Best poster prize winners of the EMBO | EMBL Symposium ‘Mechanisms of drug resistance and tolerance in bacteria, fungi, and cancer’
Recently the first EMBO | EMBL Symposium of the year ended. It was also the first meeting we held at EMBL on the topic of drug resistance and tolerance. It is a hot topic that attracted 124 participants on site and 61 participants who joined us virtually.
A highly international group of researchers came together and spent four days discussing the latest work on biological mechanisms that mediate drug resistance and tolerance across species barriers.
The meeting also saw 17 flash talks and 70 poster abstract submissions! These posters were presented and discussed in two poster sessions, and the best posters were voted on by the participants.
We are pleased to announce the five winners of the poster sessions. Please give a round of applause to these brilliant minds!
The e3 ubiquitin ligase mycbp2-spryd3 regulates mitotic cell fate decision
Presenter: Alexandra Rita Turi da Fonte Dias
Collaborators: Ingrid Hoffmann
Abstract:
Ubiquitylation, a reversible post-translational modification, is orchestrated through the interplay of three enzymes referred to as E1, E2 and E3, which activate, relay and ligate ubiquitin onto a final target protein, respectively. E3 ubiquitin-ligases confer specificity to the whole cascade by mediating the last step of substrate ubiquitylation. The implication of E3 ligases in cancer is well-described. MYCBP2 forms together with its substrate specificity factor FBXO45 an E3 ligase complex involved in promotion of mitotic slippage, a process which can result in acquisition of drug resistance against microtubule poisons. E3 ligases are antagonized by deubiquitylases (DUBs) which in turn remove ubiquitin from modified substrates. Despite their opposing activities, it is not uncommon for DUBs and E3 ligases to form complexes. Such DUB-E3 complexes can protect E3 ligases from autoubiquitylation. However, ubiquitylation of DUBs by E3 ligases may also recruit substrates for deubiquitylation. Recent data from our team suggests that SPRYD3 could act as a new substrate specificity factor of the E3 ligase MYCBP2, which in complex might regulate mitotic slippage. Here we show that SPRYD3 positively regulates mitotic slippage in U2OS and RPE1 cells after treatment with microtubule poisons Nocodazole and Paclitaxel. Additionally, SPRYD3 directly binds to MYCBP2 independently from FBXO45 in vivo and in vitro, pointing to the existence of a new E3 ligase complex. Interestingly, we identify the DUB USP11 as dircet substrate and binding partner of the MYCBP2-SPRYD3 E3 ligase. Depletion of either SPRYD3, MYCBP2 or USP11 increases the number of multipolar spindles containing cells, a phenotype that can lead to mitotic cell death. Our data suggests that MYCBP2-SPRYD3 mediated ubiquitylation of USP11 is linked to proper bipolar spindle formation during mitosis. Abolishment of either USP11 ubiquitylation or MYCBP2-SPRYD3 E3 ligase activity leads to increased multipolar spindle formation during mitosis, which is linked to higher mitotic cell death rates after microtubule poison treatment. Our study points to a new mechanism of mitotic cell fate regulation potentially mediated through a DUB/E3 ligase complex consisting of the new E3 ligase complex MYCBP2-SPRYD3 and the DUB USP11.
Due to the confidentiality of the unpublished data, we cannot share the poster.
FungAMR: a comprehensive portrait of antimicrobial resistance mutations in fungi
Presenter: Camille Bédard
Collaborators: Alicia Pageau, Anna Fijarczyk, David Mendoza-Salido, Alejandro J. Alcaniz, Philippe C. Després, Romain Durand, Samuel Plante, Emilie M. M. Alexander, François D. Rouleau, Mathieu Giguère, Mégane Bernier, Jehoshua Sharma, Laetitia Maroc, Nicholas Gervais, Anagha C. T. Menon, Isabelle Gagnon-Arsenault, Sibbe Bakker, Johanna Rhodes, Philippe Dufresne, Amrita Bharat, Adnane Sellam, Domenica G. De Luca, Aleeza Gerstein, Rebecca Shapiro8, Narciso M. Quijada, Christian R. Landry
Abstract:
Infections caused by fungal pathogens constitute a significant health threat and socio-economic burden. The widespread use of antifungals has driven the emergence of resistant strains and populations unresponsive to treatments. Unlike antibiotic resistance, which often emerges from the acquisition of genes, antifungal resistance emerges through de novo mutations in the genome, resulting in a wide array of possible resistance mechanisms. Accordingly, various mechanisms of AMR have been described for allavailable antifungal classes. However, reports of fungal AMR mutations are scattered across multiple studies, which limits our ability to overview the current state of our knowledge and to develop genomic tools to interpret genetic variants. To address this, we performed a thorough manual curation of published AMR mutations in fungal pathogens to produce the FungAMR reference dataset. A total of 462 papers were curated, leading to 54,666 mutation entries, all classified with a degree of evidence that supports their role in resistance. FungAMR covers 92 species, 202 genes, and 184 drugs. We have taken advantage of this new resource to better understand resistance mechanisms among species and antifungals. We combined variant effect predictors with FungAMR resistance mutations and showed that these tools could be used to help predict the potential impact of mutations on AMR. Additionally, a comparative analysis among species revealed a high level of convergence in the molecular basis of resistance, revealing some potentially universal resistance mutations. The analyses also showed that a significant number of resistance mutations lead to cross-resistance within antifungals of a class, as well as between classes for specific genes. Finally, we provide a computational tool, ChroQueTas, that leverages FungAMR to screen fungal genomes for AMR mutations. Overall, the analysis of the content of FungAMR revealed biases in the study of certain species, proteins and antifungals, and highlighted where more research is needed. This resource will help the scientific community to address the serious threat of antifungal resistance, and has the potential to provide a launchpad for fundamental and applied research.
EccDNA linked resistance and adaptation to copper stress in s. cerevisiae
Presenter: Amy Wolstenholme
Collaborators: Jon Houseley
Abstract:
Extrachromosomal circular DNAs (eccDNAs) are closed circular structures that exist independently of the genome, and have been observed in numerous eukaryotic species. They vary widely in size and can be produced from a diversity of sites across the genome, including carrying and expressing functional genes. Unlike chromosomes, eccDNAs do not have centromeres, and thus are not segregated equally between daughter cells in a Mendelian fashion. In some studies, genes represented on eccDNA have been correlated to resistant phenotypes, including treatment resistant cancer, drug resistance in pathogens and pesticide resistance in plants. However, the inheritance of resistant eccDNA within a population, and whether this is underpinned by a specific mechanism, is poorly understood. We aim to understand how eccDNAs can be harnessed for adaptation by using the model organism S. cerevisiae, providing for the first time a direct link between a single eccDNA and a specific adaptive phenotype. Under non-stress conditions in S. cerevisiae, eccDNA accumulates in the Mother cell, rather than passing to daughters. In this study we demonstrate that the accumulation of a single copper resistant gene on eccDNA in aged cells under non-stress conditions, leads to the robust and rapid appearance of an entire population resistant to copper upon encountering the stress for the first time. This resistance is maintained solely on circular DNA with no underlying genomic change, supporting the hypothesis that eccDNAs provide a pool of genetic variability independent of the genome, which can be drawn upon for adaptation when required. Currently, we are investigating how daughter cells can mechanistically inherit eccDNA under copper stress, which does not occur under non-stress conditions.
CedIVA, a novel DivIVA-domain containing protein of mycobacteria, augments Mtb envelope synthesis and integrity, and susceptibility to anti-TB drugs
Presenter: Yogita Kapoor
Collaborators: Vinay Kumar Nandicoori
Abstract:
According to the 2024 WHO report, tuberculosis has regained the top spot of being the deadliest infectious disease, with multidrug-resistance (MDR) emerging as a health security threat worldwide. Numerous studies in the field have implicated the presence of unique lipids in the cell wall, & the asymmetric cell division pattern of Mycobacterium tuberculosis (Mtb) in causing MDR. While the molecular players of division are fairly characterized for model species such as E. coli , they remain poorly investigated for Mtb . Here, we report the identification & characterization of the novel DivIVA proteins of Mtb . They share homology with Wag31 & SepIVA, the known DivIVA proteins that facilitate Mtb cell division. Our work using the deletion mutants of novel DivIVA proteins suggests that they are non-essential for the survival of M. smegmatis (Msm) & Mtb in vitro . Interestingly, their loss leads to a shortening of cell length, indicating a role for them in cellular growth. The loss of the novel DivIVA protein which we have named as CedIVA leads to aberrant membrane architecture & defective V-snapping, which leads to the formation of chains of undivided cells. The loss of membrane architecture & integrity arises due to a decrease in membrane lipids, as revealed by lipidome analysis. The mutant suffers from a reduction in phospholipids, neutral lipids, mycolic acids & glycolipids, suggesting that CedIVA helps regulate membrane lipid homeostasis. It does so by interacting with membrane-associated proteins involved in cell wall elongation & division, envelope maintenance & synthesis, and lipid & protein transport system, as divulged by the interactome study of FLAG-tagged CedIVA. mCherry-tagged CedIVA localizes at the membrane & septum, which is congruent with its roles in maintaining membrane integrity & V-snapping post-cell division. A deformed membrane makes the mutant susceptible to cell wall-targeting antibiotics such as isoniazid, meropenem, ethambutol, & ethionamide. Moreover, the absence of CedIVA also compromises the pathogenicity of Mtb , rendering it incompetent to establish and disseminate infection in the lungs and spleen of the murine model. Taken together, our work identifies a novel DivIVA-protein that maintains membrane lipid homeostasis & integrity and modulates the susceptibility of anti-TB drugs.
Due to the confidentiality, we cannot share the poster.
Antibiotics of the future are prone to resistance in Gram-negative pathogens
Presenter: Márton Czikkely
Collaborators: Lejla Daruka, Petra Szili, Zoltán Farkas, Elvin Maharramov, Gábor Grézal, Balázs Papp, Bálint Kintses, Csaba Pál
Abstract:
Despite the ongoing development of new antibiotics, the future evolution of bacterial resistance may render them ineffective. We demonstrate that antibiotic candidates currently under development are as prone to resistance evolution in Gram-negative ESKAPE pathogens (e.g. Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa) as clinically employed antibiotics. Resistance generally stems from both genomic mutations and the transfer of antibiotic resistance genes from microbiomes associated with humans, both factors carrying equal significance. In total, 604 mutated protein coding genes were detected, of which 193 mutated in at least two independently evolved lines per species. The molecular mechanisms of resistance overlap with those found in commonly used antibiotics. Remarkably, 69.4% of all parallel mutated genes carried mutation in lines adapted to different antibiotics. Therefore, these mechanisms are already present in natural populations of pathogens, indicating that resistance can rapidly emerge through selection of pre-existing bacterial variants. In case of E. coli, as high as 31.4% of the 245 laboratory observed non-synonymous mutations were identified in at least one of the investigated genomes (n=20,786), while the same figure is 27.3% of 216 mutations for A. baumannii (n=15,185). However, certain combinations of antibiotics and bacterial strains are less prone to developing resistance, emphasizing the potential of narrow-spectrum antibacterial therapies that could remain effective. Our comprehensive framework allows for predicting future health risks associated with bacterial resistance to new antibiotics
The EMBO | EMBL Symposium ‘Mechanisms of drug resistance and tolerance in bacteria, fungi, and cancer‘ took place from 18 – 21 March 2025 at EMBL Heidelberg and virtually.