omics" to the one of numerical analysis and interpretation of data obtained by means of next generation sequencing (NGS) techniques.
Expected learning outcomes
By the end of the course, students are expected to be able to:
1. Understand the principles and techniques of bioimaging in neuroscience.
2. Describe the functional anatomy of the human brain and its role in cognition and behavior.
3. Interpret neuroimaging data in relation to brain function.
4. Compare different imaging techniques (e.g., MRI, fMRI, EEG) and their applications.
5. Evaluate structural and functional connectivity methods.
6. Understand lesion-based approaches for studying brain function in patients.
7. Discuss the use of functional neuroimaging to investigate complex cognitive and behavioral processes.
8. Understand the principles underlying mass spectrometry techniques, in particular matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI)
10. Understand the working principle of common computational tools and methods used for analysing and interpreting data derived from mass spectrometry imaging experiments.
11. Understand the basic principle of cell mechanics and mechanobiology
12. Understand the principles underlying common methods for the imaging-based characterization of single and collective cell behavior.
12. Use selected image analysis tools to obtain quantitative information on single and collective cell behavior from time-resolved imaging data
13. Understand the fundamental principles underlying spatial transcriptomic technologies
14. Understand the key steps in the design spatial transcriptomic experiments and in the analysis of the data
1. Understand the principles and techniques of bioimaging in neuroscience.
2. Describe the functional anatomy of the human brain and its role in cognition and behavior.
3. Interpret neuroimaging data in relation to brain function.
4. Compare different imaging techniques (e.g., MRI, fMRI, EEG) and their applications.
5. Evaluate structural and functional connectivity methods.
6. Understand lesion-based approaches for studying brain function in patients.
7. Discuss the use of functional neuroimaging to investigate complex cognitive and behavioral processes.
8. Understand the principles underlying mass spectrometry techniques, in particular matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI)
10. Understand the working principle of common computational tools and methods used for analysing and interpreting data derived from mass spectrometry imaging experiments.
11. Understand the basic principle of cell mechanics and mechanobiology
12. Understand the principles underlying common methods for the imaging-based characterization of single and collective cell behavior.
12. Use selected image analysis tools to obtain quantitative information on single and collective cell behavior from time-resolved imaging data
13. Understand the fundamental principles underlying spatial transcriptomic technologies
14. Understand the key steps in the design spatial transcriptomic experiments and in the analysis of the data
Lesson period: Third trimester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course cannot be attended as a single course. Please check our list of single courses to find the ones available for enrolment.
Course syllabus and organization
Single session
Responsible
Lesson period
Third trimester
Course syllabus
1 - High-content imaging and computational aspects of in vitro and animal model systems (21h)
1.1 Human brain diseases through the lens of neuroimaging techniques (7h)
The module provides an in-depth exploration of neuroimaging techniques and their application in mapping human brain functions.
Fundamental concepts.
The first part introduces fundamental concepts of bioimaging in humans, focusing on its role in functional brain mapping. In parallel, students will develop a foundational understanding of functional neuroanatomy, linking brain structures to their respective cognitive and motor functions.
Advanced neuroimaging methods.
The second part delves into advanced neuroimaging methodologies, including techniques for investigating structural and functional connectivity in the brain, lesion-based approaches for causal mapping of specific functions in patients with brain damage, and functional neuroimaging in healthy individuals to explore the neural basis of complex behaviors.
1.2 - Technical aspects of mass spectroscopy imaging (7h)
Mass spectrometry and laser.
Initial lectures will focus on the chemical-analytical description of mass spectrometry techniques, giving fundamental principles and technical principles, and the functioning mechanisms of lasers.
MALDI-MSI.
Lectures will cover fundamental principles and applications of matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI), a very promising technology to detect the presence of biomolecules in a cell sample. Part of the lectures will be also devoted to the description of computational tools and methods for analysing and interpreting data derived from mass spectrometry imaging experiments.
1.3 - Biophysical characterization and modelling of cells and tissues (7h)
It's a material world: biomechanical characterization of cells and tissues.
Basics of mechanics of biomaterials (elasticity, viscoelasticity, plasticity), tools and methods for the biomechanical characterization of cells and tissues (rheology, pipette aspiration, atomic force microscopy, active and passive microrheology, traction force microscopy).
It's an emergence: collective cells behaviors.
Cell-cell and cell-extracellular matrix interactions, mechanisms of force generation and transmission, emerging properties of cell collectives (polarized collective cell migration, coordinated contractile processes), two- and three-dimensional in vitro models (wound healing assays, adhesion and invasion assays).
Panta rei: phase transitions in tissue morphogenesis, regeneration and disease.
Capturing transitions in the physical state of tissues: morphology, structure, dynamics, methods and mathematical models. Application: the cell jamming / unjamming paradigm in cancer invasion.
2 - Analytical challenges and opportunities from multi-omics (21 h)
I. Fundamental principles underlying spatial transcriptomic technologies: from imaging-based to sequencing-based technologies and beyond. Strength and limitations of different platforms. Spatial multi-omics.
II. Key factors in designing spatial transcriptomic experiments: capture efficiency, transcriptome-wide profiling, spatial resolution, and tissue area considerations.
III. Main steps and bioinformatics approaches for analysing spatial transcriptomic data. Computational frameworks for image pre-processing, annotation transfer, cell-type deconvolution, imputation, inference of cell-cell interactions, analysis of gene modules and integration with single-cell RNA sequencing.
IV. Hands-on sessions on basic analyses of spatial datasets.
V. Case studies highlighting the application of spatial transcriptomics in biomedical research through journal club presentations and discussion of scientific papers.
1.1 Human brain diseases through the lens of neuroimaging techniques (7h)
The module provides an in-depth exploration of neuroimaging techniques and their application in mapping human brain functions.
Fundamental concepts.
The first part introduces fundamental concepts of bioimaging in humans, focusing on its role in functional brain mapping. In parallel, students will develop a foundational understanding of functional neuroanatomy, linking brain structures to their respective cognitive and motor functions.
Advanced neuroimaging methods.
The second part delves into advanced neuroimaging methodologies, including techniques for investigating structural and functional connectivity in the brain, lesion-based approaches for causal mapping of specific functions in patients with brain damage, and functional neuroimaging in healthy individuals to explore the neural basis of complex behaviors.
1.2 - Technical aspects of mass spectroscopy imaging (7h)
Mass spectrometry and laser.
Initial lectures will focus on the chemical-analytical description of mass spectrometry techniques, giving fundamental principles and technical principles, and the functioning mechanisms of lasers.
MALDI-MSI.
Lectures will cover fundamental principles and applications of matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI), a very promising technology to detect the presence of biomolecules in a cell sample. Part of the lectures will be also devoted to the description of computational tools and methods for analysing and interpreting data derived from mass spectrometry imaging experiments.
1.3 - Biophysical characterization and modelling of cells and tissues (7h)
It's a material world: biomechanical characterization of cells and tissues.
Basics of mechanics of biomaterials (elasticity, viscoelasticity, plasticity), tools and methods for the biomechanical characterization of cells and tissues (rheology, pipette aspiration, atomic force microscopy, active and passive microrheology, traction force microscopy).
It's an emergence: collective cells behaviors.
Cell-cell and cell-extracellular matrix interactions, mechanisms of force generation and transmission, emerging properties of cell collectives (polarized collective cell migration, coordinated contractile processes), two- and three-dimensional in vitro models (wound healing assays, adhesion and invasion assays).
Panta rei: phase transitions in tissue morphogenesis, regeneration and disease.
Capturing transitions in the physical state of tissues: morphology, structure, dynamics, methods and mathematical models. Application: the cell jamming / unjamming paradigm in cancer invasion.
2 - Analytical challenges and opportunities from multi-omics (21 h)
I. Fundamental principles underlying spatial transcriptomic technologies: from imaging-based to sequencing-based technologies and beyond. Strength and limitations of different platforms. Spatial multi-omics.
II. Key factors in designing spatial transcriptomic experiments: capture efficiency, transcriptome-wide profiling, spatial resolution, and tissue area considerations.
III. Main steps and bioinformatics approaches for analysing spatial transcriptomic data. Computational frameworks for image pre-processing, annotation transfer, cell-type deconvolution, imputation, inference of cell-cell interactions, analysis of gene modules and integration with single-cell RNA sequencing.
IV. Hands-on sessions on basic analyses of spatial datasets.
V. Case studies highlighting the application of spatial transcriptomics in biomedical research through journal club presentations and discussion of scientific papers.
Prerequisites for admission
The competences acquired during Bachelor's years in Chemistry, Physics, Mathematics, Biochemistry and Molecular Biology are the only required prerequisites of the course.
Teaching methods
All the lectures will be given in the form of frontal lessons, alternated with hands-on practical sessions.
Teaching Resources
Slides of the lectures will be shared by the instructors, as well as original articles from up-to-date literature.
Assessment methods and Criteria
The exam will be based on a presentation by the student of two scientific papers, followed by an open discussion. The two papers will be selected by the students from a list which will be provided to them in advance with respect to the day of the exam.
BIO/09 - PHYSIOLOGY - University credits: 1
BIO/10 - BIOCHEMISTRY - University credits: 1
BIO/11 - MOLECULAR BIOLOGY - University credits: 3
FIS/07 - APPLIED PHYSICS - University credits: 1
BIO/10 - BIOCHEMISTRY - University credits: 1
BIO/11 - MOLECULAR BIOLOGY - University credits: 3
FIS/07 - APPLIED PHYSICS - University credits: 1
Lessons: 42 hours
Shifts:
Professor(s)