Ateneo - UPO

The course provides an overview of the application of Omics technologies in different areas of translational medicine, including nephrology, haematology, and oncology. Particular attention will be given to genomics, biomarker discovery, liquid biopsy approaches, and the analysis of biological samples such as urine, blood, and tumor-derived material. The course will also introduce advanced single-cell and multiparametric techniques, including flow cytometry, scRNA-seq, and mass imaging, with a focus on their application to the study of hematological and solid malignancies, tumor heterogeneity, immune profiling, and treatment response. Practical exercises, self-assessment activities, and group presentations will support the understanding of the main methodological and professional applications relevant to Medical Biotechnology.

The slides presented during the lectures will be made available on the University’s dedicated platform. Additional scientific papers and supplementary materials will be provided during the course.
Recommended reference textbook for the hematology module:
Williams Hematology, 9th Edition
Kenneth Kaushansky, Marshall A. Lichtman, Josef T. Prchal, Marcel M. Levi, Oliver W. Press, Linda J. Burns, Michael Caligiuri.
Available through the UPO Off-Campus Library via AccessMedicine.

The course aims to provide students with an integrated understanding of the main applications of Omics technologies and advanced cellular analysis methods in translational medicine, with particular emphasis on nephrology, haematology, and oncology. Students will acquire basic knowledge of genomics, liquid biopsy, multiparametric flow cytometry, scRNA-seq, and imaging-based approaches for the study of disease mechanisms, biomarker discovery, and the characterization of biological and immune heterogeneity.
Particular attention will be given to applications in oncology, including molecular tumor characterization, immune profiling, treatment response, and mechanisms of resistance. The course also aims to develop students’ ability to critically interpret experimental data and scientific literature and to understand how different technologies can be translated into diagnostic, prognostic, and predictive applications.

Molecular biology and biochemistry

Lectures supported by slides, interactive discussion of clinical cases, and group activities involving the presentation and critical discussion of scientific papers.

NA

Written examination consisting of three open-ended questions for each module.

Oncology

Principles of carcinogenesis, including the two-hit hypothesis and the endosymbiosis disruption hypothesis

Biology of tumor progression and metastatic dissemination

Principles of pharmacology of the main anticancer treatments, including chemotherapy, targeted therapies, immunotherapy, and antibody-drug conjugates

Molecular mechanisms of primary and acquired resistance to anticancer therapies

Hereditary cancer syndromes and their molecular basis

Integration of molecular and genomic biomarkers into clinical decision-making and clinical trials

Liquid biopsy and circulating biomarkers in oncology

Prognostic and predictive genomic assays

Principles of design and statistical methodology of phase III clinical trials

Role of Omics technologies in precision oncology, biomarker discovery, patient stratification, and treatment selection

Nephrology

Omics technologies will be explored across major nephrological settings, with particular emphasis on biomarker discovery through liquid biopsy and molecular characterization of injured tissues.

Glomerular diseases: application of Omics technologies to primary glomerulonephritis, including IgA nephropathy and membranous nephropathy, and secondary glomerulonephritis, including ANCA-associated vasculitis and lupus nephritis

Genetic and rare kidney diseases: Omics approaches in hereditary glomerular diseases causing nephrotic syndrome and in tubulo-cystic disorders

Acute kidney injury (AKI): molecular mechanisms of endothelial and tubular epithelial injury, distant organ dysfunction, and progression from AKI to chronic kidney disease through tissue fibrosis

Chronic kidney disease (CKD): application of Omics technologies to the study of CKD-associated systemic dysfunction, including cardiovascular, neurological, and immunological alterations

Kidney transplantation: tissue- and fluid-derived biomarkers of delayed graft function related to ischemia-reperfusion injury, T cell-mediated rejection, and antibody-mediated rejection

Genetic polymorphisms associated with graft rejection and post-transplant complications, including diabetes, cardiovascular disease, infections, and malignancies

Extracellular vesicles (EVs): application of Omics technologies to EVs isolated from biological fluids, with particular emphasis on urine

EV isolation by ultracentrifugation

Phenotypic characterization of EVs, including size and concentration assessment by nanoparticle tracking analysis

Proteomic, transcriptomic, and microRNA profiling of extracellular vesicles

Hematology

Clinical Omics in chronic lymphocytic leukemia: implications for diagnosis, prognostic stratification, and precision medicine

Clinical Omics in diffuse large B-cell lymphoma: implications for prognosis, molecular classification, and targeted treatment

Clinical Omics in acute lymphoblastic leukemia: applications in diagnosis, risk stratification, and precision medicine

Clinical Omics in acute myeloid leukemia: implications for disease classification, prognosis, and targeted therapies

Clinical Omics in myeloproliferative neoplasms

Clinical Omics in multiple myeloma

Integration of genomic and molecular biomarkers into the design and conduct of clinical trials in hematological malignancies

Role of Omics technologies in disease classification, treatment selection, response assessment, and measurable residual disease evaluation

Cytomics

Basic principles of flow cytometry and its biomedical applications

Multiparametric flow cytometry and high-dimensional cellular phenotyping

Basic principles and applications of single-cell RNA sequencing (scRNA-seq)

Basic principles and applications of imaging mass cytometry

Computational approaches for single-cell data analysis

Dimensionality reduction techniques

Unsupervised clustering algorithms

Classification and supervised learning approaches

Integration and visualization of high-dimensional single-cell datasets

Introduction to the Seurat workflow for scRNA-seq data preprocessing, analysis, clustering, and visualization

Learning Objectives

By the end of the course, students should be able to:

- Describe the principles and major applications of Omics technologies in translational medicine.
- Explain how genomic, transcriptomic, proteomic, and single-cell approaches can be applied to the study of human disease.
- Understand the molecular basis of selected oncological, hematological, and nephrological diseases.
- Explain the role of molecular biomarkers in diagnosis, prognosis, patient stratification, treatment selection, and response assessment.
- Understand the principles and clinical applications of liquid biopsy and other minimally invasive biomarker-based approaches.
- Describe the main applications of precision medicine in oncology, hematology, nephrology, and transplantation.
- Understand the basic principles of flow cytometry, scRNA-seq, imaging mass cytometry, and computational single-cell analysis.
- Interpret the main concepts underlying high-dimensional and single-cell data analysis, including dimensionality reduction, clustering, and classification.
- Understand how molecular biomarkers are integrated into clinical trials and the basic principles of phase III trial design and statistical analysis.
- Critically evaluate scientific data and literature concerning Omics technologies and their potential translation into clinical practice.
- Integrate biological, technological, and clinical information in the discussion of translational medicine research questions.