3. Identifying New Genes Involved in Brain Size Regulation 

Ilaria Dutto (Genomic Instability and Cancer Laboratory)

To identify regulators of human brain size, we screened candidate genes that carried fixed sequence changes in H. sapiens compared to H. neanderthalensis. The screening identified a protein that plays a role in de novo synthesis of purine, one of the building blocks of nucleic acids (DNA and RNA). This protein is crucial for correct DNA replication and ATP/ADP ratio in the cell, and mutations in its sequence cause a disease characterised by a spectrum of central nervous system defects, including mental retardation, epilepsy, autism and microcephaly, as well as growth delay.

We use a human cell line to delineate the mechanisms at a cellular level, and zebrafish and chicken embryos to understand what defects protein depletion causes during development.

In this course, we will learn how identify an adequate model system for our research project, and how to culture human cell lines and prepare experiments to test cell proliferation.

4. Mirror, Mirror on the Wall… Who Is the Most Helpful Insect of Them All? – Getting to Know Tumorigenesis Through the Fly 

 Elena Gaspar and Daniela Ferreira (Development and Growth Control Laboratory)

The fruit fly Drosophila melanogaster is an impressive model organism that has a long history of helping researchers understand the basic processes behind several diseases and systemic behaviours. This tiny organism has emerged as a potent tool for genetic manipulation, offering innumerable possibilities to analyse the detailed interaction between cells and tissues. 

On the molecular level, the fruit fly shares many similarities and conserved pathways with humans, and 60% of genes identified to be mutated, amplified or deleted in diverse human diseases have a counterpart in Drosophila.

During this semester, we will learn how to study the complex process of tumorigenesis using this model organism, both with a local and systemic approach. We will focus mainly on carcinomas, the most common type of tumour diagnosed in humans.

Carcinomas are derived from epithelial tissue, such as the skin, and they can become invasive or metastatic by spreading beyond the primary tissue layer and surrounding tissues or organs. In aggressive cancer cells, this transition is mediated by the activation of the EMT (Epithelial to Mesenchymal Transition) programme, which causes the cells to undergo morphogenetic alterations that increase invasive capacity.

In this course, we will introduce you to the first steps in fly genetics. We will cross flies, identify genetic markers and balancer chromosomes, and apply other genetic tools that we use in the lab every day. We will also learn about the anatomy of the fly in adult and larvae stages and use advanced microscopy to see several genetic markers. We will also perform in vivo dissections and their respective immunohistochemistry.

5. Proteins: Powerful Tools in Biomedicine 

Mateusz Biesaga (Laboratory of Molecular Biophysics)

Proteins comprise a major part of living matter. They are key players in all cellular processes…they regulate, organise, transport, store, provide structure, and support other functions. Thanks to advances in biotechnology, scientists are now able to precisely design, produce and purify many proteins, thus allowing them to study the features of these molecules. Indeed, proteins are not only the focus of research activity but are also pivotal in many biomedical applications. One example is synthetic human insulin, which is produced in bacteria or yeast, used to treat millions of diabetes patients worldwide. A second example is the protein complex biotin and streptavidin, which is widely employed in molecular diagnostic tests.

In this course, we will learn how to produce proteins in vitro and understand their main structural and functional features. We will employ laboratory techniques that are used to obtain pure protein solutions. Furthermore, we will discuss how to engineer a protein, from the design of DNA that encodes it to the purification process, and also the use of recombinant proteins in biomedicine.

6. Dealing with Stress

Anna Pijuan and Maria Caballero (Cell Signaling)

A fundamental property of living cells is the ability to sense and respond to fluctuations in their environment. Cells have developed a number of signal transduction pathways that serve to adapt to and survive these changes. 

The budding yeast Saccharomyces cerevisiae, a well-established eukaryotic model organism, has several advantages: ease of manipulation; short life span; ability to produce a large number of offspring; and a sequenced genome. We use S. cerevisiae to study the adaptive eukaryotic responses to a variety of environmental stresses. Remarkably, many processes initially discovered and studied in yeast, such as transcription regulation, stress-signalling transduction, and cell cycle regulation, are conserved in higher eukaryotes and therefore allow for translational studies.

Yeast and mammals have a conserved family of mitogen-activated protein kinase (MAPKs)—known as stress-activated signalling pathways (SAPKs) of the Hog1/p38 family—that sense and respond to changes in the extracellular environment. The activation of SAPKs leads to the generation of a set of adaptive responses that involves modulation of several physiological processes, such as changes in gene transcription, cell metabolism, protein translation and cell cycle progression.

In this course, we will learn how to manipulate and work with S. cerevisiae. To understand how cells detect an external signal and transduce it in order to elicit a proper response to ensure survival, we will study the activation of Hog1 MAPK at the protein level upon different stress conditions and also examine mutant strains. We will also learn how mutations in distinct genes can produce different phenotypes in response to stress.

SEMESTER 2

1. How Do Pro-Metastatic Fats Affect the Proteome? 

Miguel Martin (Stem Cells and Cancer)

Cancer is a disease involving abnormal cell growth (tumour) with the potential to invade or spread to other parts of the body (metastasis). It is the fifth leading cause of death worldwide, and most cancer-related deaths are due to metastasis. Our group recently identified a group of cells responsible for initiating and promoting metastasis in several types of human tumour. These cells are characterised by the overexpression of the protein CD36, which absorbs fatty acids from the cell membrane. The metastatic process is enhanced by fat intake, and tumour cells produce more aggressive metastases in the presence of specific fatty acids, such as palmitic acid. In the absence of CD36, the tumours do not develop metastasis, or existing metastases shrink. Thus, blocking fat metabolism may provide an effective therapy to treat cancer patients.

Our research group is interested in why some specific fatty acids are pro-metastatic. One hypothesis is that these fatty acids (e.g. palmitic acid) can covalently attach to proteins and modify their function.

In this course, we will learn how to detect ‘palmitoylated’ proteins by metabolic labelling of proteins in cell culture with a palmitic acid-mimic compound.

2. Strategies to Understand Aging and Senescence

Marta Kovatcheva (Cellular Plasticity and Disease)

Scientific research and modern medicine have dramatically extended life expectancy, with the average person in the developed world expected to reach 80 years of age or more. However, this extension in lifespan has had no effect on health span; that is, the number of healthy years a human lives. Aging is still characterised by multiple pathologies including frailty, heart disease, cancer, and neurodegenerative diseases, among many others. 

One of the main hallmarks of ageing is cellular senescence, the phenomenon by which normal cells stop dividing. Senescent cells accumulate in an organism over time, secreting pro-inflammatory molecules and contributing to age-related diseases. There is an increasing interest in clinical medicine to better identify and target senescent cells, as their elimination may delay and ameliorate some age-associated diseases. 

This course provides hands-on experience using different techniques to induce cellular senescence in normal cells. We will learn state-of-the-art techniques to study the molecular biology of senescent cells, analysing in vitro and in vivo samples. Finally, we will perform classical protocols, such as SAβgal staining, to detect senescent cells. These techniques will help us to understand, identify and target senescent cells for clearance, which is a promising therapeutic approach to extend health span.