Liquid Biopsy and Cancer Interception

In the era of Precision Medicine, liquid biopsy has emerged as a pivotal clinical tool due to its non-invasive nature, allowing real-time monitoring of the tumoral process in each patient. The methodology’s non-invasiveness is crucial not only for identifying early resistance to treatment or predicting relapse but also for identifying cancer risk through molecular analyses in populations predisposed to certain cancers (such as colorectal cancer in individuals with polyposis, hepatocellular carcinoma in those with cirrhosis, lung cancer in COPD patients with lung nodules, or ovarian cancer in individuals with ovarian polyps, among others). 79 STRATEGIC PLAN 2024-2027 Beyond its clinical applications, liquid biopsy enables deeper insights into cancer biology. Analysis of liquid biopsy components provides valuable biological information about the initiation of carcinogenesis and the progression of cancer through various stages of tumoral dissemination. This knowledge enhances our understanding of the underlying mechanisms driving cancer development and progression, facilitating the development of more effective diagnostic and therapeutic strategies tailored to individual patients.

To achieve this goal, the following sub-lines are our focus of interest:

Molecular analyses of circulating tumor DNA (ctDNA) and cell-free DNA (cfDNA) in the early stages of cancer and chronic inflammatory diseases signify a groundbreaking approach in precision medicine. By employing fragmentomic and epigenomic methodologies, we delve into the intricate molecular signatures present in these circulating nucleic acids, providing valuable insights into disease onset, progression, and treatment response.

In cancer, the presence of ctDNA and cfDNA in circulation offers a glimpse into the genomic landscape of tumors. However, the reliance on mutation-based detection assays for ctDNA raises concerns, particularly regarding their utility in identifying mutations, copy number alterations, and chromosomal rearrangements associated with early-stage malignancies. Fragmentomic techniques, encompassing not just fragment size but also other properties of cfDNA, enable the characterization of DNA fragments shed by tumors, aiding in the identification of specific genetic aberrations linked to early-stage cancers.

This molecular information holds immense potential for facilitating the early detection of cancer, allowing for timely intervention and improved treatment outcomes. Additionally, epigenomic analyses of ctDNA and cfDNA unveil dynamic changes in DNA methylation patterns, histone modifications, and chromatin structure, which play crucial roles in regulating gene expression. These epigenetic alterations serve as sensitive biomarkers for cancer and chronic inflammatory diseases, reflecting underlying pathogenic processes and disease progression.

By integrating epigenomic approaches with fragmentomic analyses, we enhance the sensitivity and specificity of liquid biopsy-based diagnostics, enabling clinicians to distinguish between malignant and benign conditions with greater accuracy. Furthermore, the fragmentation pattern of cfDNA mirrors epigenetic regulation, with breakpoint coordinates clustering at specific locations in the genome. These clusters, termed preferred end coordinates, provide insights into chromatin accessibility and tissue-specific nucleosome positioning, transcription factor binding sites, and gene expression.

Overall, molecular analyses of ctDNA and cfDNA in the early stages of cancer and chronic inflammatory diseases represent a paradigm shift in disease diagnosis and 80 STRATEGIC PLAN 2024-2027 management, offering promising avenues for personalized medicine and improved patient outcomes.

The interaction between the immune system and tumor cells is a complex and dynamic process that plays a critical role in cancer development, progression, and response to therapy. The immune system serves as a crucial defense mechanism against cancer by recognizing and eliminating abnormal cells. However, tumor cells have evolved various strategies to evade immune surveillance and manipulate the immune microenvironment to their advantage. Our research is focused on understanding the survival mechanisms of circulating tumor cells (CTCs) in the bloodstream, where they face attacks from the immune system. Despite this hostile environment, CTCs engage in active interactions with various immune cell types , including platelets, myeloid cells, macrophages, and neutrophils. These interactions contribute to CTC survival and acquisition of a metastatic phenotype, promoting metastasis formation. The acquisition of these characteristics involves the exchange of biomolecules from immune cells to circulating tumor cells (CTCs).

The term «extracellular vesicles» (EVs) refers to a diverse group of membranous structures released by cells into their extracellular environment. These vesicles play crucial roles in intercellular communication by transferring bioactive molecules, including proteins, lipids, and nucleic acids, between cells.

One key role of EVs in cancer is their ability to facilitate tumor cell communication with the surrounding microenvironment. Cancer cells release EVs containing signaling molecules that can influence neighbouring cells, such as stromal cells, endothelial cells, and immune cells, promoting tumor growth, angiogenesis, and immune evasion. Additionally, EVs derived from tumor-associated stromal cells can contribute to the establishment of a tumor-supportive microenvironment by modulating the behavior of cancer cells and other stromal components.

Moreover, EVs play a crucial role in mediating communication between primary tumor cells and distant metastatic sites. Tumor-derived EVs can travel through the bloodstream or lymphatic system, carrying bioactive molecules that prepare premetastatic niches and facilitate the seeding and colonization of metastatic cells at distant sites. These EV-mediated interactions contribute to the formation of secondary tumors and the spread of cancer throughout the body.

In our lab, we aim to identify the diverse cargo carried by these EVs, with a particular focus on their proteomic and miRNA components, and their relationship with the induction of metastasis and resistance to treatment.

The social impact of this line of research is profound and multifaceted. Firstly, in the era of Precision Medicine, advancements in liquid biopsy techniques offer noninvasive methods for early cancer detection and monitoring, providing individuals with more accessible and timely diagnosis. This can lead to improved treatment outcomes and increased survival rates. Moreover, the ability to identify cancer risk through molecular analyses in predisposed populations holds the potential to revolutionize preventive healthcare strategies, empowering individuals to take proactive steps in managing their health. Recently, our hospitals implemented ctDNA analyses according to our protocol in clinical practice for metastatic lung cancer. In this way, we are developing the first Clinical trial of Liquid Biopsy using NovaSeq in Andalucia; this project involves all provinces of this region. Additionally, regarding our analyses based on CTCs, we have developed three different patents in the GENyO center. Similarly, and more recently, we have developed a patent for the therapeutic use of EVs.

Our group is continuously pursuing new projects both on a national and international scale. Establishing international networks is essential for us, and we have strong collaborations with France, Italy, and the USA. Our objectives include not only translational research but also clinical trials, given our strong collaboration with hospitals and clinicians. Additionally, our lab is a reference for liquid biopsy, and we host students from different countries, enhancing our international visibility.