Biology subjects

Pages, G.

Publications and source records attributed to Pages, G..

8 recordsLinked to original sources

bioRxiv2025

Improving angiogenesis ameliorates the efficacy of ASO-based exon-skipping for the treatment of Duchenne muscular dystrophy

Duchenne muscular dystrophy (DMD) is a severe X-linked disease caused by mutations in the DMD gene, resulting in the absence of functional dystrophin. Antisense oligonucleotide (ASO)-based therapies aim to restore the open reading frame and produce a truncated but functional dystrophin protein. Although several ASOs are FDA-approved, dystrophin restoration in patient biopsies remains low, underlining the need to improve ASO efficacy. One major limitation is poor ASO biodistribution to skeletal muscle, influenced by both ASO chemistry and pathological features of dystrophic tissue. In DMD patients and mdx mice, microvascular abnormalities and impaired angiogenesis likely restrict ASO delivery. Here, we hypothesized that enhancing muscle vascularization could improve ASO biodistribution and therapeutic outcomes. Mdx mice were treated with a pro-angiogenic treatment prior to ASO administration targeting exon 23 of dystrophin pre-mRNA. Angiogenic stimulation increased capillary density and improved ASO delivery, exon skipping, and dystrophin expression compared to ASO alone. These molecular improvements were associated with increased myofiber size, larger mean cross-sectional area, and decreased serum myomesin levels, without signs of toxicity. This study provides proof-of-concept that promoting angiogenesis can enhance the efficacy of ASO-based treatments, offering a complementary strategy to improve therapeutic outcomes in DMD.

molecular biology↗

bioRxiv2024

Comparative effects of proton and photon irradiation on the molecular and cellular profiles of triple-negative breast cancer: the crucial impact of VEGFC on tumor microenvironment remodeling

Metastatic triple-negative breast cancers (TNBC) are among the most aggressive types of breast cancer and are often treated with adjuvant radiotherapy and chemotherapy. Despite initial efficacy, relapses are common, leading to poor prognosis. Understanding the response of tumor microenvironment to radiotherapy is crucial, particularly comparing photon (X) and proton (P) radiotherapy due to proton radiations reduced side effects. MethodsWe investigated the effects of single and multiple X and P irradiations on various cell types within the tumor microenvironment, including vascular and lymphatic endothelial cells, fibroblasts, and TNBC tumor cells. VEGFC, a key factor in lymphatic vessel formation and metastasis, was a primary focus. We used protein arrays to evaluate the effects of irradiation and examined the impact of VEGFC inactivation on the sensitivity to X and P radiation. Additionally, we tested tumor-forming capabilities of irradiated cells and assessed the impact of genetic or therapeutic VEGFC inhibition on TNBC growth. Transcriptomic and proteomic analyses further characterized the differences between X and P tumors, providing deeper insights into their distinct molecular profiles. ResultsBoth X and P irradiations caused a transient increase in VEGFC levels, along with other pro-angiogenic, pro-lymphangiogenic, and pro-fibrotic factors, such as angiopoietin 2, artemin, endostatin, IGFBP2, serpinE1, PDGFA, and DPPIV. Endothelial cells exposed to multiple rounds of radiation showed enhanced proliferation but lost the ability to form pseudo vessels, indicating an endothelial-mesenchymal transition. Tumor cells lacking VEGFC were more sensitive to radiation, and anti-VEGFC antibodies significantly suppressed TNBC cells proliferation, both naive and multi-irradiated. Tumor xenografts formed by multi-irradiated cells grew larger in nude mice, particularly following proton irradiation, while X-irradiated tumors exhibited a more pro-lymphangiogenic phenotype compared to P-irradiated tumors. ConclusionsOur findings show that while P multi-irradiated TNBC cells form larger tumors, X multi-irradiated tumors are more aggressive, with elevated expression of genes linked to angiogenesis, lymphangiogenesis, and endothelial-mesenchymal transition. Targeting VEGFC during photon or proton radiotherapy could reduce metastasis and improve TNBC prognosis.

cancer biology↗

bioRxiv2024

Disrupting USP39 deubiquitinase Function Impairs the Survival and Migration of Multiple Myeloma Cells through ZEB1 Degradation

RationaleMultiple Myeloma (MM) stands as the second most common hematological malignancy characterized by the accumulation of monoclonal plasmocytes within the bone marrow. Despite the introduction of proteasome inhibitors, immunomodulatory agents and CD38-targeting antibodies which have extended survival rates, the disease remains incurable for most patients due to the emergence of resistant clones and frequent relapses. The efficacy of the proteasome inhibitor bortezomib (BTZ) in MM treatment underscores the critical role of the ubiquitin proteasome system (UPS) in this cancer. Deubiquitinases (DUBs), a class of enzymes governing the stability, interactions or localization of cellular proteins by removing ubiquitin modifications, have emerged as promising therapeutic targets across various cancers, including MM. MethodsThrough an exhaustive loss-of-function approach, we have identified for the first time USP39 DUB as a pivotal survival determinant for MM cells. ResultsOur analysis reveals a direct correlation between heightened USP39 mRNA levels and shorter survival in MM patients. Additionally, robust USP39 protein expression is observed in MM patient plasmocytes compared to healthy counterparts. Knockdown of Usp39 not only impedes clonogenic capabilities, but also induces apoptosis, triggers cell cycle arrest and overcomes BTZ resistance. Complementary gain-of-function assays, further elucidate how USP39, by stabilizing the transcription factor ZEB1, enhances the trans-migratory potential of MM cells. ConclusionsIn summary, our findings underscores the pivotal role of the deubiquitinase USP39, suggesting that targeting the USP39/ZEB1 axis hold promise as a prospective diagnostic marker and therapeutic target in MM.

cancer biology↗

bioRxiv2024

Exploiting De Novo Serine Synthesis as a Metabolic Vulnerability to Overcome Sunitinib Resistance in Advanced Renal Cell Carcinoma

Sunitinib, an oral tyrosine kinase inhibitor used in advanced renal cell carcinoma (RCC), exhibits significant efficacy but faces resistance in 30% of patients. Yet, the molecular mechanisms underlying this therapy resistance remain elusive. Here, we show that sunitinib induces a metabolic shift leading to increased serine synthesis in RCC cells. The activation of the GCN2-ATF4 stress response pathway is identified as the mechanistic link between sunitinib treatment and elevated serine production. Inhibiting key enzymes in the serine synthesis pathway, such as PHGDH and PSAT1, enhances the sensitivity of resistant cells to sunitinib. The study underscores the role of serine biosynthesis in nucleotide synthesis, influencing cell proliferation, migration, and invasion. Beyond RCC, similar activation of serine synthesis occurs in other cancer types, suggesting a shared adaptive response to sunitinib therapy. This research identifies serine synthesis as a potential target to overcome sunitinib resistance, offering insights into therapeutic strategies applicable across diverse cancer contexts. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/586287v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@47d331org.highwire.dtl.DTLVardef@17a4892org.highwire.dtl.DTLVardef@1329e51org.highwire.dtl.DTLVardef@37de9b_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LISunitinib induces an increase in endogenous serine production in metastatic ccRCC. C_LIO_LIThe heightened serine biosynthesis promoted by sunitinib facilitates nucleotide synthesis, thereby sustaining tumor cell proliferation. C_LIO_LISunitinib-induced enhancement of serine biosynthesis enables cell migration and invasion. C_LIO_LIThe stimulation in serine synthesis is also observed in other cancer models treated with sunitinib. C_LI

cancer biology↗

bioRxiv2020

The antiangiogenic compound axitinib demonstrates low toxicity and anti-tumoral effects against medulloblastoma

Evolution of medulloblastoma (MB) treatments has increased the 5-year overall survival of to more than 70%. However, an increasing number of survivors face severe long-term adverse effects and associated morbidity due to multimodal treatments particularly harsh for the younger patients. Chemotherapeutic compounds inducing less adverse effects are key to improving the care of MB patients. The preclinical relevance of last generation anti-angiogenic compounds deserves to be fully assessed. Among these, axitinib showed the highest selectivity index for MB cells, efficiently reduced the growth rate of experimental tumors and led to less toxicity towards normal cells than did a reference treatment. In vivo, axitinib did not lead to acute toxicity in very young rats and was able to cross the blood brain barrier. Analysis of public databases shows that high expression of axitinib targets are of poor prognosis. Altogether, our results suggest that axitinib is a compelling candidate for MB treatment.

cancer biology↗

bioRxiv2020

A multi-layered systems approach for renal cell carcinoma

Renal cell carcinoma (RCC) still lacks prognostic and predictive biomarkers to monitor the disease and the response to therapy. The usual strategy in translational research is to start from human samples, to identify molecular markers and gene networks and then to functionally validate them in vitro and in animal models. We devised herein a completely opposite strategy from "mouse to man" by performing an aggressiveness screen and used functional genomics, imaging, clinical data and computational approaches in order to discover molecular pathways and players in renal cancer development and metastasis. Multiple cell lines for primary tumor growth, survival in the blood circulation and lung metastasis or metastatic spread from the primary tumor were generated and analyzed using a multi-layered approach which includes large-scale transcriptome, genome and methylome analyses. Transcriptome and methylome analyses demonstrated distinct clustering in three different groups. Remarkably, DNA sequencing did not show significant genomic variations in the different groups which indicates absence of clonal selection during the in vivo amplification process. Transcriptome analysis revealed distinct signatures of tumor aggressiveness which were validated in patient cohorts. Methylome analysis of full-length DNA allowed clustering of the same groups and revealed clinically relevant signatures. Furthermore, we identified SAA2 and CFB as soluble prognostic and predictive biomarkers of the therapeutic response. We also uncovered IL34 as another soluble prognostic biomarker and key regulator of renal cell carcinoma (RCC) progression. This was also functionally validated in vivo, and a mathematical model of IL34-dependent primary tumor growth and metastasis development was provided. These results indicate that such multilayered analysis in a RCC animal model leads to meaningful results that are of translational significance. One Sentence SummaryAn aggressiveness screen with multilayer systems analysis to identify signatures and biomarkers for renal cell carcinoma aggressiveness.

cancer biology↗

bioRxiv2018

Protein model quality assessment using 3D oriented convolutional neural networks

Protein model quality assessment (QA) is a crucial and yet open problem in structural bioinformatics. The current best methods for single-model QA typically combine results from different approaches, each based on different input features constructed by experts in the field. Then, the prediction model is trained using a machine-learning algorithm. Recently, with the development of convolutional neural networks (CNN), the training paradigm has changed. In computer vision, the expert-developed features have been significantly overpassed by automatically trained convolutional filters. This motivated us to apply a three-dimensional (3D) CNN to the problem of protein model QA.\n\nWe developed a novel method for single-model QA called Ornate. Ornate (Oriented Routed Neural network with Automatic Typing) is a residue-wise scoring function that takes as input 3D density maps. It predicts the local (residue-wise) and the global model quality through a deep 3D CNN. Specifically, Ornate aligns the input density map, corresponding to each residue and its neighborhood, with the backbone topology of this residue. This circumvents the problem of ambiguous orientations of the initial models. Also, Ornate includes automatic identification of atom types and dynamic routing of the data in the network. Established benchmarks (CASP 11 and CASP 12) demonstrate the state-of-the-art performance of our approach among singlemodel QA methods.\n\nThe method is available at https://team.inria.fr/nanod/software/Ornate/. It consists of a C++ executable that transforms molecular structures into volumetric density maps, and a Python code based on the TensorFlow framework for applying the Ornate model to these maps.

bioinformatics↗

bioRxiv2018

Pharmacological inhibition of the amino-acid transporter LAT1 demonstrates in vitro anti-neoplastic activity towards medulloblastoma

Most cases of medulloblastoma (MB) occur in young children. While the overall survival rate can be relatively high, current treatments combining surgery, chemo- and radiotherapy are very destructive for patient development and quality of life. Moreover, aggressive forms and recurrences of MB cannot be controlled by classical therapies. Therefore, new therapeutic approaches yielding good efficacy and low toxicity for healthy tissues are required to improve patient outcome. Cancer cells sustain their proliferation by optimizing their nutrient uptake capacities. The L-type amino acid transporter 1 (LAT1) is an essential amino acid carrier overexpressed in aggressive human cancers that was described as a potential therapeutic target. In this study, we investigated the therapeutic potential of JPH203, a LAT1-specific pharmacological inhibitor, on two independent MB cell lines belonging to subgroups 3 (HD-MB03) and Shh (DAOY). We show that while displaying low toxicity towards normal cerebral cells, JPH203 disrupts AA homeostasis, mTORC1 activity, proliferation and survival in MB cells. Moreover, we demonstrate that a long-term treatment with JPH203 does not lead to resistance in MB cells. Therefore, the present study suggests that targeting LAT1 with JPH203 is a promising therapeutic approach for MB treatment.

cancer biology↗