Research
Biomarkers for Precision Oncology : A. Thierry

The cancerous tumor releases nucleic acids into the blood, providing a biological source whose analysis constitutes a breakthrough approach in oncology diagnosis. Our team is amongst those which has contributed most in the study of the origins, structures and functions of circulating DNA (cirDNA) in particular, as well as evaluating its various clinical potentials, such as therapeutic prediction, screening, and longitudinal disease management (detection of residual disease, monitoring of treatment efficacy and recurrence, highlighting resistance mechanisms) and screening. Our team's program combines fundamental, technological and translational research. This has also opened up new avenues of research, particularly concerning (1), the detection of specific circulating RNAs in cancer patients; (2), the development of new strategies of targeted drug therapies; (3), the relationship between tumor progression/cirDNA/innate immune response; and (4), the discovery of free circulating mitochondria.

Axis 1 : Study of the origins and structures of circulating DNA (E. Pisareva)

We discovered that (1) cirDNA are highly fragmented, which enables a higher level of detection; and (2), that tumor-derived cirDNA are characterized by a particularly high degree of fragmentation. We contributed to the elucidation of the cirDNA stuctures ) in the blood stream, using shallow WGS. This led to the pioneering emergence of a new field of research: Fragmentomics. We showed than the comparison of mitochondrial and nuclear cirDNA structures and topologies enables discrimination between healthy and cancer individuals. We use AI and machine learning assistance to further characterize cirDNA (nucleosome positioning and end-motif sequences, …) potentially enabling the genomic discrimination of various physiological states, including cancer. Lastly, we are currently characterizing the cell-free DNA released from tumoroids in order to evaluate the potential this model may have in optimizing treatment selection.

Axis 2: Study of mitochondrial cirDNA and evaluation of the diagnostic power of circulating cell-free mitochondria (B. Roch, E. Pisareva, C. Prevostel).

Through in vitro and in vivo work on the origin of cirDNA, we have demonstrated that circulating mitochondrial DNA corresponds almost entirely to circulating cell-free mitochondria (cir-exMito) in the blood. This discovery concerning a new blood constituent opens up new avenue of research in both cognitive and applied research. We are currently studying the possibility that cir-exMito function as elements of communication between cells. Within a diagnostic perspective, we are studying differences in mitochondrial production and metabolism, particularly in cancer patients. In applied research, we are collaborating on work concerning the transfer of ex-Mito, which offers potential applications in cardiology, aging, neurology, etc.

Axis 3 : Optimization of circulating DNA analysis (E. Crapez, B. Pastor)

Building on these pioneering discoveries concerning the structure and origins of cirDNA, the team developed and patented a specific and optimal q-PCR method by which qualitative (mutation test) and quantitative information can be obtained from cirDNA (IntPlex Technology). To optimize standardization of cirDNA analysis in a clinical study setting, we provided the first guidelines for its pre-analytical conditions. In this context, we continue to study the impact of epidemiological factors on cirDNA detection. We are currently studying the effects on cirDNA analysis of the non-conventional use of single strand DNA library preparation for sWGS, and working in particular on a better characterization of cirDNA structures and on the application of fragmentomics.

Axis 4 : Clinical evaluation of cirDNA analysis during the various phases of cancer patient care

 (M. Ychou, T. Mazard, B. Roch and E. Crapez),

Our team is working towards the development of predictive and prognostic biomarkers for personalized, ‘precision’ medicine in the field of oncology. Following our first clinical evaluations in predictive medicine, we are currently studying the potentials offered by cirDNA analysis across all phases of cancer patient care. Specifically, our areas of investigation include detection of minimal residual disease, early detection of resistance, monitoring treatment effectiveness, monitoring recurrence, and early cancer detection/screening. Thus, nine clinical trials are underway, following the three trials already completed, which address not only the potentials described above but also extend to multiple cancer types (colon, rectum, breast, lung, pancreas). For instance, we are finalizing the first prospective multicenter interventional study to employ cirDNA analysis to guide the first-line use of anti-EGFR. To date, our team has tested ~4,000 tested individuals and analysed more than 10,000 plasmas.

Axis 5 : Targeting the Wnt/β-catenin signaling pathway  and development of a nanovectorization strategy for anticancer drugs (C. Prevostel, L. Picque Lasorsa, T. Mazard)

We have long been committed to deciphering the molecular mechanisms regulating Wnt/β-catenin activity. This oncogenic signaling pathway plays a crucial role in the initiation, development and recurrence of various cancers. However, this pathway is also vital for the homeostasis and self-renewal of healthy tissues, which compromises the use of Wnt/β-catenin inhibitors in cancer therapy, given their significant toxic effects on healthy tissues [4]. To overcome these limitations, we are currently designing an innovative nanovectorization strategy to selectively target the delivery of Wnt/β-catenin inhibitors into cancer cells, alone or in combination. Our aim is to develop new, more effective and less toxic therapeutic options for cancer treatment.

Axis 6: Study of circulating mRNA in cancer patients (P. Blache, T.Mazard)

We have developed a straightforward method to quantify circulating mRNAs as biomarkers of colorectal cancer, we termed low-cost RNA-2C method (Plasma mRNA for Cancer Check-up) to identify patients with metastatic colorectal cancer. This approach relies on the quantification of three circulating plasma mRNAs: Beta2-Microglobulin (B2M), Tissue Inhibitor of Metalloproteinases-1 (TIMP-1), and Clusterin (CLU), achieving a sensitivity of 82% and a specificity of 93%. We are working on sequencing cir-RNA for better characterization. Currently, we are extending our analysis of these mRNAs to other stages of colorectal cancer, as well as to the treatment period. The goal of these studies is to establish multi-parametric blood tests for early diagnosis, prognosis, and recurrence monitoring.

Axis 7: Study of the impact of Neutrophil Extracellular Traps (NETs) on tumor progression and other inflammatory diseases

During our study on the origin of total cirDNA we observed that, in the presence of infection (such as COVID-19) or in the case of cancer, they can derive principally from neutrophil extracellular traps (NETs). We are currently working on the association of NETs production with tumor progression. Our hypothesize is that NETs support and/or assist tumor progression and the phenomenon of metastases. In addition, we have observed that NETs and the cirDNA from which they derive associate in the circulation with micro-clots which appear in high numbers in inflammatory diseases and cancer. These findings are particularly significant given the prevalence of thrombotic events in cancer patients.

Axis 8: Research on the development of an early detection test for cancers (E. Pisareva)

We are convinced that any viable blood test for the early detection or screening of cancer must involve circulating DNA analysis. To this end, we are working on fragmentomics with the assistance of artificial intelligence (machine learning), of which we are amongst the very first users. We are currently studying variables related to the position of nucleosomes, fragment size, and terminal sequences. We are also evaluating a pancancer test that could potentially differentiate cancer types in large cohorts of breast, lung, and colorectal cancer patients.