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Abstract The main critical step in single-cell transcriptomics is sample preparation. Several methods have been developed to preserve cells after dissociation to uncouple sample handling from library preparation. Yet, the suitability of these methods depends on the cell types to be processed. In this project, we perform a systematic comparison of preservation methods for droplet-based single-cell RNA-seq on neural and glial cells derived from induced pluripotent stem cells. Our results show that while DMSO provides the highest cell quality in terms of RNA molecules and genes detected per cell, it strongly affects the cellular composition and induces the expression of stress and apoptosis genes. In contrast, methanol fixed samples display a cellular composition similar to fresh samples and provide a good cell quality and little expression biases. Taken together, our results show that methanol fixation is the method of choice for performing droplet-based single-cell transcriptomics experiments on neural cell populations.

Invasive candidiasis poses a worldwide threat because of the rising prevalence of antifungal resistance, resulting in higher rates of morbidity and mortality. Additionally, Candida species, which are opportunistic infections, have significant medical and economic consequences for immunocompromised individuals. This study explores the antifungal potential of chitosan to mitigate caspofungin resistance in caspofungin-resistant Candida albicans, C. krusei, and C. tropicalis isolates originating from human and animal sources using agar well diffusion, broth microdilution tests, and transmission electron microscope (TEM) analysis of treated Candida cells. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) was performed to assess the expression of SAGA complex genes (GCN5 and ADA2) and the caspofungin resistance gene (FKS) in Candida species isolates after chitosan treatment. The highest resistance rate was observed to ketoconazole (80%) followed by clotrimazole (62.7%), fluconazole (60%), terbinafine (58%), itraconazole (57%), miconazole (54.2%), amphotericin B (51.4%), voriconazole (34.28%), and caspofungin (25.7%). Nine unique FKS mutations were detected, including S645P (n = 3 isolates), S645F, L644F, S645Y, L688M, E663G, and F641S (one isolate in each). The caspofungin minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) values before chitosan treatment ranged from 2 to 8 µg/mL and 4 to 16 µg/mL, respectively. However, the MIC and MFC values were decreased after chitosan treatment (0.0625–1 µg/mL) and (0.125–2 µg/mL), respectively. Caspofungin MIC was significantly decreased (p = 0.0007) threefold following chitosan treatment compared with the MIC values before treatment. TEM analysis revealed that 0.5% chitosan disrupted the integrity of the cell surface, causing irregular morphologies and obvious aberrant changes in cell wall thickness in caspofungin-resistant and sensitive Candida isolates. The cell wall thickness of untreated isolates was 0.145 μm in caspofungin-resistant isolate and 0.125 μm in sensitive isolate, while it was significantly lower in chitosan-treated isolates, ranging from 0.05 to 0.08 μm when compared with the cell wall thickness of sensitive isolate (0.03 to 0.06 μm). Moreover, RT-qPCR demonstrated a significant (p < 0.05) decrease in the expression levels of histone acetyltransferase genes (GCN5 and ADA2) and FKS gene of caspofungin-resistant Candida species isolates treated with 0.5% chitosan when compared with before treatment (fold change values ranged from 0.001 to 0.0473 for GCN5, 1.028 to 4.856 for ADA2, and 2.713 to 12.38 for FKS gene). A comparison of the expression levels of cell wall-related genes (ADA2 and GCN5) between caspofungin-resistant and -sensitive isolates demonstrated a significant decrease following chitosan treatment (p < 0.001). The antifungal potential of chitosan enhances the efficacy of caspofungin against various caspofungin-resistant Candida species isolates and prevents the development of further antifungal resistance. The results of this study contribute to the progress in repurposing caspofungin and inform a development strategy to enhance its efficacy, appropriate antifungal activity against Candida species, and mitigate resistance. Consequently, chitosan could be used in combination with caspofungin for the treatment of candidiasis.

Little is known about the interactions among phagocytes and antifungal agents and the antifungal immunomodulatory activities on Candida species biofilms. Here, inhibition of C. albicans biofilms and the interactions among biofilms and phagocytes alone or in combination with essential oils, biological, and chemical agents, or fluconazole were investigated. Biofilm formation by a panel of 28 C. albicans clinical isolates from hospitalized patients, birds, and cattle was tested. The anti-biofilm activities of cinnamon and clove oils, sodium dodecyl sulfate (SDS), cetyltrimethylammonium bromide (CTAB), and Enterococcus faecalis cell-free supernatant (CFS) in comparison with fluconazole were investigated using crystal violet and XTT reduction assays, expression of hypha-specific and hyphal regulator genes, and scanning electron microscopy (SEM) analysis. Of the tested C. albicans isolates, 15 of 28 (53.6%) were biofilm producers. Cinnamon followed by E. faecalis–CFS, SDS, and CTAB was the most effective inhibitors of planktonic C. albicans and biofilms. Fluconazole was an ineffective inhibitor of C. albicans biofilms. Sessile minimal inhibitory concentration (SMIC50) of cinnamon, SDS, CTAB, and E. faecalis–CFS downregulated the hypha-specific and regulator genes, albeit to various extents, when compared with untreated biofilms (P < 0.001). SEM analysis revealed disruption and deformity of three-dimensional structures in cinnamon oil–treated biofilms. C. albicans sessile cells within biofilm were less susceptible to phagocytosis than planktonic cells. The additive effects of phagocytes and the tested antifungals enabled phagocytes to engulf C. albicans cells rapidly in cinnamon, E. faecalis–CFS, or SDS-treated biofilms. No differences in anti-Candida or anti-biofilm eradication activities were detected among the tested isolates. Our findings reinforce the substantial anti-biofilm activity of cinnamon oil, SDS, and E. faecalis–CFS and provide new avenues for the development of novel anti-biofilm immunotherapies or antifungals that could be used prior to or during the management of cases with biofilm-associated infections.