Omics: from bench to bedside
A.A. 2023/2024
Obiettivi formativi
The aim of the course is to present to the students the fundamental logic in the use of omic methodologies, to introduce the theoretical and practical bases and the principles on which the different omic techniques are based, to describe the main protocols of use both in the preparation of the sample and of the instrumentation and their control, and finally to provide the basis for the management and analysis of the results including the possibility of integration of the data obtained with different omic methodologies.
In addition, since omics-based recent approaches have unveiled the molecular mechanism behind tumorigenesis of several human tumors and promoted the identification of next-generation molecular markers for early diagnosis, prognosis and even personalized targeted therapy, the course will introduce the student to the most promising omics approaches and their outcomes for the diagnosis and therapy of cancer.
In addition, since omics-based recent approaches have unveiled the molecular mechanism behind tumorigenesis of several human tumors and promoted the identification of next-generation molecular markers for early diagnosis, prognosis and even personalized targeted therapy, the course will introduce the student to the most promising omics approaches and their outcomes for the diagnosis and therapy of cancer.
Risultati apprendimento attesi
At the end of the course, the students will be able to address different scientific issues and to choose and apply the best omics approaches to understand the biochemical bases of tissue functions in health and disease. The student will be prepared to discuss the available modern high technologies to identify novel tumor markers and understand personalized therapies; they will learn the "omics" work flow from different clinical matrices (i.e. tumor specimen) to data analysis.
Periodo: Secondo semestre
Modalità di valutazione: Esame
Giudizio di valutazione: voto verbalizzato in trentesimi
Corso singolo
Questo insegnamento può essere seguito come corso singolo.
Programma e organizzazione didattica
Edizione unica
Responsabile
Periodo
Secondo semestre
Programma
The following topics will be explained during the teaching unit "Omics technology and approaches":
- An overview on Precision Medicine
- Large Scale Genome Sequencing Project
- Next Generation Sequencing Platforms
- Next Generation Sequencing libraries preparations and sequencing
- Next Generation Sequencing Applications: Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS)
- Next Generation Sequencing Applications: ATAC-seq, ChIP-seq, bulk-RNA-seq
- Spatial Transcriptomics
- Single Cell RNA-seq
- Introduction to proteomics
- Proteomic platform and instrumentation (high-resolution nanoLC-MS/MS system)
- Quantitative analysis in proteomics: Labelled and label-free approaches
- Imaging proteomics and applications
- Structural proteomics
- Introduction to metabolomics
- Metabolic platform: targeted vs untargeted metabolomics
- Lipidomics
- Fluxomics
- Introduction to bioinformatics
- Omics data integration
- Principle of system biology and application to disease
The following topics will be covered during the teaching unit "Omics approaches in oncodiagnostics and therapy":
- Elements of oncogenic transformation, tumor classification and phenotype, epidemiology, and risk factors of most common neoplasia. Hereditary cancers.
- Omics-based approaches to investigate the molecular mechanisms of cancer transformation focusing on the description of the hallmarks of cancer.
- Omics-based approaches to identify molecular markers for early diagnosis and prognosis of the most common tumors (from histology to liquid biopsy). Definition and usage of tumor markers.
- Experimental data obtained from animal models with chemically induced tumors and their relevance to disease.
- An overview on Precision Medicine
- Large Scale Genome Sequencing Project
- Next Generation Sequencing Platforms
- Next Generation Sequencing libraries preparations and sequencing
- Next Generation Sequencing Applications: Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS)
- Next Generation Sequencing Applications: ATAC-seq, ChIP-seq, bulk-RNA-seq
- Spatial Transcriptomics
- Single Cell RNA-seq
- Introduction to proteomics
- Proteomic platform and instrumentation (high-resolution nanoLC-MS/MS system)
- Quantitative analysis in proteomics: Labelled and label-free approaches
- Imaging proteomics and applications
- Structural proteomics
- Introduction to metabolomics
- Metabolic platform: targeted vs untargeted metabolomics
- Lipidomics
- Fluxomics
- Introduction to bioinformatics
- Omics data integration
- Principle of system biology and application to disease
The following topics will be covered during the teaching unit "Omics approaches in oncodiagnostics and therapy":
- Elements of oncogenic transformation, tumor classification and phenotype, epidemiology, and risk factors of most common neoplasia. Hereditary cancers.
- Omics-based approaches to investigate the molecular mechanisms of cancer transformation focusing on the description of the hallmarks of cancer.
- Omics-based approaches to identify molecular markers for early diagnosis and prognosis of the most common tumors (from histology to liquid biopsy). Definition and usage of tumor markers.
- Experimental data obtained from animal models with chemically induced tumors and their relevance to disease.
Prerequisiti
Basic knowledge in Biochemistry, Applied Biochemistry, Molecular Biology, Immunology, and elements of human physiopathology are strongly recommended for omics technology and approaches course.
Metodi didattici
The course is composed of two teaching units: 1. "Omics technology and approaches" (32 h) and 2. "Omics approaches in oncodiagnostics and therapy" (16 h). Both teaching units consist of lectures given by the Teachers and, occasionally, seminars by external experts on particular topics. Additionally, for the teaching unit "Omics Approaches in Oncodiagnostics and Therapy", team-based work will be assigned. Further details will be made available on the Ariel website.
Powerpoint presentations or short videos are usually used and are provided to the students on the Ariel site of the course.
Powerpoint presentations or short videos are usually used and are provided to the students on the Ariel site of the course.
Materiale di riferimento
For the teaching unit "Omics technology and approaches" the iconographic materials shown during the lessons and bibliographic references can be downloaded from the Ariel portal.
For the teaching unit "Omics approaches in oncodiagnostics and therapy", Pathological bases for precision medicine interventions (Robbins and Cotran) is suggested.
For the teaching unit "Omics approaches in oncodiagnostics and therapy", Pathological bases for precision medicine interventions (Robbins and Cotran) is suggested.
Modalità di verifica dell’apprendimento e criteri di valutazione
The students' learning outcomes will be evaluated by written examination on the omics methodologies and their applications according to the program carried out during the teaching unit "Omics technology and approaches". Specifically, the written exam will consist of multiple-choice questions on the topics covered during the course.
For the teaching unit "Omics approaches in oncodiagnostics and therapy", the group work will be evaluated throughout the course, with each student receiving a personal score. For those who do not attend the course, an oral exam will be conducted which involves discussing a scientific paper selected from a provided list. Further details will be published on the Ariel website.
The final grade will be the weighted average of the grades obtained in "Omics technology and approaches" and "Omics approaches in oncodiagnostics and therapy" exams, based on the credits assigned to each teaching unit.
For the teaching unit "Omics approaches in oncodiagnostics and therapy", the group work will be evaluated throughout the course, with each student receiving a personal score. For those who do not attend the course, an oral exam will be conducted which involves discussing a scientific paper selected from a provided list. Further details will be published on the Ariel website.
The final grade will be the weighted average of the grades obtained in "Omics technology and approaches" and "Omics approaches in oncodiagnostics and therapy" exams, based on the credits assigned to each teaching unit.
Moduli o unità didattiche
Omics approaches in oncodiagnostics and therapy
BIO/10 - BIOCHIMICA
MED/04 - PATOLOGIA GENERALE
MED/04 - PATOLOGIA GENERALE
Lezioni: 16 ore
Docente:
Calvo Alvarez Estefania
Omics technology and approaches
BIO/10 - BIOCHIMICA
MED/04 - PATOLOGIA GENERALE
MED/04 - PATOLOGIA GENERALE
Lezioni: 32 ore
Docenti:
Ghisletti Serena Maria Luisa, Mitro Nico
Siti didattici
Docente/i
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