Omics: from bench to bedside

A.Y. 2021/2022
Overall hours
BIO/10 MED/04
Learning objectives
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.
Expected learning outcomes
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.
Course syllabus and organization

Single session

Lesson period
Second semester
More specific information on the delivery modes of training activities for the academic year 2021/2022 will be provided over the coming months, based on the evolution of the public health situation.
Course syllabus
The following topics will be explained during the course of omics technology and approaches:
- Introduction to genomics
- Sequencing technology platform
- Single Nucleotide polymorphisms (SNPs), exome sequencing and genome-wide association study (GWAS)
- DNA-protein interaction at the genome level (chromatin immunoprecipitation coupled to next-generation sequencing-ChIP-Seq)
- Functional genomics screens
- Epigenomics
- Metagenomics
- Introduction to transcriptomics
- Nascent RNA and total RNA sequencing
- Splicing analysis
- Other RNAs analysis (miRNAs, long non-coding RNAs, small nuclear RNAs and others)
- Introduction to proteomics
- Proteomic platform and instrumentation (high-resolution nanoLC-MS/MS system)
- Labelled and label-free proteomics
- 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 section of "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 mechanism 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.
- Cancer therapy and immunotherapy. Basic concepts of tumor antigens and the rationale for immunotherapy. Experimental data obtained in mice with chemically induced tumors. Passive immunotherapy: clinical use of monoclonal antibodies; Active immunotherapy: use of checkpoints inhibitors, use of CART cells; examples of personalized treatments based on novel biotech drugs and/or treatments.
Prerequisites for admission
Basic knowledge in Biochemistry and Applied Biochemistry, Immunology and elements Human physio-pathology are strongly recommended for omics technology and approaches course.
Teaching methods
The course is composed of two sections: 1. Omics technology and approaches (32 h) and 2. Omics approaches in oncodiagnostics and therapy (16 h). Both sections consist of lectures given by the Teacher and occasionally seminars by external experts on particular subjects.
Power point presentations or short videos are usually used and are provided to the students in the Ariel site of the course.
Teaching Resources
The iconographic material shown during the lessons and bibliographic references can be downloaded from the Ariel portal.
Assessment methods and Criteria
The students' learning outcomes will be evaluated by the teacher through an oral examination of the learning of the omic methodologies and their use on the basis of the program carried out during the course. Additional learning activities conducted as a group by the students will be evaluated after the oral presentation of the group.
Omics approaches in oncodiagnostics and therapy
Lessons: 16 hours
Omics technology and approaches
Lessons: 32 hours
Educational website(s)
to be defined
via Carlo Pascal, 36 - 20133 MILANO