Biology subjects

Duhamel, M.

Publications and source records attributed to Duhamel, M..

12 recordsLinked to original sources

bioRxiv2025

Distinct tumor immune microenvironmental (TIME) landscapes drive divergent immunotherapy responses in glioblastoma

BackgroundImmunotherapies have improved outcomes in many cancers but show limited efficacy in glioblastoma (GBM). This study aimed to determine whether immunotherapy could be tailored to GBM by functional subtyping of vascular-immune landscapes. MethodsWe employed single-cell RNA sequencing, multiplex immunohistochemistry to characterize three distinct TIME subtypes in human and murine GBMs. We evaluated responses to combination of anti-angiogenic immunomodulating therapies (CD40 Ag, anti-PDL1, PI3K{gamma}/{delta} inhibition) in orthotopic syngeneic GBM mouse models. ResultsWe identified three distinct functional TIME subtypes with unique vascular-immune landscapes in human and murine GBM: TIME-low (immune-low/deserted, leaky vasculature), TIME-med (intermediate immune-infiltration, angiogenic), and TIME-high (heavily infiltrated with immunosuppressive myeloid cells and dysfunctional T cells). Representative mouse models of TIME-GBMs responded in subtype specific ways to anti-angiogenic immunomodulating therapies. TIME-low GBMs enhanced T-cell activity but relapsed due to emerging myeloid immunosuppression, concomitant with mesenchymal transition. TIME-med displayed the most immune-activated, yet angiogenic phenotype, and showed overall good responses to various anti-angiogenic immunomodulating therapies. TIME-high GBMs were mostly non-responsive but improved when the myeloid-cell PI3K{gamma} was targeted. However, CD40 agonist treatment, expected to enhance APC function, unexpectedly worsened survival by promoting angiogenesis and heightening immunosuppression, leading to dysfunctional T cells and reduced NK cell recruitment, and subsequent enhanced tumor propagation. ConclusionsOur study reveals three GBM TIME subtypes with distinct vascular-immune landscapes that require tailored therapies. TIME-med tumors are predicted to respond best to immunotherapies, TIME-low tumors show transient effects with anti-angiogenic immunomodulating therapies, while TIME-high tumors, due to their profound immunosuppression, can even have worse outcomes. Key pointsO_LIThree TIME subtypes were identified in GBM with distinct vascular-immune landscapes C_LIO_LITIME subtypes show divergent immunotherapy responses C_LIO_LITIME classification supports personalized treatment strategy for GBM immunotherapy C_LI Importance of the StudyThis study advances glioblastoma immunotherapy by providing the first comprehensive single-cell characterization of TIME subtypes, moving beyond bulk RNA-sequencing to reveal detailed functional states of immune cells. We establish clinically relevant murine models that recapitulate human TIME subtypes, enabling preclinical testing of TIME-targeted therapies. Our findings identify TIME-low GBM as immune deserted and TIME-med tumors as the most immunotherapy-responsive subtype that should be prioritized for clinical selection. We found that high immune infiltration correlates with non-responsiveness and even unexpected detrimental effects with CD40 agonist treatment in TIME-high tumors--critical information given ongoing clinical trials. Identifying distinct immunosuppressive mechanisms across TIME subtypes and differential treatment responses provides a framework for personalized immunotherapy selection. The immediate translational impact of this work highlights the importance of TIME classification for treatment stratification and the urgent need to consider TIME status in clinical trial design, potentially explaining variable patient responses in previous GBM immunotherapy trials.

cancer biology↗

bioRxiv2024

An NAMPT Inhibitor Decreases NAMPT Capture by an Antibody Directed against the 5-Phosphoribosyl-1-Pyrophosphate-Binding Loop: A Rational for an NAMPT Occupancy Assay

Nicotinamide phosphoribosyltransferase (NAMPT) catalyzes the rate-limiting step of nicotinamide adenine dinucleotide (NAD) biosynthesis. NAMPT inhibitors (NAMPTi) have been shown to be NAMPT substrates. The resulting NAMPTi-phosphoribose (RP) adduct binds tightly to NAMPT and inhibits the enzyme. Using new NAMPTi, SAR154782, structural analyses performed in this study unveiled a close proximity of the SAR154782-RP complex to the 5-phosphoribosyl-1-pyrophosphate-binding (PRPP-binding) loop within the NAMPT catalytic site. The PRPP-binding loop of NAMPT is subject to conformational flexibility. Interestingly, the PRPP-binding loop domain is oriented to the outer side of the NAMPT dimer and can potentially serve as an antigen-binding site for antibodies. Here we report for the first time that the NAMPTi-RP adduct bound to NAMPT decreases NAMPT capture by an antibody directed against the c-terminal PRPP-binding loop in NAMPT. This finding was then used to explore cellular NAMPT occupancy. The NAMPTi-RP complex displays a sustained, cellular NAMPT occupancy that correlates with the inhibition of NAMPT activity. Moreover, a good correlation between NAMPT occupancy, NAD decrease, and NAMPTi efficacy was observed in-vivo in a NCI-H82 small cell lung cancer (SCLC) xenograft model. NAMPT-occupancy assay can be used in clinical settings to better define the optimal dose levels and dose regimen for effective NAMPT inhibition.

cancer biology↗

bioRxiv2024

Repeated loss of function at HD mating-type genes and of recombination suppression without mating-type locus linkage in anther-smut fungi

A wide diversity of mating systems occur in nature, with frequent evolutionary transitions in mating-compatibility mechanisms. Basidiomycete fungi typically have two mating-type loci controlling mating compatibility, HD and PR, usually residing on different chromosomes. In Microbotryum anther-smut fungi, there have been repeated events of linkage between the two mating-type loci through chromosome fusions, leading to large non-recombining regions. By generating high-quality genome assemblies, we found that two sister Microbotryum species parasitizing Dianthus plants, M. superbum and M. shykoffianum, as well as the distantly related M. scorzonarae, have their HD and PR mating-type loci on different chromosomes, but with the PR mating-type chromosome fused with part of the ancestral HD chromosome. Furthermore, progressive extensions of recombination suppression have generated evolutionary strata. In all three species, rearrangements suggest the existence of a transient stage of HD-PR linkage by whole chromosome fusion, and, unexpectedly, the HD genes lost their function. In M. superbum, multiple natural diploid strains were homozygous, and the disrupted HD2 gene was hardly expressed. Mating tests confirmed that a single genetic factor controlled mating compatibility (i.e. PR) and that haploid strains with identical HD alleles could mate and produce infectious hyphae. The HD genes have therefore lost their function in the control of mating compatibility in these Microbotryum species. While the loss of function of PR genes in mating compatibility has been reported in a few basidiomycete fungi, these are the first documented cases for the loss of mating-type determination by HD genes in heterothallic fungi. The control of mating compatibility by a single genetic factor is beneficial under selfing and can thus be achieved repeatedly, through evolutionary convergence in distant lineages, involving different genomic or similar pathways.

evolutionary biology↗

bioRxiv2023

Comparative genomics of smut fungi suggest the ability of meiosis and mating in asexual species of the genus Pseudozyma (Ustilaginales)

BackgroundThe Ustilaginales comprise hundreds of plant-parasitic fungi with a characteristic life cycle that directly links sexual reproduction and parasitism: One of the two mating-type loci codes for a transcription factor that not only facilitates mating, but also initiates the infection process. However, several species within the Ustilaginales have no described parasitic stage and were historically assigned to the genus Pseudozyma. Molecular studies have shown that the group is polyphyletic, with members being scattered in various lineages of the Ustilag-inales. Together with recent findings of conserved fungal effectors in these non-parasitic species, this raises the question if parasitism has been lost recently and in multiple independent events or if there are hitherto undescribed parasitic stages of these fungi. ResultsIn this study, we sequenced genomes of five Pseudozyma species together with parasitic species from the Ustilaginales to compare their genomic capability to perform two central functions in sexual reproduction: mating and meiosis. While the loss of sexual capability is assumed in certain lineages and asexual species are common in Asco- and Basidiomycota, we were able to successfully annotate functional mating and meiosis genes that are conserved throughout the whole group. ConclusionOur data suggest that at least the key functions of a sexual lifestyle are maintained in the analyzed genomes, challenging the current understanding of the so-called asexual species with respect to their evolution and ecological role.

genomics↗

bioRxiv2022

Establishment and characterization of a tumoroid biobank derived from dog patients' mammary tumors for translational research

Breast cancer is the most frequent cancer among women causing the greatest number of cancer-related deaths. Cancer heterogeneity is a main obstacle to therapies. Around 96% of the drugs fail from discovery to the clinical trial phase probably because of the current unreliable preclinical models. New models emerge such as companion dogs who develop spontaneous mammary tumors resembling human breast cancer in many clinical and molecular aspects. The present work aimed at developing a robust canine mammary tumor model in the form of tumoroids which recapitulate the tumor diversity and heterogeneity. We conducted a complete characterization of these canine mammary tumoroids through histologic, molecular and proteomic analysis, demonstrating their strong similarity to the primary tumor. We demonstrated that these tumoroids can be used as a drug screening model. In fact, we showed that Paclitaxel, a human chemotherapeutic, could killed canine tumoroids with the same efficacy as human tumoroids with 0.1 to 1 M of drug needed to kill 50% of the cells. Due to easy tissue availability, canine tumoroids can be produced at larger scale and cryopreserved to constitute a biobank. We have demonstrated that cryopreserved tumoroids keep the same histologic and molecular features (ER, PR and HER2 expression) as fresh tumoroids. Two techniques of cryopreservation were compared demonstrating that tumoroids made from frozen tumor material allowed to maintain a higher molecular diversity. These findings revealed that canine mammary tumoroids can be easily generated at large scale and can represent a more reliable preclinical model to investigate tumorigenesis mechanisms and develop new treatments for both veterinary and human medicine.

cancer biology↗

bioRxiv2022

Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi

BackgroundTransposable element (TE) activity is generally deleterious to the host fitness, such that TE copies are often purged by selection, which is facilitated when meiotic recombination reshuffles variation among loci. In the absence of recombination, the number of TE insertions usually increases, but the dynamics of such TE accumulations is unknown. ResultsIn this study, we investigated the temporal dynamics of TE accumulation in the non-recombining genomic regions of 15 Microbotryum species, leveraging on a unique dataset of 21 independent evolutionary strata of recombination cessation of different ages. We show that TEs rapidly accumulated in regions lacking recombination, but that the TE content reached a plateau at ca. 50% of occupied base pairs by 1.5 MY following recombination suppression. The same TE superfamilies have repeatedly expanded in independently evolved non-recombining regions, in particular rolling-circle replication elements (Helitrons), despite being scarce before recombination suppression. The most abundant elements, long-terminal repeat (LTR) retrotransposons of the Copia and Ty3 superfamilies, expanded through transposition bursts affecting both the non-recombining regions of mating-type chromosomes and autosomes, thus suggesting that non-recombining regions constitute a reservoir of TEs that transpose to recombining regions. Based on LTR sequence divergence within and among copies, we could distinguish bursts of transposition from gene conversion. ConclusionOur study supports the TE reservoir hypothesis, by showing that TE accumulation in non-recombining has a genome-wide impact. TEs accumulated through bursts, and following a non-linear, decelerating dynamics, thus improving our knowledge on genome evolution, particularly in association with sex or mating-type chromosomes.

evolutionary biology↗

bioRxiv2021

Anticancer immunotherapies transition postcapillary venules into high-endothelial venules that generate TCF1+ T lymphocyte niches through a feed-forward loop

The lack of T-cell infiltrates is a major obstacle to effective immunotherapy in cancer. Conversely, the formation of tumor-associated tertiary-lymphoid-like structures (TA-TLS), which are the local site of humoral and cellular immune responses against cancers, are associated with good prognosis and have recently been detected in Immune Checkpoint Blockade (ICB)-responding patients. However, how these lymphoid aggregates develop remains poorly understood. By employing scRNA sequencing, endothelial fate mapping, and functional multiplex immune profiling, we demonstrate that antiangiogenic immune-modulating therapies evoke the transition of postcapillary venules into inflamed high endothelial venules (HEVs), which generate permissive TA-TLS-like lymphocyte niches with PD1neg and PD1+TCF1+CD8 T cell progenitors that differentiate into GrzB+TCF1neg TIM3+ PD1+ CD8 T effector cells. Tumor-HEVs require continuous CD8 and NK cell-derived lymphotoxin signals revealing that tumor-HEV maintenance is actively sculpted by the adaptive immune system through a feed-forward loop. In BriefHua & Vella et al. reveal that effective antiangiogenic immunotherapy transitions postcapillary venules into inflamed high-endothelial venules (HEV), sustained by CD8 T and NK cell-derived signals through a feed-forward loop. Thereby, tumoral HEVs establish perivascular niches in which TCF1+ PD1+ lymphocytes expand and produce cytolytic PD1+ TIM3+ CD8 T cells that facilitate anti-tumoral immunity. HighlightsO_LIHigh endothelial venule induction by anticancer immunotherapies generates perivascular immune niches permissive for TCF1+ PD1+ CD8 progenitor T cell expansion and production of TCF1neg PD1+ TIM3+ CD8 effector T cells C_LIO_LITumoral high-endothelial venules exhibit characteristics of inflamed lymph node HEVs and postcapillary venules C_LIO_LIPostcapillary venules dynamically transdifferentiate into high-endothelial venules in tumors, which requires continuous signals from surrounding immune cells C_LIO_LICD8 and NK cells drive tumoral high-endothelial venule formation during antiangiogenic immunotherapies in a feed-forward loop via lymphotoxin beta receptor signaling C_LI

cancer biology↗

bioRxiv2021

Onset and stepwise extensions of recombination suppression are common in mating-type chromosomes of Microbotryum anther-smut fungi

Sex chromosomes and mating-type chromosomes can display large genomic regions without recombination. Recombination suppression often extended stepwise with time away from the sex- or mating-type-determining genes, generating evolutionary strata of differentiation between alternative sex or mating-type chromosomes. In anther-smut fungi of the Microbotryum genus, recombination suppression evolved repeatedly, linking the two mating-type loci and extended multiple times in regions distal to the mating-type genes. Here, we obtained high-quality genome assemblies of alternative mating types for four Microbotryum fungi. We found an additional event of independent chromosomal rearrangements bringing the two mating-type loci on the same chromosome followed by recombination suppression linking them. We also found, in a new clade analysed here, that recombination suppression between the two mating-type loci occurred in several steps, with first an ancestral recombination suppression between one of the mating-type locus and its centromere; later, completion of recombination suppression up to the second mating-type locus occurred independently in three species. The estimated dates of recombination suppression between the mating-type loci ranged from 0.15 to 3.58 million years ago. In total, this makes at least nine independent events of linkage between the mating-type loci across the Microbotryum genus. Several mating-type locus linkage events occurred through the same types of chromosomal rearrangements, where similar chromosome fissions at centromeres represent convergence in the genomic changes leading to the phenotypic convergence. These findings further highlight Microbotryum fungi as excellent models to study the evolution of recombination suppression.

evolutionary biology↗

bioRxiv2020

Overall patient's survival of glioblastoma associated to molecular markers: a pan-proteomic prospective study

Molecular heterogeneities are a key feature of glioblastoma (GBM) pathology impeding patients stratification and leading to high discrepancies between patients mean survivals. Here, we established a molecular classification of GBM tumors using a pan-proteomic analysis. Then, we identified, from our proteomic data, 2 clusters of biomarkers associated with good or bad patient survival from 46 IDH wild-type GBMs. Three molecular groups have been identified and associated with systemic biology analyses. Group A tumors exhibit neurogenesis characteristics and tumorigenesis. Group B shows a strong immune cell signature and express poor prognosis markers while group C tumors are characterized by an anti-viral signature and tumor growth proteins. 124 proteins were found statistically different based on patients survival times, of which 10 are issued from alternative AltORF or non-coding RNA. After statistical analysis, a panel of markers associated to higher survival (PPP1R12A, RPS14, HSPD1 and LASP1) and another panel associated to lower survival (ALCAM, ANXA11, MAOB, IP_652563 and IGHM) has been validated by immunofluorescence. Taken together, our data will guide GBM prognosis and help to improve the current GBM classification by stratifying the patients and may open new opportunities for therapeutic development. SignificanceGlioblastoma are very heterogeneous tumors with median survivals usually inferior to 20 months. We conducted a pan-proteomics analysis of glioblastoma (GBM) in order to stratify GBM based on the molecular contained. Forty-six GBM cases were classified into three groups where proteins are involved in specific pathways i.e. the first group has a neurogenesis signature and is associated with a better prognosis while the second group of patients has an immune profile with a bad prognosis. The third group is more associated to tumorigenesis. We correlated these results with the TCGA data. Finally, we have identified 28 new prognostic markers of GBM and from these 28, a panel of 4 higher and 5 lower survival markers were validated. With these 9 markers in hand, now pathologist can stratify GBM patients and can guide the therapeutic decision. HighlightsO_LIA novel stratification of glioblastoma based on mass spectrometry was established. C_LIO_LIThree groups with different molecular features and survival were identified. C_LIO_LIThis new classification could improve prognostication and may help therapeutic options. C_LIO_LI8 prognosis markers for oncologist therapeutic decision have been validated. C_LI

cancer biology↗

bioRxiv2020

Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms

The worldwide SARS-CoV-2 outbreak poses a serious challenge to human societies and economies. SARS-CoV-2 proteins orchestrate complex pathogenic mechanisms that underlie COVID-19 disease. Thus, understanding how viral polypeptides rewire host protein networks enables better-founded therapeutic research. In complement to existing proteomic studies, in this study we define the first proximal interaction network of SARS-CoV-2 proteins, at the whole proteome level in human cells. Applying a proximity-dependent biotinylation (BioID)-based approach greatly expanded the current knowledge by detecting interactions within poorly soluble compartments, transient, and/or of weak affinity in living cells. Our BioID study was complemented by a stringent filtering and uncovered 2,128 unique cellular targets (1,717 not previously associated with SARS-CoV-1 or 2 proteins) connected to the N- and C-ter BioID-tagged 28 SARS-CoV-2 proteins by a total of 5,415 (5,236 new) proximal interactions. In order to facilitate data exploitation, an innovative interactive 3D web interface was developed to allow customized analysis and exploration of the landscape of interactions (accessible at http://www.sars-cov-2-interactome.org/). Interestingly, 342 membrane proteins including interferon and interleukin pathways factors, were associated with specific viral proteins. We uncovered ORF7a and ORF7b protein proximal partners that could be related to anosmia and ageusia symptoms. Moreover, comparing proximal interactomes in basal and infection-mimicking conditions (poly(I:C) treatment) allowed us to detect novel links with major antiviral response pathway components, such as ORF9b with MAVS and ISG20; N with PKR and TARB2; NSP2 with RIG-I and STAT1; NSP16 with PARP9-DTX3L. Altogether, our study provides an unprecedented comprehensive resource for understanding how SARS-CoV-2 proteins orchestrate host proteome remodeling and innate immune response evasion, which can inform development of targeted therapeutic strategies.

systems biology↗

bioRxiv2018

Keystone mutualists can facilitate transition between alternative ecosystem states in the soil

Symbioses between plants and microbial organisms can fundamentally alter the structure of ecosystems, from their species diversity to rates of nutrient cycling. Yet, many aspects of how differences in the prevalence of microbial symbioses arise are unclear. This is a key knowledge gap, as if co-variation in plant and microbial distributions are primarily determined by extrinsic abiotic factors then symbioses should exert little independent control over ecosystems. To examine the potential for alternative symbiotic communities to arise under similar conditions we examined biogeochemical cycling and microbial community structure in a coastal landscape where historical patterns of vegetation transition are known, allowing us to eliminate abiotic determinism. We found that alternative states in microbial community structure and ecosystem processes emerged under different plant species. Greenhouse studies further demonstrated that plant selection of symbiotic microbes is central to emergence of these alternative states and occurs independent of soil abiotic conditions. Moreover, we provide evidence that transition between states may be highly dependent on the presence of a small set of ruderal symbionts that are rare in mature systems but may act as keystone mutualists. Because differences between these alternative states can be directly linked to plant-microbe symbioses, independent of initial conditions, our results suggesting that biotic feedbacks between keystone symbiotic microbes and plants play a foundational role in the diversity and function of soils.

ecology↗

bioRxiv2017

FIGL1 and its novel partner FLIP form a conserved complex that regulates homologous recombination.

Homologous recombination is central to repair DNA double-strand breaks (DSB), either accidently arising in mitotic cells or in a programed manner at meiosis. Crossovers resulting from the repair of meiotic breaks are essential for proper chromosome segregation and increase genetic diversity of the progeny. However, mechanisms regulating CO formation remain elusive. Here, we identified through protein-protein interaction and genetic screens FIDGETIN-LIKE-1 INTERACTING PROTEIN (FLIP) as a new partner of the previously characterized anti-crossover factor FIDGETIN-LIKE-1 (FIGL1) in Arabidopsis thaliana. We showed that FLIP limits meiotic crossover together with FIGL1. Further, FLIP and FIGL1 form a protein complex conserved from Arabidopsis to Human. FIGL1 interacts with the recombinases RAD51 and DMC1, the enzymes that catalyze the DNA stand exchange step of homologous recombination. Arabidopsis flip mutants recapitulates the figl1 phenotype, with enhanced meiotic recombination associated with change in DMC1 dynamics. Our data thus suggest that FLIP and FIGL1 form a conserved complex that regulates the crucial step of strand invasion in homologous recombination.

genetics↗