Biology subjects

Hoda, S.

Publications and source records attributed to Hoda, S..

5 recordsLinked to original sources

bioRxiv2023

Patient-derived tumor organoids with p53 mutations, and not wild-type p53, are sensitive to synergistic combination PARP inhibitor treatment

Poly (ADP-ribose) polymerase inhibitors (PARPi) are used for patients with BRCA1/2 mutations, but patients with other mutations may benefit from PARPi treatment. Another mutation that is present in more cancers than BRCA1/2 is mutation to the TP53 gene. In 2D breast cancer cell lines, mutant p53 (mtp53) proteins tightly associate with replicating DNA and Poly (ADP-ribose) polymerase (PARP) protein. Combination drug treatment with the alkylating agent temozolomide and the PARPi talazoparib kills mtp53 expressing 2D grown breast cancer cell lines. We evaluated the sensitivity to the combination of temozolomide plus PARPi talazoparib treatment to breast and lung cancer patient-derived tumor organoids (PDTOs). The combination of the two drugs was synergistic for a cytotoxic response in PDTOs with mtp53 but not for PDTOs with wtp53. The combination of talazoparib and temozolomide induced more DNA double-strand breaks in mtp53 expressing organoids than in wild-type p53 expressing organoids as shown by increased {psi}-H2AX protein expression. Moreover, breast cancer tissue microarrays (TMAs) showed a positive correlation between stable p53 and high PARP1 expression in sub-groups of breast cancers, which may indicate sub-classes of breast cancers sensitive to PARPi therapy. These results suggest that mtp53 could be a biomarker to predict response to the combination of PARPi talazoparib-temozolomide treatment.

cancer biology↗

bioRxiv2023

xpanding the toolkit for genetic manipulation and discovery in Candida species using a CRISPR ribonucleoprotein-based approach

The World Health Organization recently published the first list of priority fungal pathogens highlighting multiple Candida species including C. glabrata, C. albicans, and C. auris. The use of CRISPR-Cas9 and auxotrophic C. glabrata and C. albicans strains have been instrumental in the study of these fungal pathogens. Dominant drug resistance cassettes are also critical for genetic manipulation and eliminate the concern of altered virulence when using auxotrophic strains. However, genetic manipulation has been mainly limited to the use of two drug resistance cassettes, NatMX and HphMX. Using an in vitro assembled CRISPR-Cas9 ribonucleoprotein (RNP)-based system and 130-150 bp homology regions for directed repair, we expand the drug resistance cassettes for Candida to include KanMX and BleMX, commonly used in S. cerevisiae. As a proof of principle, we demonstrated efficient deletion of ERG genes using KanMX and BleMX. We also showed the utility of the CRISPR-Cas9 RNP system for generating double deletions of genes in the ergosterol pathway and endogenous epitope tagging of ERG genes using an existing KanMX cassette. This indicates that CRISPR-Cas9 RNP can be used to repurpose the S. cerevisiae toolkit. Furthermore, we demonstrated that this method is effective at deleting ERG3 in C. auris using a codon optimized BleMX cassette and effective at deleting the epigenetic factor, SET1, in C. albicans using a recyclable SAT1. Using this expanded toolkit, we discovered new insights into fungal biology and drug resistance. IMPORTANCEThe increasing problem of drug resistance and emerging pathogens is an urgent global health problem that necessitates the development and expansion of tools for studying fungal drug resistance and pathogenesis. We have demonstrated the effectiveness of an expression-free CRISPR-Cas9 RNP-based approach employing 130-150 bp homology regions for directed repair. Our approach is robust and efficient for making gene deletions in C. glabrata, C. auris and C. albicans as well as epitope tagging in C. glabrata. Furthermore, we demonstrated that KanMX and BleMX drug resistance cassettes can be repurposed in C. glabrata and BleMX in C. auris. Overall, we have expanded the toolkit for genetic manipulation and discovery in fungal pathogens.

genetics↗

bioRxiv2023

Rapid, efficient auxin-inducible protein degradation in Candida pathogens

A variety of inducible protein degradation (IPD) systems have been developed as powerful tools for protein functional characterization. IPD systems provide a convenient mechanism for rapid inactivation of almost any target protein of interest. Auxin-inducible degradation (AID) is one of the most common IPD systems and has been established in diverse eukaryotic research model organisms. Thus far, IPD tools have not been developed for use in pathogenic fungal species. Here, we demonstrate that the original AID and the second generation AID2 systems work efficiently and rapidly in the human pathogenic yeasts Candida albicans and Candida glabrata. We developed a collection of plasmids that support AID system use in laboratory strains of these pathogens. These systems can induce >95% degradation of target proteins within minutes. In the case of AID2, maximal degradation was achieved at low nanomolar concentrations of the synthetic auxin analog 5-adamantyl-indole-3-acetic acid (5-Ad-IAA). Auxin-induced target degradation successfully phenocopied gene deletions in both species. The system should be readily adaptable to other fungal species and to clinical pathogen strains. Our results define the AID system as a powerful and convenient functional genomics tool for protein characterization in fungal pathogens.

molecular biology↗

bioRxiv2022

Reduced Cdc14 phosphatase activity impairs septation, hyphal differentiation and pathogenesis and causes echinocandin hypersensitivity in Candida albicans

The Cdc14 phosphatase family is highly conserved in fungi. In Saccharomyces cerevisiae, Cdc14 is essential for down-regulation of cyclin-dependent kinase activity at mitotic exit. However, this essential function is not broadly conserved and requires a small fraction of normal Cdc14 activity. It remains unclear what fungal Cdc14 functions require high Cdc14 activity. We identified an invariant motif in the disordered C-terminal tail of fungal Cdc14 enzymes that is required for full enzyme activity. Mutation of this motif reduced Cdc14 catalytic rate and provided a tool for studying the biological significance of high Cdc14 activity. A S. cerevisiae strain expressing the reduced-activity hypomorphic mutant allele (cdc14hm) as the sole source of Cdc14 exhibited an unexpected sensitivity to cell wall stresses, including chitin-binding compounds and echinocandin antifungal drugs. Sensitivity to echinocandins was also observed in Schizosaccharomyces pombe and Candida albicans strains lacking CDC14, suggesting this phenotype reflects a conserved function of Cdc14 orthologs in mediating fungal cell wall integrity. In C. albicans, the orthologous cdc14hm allele was sufficient to elicit echinocandin hypersensitivity and perturb cell wall integrity signaling. It also caused striking abnormalities in septum structure and the same cell separation and hyphal differentiation defects previously observed with cdc14 gene deletions. Since hyphal differentiation is important for C. albicans pathogenesis, we assessed the effect of reducing Cdc14 activity on virulence in Galleria mellonella and mouse models of invasive candidiasis. Partial reduction in Cdc14 activity via cdc14hm mutation severely impaired C. albicans virulence in both assays. Our results reveal that high Cdc14 activity promotes fungal cell wall integrity and, in C. albicans, is needed to orchestrate septation and hyphal differentiation, and for pathogenesis. Cdc14 may therefore be worth future exploration as an antifungal drug target. AUTHOR SUMMARYInvasive fungal infections are a serious concern for the immune-compromised. Antifungal drugs to treat invasive infections are limited and pathogens are developing resistance to them. Novel targets for antifungal drug development are needed. In this study we developed a system to test if partial therapeutic reduction in activity of a protein phosphatase called Cdc14 could reduce virulence of the opportunistic human pathogen Candida albicans. This idea arose from prior studies in fungal pathogens of plants, where Cdc14 was unexpectedly required for host infection through an unknown mechanism. We found that successful C. albicans infections in two animal models of invasive candidiasis were dependent on high Cdc14 activity. Moreover, we made the surprising observation that integrity of the C. albicans cell wall is also dependent on high Cdc14 activity, with Cdc14-deficient cells becoming hypersensitive to cell wall-targeted antifungal drugs. We conclude that even modest reduction in Cdc14 activity could have therapeutic benefit for human fungal infections and possibly help overcome resistance to some antifungal drugs. Cdc14 structure and specificity are unique among phosphatases and highly conserved in pathogenic fungi, suggesting that highly selective inhibitors can be developed that would be useful against a broad range of fungal pathogens.

molecular biology↗

bioRxiv2021

Set1-mediated histone H3K4 methylation is required for azole induction of the ergosterol biosynthesis genes and antifungal drug resistance in Candida glabrata.

Candida glabrata is an opportunistic pathogen that has developed the ability to adapt and thrive under azole treated conditions. The common mechanisms that can result in Candida drug resistance are due to mutations or overexpression of the drug efflux pump or the target of azole drugs, Cdr1 and Erg11, respectively. However, the role of epigenetic histone modifications in azole-induced gene expression and drug resistance are poorly understood in C. glabrata. In this study, we show for the first time that Set1 mediates histone H3K4 mono-, di-, and trimethylation in C. glabrata. In addition, loss of SET1 and histone H3K4 methylation results in increased susceptibility to azole drugs in both C. glabrata and S. cerevisiae. Intriguingly, this increase in susceptibility to azole drugs in strains lacking Set1-mediated histone H3K4 methylation is not due to altered transcript levels of CDR1, PDR1 or Cdr1s ability to efflux drugs. Genome-wide transcript analysis revealed that Set1 is necessary for azole-induced expression of 12 genes involved in the late biosynthesis of ergosterol including ERG11 and ERG3. Importantly, chromatin immunoprecipitation analysis showed that histone H3K4 trimethylation was detected on chromatin of actively transcribed ERG genes. Furthermore, H3K4 trimethylation increased upon azole-induced gene expression which was also found to be dependent on the catalytic activity of Set1. Altogether, our findings show that Set1-mediated histone H3K4 methylation governs the intrinsic drug resistant status in C. glabrata via epigenetic control of azole-induced ERG gene expression. IMPORTANCEC. glabrata is the second most commonly isolated species from Candida infections, coming in second to C. albicans. Treatment of C. glabrata infections are difficult due to their natural resistance to antifungal azole drugs and their ability to adapt and become multidrug resistant. In this study, we investigated the contributing cellular factors for controlling drug resistance. We have determined that an epigenetic mechanism governs the expression of genes involved in the late ergosterol biosynthesis pathway, an essential pathway that antifungal drugs target. This epigenetic mechanism involves histone H3K4 methylation catalyzed by the Set1 methyltransferase complex (COMPASS). We also show that Set1-mediated histone H3K4 methylation is needed for expression of specific azole induced genes and azole drug resistance in C. glabrata. Identifying epigenetic mechanisms contributing to drug resistance and pathogenesis could provide alternative targets for treating patients with fungal infections.

genetics↗