Pathogen-Host Interaction Repertoire at Proteome and Posttranslational Modification Levels During Fungal Infections

Prevalence of fungal diseases has increased globally in recent years, which often associated with increased immunocompromised patients, aging populations, and the novel Coronavirus pandemic. Furthermore, due to the limitation of available antifungal agents mortality and morbidity rates of invasion fungal disease remain stubbornly high, and the emergence of multidrug-resistant fungi exacerbates the problem. Fungal pathogenicity and interactions between fungi and host have been the focus of many studies, as a result, lots of pathogenic mechanisms and fungal virulence factors have been identified. Mass spectrometry (MS)-based proteomics is a novel approach to better understand fungal pathogenicities and host–pathogen interactions at protein and protein posttranslational modification (PTM) levels. The approach has successfully elucidated interactions between pathogens and hosts by examining, for example, samples of fungal cells under different conditions, body fluids from infected patients, and exosomes. Many studies conclude that protein and PTM levels in both pathogens and hosts play important roles in progression of fungal diseases. This review summarizes mass spectrometry studies of protein and PTM levels from perspectives of both pathogens and hosts and provides an integrative conceptual outlook on fungal pathogenesis, antifungal agents development, and host–pathogen interactions.

Effects of antifungal agents on the fungal proteome: informing on mechanisms of sensitivity and resistance

INTRODUCTION

Antifungal agents are essential in the fight against serious fungal disease, however emerging resistance is threatening an already limited collection of therapeutics. Proteomic analyses of effects of antifungal agents can expand our understanding of multifactorial mechanisms of action and have also proven valuable to elucidate proteomic changes associated with antifungal resistance.

AREAS COVERED

This review covers the application of proteomic techniques to examine sensitivity and resistance to antifungals including commonly used therapeutics, amphotericin B, echinocandins and the azoles, based predominantly on studies involving Aspergillus fumigatus, Candida albicans and Candida glabrata from the last 10 years. In addition, non-clinical antimicrobial agents are also discussed, which highlight the potential of proteomics to identify new antifungal targets.

EXPERT COMMENTARY

Fungal proteomics has evolved in the last decade with increased genome availability and developments in mass spectrometry. Collectively, these have led to the advancement of proteomic techniques, allowing increased coverage of the proteome. Gel-based proteomics laid the foundation for these types of studies, which has now shifted to the more powerful gel-free proteomics. This has resulted in the identification of key mediators and potential biomarkers of antifungal resistance, as well as elucidating the mechanisms of action of novel and established antifungal agents.

Octominin: A Novel Synthetic Anticandidal Peptide Derived from Defense Protein of Octopus minor

The rapid emergence of multidrug-resistant pathogens makes an urgent need for discovering novel antimicrobial agents as alternatives to conventional antibiotics. Towards this end, we designed and synthesized a synthetic peptide of 23 amino acids (AAs) (¹GWLIRGAIHAGKAIHGLIHRRRH²³) from a defense protein 3 cDNA sequence of Octopus minor. The sequence of the peptide, which was named Octominin, had characteristic features of known antimicrobial peptides (AMPs) such as a positive charge (+5), high hydrophobic residue ratio (43%), and 1.86 kcal/mol of Boman index. Octominin was predicted to have an alpha-helix secondary structure. The synthesized Octominin was 2625.2 Da with 92.5% purity. The peptide showed a minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) of 50 and 200 μg/mL, respectively, against Candida albicans. Field emission scanning electron microscopy observation confirmed that Octominin caused ultrastructural cell wall deformities in C. albicans. In addition, propidium iodide penetrated the Octominin-treated C. albicans cells, further demonstrating loss of cell membrane integrity that caused cell death at both MIC and MFC. Octominin treatment increased the production of intracellular reactive oxygen species and decreased cell viability in a concentration dependent manner. Cytotoxicity assays revealed no significant influence of Octominin on the viability of human embryonic kidney 293T cell line, with over 95% live cells in the Octominin-treated group observed up to 100 µg/mL. Moreover, we confirmed the antifungal action of Octominin in vivo using a zebrafish experimental infection model. Overall, our results demonstrate the Octominin is a lead compound for further studies, which exerts its effects by inducing cell wall damage, causing loss of cell membrane integrity, and elevating oxidative stress.

Antifungal, Antitumoral and Antioxidant Potential of the Danube Delta Nymphaea alba Extracts

This study aimed to explore for the first time the biological properties such as antifungal, antitumoral and antioxidant of Danube Delta Nymphaea alba (N. alba) leaf and root methanolic extracts. The toxicity studies of N. alba extracts showed no inhibitory effect on wheat seed germination by evaluating the most sensitive physiological parameters (Germination %, Germination index, Vigor index) and using confocal laser scanning microscopy images. The analyzed extracts were found to have high antifungal activity against Candida glabrata with MIC values of 1.717 µg/mL for leaf and 1.935 µg/mL for root. The antitumor activity of the both extracts against A2780/A2780cisR ovarian, LNCaP prostate and MCF-7 breast cancer cells was promising with IC₅₀ values ranging from 23–274 µg/mL for leaf and 18–152 µg/mL for root, and the combination of N. alba extracts with cisplatin showed a synergistic effect (coefficient of drug interaction <1). The antioxidant properties were assessed by β-carotene bleaching, ABTS and FRAP assays and cyclic voltammetry. Quercetin, the most prominent antioxidant, was quantified in very good yields by spectroelectrochemical assay.

Mechanisms of azole resistance in clinical isolates of Candida glabrata from two hospitals in China

Purpose: Candida glabrata has emerged as the second or third most common non-albicans species responsible for an increasing number of systemic infections. Moreover, its high-level of resistance to azole is associated with a high mortality rate. This study aimed to evaluate nosocomial infections and resistance characteristics of C. glabrata and to explore the mechanism of azole resistance in C. glabrata.

Patients and methods: Fifty-nine clinical C. glabrata isolates were collected from two hospitals in China. The susceptibility of the strains to antifungal agents was determined by both the ATB Fungus 3 strip and CLSI M27 broth microdilution method. Efflux of rhodamine 6G was examined to evaluate the effects of efflux pumps. The expression levels of CgCDR1, CgCDR2, CgSNQ2, CgERG11, and CgPDR1 were examined by real-time PCR. The sequences of CgERG11 and CgPDR1 were determined by PCR-based DNA sequencing.

Results: All 59 isolates of C. glabrata were susceptible to flucytosine and amphotericin B. Twelve (20.3%) isolates were determined to be fluconazole-resistant, whereas 13 (22.0%) and 27 (45.7%) isolates were categorized as non-wild-type for itraconazole and voriconazole, respectively. Efflux pumps in azole-resistant isolates showed stronger effects than those in azole-susceptible-dose dependent isolates, which is consistent with the significant upregulation of CgCDR1 and CgCDR2 (P<0.05), whereas no obvious differences were found for CgSNQ2, CgERG11, and CgPDR1 (P>0.05). Sequencing of CgERG11 showed no alteration favoring the hypothesis that CgERG11 is not involved in the azole resistance of C. glabrata. Four CgPDR1 missense mutations were found in azole-resistant isolates, of which the high frequency of the CgPDR1 mutation, A848V, has not been reported previously.

Conclusion: Efflux pump function is the main mechanism of resistance to fluconazole in our collected clinical isolates of C. glabrata, and further studies of the related gene disruption and genome-wide expression are needed to verify the function.

Fluconazole induces ROS in Cryptococcus neoformans and contributes to DNA damage in vitro

Pathogenic basidiomycetous yeast, Cryptococcus neoformans, causes fatal meningitis in immunocompromised individuals. Fluconazole (FLC) is a fungistatic drug commonly administered to treat cryptococcosis. Unfortunately, FLC-resistant strains characterized by various degree of chromosomal instability were isolated from clinical patients. Importantly, the underlying mechanisms that lead to chromosomal instability in FLC-treated C. neoformans remain elusive. Previous studies in fungal and mammalian cells link chromosomal instability to the reactive oxygen species (ROS). This study provides the evidence that exposure of C. neoformans to FLC induces accumulation of intracellular ROS, which correlates with plasma membrane damage. FLC caused transcription changes of oxidative stress related genes encoding superoxide dismutase (SOD1), catalase (CAT3), and thioredoxin reductase (TRR1). Strikingly, FLC contributed to an increase of the DNA damage in vitro, when complexed with iron or copper in the presence of hydrogen peroxide. Strains with isogenic deletion of copper response protein metallothionein were more susceptible to FLC. Addition of ascorbic acid (AA), an anti-oxidant at 10 mM, reduced the inhibitory effects of FLC. Consistent with potential effects of FLC on DNA integrity and chromosomal segregation, FLC treatment led to elevated transcription of RAD54 and repression of cohesin-encoding gene SCC1. We propose that FLC forms complexes with metals and contributes to elevated ROS, which may lead to chromosomal instability in C. neoformans.

ABC transportome inventory of human pathogenic yeast Candida glabrata: Phylogenetic and expression analysis

ATP-binding cassette (ABC) is one of the two major superfamilies of transporters present across the evolutionary scale. ABC superfamily members came to prominence due to their ability to extrude broad spectrum of substrates and to confer multi drug resistance (MDR). Overexpression of some ABC transporters in clinical isolates of Candida species was attributed to the development of MDR phenotypes. Among Candida species, Candida glabrata is an emerging drug resistant species in human fungal infections. A comprehensive analysis of such proteins in C. glabrata is required to untangle their role not only in MDR but also in other biological processes. Bioinformatic analysis of proteins encoded by genome of human pathogenic yeast C. glabrata identified 25 putative ABC protein coding genes. On the basis of phylogenetic analysis, domain organization and nomenclature adopted by the Human Genome Organization (HUGO) scheme, these proteins were categorized into six subfamilies such as Pleiotropic Drug Resistance (PDR)/ABCG, Multi Drug Resistance (MDR)/ABCB, Multi Drug Resistance associated Protein (MRP)/ABCC, Adrenoleukodystrophy protein (ALDp)/ABCD, RNase L Inhibitor (RLI)/ABCE and Elongation Factor 3 (EF3)/ABCF. Among these, only 18 ABC proteins contained transmembrane domains (TMDs) and were grouped as membrane proteins, predominantly belonging to PDR, MDR, MRP, and ALDp subfamilies. A comparative phylogenetic analysis of these ABC proteins with other yeast species revealed their orthologous relationship and pointed towards their conserved functions. Quantitative real time PCR (qRT-PCR) analysis of putative membrane localized ABC protein encoding genes of C. glabrata confirmed their basal expression and showed variable transcriptional response towards antimycotic drugs. This study presents first comprehensive overview of ABC superfamily proteins of a human fungal pathogen C. glabrata, which is expected to provide an important platform for in depth analysis of their physiological relevance in cellular processes and drug resistance.

Triazole Resistance in Aspergillus Species: An Emerging Problem

Aspergillus species are ubiquitous fungal saprophytes found in diverse ecological niches worldwide. Among them, Aspergillus fumigatus is the most prevalent and is largely responsible for the increased incidence of invasive aspergillosis with high mortality rates in some immunocompromised hosts. Azoles are the first-line drugs in treating diseases caused by Aspergillus spp. However, increasing reports in A. fumigatus azole resistance, both in the clinical setting and in the environment, are threatening the effectiveness of clinical and agricultural azole drugs. The azole target is the 14-α sterol demethylase encoded by cyp51A gene and the main mechanisms of resistance involve the integration of tandem repeats in its promoter and/or single point mutations in this gene. In A. fumigatus, azole resistance can emerge in two different scenarios: a medical route in which azole resistance is generated during long periods of azole treatment in the clinical setting and a route of resistance derived from environmental origin due to extended use of demethylation inhibitors in agriculture. The understanding of A. fumigatus azole resistance development and its evolution is needed in order to prevent or minimize its impact. In this article, we review the current situation of azole resistance epidemiology and the predominant molecular mechanisms described based on the resistance acquisition routes. In addition, the clinical implications of A. fumigatus azole resistance and future research are discussed.

A case report of invasive candidiasis and fungal osteomyelitis mimicking oropharyngeal carcinoma recurrence in an immunocompetent patient following transoral robotic surgery

INTRODUCTION

Transoral robotic surgery(TORS) for the excision of oropharyngeal tumour is increasingly considered for its lower rates of postoperative complications and better functional outcomes. However, we report a case of invasive candidiasis in an immunocompetent patient with previous radiation therapy years ago who underwent TORS recently.

CASE PRESENTATION

A 55year old Chinese female with previous radiation therapy for nasopharyngeal carcinoma diagnosed in 1986 underwent wide excision of a newly diagnosed oropharyngeal carcinoma with TORS. From 4 to 8 weeks post-op, an enlarging exophytic lesion at the surgical excision site was noted. Initial biopsy did not show malignancy or fungal organisms. A repeat biopsy under anaesthesia was done as CT imaging showed suspicion of either infective or tumour recurrence. The patient was treated with long term antifungals as final culture results showed invasive candidiasis. The surgical site showed no further lesions 6 months post-op.

DISCUSSION

Previous radiation therapy to the oropharyngeal area predisposes a patient to colonization of fungal organisms. Despite TORS showing lower rates of infection, patients who have had previous radiotherapy may be more susceptible to infections as the dissection involves down to the pre-vertebral fascia. Hence, it is appropriate for such patients to have microbiological and fungal cultures performed for a lesion such as this and be treated according to the results of the culture.

CONCLUSION

This case serves as a reminder of the risk of invasive candidiasis requiring early investigation and treatment in an immunocompetent patient with prior history of both radiation therapy and recent TORS.

Rapid Assays for Specific Detection of Fungi of Scopulariopsis and Microascus Genera and Scopulariopsis brevicaulis Species

Purpose

Fungi of Scopulariopsis and Microascus genera cause a wide range of infections, with S. brevicaulis being the most prevalent aetiological agent of mould onychomycosis. Proper identification of these pathogens requires sporulating culture, which considerably delays the diagnosis. So far, sequencing of rDNA regions of clinical isolates has produced ambiguous results due to the lack of reference sequences in publicly available databases. Thus, there is a clear need for the development of new molecular methods that would provide simple, rapid and highly specific identification of Scopulariopsis and Microascus species. The objective of this study was to develop simple and fast assays based on PCR and real-time PCR for specific detection of fungi from Scopulariopsis and Microascus genera, and separately, S. brevicaulis species.

Methods

On the basis of alignment of β-tubulin gene sequences, Microascus/Scopulariopsis-specific primers were designed and S. brevicaulis-specific primers were reevaluated. DNA from cultured fungal isolates, extracted in a two-step procedure, was used in Microascus/Scopulariopsis-specific and S. brevicaulis-specific PCR and real-time PCR followed by electrophoresis or melting temperature analysis, respectively.

Results

The specificity of the assays was confirmed, as positive results were obtained only for Scopulariopsis spp. and Microascus spp. isolates tested in Microascus/Scopulariopsis-specific assay, and only for S. brevicaulis and S. koningii (syn. S. brevicaulis) isolates in a S. brevicaulis-specific assay, respectively, and no positive results were obtained neither for other moulds, dermatophytes, yeast-like fungi, nor for human DNA.

Conclusions

The developed assays enable fast and unambiguous identification of Microascus spp. and Scopulariopsis spp. pathogens.

Multiple mechanisms contribute to the development of clinically significant azole resistance in Aspergillus fumigatus

Infections caused by the filamentous fungus Aspergillus fumigatus are a significant clinical issue and represent the second most-common form of fungal infection. Azole drugs are effective against this pathogen but resistant isolates are being found more frequently. Infections associated with azole resistant A. fumigatus have a significantly increased mortality making understanding drug resistance in this organism a priority. The target of azole drugs is the lanosterol α-14 demethylase enzyme encoded by the cyp51A gene in A. fumigatus. Mutations in cyp51A have been described that give rise to azole resistance and been argued to be the primary, if not sole, contributor to azole resistance. Here, I discuss recent developments that indicate multiple mechanisms, including increased expression of ATP-binding cassette (ABC) transporter proteins, contribute to azole resistance. ABC transporters are well-established determinants of drug resistance in other fungal pathogens and seem likely to play a similar role in A. fumigatus.

Silver and gold nanostructures: antifungal property of different shapes of these nanostructures on Candida species

The shape of nanoparticles is an important determinant of their physical and chemical properties, possibly including the little-explored area of their use as antifungal agents. Therefore, we evaluated the in vitro antifungal activities of three different shapes of silver and gold nanostructures, including nanocubes, nanospheres, and nanowires, on Candida albicans, C. glabrata and C. tropicalis, using the microdilution and disk diffusion methods as per the guidelines of the Clinical and Laboratory Standards Institute. We found that silver and gold nanocubes had higher antifungal properties against the test species than nanospheres and nanowires. While some isolates were resistant to silver and gold nanospheres and nanowires, none of the isolates were resistant to silver and gold nanocubes. The occurrence of resistance is a new finding which should be further explored.

Sub-inhibitory concentrations of antifungals suppress hemolysin activity of oral Candida albicans and Candida tropicalis isolates from HIV-infected individuals

Secretion of hydrolytic enzymes such as hemolysin is considered an important virulence attribute of the opportunistic pathogenic fungus Candida. It is known that Candida spp. isolated from HIV-infected patients produce copious hemolysins. As common antifungal agents may perturb the production of extracellular enzymes, we evaluated the effect of three antifungals nystatin, amphotericin B and fluconazole on the hemolytic activity of Candida albicans and Candida tropicalis isolates from HIV-infected individuals. The impact of antimycotics on hemolytic activity was assessed by a previously described in vitro plate assay, after exposing ten isolates each of C. albicans and C. tropicalis recovered from HIV-infected individuals to sub-minimum inhibitory concentrations (sub-MIC) of nystatin, amphotericin B and fluconazole. All Candida isolates showed a significant reduction in hemolytic activity. The reduction was highest for amphotericin B-exposed C. albicans and C. tropicalis followed by nystatin and fluconazole. The effect of antimycotics was more pronounced on the hemolytic activity of C. tropicalis compared to that of C. albicans. Commonly used antifungal agents significantly suppress hemolysin activity of Candida species. This implies that the antifungals, in addition to their lethality, may modulate key virulence attributes of the yeast. The clinical relevance of this phenomenon in HIV disease and other similar pathologies remains to be determined.

Effects of fluconazole on Candida glabrata biofilms and its relationship with ABC transporter gene expression

Candida glabrata has emerged as the second most prevalent fungal pathogen and its ability to form biofilms has been considered one of the most important virulence factors, since biofilms present a high tolerance to antifungal agents used in fungal infection treatment. The mechanisms of biofilm tolerance to antifungal agents remain poorly understood. Thus, the aim of this study was to evaluate the effects of fluconazole (FLU) on the formation and control of C. glabrata biofilms and its relation with the expression of genes encoding for ABC transporters, CDR1, SNQ2, and PDR1. For that, minimal inhibitory concentration values for seven C. glabrata strains were determined and the effect of FLU against C. glabrata biofilms was evaluated by total biomass quantification and viable cell enumeration. Matrices from biofilms were analyzed in terms of protein, carbohydrate and DNA content. ABC transporter gene expression was analyzed for quantitative real-time PCR. In addition to the high amounts of proteins and carbohydrates detected in the extracellular matrices in the presence of FLU, this work showed that the overexpression of efflux pumps is a possible mechanism of biofilm tolerance to FLU and this phenomenon alters the structure of C. glabrata biofilms by creating cell clusters.

The yeast anaerobic response element AR1b regulates aerobic antifungal drug-dependent sterol gene expression

Saccharomyces cerevisiae ergosterol biosynthesis, like cholesterol biosynthesis in mammals, is regulated at the transcriptional level by a sterol feedback mechanism. Yeast studies defined a 7-bp consensus sterol-response element (SRE) common to genes involved in sterol biosynthesis and two transcription factors, Upc2 and Ecm22, which direct transcription of sterol biosynthetic genes. The 7-bp consensus SRE is identical to the anaerobic response element, AR1c. Data indicate that Upc2 and Ecm22 function through binding to this SRE site. We now show that it is two novel anaerobic AR1b elements in the UPC2 promoter that direct global ERG gene expression in response to a block in de novo ergosterol biosynthesis, brought about by antifungal drug treatment. The AR1b elements are absolutely required for auto-induction of UPC2 gene expression and protein and require Upc2 and Ecm22 for function. We further demonstrate the direct binding of recombinant expressed S. cerevisiae ScUpc2 and pathogenic Candida albicans CaUpc2 and Candida glabrata CgUpc2 to AR1b and SRE/AR1c elements. Recombinant endogenous promoter studies show that the UPC2 anaerobic AR1b elements act in trans to regulate ergosterol gene expression. Our results indicate that Upc2 must occupy UPC2 AR1b elements in order for ERG gene expression induction to take place. Thus, the two UPC2-AR1b elements drive expression of all ERG genes necessary for maintaining normal antifungal susceptibility, as wild type cells lacking these elements have increased susceptibility to azole antifungal drugs. Therefore, targeting these specific sites for antifungal therapy represents a novel approach to treat systemic fungal infections.