Molecular Biology, Medicinal Chemistry and Computer Science for Pharmaceutical Applications

Activity type

Discipline Mediche

SSD

MED/46

Year

3rd year

Semester

1st semester

CFU

6

Hours distribution

32 classroom hours, 40 laboratory hours

Lecturers

VITTORIO PICCHIO
ISOTTA CHIMENTI
Francesca PAGANO

Activity type

Discipline Mediche

SSD

MED/04

Year

3rd year

Semester

1st semester

CFU

6

Hours distribution

48 classroom hours

Lecturers

DONATELLA PONTI
PAOLO ROSA

Students will learn the general principles and fundamental mechanisms of pathology and pathophysiology, with a particular focus on immunology. The module will also address advanced molecular biology techniques—covering diagnostics, basic research, and, above all, their integration with advanced cellular models. Additionally, the module will foster familiarity with scientific publishing and the critical reading of manuscripts from high-impact journals.

Essential: Cell biology and molecular biology
Important: Biochemistry
Useful: Chemistry and physics

MODULE 1 – PATHOLOGY AND IMMUNOLOGY

General Pathology

Concepts of etiology and pathogenesis: causes of disease and biological mechanisms underlying disease development; chemical, physical, and biological pathogenic agents.

Cellular adaptations and cell death: hyperplasia, hypoplasia, hypertrophy, atrophy, metaplasia, dysplasia, and autophagy; necrosis and apoptosis.

Inflammation: acute and chronic inflammation; vascular and cellular events, microcirculation, exudate formation, chemotaxis, diapedesis, and phagocytosis; inflammatory mediators, cytokines, complement, and innate immune receptors; systemic effects of inflammation, fever, hyperthermia, and septic shock; chronic inflammation, role of macrophages, granulomas, fibrosis, and tissue repair.

Tumors: tumor initiation and progression; classification of benign and malignant tumors, grading and staging; cancer epidemiology, risk factors, and hereditary cancer syndromes; characteristics of malignant cells, uncontrolled proliferation, evasion of apoptosis, and metabolic reprogramming; tumor heterogeneity and cancer stem cells; invasion, angiogenesis, and metastasis; oncogenes, tumor suppressor genes, non-coding RNAs, and oxidative stress; chemical and viral carcinogenesis and cell cycle dysregulation.

Genetic diseases: chromosomal abnormalities, Mendelian inheritance, complex genetic disorders, and genotype-phenotype correlations.

Immunology

Structure and function of the immune system: primary and secondary lymphoid organs; major immune cell populations; coordination of local and systemic immune responses.

Innate immunity: physical and chemical barriers; complement system; acute-phase proteins; phagocytes; natural killer (NK) cells and innate lymphoid cells; pattern recognition receptors.

Humoral immunity: B-cell activation and differentiation and antibody production; immunoglobulin classes (IgM, IgG, IgA, IgE, and IgD); BCR signaling; T-dependent and T-independent responses; class switching and affinity maturation; antibody functions: neutralization, opsonization, and complement activation.

Cell-mediated immunity: helper T cells (Th1, Th2, Th17, and Treg), cytotoxic T cells, and memory T cells; antigen presentation through MHC class I and II molecules; antigen processing through proteasomes, phagolysosomes, and autophagy; T-cell activation and co-stimulation; cytokine production and major signaling pathways.

MODULE 2 – ADVANCED MOLECULAR BIOLOGY TECHNIQUES

Discovery and profiling techniques: introduction to omics technologies; principles and chemistry of sequencing and Next Generation Sequencing (NGS); human genomics and its applications; transcriptomics and analysis of coding and non-coding RNAs; single-cell sequencing; spatial omics; liquid biopsy and circulating DNA analysis; protein analysis techniques, proteomics, and arrays; circulating biomarkers.

Principles of bioinformatics analysis: Principal Component Analysis (PCA), heatmaps, and clustering; data representation and visualization using Venn and Sankey diagrams; Gene Ontology enrichment; network analysis and pathway analysis.

Gene interference and editing techniques: biology of non-coding RNAs and their biotechnological applications; gene expression vectors; genome editing technologies.

Laboratory activities: RNA extraction and quantification; reverse transcription; real-time PCR preparation and data analysis; antibody array protocol and data analysis; principles and application of a Next Generation Sequencing protocol in molecular diagnostics.

Molecular Biology – Zlatanova, van Holde – 2018
Genetics and Genomics in Medicine – Strachan, Goodship, Chinnery
Molecular Biotechnology – Brown – 2nd edition, 2017
Basic Immunology, Shiv Pillai, Abul K. Abbas, Andrew H. Lichtman, Elsevier
Robbins, Basic Pathology, Kumar Abbas Aster, Elsevier Saunders

Scientific articles and material provided by the professor

Lectures: traditional classes featuring slide presentations by the instructor.
Seminars: lectures will be supplemented by relevant seminars within the university network, should any arise during the course.
Laboratory experience: exposure to and interaction with research laboratories and key diagnostic techniques, including hands-on laboratory practice.
Group work: potential group workshops featuring dynamic discussions throughout the course.

Not mandatory but highly recommended

A written exam in multiple-choice quiz format is required for all modules.
For the molecular biology module, an oral exam component is also included, but only after the written exam has been passed.

1 - Describe the main mechanisms of acute and chronic inflammation, highlighting the role of immune cells and mediators and the possible pathological consequences.
2 - Describe the principles of Next Generation Sequencing (NGS) and discuss its main applications in genomics, transcriptomics, and molecular diagnostics.
3 - Describe the principles of genome editing technologies, with particular reference to the CRISPR/Cas9 system, and discuss their main applications in biomedical research and disease investigation.
4 - What are circulating biomarkers and liquid biopsy? Describe the main molecules that can be analyzed, the techniques used for their identification, and their possible applications in disease diagnosis and monitoring.

• Concepts of etiology and pathogenesis: causes of disease and biological mechanisms underlying disease
  development; chemical, physical, and biological pathogenic agents.
  • Books: Robbins,
    
    Basic Pathology, Kumar Abbas Aster, Elsevier Saunders


• Cellular adaptations and cell death: hyperplasia, hypoplasia, hypertrophy, atrophy, metaplasia,
  dysplasia, and autophagy; necrosis and apoptosis.
  • Books: Robbins,
    
    Basic Pathology, Kumar Abbas Aster, Elsevier Saunders


• Structure and function of the immune
  system: primary and secondary lymphoid organs;
  major immune cell populations; coordination of local and systemic immune
  responses.
  
  Innate immunity: physical and chemical barriers; complement system; acute-phase
  proteins; phagocytes; natural killer (NK) cells and innate lymphoid cells;
  pattern recognition receptors.
  • Books: Basic Immunology, Shiv Pillai, Abul K. Abbas, Andrew H. Lichtman, Elsevier


• Inflammation: acute and chronic inflammation; vascular and
  cellular events, microcirculation, exudate formation, chemotaxis, diapedesis,
  and phagocytosis; inflammatory mediators, cytokines, complement, and innate
  immune receptors; 
  • Books: Robbins,
    
    Basic Pathology, Kumar Abbas Aster, Elsevier Saunders


• systemic effects of inflammation, fever,
  hyperthermia, and septic shock; chronic inflammation, role of macrophages,
  granulomas, fibrosis, and tissue repair.
  • Books: Robbins,
    
    Basic Pathology, Kumar Abbas Aster, Elsevier Saunders


• introduction
  to omics technologies; principles and chemistry of sequencing and Next
  Generation Sequencing (NGS); human genomics and its applications;
  • Books: Biologia molecolare - Zlatanova, van Holde - Anno 2018
    
    
    
    Genetica e Genomica nelle scienze mediche.
    
    Strachan-Goodship-Chinnery
    
    
    
    Biotecnologie Molecolari Brown - seconda edizione 2017


• Humoral immunity: B-cell activation and differentiation and antibody production;
  immunoglobulin classes (IgM, IgG, IgA, IgE, and IgD); BCR signaling;
  T-dependent and T-independent responses; class switching and affinity
  maturation; antibody functions: neutralization, opsonization, and complement
  activation.
  • Books: Basic Immunology, Shiv Pillai, Abul K. Abbas, Andrew H. Lichtman, Elsevier


• Cell-mediated immunity: helper T cells (Th1, Th2, Th17, and Treg), cytotoxic T cells, and
  memory T cells; antigen presentation through MHC class I and II molecules;
  antigen processing through proteasomes, phagolysosomes, and autophagy; T-cell
  activation and co-stimulation; cytokine production and major signaling
  pathways.
  • Books: Basic Immunology, Shiv Pillai, Abul K. Abbas, Andrew H. Lichtman, Elsevier


• Tumors: tumor initiation and progression;
  classification of benign and malignant tumors, grading and staging; cancer
  epidemiology, risk factors, and hereditary cancer syndromes; characteristics of
  malignant cells, uncontrolled proliferation, evasion of apoptosis, and
  metabolic reprogramming; 
  • Books: Robbins,
    
    Basic Pathology, Kumar Abbas Aster, Elsevier Saunders


• tumor heterogeneity and cancer stem
  cells; invasion, angiogenesis, and metastasis; oncogenes, tumor suppressor
  genes, non-coding RNAs, and oxidative stress; chemical and viral carcinogenesis
  and cell cycle dysregulation.
  • Books: Robbins,
    
    Basic Pathology, Kumar Abbas Aster, Elsevier Saunders


• transcriptomics and analysis of coding
  and non-coding RNAs; single-cell sequencing; spatial omics;  circulating biomarkers.
  • Books: Biologia molecolare - Zlatanova, van Holde - Anno 2018 Genetica e Genomica nelle scienze mediche. Strachan-Goodship-Chinnery Biotecnologie Molecolari Brown - seconda edizione 2017


• liquid biopsy and circulating DNA analysis; protein analysis techniques, proteomics, and arrays;
  • Books: Biologia molecolare - Zlatanova, van Holde - Anno 2018 Genetica e Genomica nelle scienze mediche. Strachan-Goodship-Chinnery Biotecnologie Molecolari Brown - seconda edizione 2017


• Genetic diseases: chromosomal abnormalities, Mendelian inheritance, complex genetic
  disorders, and genotype-phenotype correlations.
  • Books: Robbins,
    
    Basic Pathology, Kumar Abbas Aster, Elsevier Saunders


• Principles of bioinformatics analysis: Principal Component Analysis (PCA), heatmaps, and clustering; data
  representation and visualization using Venn and Sankey diagrams; Gene Ontology
  enrichment; network analysis and pathway analysis.
  • Books: Biologia molecolare - Zlatanova, van Holde - Anno 2018 Genetica e Genomica nelle scienze mediche. Strachan-Goodship-Chinnery Biotecnologie Molecolari Brown - seconda edizione 2017


• Gene interference and editing
  techniques: biology of non-coding RNAs and their
  biotechnological applications; gene expression vectors; genome editing
  technologies.
  • Books: Biologia molecolare - Zlatanova, van Holde - Anno 2018 Genetica e Genomica nelle scienze mediche. Strachan-Goodship-Chinnery Biotecnologie Molecolari Brown - seconda edizione 2017


• Laboratory
  activities:
  RNA extraction and quantification; reverse transcription; 
  • Books: Materials and protocols provided during the activities


• Laboratory activities: antibody array protocol and data analysis
  • Books: Materials and protocols provided during the activities


• Laboratory activities: real-time
  PCR preparation and data analysis; 
  • Books: Materials and protocols provided during the activities


• Laboratory activities: principles and application of a Next
  Generation Sequencing protocol in molecular diagnostics.
  • Books: Materials and protocols provided during the activities