# Molecular Pathology in Modern Medicine: A Review of Genomic, Proteomic, and Epigenetic Insights Into Disease Mechanisms

## TL;DR

This paper reviews how molecular pathology uses genomic, proteomic, and epigenetic data to better understand disease mechanisms and improve diagnostics and treatment in modern medicine.

## Contribution

The paper provides a comprehensive review of integrative molecular pathology platforms and computational strategies for disease mechanism elucidation and clinical translation.

## Key findings

- Molecular pathology platforms like whole-genome sequencing and proteomics help uncover disease mechanisms.
- Computational strategies such as multimodal data harmonisation and AI improve patient endotyping and therapy selection.
- Challenges include data harmonisation, model interpretability, and the need for prospective clinical validation.

## Abstract

Molecular pathology has become a central discipline in modern medicine by enabling the systematic interrogation of genomic, proteomic, and epigenetic alterations that underlie human disease mechanisms. This review synthesises how genomic variants, proteomic dysregulation, and epigenetic alterations interact to drive disease initiation, progression, and phenotypic heterogeneity. Key molecular pathology platforms, including whole-genome sequencing, mass spectrometry-based proteomics, and epigenetic profiling, are examined as tools for elucidating disease mechanisms in modern medicine. Computational strategies, including multimodal data harmonisation, causal and network models, and interpretable artificial intelligence (AI), enable mechanism-anchored patient endotyping and therapy selection; clinical decision support and pharmacogenomics (PGx) translate molecular evidence into action. Considerations influencing the implementation of integrative molecular pathology include pre-analytical handling, platform-specific characteristics, data harmonisation, economic feasibility, model interpretability, reproducibility, and the extent of prospective clinical validation and reimbursement pathways. Recommended priorities include standards for pipeline validation, longitudinal and minimally invasive monitoring, deployable multimodal AI with uncertainty estimates, and equitable data governance. Molecular pathology reframes diagnostics in modern medicine by shifting from isolated markers toward a mechanistic understanding of disease biology across oncology and complex disorders.