Ateneo - UPO

The course examines the main molecular and biochemical processes that drive biological aging and the progressive loss of cellular and systemic homeostasis, using the Hallmarks of Aging as an integrated conceptual framework. Topics include genomic and telomeric instability, somatic mosaicism, epigenetic alterations, loss of proteostasis, mitochondrial dysfunction, oxidative stress, dysregulation of nutrient-sensing pathways, cellular senescence, chronic inflammation and stem cell exhaustion.Particular emphasis will be placed on translating these mechanisms into measurable molecular alterations. For each process, the course will consider the associated biomarkers, the most appropriate biological sample, the main analytical platforms and the clinical significance of the results. Genomic, epigenetic, protein, metabolic and inflammatory biomarkers will be addressed, together with biological clocks, laboratory-based frailty indices and biomarkers of neurodegenerative diseases.The course will also cover the principles of analytical and clinical biomarker validation, the integration of multi-omics and longitudinal data, and their use for early diagnosis, biological-age estimation, risk stratification, identification of intervention windows and monitoring of responses to preventive and therapeutic strategies. Transversal case-based discussions and structured debates will connect biological mechanisms with biomarker selection, result interpretation and the related clinical, ethical and regulatory implications

No compulsory textbook is prescribed. The reference materials for the course consist of the lecture slides and supplementary materials provided by the instructor through the University Moodle DIR platform. Selected scientific articles and reviews may also be recommended during the course for further study and discussion.

The course aims to provide an integrated understanding of the main molecular and biochemical mechanisms that drive biological aging and the progressive loss of cellular and systemic homeostasis, using the Hallmarks of Aging as the main conceptual framework.The course is intended to enable students to connect the biological processes of aging with measurable molecular alterations and to identify, for each context, the most appropriate biomarkers, biological samples and analytical technologies. Particular attention will be given to genomic, epigenetic, protein, metabolic and inflammatory biomarkers, as well as to indicators of biological age, frailty and neurodegenerative diseases.The course also aims to provide the conceptual tools required to understand the principles of analytical and clinical biomarker validation and to critically assess their use in early diagnosis, risk stratification, identification of intervention windows and monitoring of responses to preventive and therapeutic strategies.Through case-based discussions and structured debates, students will be guided in integrating biological, biochemical and diagnostic knowledge, while considering pre-analytical factors, confounders, interpretative limitations and the clinical, ethical and regulatory implications of molecular diagnostics applied to aging.

Basic knowledge of cell and molecular biology, biochemistry and genetics is required, particularly regarding the structure and function of DNA, RNA and proteins, the main cellular processes and the regulation of gene expression. No specialised knowledge of geroscience or molecular diagnostics is required.

The course will be delivered through lectures supported by slides, diagrams, experimental examples and selected scientific literature. The lessons will integrate the main molecular and biochemical mechanisms of aging with their application to molecular diagnostics and biomarker interpretation.Transversal activities will include case-based discussions, structured debates and Translational Controversy Journal Clubs. These activities will guide students in the critical analysis of scientific studies and controversial translational issues, with particular attention to the selection of the most appropriate biological sample, analytical method and biomarker, the assessment of the quality of the evidence and the interpretation of results within the clinical context.The main pre-analytical factors and confounders, the limitations of the technologies and biomarkers considered, and their clinical, ethical and regulatory implications will also be discussed.Slides, scientific articles and supplementary teaching materials will be made available through the University Moodle DIR platform.

Lecture slides, scientific articles and supplementary materials will be made available through the University Moodle DIR platform, which will also be used for course-related communications.
Exam preparation must be based on the programme and teaching materials of the current academic year, including for students enrolled in previous years.
The consultation of scientific literature in English is an integral part of the course activities and of the Translational Controversy Journal Clubs.

Learning will be assessed through an individual computer-based written examination, held in person in a computer room using the University Moodle DIR platform.The examination will consist of 30 questions to be completed within 40 minutes. It may include multiple-choice questions and questions requiring completion, matching, ordering, classification or application of knowledge to short cases. The questions will cover the entire course programme and will assess:knowledge of the main molecular and biochemical mechanisms of aging;the ability to relate biological processes to biomarkers, biological samples and analytical technologies;the ability to interpret data and results in the context of early diagnosis, risk stratification and intervention monitoring.Incorrect and unanswered questions will not be penalised. The final score will be expressed on a 30-point scale, and the examination will be passed with a minimum mark of 18/30.As this module is part of an integrated course, the final grade will be determined jointly by the teaching staff, according to the procedures described in the syllabus of the integrated course.

The course follows a translational sequence linking each molecular or biochemical mechanism to a measurable alteration, the appropriate biological sample, the analytical method, biomarker interpretation, clinical application and potential intervention.

1. Aging, epidemiology, geroscience and molecular medicine
Demographic transition, increased longevity and the gap between lifespan and healthspan. Healthy aging, intrinsic capacity, resilience, vulnerability, multimorbidity and frailty. Biological aging as a continuous process preceding overt age-related disease. The geroscience paradigm and interventions targeting shared mechanisms. Social determinants, environmental exposures and the exposome. Role of molecular diagnostics in the early identification of loss of homeostasis and windows for prevention.

2. Hallmarks of Aging as a molecular and diagnostic framework
The Hallmarks of Aging as an integrated model of functional decline and disease susceptibility. Primary, antagonistic and integrative mechanisms: biological meaning, interactions and limitations. Cross-talk among genomic damage, epigenetic alterations, loss of proteostasis, metabolic dysfunction, senescence, inflammation and reduced regenerative capacity. Hallmarks as sources of candidate biomarkers and therapeutic targets. From mechanism to molecular readout: analyte, sample, platform and intended clinical use. Limitations of single biomarkers and rationale for composite and longitudinal models.

3. Genomic instability, telomeres and somatic mosaicism
Endogenous and exogenous sources of DNA damage and main classes of lesions. DNA damage response and repair systems; consequences of persistent or incorrectly repaired damage. Telomere structure, shortening and dysfunction. Somatic mutations, genomic mosaicism and age-related clonal expansions, including clonal hematopoiesis. Molecular methods for assessing genomic damage, telomere length and clonal variants. Use of genomic biomarkers for risk estimation, stratification and longitudinal monitoring.

4. Epigenetic alterations, biological clocks and multi-omics
DNA methylation, histone modifications, chromatin remodelling and non-coding RNAs in the regulation of cellular identity and plasticity. Epigenetic drift, locus-specific changes and environmental interactions. Epigenetic clocks estimating chronological age, risk, mortality and pace of aging. Age acceleration, tissue specificity, cell composition and reversibility. Methylation arrays, bisulfite conversion and sequencing. Proteomic and metabolomic clocks. Integration of epigenomic, transcriptomic, proteomic and metabolomic data using statistical and machine-learning approaches. Validity, reproducibility, confounders and interpretative limitations.

5. Proteostasis and proteinopathies
The proteostasis network: protein synthesis, folding, conformational maintenance, refolding and degradation. Molecular chaperones, ribosome-associated quality control, the ubiquitin–proteasome system, ER-associated degradation and the unfolded protein response. Autophagy and the lysosomal system in protein and organelle quality control. Age-related decline of proteostasis, misfolding and aggregation. Oligomers, amyloid fibrils and amorphous aggregates; mechanisms of toxicity. Proteinopathies as models of age-related disease. Protein and proteomic biomarkers, analytical platforms and markers of target engagement and response.

6. Mitochondrial dysfunction, oxidative stress and nutrient sensing
Mitochondrial bioenergetics, biogenesis, dynamics and quality control; age-related mitochondrial DNA alterations. Communication among mitochondria, endoplasmic reticulum and calcium signalling. Reactive oxygen species as signals and mediators of damage; redox adaptation and hormesis. Oxidative modifications of DNA, proteins and lipids as biomarkers. Nutrient-sensing pathways: insulin/IGF-1, mTOR, AMPK and sirtuins. Metabolic reprogramming and the contribution of metabolomics to biological-age and risk assessment. Caloric restriction, exercise and metabolic modulators as models of biomarker-guided prevention and monitoring.

7. Cellular senescence, inflammaging and stem cell exhaustion
Replicative, stress-induced, oncogene-induced and mitochondrial dysfunction-associated senescence. DNA damage response, p53/p21 and p16/Rb pathways, stable cell-cycle arrest and resistance to apoptosis. Senescence markers: SA-β-galactosidase, lipofuscin, persistent DNA-damage foci and cell-cycle inhibitors. SASP, paracrine senescence and tissue remodelling. Heterogeneity of senescent cells and the need for multi-marker and tissue-specific assessment. Immunosenescence and inflammaging. Stem cell exhaustion, niche alterations and loss of regenerative capacity. Senolytics, senomorphics and regenerative strategies: targets, safety, biomarkers and response assessment.

8. Biological age, frailty and integrated biomarkers
Chronological, biological and functional age and pace of aging. Frailty phenotype, deficit accumulation and biological frailty. Construction and interpretation of laboratory-based frailty indices, including FI-LAB. Biochemical, hematological, inflammatory and metabolic markers associated with vulnerability and adverse outcomes. Genomic, epigenetic, proteomic and metabolomic signatures. Composite biomarkers, longitudinal trajectories and multi-omics integration for predictive risk stratification. Validation, reference populations, confounders, transportability and limitations of clinical implementation.

9. Neurodegeneration and molecular diagnostics
Neurodegenerative diseases as age-related proteinopathies with shared and disease-specific mechanisms. APP processing, amyloid-β and tau in Alzheimer’s disease. α-Synuclein, TDP-43, SOD1, FUS and other aggregating proteins in parkinsonian disorders and motor neuron diseases. Genetic susceptibility, proteostasis failure, mitochondrial dysfunction and neuroinflammation. Blood- and cerebrospinal-fluid biomarkers: amyloid-β ratios, phosphorylated tau, neurofilament light chain and GFAP. Use for preclinical detection, differential diagnosis, risk stratification and monitoring. Pre-analytical and analytical variables, standardisation, discordant results and ethical implications.

10. From molecular diagnosis to intervention and monitoring
Susceptibility/risk, diagnostic, prognostic, predictive, pharmacodynamic and monitoring biomarkers. Sample selection and pre-analytical variability. Main platforms: qPCR, digital PCR, sequencing, immunoassays, mass spectrometry and omics technologies. Analytical and clinical validation, cut-offs, reference intervals, sensitivity, specificity and clinical utility. Early diagnosis and biological windows of intervention. Biomarkers of target engagement, response, toxicity and disease modification. Composite scores, artificial intelligence and longitudinal models for personalised strategies. Ethical, regulatory and societal issues: communication of biological age and future risk, overdiagnosis, medicalisation of aging, equity and access.

Transversal learning activities
Case-based discussions, structured debates and Translational Controversy Journal Clubs will be integrated throughout all modules. Activities will connect the biological problem with the selection of the sample, method and biomarker, the assessment of evidence and the interpretation of results in the clinical context, considering confounders, feasibility, risks, limitations and ethical implications.

By the end of the course, students will be able to:
Knowledge and understanding
• describe the main molecular and biochemical mechanisms of aging and their interconnections within the Hallmarks of Aging framework;
• understand the role of genomic and telomeric instability, epigenetic alterations, loss of proteostasis, mitochondrial dysfunction, oxidative stress, cellular senescence, chronic inflammation and stem cell exhaustion;
• identify the main categories of biomarkers related to aging, biological age, frailty and neurodegenerative diseases;
• understand the general principles of the molecular, biochemical and omics technologies used for biomarker measurement;
• understand the principles of analytical and clinical validation and the main pre-analytical and biological factors that may influence results.
Applying knowledge and understanding
• link a specific molecular or biochemical process to the corresponding measurable alteration;
• identify the most appropriate biological sample, biomarker and analytical approach for a specific diagnostic or research question;
• interpret molecular and biochemical results in the context of early diagnosis, biological-age estimation, risk stratification and intervention monitoring;
• distinguish among susceptibility/risk, diagnostic, prognostic, predictive, pharmacodynamic and monitoring biomarkers;
• apply the acquired knowledge to the analysis of cases and problems of translational relevance.
Making judgements
• critically assess the appropriateness, validity and limitations of a biomarker or biomarker panel;
• recognise the possible effects of pre-analytical variables, confounders, cell composition, tissue specificity and characteristics of the study population;
• compare alternative diagnostic strategies on the basis of the quality of evidence, feasibility and clinical utility;
• critically discuss the limitations of risk and biological-age prediction and their ethical, regulatory and societal implications.
Communication skills
• use appropriate scientific terminology related to the mechanisms of aging and molecular diagnostics;
• clearly present and discuss the rationale for selecting a biomarker, biological sample and analytical method;
• communicate results and analytical limitations to specialist audiences, including during case-based discussions, structured debates and Translational Controversy Journal Clubs.
Learning skills
• read and understand scientific articles and reviews in English;
• independently update knowledge on biomarkers, omics technologies and translational applications in aging research;
• integrate information from different sources and biological levels to address new problems in molecular diagnostics and precision medicine.