Biology subjects

Bieche, I.

Publications and source records attributed to Bieche, I..

10 recordsLinked to original sources

bioRxiv2025

Pathogenic Viruses, Genome Integrations, and Viral::Human Chimeric Transcripts Detected by VirusIntegrationFinder Across >30k Human Tumor and Normal Samples

Viruses are a leading cause of human morbidity and mortality. Certain viruses, including human papillomaviruses (HPVs), play a significant role in the etiology of cancer. Detection of viral DNA insertions in the human genome from next generation sequencing data defines viral associations with cancer and other diseases, identifies impacted organs and tissues, provides insights into disease mechanisms and has the potential to enhance clinical evaluations. In this study, we developed VirusIntegrationFinder (CTAT-VIF), a tool for surveying human genome insertions of various human viruses using both DNA and RNA sequencing data. We applied CTAT-VIF to analyze a dataset of over 30,000 tumor and normal samples, as well as more than 1,000 cancer cell lines. This effort resulted in the compilation of a catalog of over 30,0000 virus-human DNA or RNA junctions at more than 20,000 insertion loci and reassessed viral cancer-insertion hotspots across the human genome. Furthermore, we characterized the functional impacts of insertions with respect to human copy number alterations, effects on the expression of flanking human genes, and the identification of potentially oncogenic chimeric human and human/virus fusion transcripts at insertion loci. In addition to confirming known viral associations with specific tumor types, our study revealed both shared and virus-specific insertion hotspots in addition to variable functional impacts based on virus type. Besides some rare events of interest, we also found evidence for sequencing contamination, which underscores the need for vigilance when studying viral content or genome integrations.

cancer biology↗

bioRxiv2025

SPARC is a new driver of early breast tumor progression via TGF-β -dependent mechanism.

Ductal carcinoma in situ (DCIS) is a pre-invasive lesion that is thought to be a precursor of invasive ductal carcinoma (IDC). The challenge lies in discriminating between DCIS progressors and DCIS non-progressors, often resulting in over- or under-treatment in many cases. Membrane type 1 (MT1)-matrix metalloproteinase (MMP) has been previously identified as an essential gene involved in DCIS progression. Here, RNA-sequencing analysis of MT1-MMPhigh subpopulation derived from invasive breast tumors in the intraductal xenograft model was compared against a dataset of human high-grade DCIS, and Secreted Protein Acidic and Cysteine Rich (SPARC) has emerged as a master candidate involved in early breast tumor progression. We report that SPARC is up-regulated in DCIS as compared to normal breast epithelial tissues, and further increased in IDC relative to synchronous DCIS foci. We found a positive correlation between SPARC and MT1-MMP expression in DCIS lesions. At the mechanistic level, depletion of SPARC reduced MT1-MMP expression, the degradative capacity of the cells and the activation of the TGF-{beta} signalling canonical pathway. Pharmacological inhibition of the TGF-{beta} signalling pathway decreased SPARC and MT1-MMP at the mRNA and protein level, and concomitantly the cell degradative capacity and 3D cell migration. Strikingly, inhibition of the TGF-{beta} signalling pathway limits the invasive transition of breast tumors in a new triple-negative mouse intraductal syngeneic xenograft model. Moreover, high SPARC expression was positively correlated with both, TGF-{beta} and its receptor, TGFBRI, in a basal type of breast cancer collection supporting our findings. This study identifies SPARC as a new driver of early breast tumor progression via a TGF-{beta}-dependent mechanism, suggesting TGF-{beta} signaling pathway as a potential target for patients with high SPARC expression.

cancer biology↗

bioRxiv2024

Conserved RNA-binding protein interactions mediate syntologous lncRNA functions

Syntologous long noncoding RNAs (lncRNAs) are loci with conserved genomic positions that often show little or no sequence similarity. Despite diverging primary sequences, lncRNA syntologs from distant species can carry out similar functions. However, determinants underlying conserved functions of syntologous lncRNA transcripts with no sequence similarity remain unknown. Using CASC15 and melanoma formation as a paradigm for fast evolving lncRNAs and their functions, we found that human and zebrafish CASC15 syntologs with no detectable sequence similarity retained their function across 450 million years of evolution. Similar to the casc15-deficient zebrafish, CASC15-mutant human melanoma cells show increased cell migration. Expression of human CASC15 in zebrafish rescues loss of casc15 function by attenuating melanoma formation. This conserved function is supported by a set of RNA-binding proteins, interacting with both zebrafish and human CASC15 transcripts. Together, our findings demonstrate that conserved RNA-protein interactions can define functions of rapidly evolving lncRNA transcripts.

molecular biology↗

bioRxiv2023

MET functions in tumour progression and therapy resistance are repressed by intronic polyadenylation

Intronic polyadenylation (IPA) leads to the production of transcript isoforms with alternative last exons in thousands of mammalian genes. Widespread regulation of IPA isoforms was observed during oncogenic transformation and in tumours versus healthy tissues, and several IPA isoforms were involved in oncogenesis. However, little is known about the potential involvement of IPA in tumour progression, such as cancer cell invasiveness and metastasis, and in resistance to anticancer therapies. Here, we show that an IPA isoform of MET (short MET) whose production is inhibited by U1 snRNP (U1), an essential ribonucleoprotein complex that recognizes the 5 exon-intron junction of pre-mRNA, is associated with better prognosis in breast cancer. Induction of the short MET isoform, using a steric-blocking antisense oligonucleotide targeting the U1 binding site in the vicinity of the short MET alternative polyadenylation site, antagonizes cell invasiveness. U1 blockade with an antisense oligonucleotide targeting the U1 snRNA also decreases breast cancer cell invasiveness, in both human and mouse cancer cell models, and this effect involves IPA induction in MET and several genes belonging to the RAS/RAF/MAPK signalling pathway. Finally, short MET relieves melanoma cell resistance to MAPK cascade-targeted therapy in vitro and in vivo. IPA isoform levels of MET and a few other genes (mTOR, EGFR and CTNNA1) help predict such resistance in patients. Altogether, our findings provide evidence for a role of IPA in both cancer cell invasiveness and resistance to therapy. This suggests that IPA isoforms can be exploited as biomarkers and therapeutic targets to combat tumour progression.

molecular biology↗

bioRxiv2023

Inactivating Negative Regulators of Cortical Branched Actin Enhances Persistence of Single Cell Migration

The Rac1-WAVE-Arp2/3 pathway pushes the plasma membrane by polymerizing branched actin at the cell cortex and thereby powering membrane protrusions that mediate cell migration. Here, using knock-down (KD) or knock-out (KO), we combine the inactivation of the Arp2/3 inhibitory protein Arpin, the Arp2/3 subunit ARPC1A and the WAVE complex subunit, CYFIP2, that all enhance the polymerization of cortical branched actin (CBA). Inactivation of the 3 CBA negative regulators increases migration persistence of human breast MCF10A cells, and of endodermal cells in the zebrafish embryo, significantly more than any single or double inactivation. In the triple KO, but not triple KD cells, the "super-migrator" phenotype was associated with a heterogenous down-regulation of vimentin expression and a lack of coordination in collective behaviors, such as wound healing and acinus morphogenesis. Re-expression of vimentin in triple KO cells restored the normal persistence of single cell migration to a large extent, suggesting that vimentin down-regulation is one of the adjustments in gene expression through which the super-migrator phenotype is stably maintained in triple KO cells. Constant excessive production of branched actin at the cell cortex thus commits cells into a motile state through changes in gene expression.

cell biology↗

bioRxiv2022

Integrated molecular and pharmacological characterization of patient-derived xenografts from bladder and ureteral cancers identifies new potential therapies.

BackgroundMuscle-invasive bladder cancer (MIBC) and upper urinary tract urothelial carcinoma (UTUC) are molecularly heterogeneous. Despite chemotherapies, immunotherapies or anti-FGFR treatments, these tumors are still of poor outcome. Our objective was to develop a bank of patient-derived xenografts (PDXs) recapitulating molecular heterogeneity of MIBC and UTUC, to facilitate preclinical identification of therapies. MethodsFresh tumors were obtained from patients and subcutaneously engrafted into immune-compromised mice. Patient tumors and matched PDXs were compared regarding histopathology, transcriptomic (microarrays) and genomic profiles (targeted-NGS). Several PDXs were treated with chemotherapy (cisplatin/gemcitabine) or targeted therapies (FGFR and EGFR inhibitors). Results31 PDXs were established from 1 non-MIBC, 25 MIBC, 5 upper urinary tract tumors, including 28 urothelial (UCC) and 3 squamous-cell carcinomas (SCC). Integrated genomic and transcriptomic profiling identified PDXs of 3 different consensus molecular subtypes (Basal/Squamous, Luminal papillary and Luminal unstable), and included FGFR3-mutated PDXs. High histological and genomic concordance was found between matched patient tumor/PDX. Discordance in molecular subtypes, such as a basal/squamous patient tumor giving rise to a luminal papillary PDX, was observed (n=5) at molecular and histological levels. Ten models were treated with cisplatin-based chemotherapy and we did not observe association between subtypes and response. Of the 3 basal/squamous models treated with anti-EGFR therapy, two models were sensitive and one model, of sarcomatoid variant, was resistant. Treatment of 3 FGFR3-mutant PDXs with combined FGFR/EGFR inhibitors was more efficient than anti-FGFR3 treatment alone. ConclusionsWe developed preclinical PDX models that recapitulate the molecular heterogeneity of MIBCs and UTUC, including actionable mutations, which will represent an essential tool in therapy development. Pharmacological characterization of the PDXs suggested that upper urinary tract and MIBCs, UCC but also SCC, with similar molecular characteristics could benefit from the same treatments including anti-FGFR for FGFR3-mutated tumors and anti-EGFR for basal ones and showed a benefit for combined FGFR/EGFR inhibition in FGFR3-mutant PDXs, compared to FGFR inhibition alone.

cancer biology↗

bioRxiv2020

CYFIP2 containing WAVE complexes inhibit cell migration

Branched actin networks polymerized by the Arp2/3 complex are critical for cell migration. The WAVE complex is the machinery that activates Arp2/3 in a RAC1-dependent manner at the leading edge of migrating cells. Multiple WAVE complexes are assembled in a cell through various combinations of paralogous subunits. Here we report the surprising phenotype associated with loss-of-function of CYFIP2, a subunit of the WAVE complex. In three different human mammary cell lines and in prechordal plate cells of gastrulating zebrafish embryos, CYFIP2 depletion promoted, rather than impaired, membrane protrusions and migration persistence. CYFIP2, however, assembled WAVE complexes that polymerize branched actin at the cell cortex and rescued membrane protrusions of CYFIP1/2 double knock-out cells, although less efficiently than CYFIP1. Point mutations of CYFIP2 associated with intellectual disability in children were gain-of-function, as they made CYFIP2 as active as CYFIP1 in this rescue experiment. Biochemical reconstitutions of CYFIP2-containing WAVE complexes showed that they bound equally well to active RAC1 as CYFIP1-containing WAVE complexes, yet they were poorly activated in response to RAC1 binding. Together these results suggest that CYFIP2-containing WAVE complexes titrate active RAC1 and thereby prevent efficient CYFIP1-containing complexes from being activated. In this context, where cell migration is governed by the balance of CYFIP1/2 expression, releasing the restrained activity of CYFIP2-containing WAVE complexes leads to pathology.

cell biology↗

bioRxiv2020

Flotillin-upregulation acts as an epithelial-mesenchymal transition driver by promoting sphingosine kinase 2-dependent AXL stabilization

Altered endocytosis and vesicular trafficking are major players during tumorigenesis. Flotillin overexpression, a feature observed in many invasive tumors, and identified as a marker of poor prognosis, induces a deregulated endocytic and trafficking pathway called Upregulated Flotillin-Induced Trafficking (UFIT). Here, we found that, in non tumoral mammary epithelial cells, induction of the UFIT pathway promotes epithelial-to-mesenchymal transition (EMT) and accelerates the endocytosis of several transmembrane receptors, including AXL, in flotillin-positive late endosomes. AXL overexpression, frequently observed in cancer cells, is linked to EMT and metastasis formation. In flotillin-overexpressing non-tumoral mammary epithelial cells and in invasive breast carcinoma cells, we found that the UFIT-pathway-mediated AXL endocytosis allows its stabilization and depends on sphingosine-kinase 2, a lipid kinase recruited in flotillin-rich plasma membrane-domains and endosomes. Thus, the deregulation of vesicular trafficking following flotillin upregulation, and through sphingosine kinase 2, emerges as a new mechanism of AXL overexpression and EMT-inducing signaling pathway activation.

cell biology↗

bioRxiv2019

MMP2 As An Independent Prognostic Stratifier In Oral Cavity Cancers

BackgroundAround 25% of oral cavity squamous cell carcinoma (OCSCC) are not controlled by standard of care. Identifying those patients could offer them possibilities for intensified and personalized regimen. However, there is currently no validated biomarker for OCSCC patient selection in a pre-treatment setting.\n\nPatients and methodsOur objectives were to determine a robust and independent predictive biomarker for disease related death in OCSCC treated with standard of care. Tumor and juxtatumor secretome were analyzed in a prospective discovery cohort of 37 OCSCC treated by primary surgery. Independent biomarker validation was performed by RTqPCR in a retrospective cohort of 145 patients with similar clinical features. An 18-gene signature (18G) predictive of the response to PD-1 blockade was evaluated in the same cohort..\n\nResultsAmong 29 deregulated molecules in a secretome analysis, we identified soluble MMP2 as a prognostic biomarker. In our validation cohort (n=145), high levels of MMP2 and CD276, and low levels of CXCL10 and STAT1 mRNA were associated with poor prognosis in univariate analysis (Kaplan-Meier). MMP2 (p = 0.001) and extra-nodal extension (ENE) (p = 0.006) were independent biomarkers of disease-specific survival (DSS) in multivariate analysis, and defined prognostic groups with 5-year DSS ranging from 36% (MMP2highENE+) to 88% (MMP2lowENE-). The expression of 18G was similar in the different prognostic groups, suggesting comparable responsiveness to anti-PD-1.\n\nConclusionHigh levels of MMP2 was an independent and validated prognostic biomarker, which may be used to select poor prognosis patients for intensified neoadjuvant or adjuvant regimens.

cancer biology↗

bioRxiv2019

A single droplet digital PCR for ESR1 activating mutations detection in plasma

BackgroundActivating mutations in the estrogen receptor 1 (ESR1) gene are recurrent mechanisms of acquired resistance to aromatase inhibitors (AI), and may be the target of other selective estrogen receptor down-regulators. To assess the clinical utility of monitoring ESR1 resistant mutations, a droplet digital PCR (ddPCR)-based assay compatible with body fluids is ideal due to its cost-effectiveness and quick turnaround.\n\nMethodsWe designed a multiplex ddPCR, which combines a drop-off assay, targeting the clustered hotspot mutations found in exon 8, with another pair of probes interrogating the E380Q mutation in exon 5. We assessed its sensitivity in vitro using synthetic oligonucleotides, harboring E380Q, L536R, Y537C, Y537N, Y537S or D538G mutations. Validation of the assay was performed on plasma samples from a prospective study and compared to next generation sequencing (NGS) data.\n\nResultsThe multiplex ESR1-ddPCR showed a high sensitivity with a limit of detection ranging from 0.07 to 0.19% in mutant allele frequency depending on the mutation tested. The screening of plasma samples from patients with AI-resistant metastatic breast cancer identified ESR1 mutations in 29% of them with perfect concordance (and higher sensitivity) to NGS data obtained in parallel. Additionally, this test identifies patients harboring polyclonal alterations. Furthermore, the monitoring of ctDNA using this technique during treatment follow-up predicts the radiological response to palbociclib-fulvestrant.\n\nConclusionThe multiplex ESR1-ddPCR detects, in a single reaction, the most frequent ESR1 activating mutations and is compatible with plasma samples. This method is thus suitable for real-time ESR1 mutation monitoring in large cohorts of patients.\n\nStatement of translational relevanceExons 5 and 8 mutations in ESR1 are recurrent mechanisms of resistance to aromatase inhibitors (AI) in estrogen receptor (ER)-positive metastatic breast cancer and may be targeted by selective ER down-regulators. We implemented a novel droplet digital PCR, which allows for the detection of the most frequent ESR1 mutations in circulating cell-free DNA. In prospectively collected plasma samples, ESR1 mutations were found in 29% of AI-resistant patients, with excellent concordance and higher sensitivity to next generation sequencing. Moreover, circulating ESR1 mutations appear to be reliable markers for ctDNA monitoring in order to predict treatment response. Ultimately, the short turnaround time, high sensitivity and limited cost of the ESR1-ddPCR are compatible with repeated samplings to detect the onset of resistance to AI before the radiological progression. This opens a window of opportunity to develop new clinical strategies for breast cancer hormone therapy, as tested in an ongoing phase 3 trial.\n\nList of abbreviations\n\nHuman genesESR1: Estrogen Receptor 1\nHER2: Human Epidermal Growth Factor Receptor 2\nEGFR: Epithelial Growth Factor Receptor\nKRAS: KRAS proto-oncogene, GTPase\nBRAF: B-Raf Proto-Oncogene, Serine/Threonine kinase

cancer biology↗