Biology subjects

Jacot, W.

Publications and source records attributed to Jacot, W..

5 recordsLinked to original sources

bioRxiv2025

Single- and double-strand circulating DNA fragmentomics for enhanced cancer detection performance

In early detection of cancer, the use of circulating cell-free DNA (cirDNA) obtained from blood samples is notable for its minimally invasive nature. We have developed an algorithm designed to discriminate cancer patients and healthy individuals based on cirDNA fragment end motif analysis assisted by machine learning, using data obtained from shallow whole genome sequencing (a method we call EMA). We applied EMA to cirDNA from the plasma of patients with stage II-III breast cancer, stage I-III non-small cell lung cancer, and metastatic colorectal cancer (mCRC). CirDNA from 158 individuals was prepared following the conventional double-stranded DNA library preparation (DSP). Using 3 bp end motifs, each tumor type was detected with a sensitivity of 0.87-1.00, a specificity of 0.95, and an AUC above 0.96. The three selected cancer types could be differentiated with an accuracy (ACC) above 0.94. Multi-cancer detection by pooling samples from the three cancer types showed ACC, AUC and sensitivity of 0.98, 0.99 and 0.98, respectively. Comparisons with 4 and 2 bp end motifs were conducted, and our main observations were confirmed using an external public dataset (N=366). We also performed a single-stranded DNA library preparation (SSP) using mCRC patients and healthy control cirDNA, which allowed us to make the first ever end motif analysis in the literature which compares the use of DSP and SSP. As compared to EMAD (use of DSP), EMAS (use of SSP) produced a very significant difference in end motif frequency and an improved cancer detection performance (ACC, AUC and sensitivity of 0.97, 1.00 and 0.99, respectively). Furthermore, optimal performance was produced when the full-size range was used for EMAS, whereas when the dataset was restricted to fragments of 115 - 220 bp for EMAD. EMAS strong performance, coupled with its compatibility with cost-effective shallow cirDNA sequencing, positions this methodology as a potentially transformative tool in early cancer screening.

genomics↗

bioRxiv2023

Replication poison treated BRCA1-deficient breast cancers are prone to MRE11 over-resection resulting in single strand DNA accumulation and mitotic catastrophe

BRCA1, BRCA2 and RAD51, key players of homologous recombination (HR) repair, are also involved in stalled DNA replication fork protection and repair. BRCA1-deficiency is encountered in 25% of Triple Negative Breast Cancer (TNBC). Here we investigated the sensitivity of BRCA1-deficient TNBC cell models to gemcitabine a frequently used replication poison that does not alter DNA structure. We show that BRCA1-deficient models, in contrast to their isogenic BRCA1-proficient counterparts, are superiorly sensitive to gemcitabine, accumulate massive levels of single strand DNA (ssDNA), in absence of RPA and RAD51 signals and elevated double strand break (DSB) numbers leading to cell death. Remarkably, ssDNA accumulation in gemcitabine-treated BRCA1-deficient cells was strongly diminished by the MRE11 inhibitor mirin, while it did not affect ssDNA levels resulting from PARP inhibitor olaparib treatment. The central role of MRE11 DNA resection strongly suggested that replication fork reversal may be important in response to replication poisoning by gemcitabine in BRCA1-deficient models. Furthermore, we demonstrate that gemcitabine-treated BRCA1-deficient cells showing massive ssDNA accumulation slipped into mitosis and produced mitotic bridges and micronuclei (MN) showing strong BrdU and {gamma}H2AX staining. Noticeably these BrdU-positive MN and DNA bridges triggered cGAS sensing. Our data, thus, strongly suggest that gemcitabine treatment could be beneficial in BRCA1-deficient TNBC both in terms of cancer cell death, but possibly as well in terms of antitumor immune response.

cancer biology↗

bioRxiv2021

SPARC in cancer-associated fibroblasts is an independent poor prognostic factor in non-metastatic triple-negative breast cancer and exhibits pro-tumor activity

PurposeTriple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype and lacks specific targeted therapeutics. The current mechanistic evidence from cell-based studies suggests that the matricellular protein SPARC has a tumor-promoting role in TNBC; however, data on the clinical relevance of SPARC expression/secretion by tumor and stromal cells in TNBC are limited. Experimental DesignThis study analyzed the prognostic value of tumor and stromal cell SPARC expression in a large series of 148 patients with non-metastatic TNBC and long follow-up (median: 5.4 years). Fibrosis, tumor-associated macrophage (TAM) infiltration, tumor-infiltrating lymphocyte (TIL) density, PD-L1 and PD-1 expression were assessed. Tumor and stromal cell SPARC expression was studied by immunofluorescence, western blotting, and meta-analysis of published single-cell mRNA sequencing data. The biological role of fibroblast-secreted SPARC was analyzed using cell adhesion, wound healing, Transwell-based motility and invasion, and tumor spheroid assays. ResultsSPARC expression was detected in cancer cells (42.4%), cancer-associated fibroblasts (CAFs) (88.1%), TAMs (77.1%), endothelial cells (75.2%), and TILs (9.8%). Recurrence-free survival was significantly lower in patients with SPARC-expressing CAFs. SPARC expression in CAFs was an independent prognostic factor in multivariate analysis. Tumor and stromal cell SPARC expression was observed in TNBC cytosols, patient-derived xenografts, and cell lines. SPARC was expressed by different CAF subsets, including myofibroblasts and inflammatory CAFs. Fibroblast-secreted SPARC inhibited TNBC cell adhesion and stimulated their migration and invasion. ConclusionsSPARC expression in CAFs is an independent predictor of recurrence-free survival in TNBC. Patients with SPARC-expressing CAFs could be eligible for anti-SPARC-targeted therapy. Statement of translational relevanceHere, we identified a subgroup of patients with triple-negative breast cancer (TNBC) with worse prognosis and eligible for therapies that target extracellular matrix proteins in the tumor stroma. Specifically, we found that expression of the matricellular protein SPARC in cancer-associated fibroblasts (CAFs) is an independent prognostic marker of poor outcome in TNBC. Furthermore, we showed that in TNBC, SPARC is expressed by different CAF subpopulations, including myofibroblasts and inflammatory fibroblasts that are involved/associated with many tumor-related processes. We then found that SPARC secreted by fibroblasts has a pro-tumor-promoting role by inhibiting TNBC cell adhesion and stimulating their motility and invasiveness. Overall, our results support the need to consider SPARC expressed/secreted by CAFs as a novel therapeutic target in TNBC in the context of treatments to modulate the tumor stroma.

cancer biology↗

bioRxiv2020

Cathepsin D exacerbates SPARC-driven aggressiveness by limited proteolysis in triple-negative breast cancer

Extracellular matrix (ECM) remodeling by proteases results in the release of protein fragments that promote tumor progression and metastasis. The protease cathepsin D (cath-D), a marker of poor prognosis in triple-negative breast cancer (TNBC), is aberrantly secreted in the tumor microenvironment. Using degradomic analyses by TAILS, we discovered that the matricellular protein SPARC is a substrate of extracellular cath-D. In vitro, cath-D induced limited proteolysis of SPARC C-terminal extracellular Ca2+ binding domain at acidic pH, leading to the production of SPARC fragments (34-, 27-, 16-, 9-, and 6-kDa). Similarly, cath-D secreted by TNBC cells cleaved fibroblast- and cancer cell-derived SPARC at the tumor pericellular acidic pH. SPARC cleavage also occurred in TNBC tumors. Among these fragments, only the 9-kDa SPARC fragment inhibited TNBC cell adhesion and spreading on fibronectin, and stimulated their migration, endothelial transmigration, and invasion. Our study establishes a novel crosstalk between proteases and matricellular proteins in the tumor microenvironment through limited proteolysis of SPARC, revealing a novel targetable 9-kDa bioactive SPARC fragment for new TNBC treatments.

cancer biology↗

bioRxiv2018

Distinct oncogenes drive distinct genome and epigenome alterations in human mammary epithelial cells

Gene expression differences, combined with distinct patterns of genomic rearrangements and epigenetic modifications, have laid the bases of molecular classification of breast cancer. Different molecular subtypes are thought to originate from different cell lineages in the mammary gland, but the early activation of an oncogene could also play a role. It is, however, difficult to discriminate the respective inputs of oncogene activation or cell type of origin in the natural history of the tumor. In this work, we have designed an experimental strategy aiming at determining whether activation of distinct oncogenic pathways in human mammary epithelial cells (HMEC) could lead to different patterns of genetic and epigenetic changes. We show that initial activation of CCNE1, WNT1 and RASv12, which activate distinct oncogenic pathways, in shp53 immortalized HMECs results in different and reproducible profiles of mRNA and miRNA expression, copy number alterations (CNA) and DNA methylation modifications. Noticeably, HMECs transformed by RAS bore very specific profiles of CNAs and DNA methylation, clearly distinct from those shown by CCNE1 and WNT1 transformed HMECs.\n\nGenes impacted by CNAs and CpG methylation in the RAS and the CCNE1/WNT1 clusters showed clear differences, illustrating the activation of distinct pathways. Our data show that early activation of distinct oncogenic pathways leads to active adaptive events resulting in specific sets of CNAs and DNA methylation changes. We, thus, propose that activation of different oncogenes could have a role in reshaping the genetic landscape of breast cancer subtypes.\n\nAuthor summaryGenetic and epigenetic changes are at the center of cancer development. Breast cancer molecular subtypes are defined on differences in genetic and epigenetic profiles and it is generally assumed these subtypes originate from different cell lineages in the mammary gland. We propose that founding oncogenic mutations could also have an impact. To address this question, we designed an experimental model, based on the ectopic expression of different oncogenes in human mammary epithelial cells (HMEC), and monitored genetic and DNA methylation changes occurring at different stages of cell transformation. We show that transformation of HMEC by distinct oncogenes resulted in clearly different and reproducible patterns of genetic and DNA methylation changes. Genes whose expression was modified by either CNAs or CpG methylation were consistent with the dominant pathways activated and reflected the phenotypes in the respective models. We propose that DNA methylation and CNA changes correspond to adaptive responses to the activation of the oncogenic pathways. Our data strongly suggest that early activation of distinct oncogenic insults will not only impinge on the phenotypic characteristics of the resulting tumors, but also have a strong impact on their genomic and epigenetic landscapes.

cancer biology↗