S2.5d Exploring multidrug resistance, fitness compensation, and collateral sensitivity in Candida auris : Fight fire with fire?

S2.5 Rare yeasts, September 21, 2022, 3:00 PM - 4:30 PM

Candida auris (C. auris) is a recently emerged human fungal pathogen of growing concern due to its ability to acquire extensive multidrug resistance (MDR) to all four antifungal drug classes. The unprecedented extent of MDR in C. auris, suggests accelerated resistance evolution, novel mechanisms of resistance, and/or potential fitness compensation. Despite being the first fungus to be officially considered an urgent antimicrobial resistance threat by the CDC (US), insights into the resistance mechanisms and evolutionary dynamics of C. auris are still scarce.

 

By using high-throughput in vitro experimental evolution with various antifungal drugs, we have obtained a library of resistant strains from four different clades. Through both genome and targeted sequencing, we have discovered novel mutations, especially for polyene resistance, which indicate new mechanisms of resistance and fitness compensation. For the validation of mutations, we have optimized a recyclable CRISPR/Cas9 tool for C. auris based on the C. albicans HIS-FLP system.

 

By mapping drug susceptibility responses of evolved strains across a library of several antifungals and repurposed drugs, we have discovered trends of cross-resistance and collateral sensitivity. Both phenomena have been extensively studied in tumors and bacteria but remain unexplored in fungi. In the light of these observations, we explore novel treatment schemes that prevent antifungal drug resistance development in C. auris and other pathogenic fungi.

Genome-wide analysis of experimentally evolved Candida auris reveals multiple novel mechanisms of multidrug-resistance

Candida auris is globally recognized as an opportunistic fungal pathogen of high concern, due to its extensive multidrug-resistance (MDR). Still, molecular mechanisms of MDR are largely unexplored. This is the first account of genome wide evolution of MDR in C. auris obtained through serial in vitro exposure to azoles, polyenes and echinocandins. We show the stepwise accumulation of multiple novel mutations in genes known and unknown in antifungal drug resistance, albeit almost all new for C. auris. Echinocandin resistance was accompanied by a codon deletion in FKS1hot spot 1 and a substitution in FKS1 ‘novel’ hot spot 3. Mutations in ERG3 and CIS2 further increased the echinocandin MIC. Decreased azole susceptibility was linked to a mutation in transcription factor TAC1b and overexpression of the drug efflux pump Cdr1; a segmental duplication of chromosome 1 containing ERG11; and a whole chromosome 5 duplication, which contains TAC1b. The latter was associated with increased expression of ERG11, TAC1band CDR2, but not CDR1. The simultaneous emergence of nonsense mutations in ERG3 and ERG11 was shown to decrease amphotericin B susceptibility, accompanied with fluconazole cross resistance. A mutation in MEC3, a gene mainly known for its role in DNA damage homeostasis, further increased the polyene MIC. Overall, this study shows the alarming potential and diversity for MDR development in C. auris, even in a clade until now not associated with MDR (clade II),hereby stressing its clinical importance and the urge for future research.

Genome-Wide Analysis of Experimentally Evolved Candida auris Reveals Multiple Novel Mechanisms of Multidrug Resistance

Candida auris is globally recognized as an opportunistic fungal pathogen of high concern, due to its extensive multidrug resistance (MDR). Still, molecular mechanisms of MDR are largely unexplored. This is the first account of genome-wide evolution of MDR in C. auris obtained through serial in vitro exposure to azoles, polyenes, and echinocandins. We show the stepwise accumulation of copy number variations and novel mutations in genes both known and unknown in antifungal drug resistance. Echinocandin resistance was accompanied by a codon deletion in FKS1 hot spot 1 and a substitution in FKS1 "novel" hot spot 3. Mutations in ERG3 and CIS2 further increased the echinocandin MIC. Decreased azole susceptibility was linked to a mutation in transcription factor TAC1b and overexpression of the drug efflux pump Cdr1, a segmental duplication of chromosome 1 containing ERG11, and a whole chromosome 5 duplication, which contains TAC1b The latter was associated with increased expression of ERG11, TAC1b, and CDR2 but not CDR1 The simultaneous emergence of nonsense mutations in ERG3 and ERG11 was shown to decrease amphotericin B susceptibility, accompanied with fluconazole cross-resistance. A mutation in MEC3, a gene mainly known for its role in DNA damage homeostasis, further increased the polyene MIC. Overall, this study shows the alarming potential for and diversity of MDR development in C. auris, even in a clade until now not associated with MDR (clade II), stressing its clinical importance and the urge for future research.IMPORTANCECandida auris is a recently discovered human fungal pathogen and has shown an alarming potential for developing multi- and pan-resistance toward all classes of antifungals most commonly used in the clinic. Currently, C. auris has been globally recognized as a nosocomial pathogen of high concern due to this evolutionary potential. So far, this is the first study in which the stepwise progression of multidrug resistance (MDR) in C. auris is monitored in vitro Multiple novel mutations in known resistance genes and genes previously not or vaguely associated with drug resistance reveal rapid MDR evolution in a C. auris clade II isolate. Additionally, this study shows that in vitro experimental evolution can be a powerful tool to discover new drug resistance mechanisms, although it has its limitations.

Amphotericin B and Other Polyenes-Discovery, Clinical Use, Mode of Action and Drug Resistance

Although polyenes were the first broad spectrum antifungal drugs on the market, after 70 years they are still the gold standard to treat a variety of fungal infections. Polyenes such as amphotericin B have a controversial image. They are the antifungal drug class with the broadest spectrum, resistance development is still relatively rare and fungicidal properties are extensive. Yet, they come with a significant host toxicity that limits their use. Relatively recently, the mode of action of polyenes has been revised, new mechanisms of drug resistance were discovered and emergent polyene resistant species such as Candida auris entered the picture. This review provides a short description of the history and clinical use of polyenes, and focusses on the ongoing debate concerning their mode of action, the diversity of resistance mechanisms discovered to date and the most recent trends in polyene resistance development.

Disruption of autophagy by the histone deacetylase inhibitor MGCD0103 and its therapeutic implication in B-cell chronic lymphocytic leukemia

Evading apoptosis is a hallmark of B-cell chronic lymphocytic leukemia (CLL) cells and an obstacle to current chemotherapeutic approaches. Inhibiting histone deacetylase (HDAC) has emerged as a promising strategy to induce cell death in malignant cells. We have previously reported that the HDAC inhibitor MGCD0103 induces CLL cell death by activating the intrinsic pathway of apoptosis. Here, we show that MGCD0103 decreases the autophagic flux in primary CLL cells. Activation of the PI3K/AKT/mTOR pathway, together with the activation of caspases, and to a minor extent CAPN1, resulting in cleavage of autophagy components, were involved in MGCD0103-mediated inhibition of autophagy. In addition, MGCD0103 directly modulated the expression of critical autophagy genes at the transcriptional level that may contribute to autophagy impairment. Besides, we demonstrate that autophagy is a pro-survival mechanism in CLL whose disruption potentiates cell death induced by anticancer molecules including HDAC and cyclin-dependent kinase inhibitors. In particular, our data highlight the therapeutic potential of MGCD0103 as not only an inducer of apoptosis but also an autophagy suppressor in both combination regimens with molecules like flavopiridol, known to induce protective autophagy in CLL cells, or as an alternative to circumvent undesired immunomodulatory effects seen in the clinic with conventional autophagy inhibitors.

Suppression of Epstein-Barr virus reactivation in lymphoblastoid cells cultured in simulated microgravity

Rotating-wall vessels allow for the growth of cells in simulated microgravity. Lymphoblastoid cells cultured in rotating-wall vessels exhibited significant differences in the expression of both early and late Epstein-Barr Virus (EBV) antigens. Viral protein expression (as measured by indirect immunofluorescence) was significantly suppressed in cells cultured in simulated microgravity. A significantly greater percentage of P3HR-1 cells and Daudi cells were positive for the expression of BamH1-Z-DNA fragment of Epstein-Barr replication activator (ZEBRA), early antigen restricted (EA-R), and viral capsid antigen (VCA) in cells cultured in static tissue culture flasks as compared to cells cultured in rotating-wall vessels. We observed a 7, 11, and 25-fold reduction, respectively, for EA-R, VCA, and ZEBRA protein in P3HR-1 cells cultured in simulated microgravity. Additionally, suspension cultures of P3HR-1 cells exhibited significantly greater ZEBRA antigen expression than cells cultured in rotating-wall vessels. As an independent confirmation of the reduction in ZEBRA-protein production in simulated microgravity in P3HR-1 cells, ZEBRA-mRNA was quantitated by reverse transcription polymerase chain reaction. We observed between a 4 to 10-fold reduction in ZEBRA-mRNA in cells cultured in simulated microgravity as compared to cells cultured at 1 x g in tissue culture flasks. Rotating-wall vessels, by virtue of providing a simple culture environment triggering marked differences in viral activation, provide a model whereby both host and viral factors involved in regulating the maintenance of EBV latency can be examined.

Rhinovirus replication in HeLa cells cultured under conditions of simulated microgravity

BACKGROUND

Rotating-wall vessels (RWVs) allow for the growth of cells under conditions of simulated microgravity. Information about the replication of viruses in simulated microgravity using RWVs has not been reported. Cells grown in RWVs are subjected to low shear motion, and the replication of certain viruses such as rhinoviruses has been reported to be enhanced by motion.

HYPOTHESIS

Our research was based on the hypothesis that rhinovirus replication would be enhanced under conditions of simulated microgravity.

METHODS

HeLa cells were cultured in three-dimensional cultures on microcarrier beads in simulated microgravity using RWVs and in sealed Teflon roller bottles. Two-dimensional cultures of HeLa cells were also grown in tissue culture flasks (T-150s). Viral infections for all cultures were carried out under standardized conditions at 1 x g. The amount of new virus released during the first viral replication cycle and the total viral yields obtained from multiple viral replication cycles were determined.

RESULTS

Viral quantitation during the first viral replication cycle showed that after 10-13 h RWV and Teflon roller bottle supernatants contained significantly more virus than the supernatants from T-150 cultures. After multiple viral replication cycles (at 24, 48, 72, and 96 h following infection), total viral samples (both free and cell-associated virus) from RWV cultures contained significantly more virus than Teflon roller bottle cultures.

CONCLUSIONS

The rhinovirus replication cycle was enhanced in cultures grown in the presence of motion (Teflon roller bottle cultures and RWV cultures). Additionally, multiple rounds of rhinovirus replication yielded more virus in simulated microgravity conditions. Viral transmission in cell cultures in RWVs was efficient and was similar to or better than what occurred in the Teflon roller bottles. The cultivation of cells in simulated microgravity possibly affected the rate of viral adsorption/uptake, the viral replication cycle, and/or the viral yield. RWVs provide an effective means for culturing human rhinoviruses.

Membrane insertion, glycosylation, and oligomerization of inositol trisphosphate receptors in a cell-free translation system

In order to study the membrane topology, processing, and oligomerization of inositol trisphosphate receptor (IP3R) isoforms, we have utilized RNA templates encoding putative transmembrane domains to program a cell-free translation system of rabbit reticulocyte lysates supplemented with canine pancreas microsomes. In the absence of microsomes, translation of the RNA templates encoding all the putative transmembrane domains present in the C-terminal segment of the type I (1TM) and type III (3TM) IP3R isoforms resulted in a 62- and 59-kDa polypeptide, respectively. In both cases, an additional band approximately 3 kDa larger was observed upon the addition of microsomes. Both bands in the translation doublet were integrated into microsomal membranes and were full-length translation products, as shown by sedimentation through a sucrose cushion and immunoprecipitation with C-terminal isoform-specific antibodies. With both isoforms, N-glycopeptidase F digestion indicates that the upper band in the doublet corresponds to a glycosylated translation product. A 17-kDa protected fragment was observed after proteinase-K digestion of 1TM translated in the presence of microsomes. The pattern and size of protected fragments was consistent with the current six-transmembrane domain model of IP3R topology. Cotranslation of both 1TM and 3TM RNA templates in the presence of microsomes followed by immunoprecipitation with isoform specific antibodies revealed coimmunoprecipitation of translation products. This was not observed when the isoforms were translated separately and then mixed, suggesting that heteroligomerization occurs cotranslationally. A construct encoding only the first putative transmembrane domain of the type I isoform was found to be sufficient for integration into membranes but was unable to oligomerize with either 1TM or 3TM. Cotranslation experiments using additional constructs indicate that the major structural determinant for homoligomerization lies between putative transmembrane domain 5 and the C terminus. A second oligomerization domain involved in stabilization of heteroligomers is present within the first four transmembrane domains.

Heteroligomers of type-I and type-III inositol trisphosphate receptors in WB rat liver epithelial cells

We have previously shown that a 222-kDa polypeptide co-immunoprecipitates together with the type-I myoinositol 1,4,5-trisphosphate receptor (IP3R) in WB rat liver epithelial cell extracts, when the immunoprecipitation is carried out with a type-I isoform specific antibody (Joseph, S. K. (1994) J. Biol. Chem. 269, 5673-5679). Utilizing isoform-specific antibodies raised to unique sequences within the COOH-terminal region of IP3 receptors, we now report that the co-immunoprecipitating 222-kDa polypeptide is the type-III IP3R isoform and that type-III IP3R antibodies (Abs) can co-immunoprecipitate the type-I IP3R isoform. Co-immunoprecipitation of IP3R isoforms was not due to cross-reactivity of the antibodies for the following reasons: (a) on immunoblots the type-III antibodies did not cross-react with type-I IP3R and vice versa; (b) inclusion of the COOH-terminal type-III peptide had no effect on the ability of type-I IP3R Ab to co-immunoprecipitate the type-III IP3R but blocked the ability of type-III IP3R Ab to coimmunoprecipitate the type-I isoform; and (c) crude hepatocyte lysates contain undetectable amounts of type-III IP3R, and immunoprecipitation with type-III IP3R Ab does not co-immunoprecipitate any other isoforms. However, type-I and type-II IP3R isoforms were co-immunoprecipitated by their respective antibodies in hepatocyte lysates. Sucrose density gradient analysis of WB cell lysates indicated that the co-immunoprecipitating fraction is exclusively located at the density expected for tetrameric receptors, suggesting that co-immunoprecipitation was not a reflection of the nonspecific aggregation of IP3R isoforms. Phosphorylation of either type-I or type-III immunoprecipitates by protein kinase A indicated that only the type-I IP3R could be phosphorylated in vitro. Fractionation of WB cell membranes and immunofluorescence studies showed that the type-I and type-III isoforms have very similar sub-cellular localizations. We conclude that the WB cell contains both type-I and type-III IP3R isoforms and that a proportion of these receptors exist as heterotetramers.

Trypsin digestion of the inositol trisphosphate receptor: implications for the conformation and domain organization of the protein

Limited digestion of rat cerebellum microsomal vesicles with trypsin resulted in the proteolysis of the 240 kDa inositol 1,4,5-trisphosphate receptor (IP3R) and the formation of a 94 kDa species that remained membrane-bound and retained immunoreactivity to an antibody raised against the C-terminal sequence of this protein. The appearance of the 94 kDa species was associated with a loss of [3H]IP3 binding sites in the membrane and the appearance of [3H]IP3 binding sites in the soluble fraction. The 94 kDa fragment retained reactivity to biotinylated concanavalin A. In vitro phosphorylation of the IP3R in membranes with cyclic AMP-dependent protein kinase and [gamma-32P]ATP produced an unlabelled 94 kDa fragment after tryptic digestion. According to current models of the cerebellar IP3R this would place the proteolytic site between the phosphorylation site at serine-1755 and the first transmembrane segment of the IP3R. A second antibody raised to amino acids 401-414 in the N-terminal region of the receptor recognizes a 68 kDa fragment released into the soluble fraction after trypsin treatment. The time course of release of the 68 kDa fragment was correlated with the appearance of soluble binding sites, and the fragment was bound by IP3-Affigel resin. A large proportion of the 68 kDa fragment remained associated with the membrane fraction and could be specifically immunoprecipitated from detergent extracts of digested membranes by anti-C-terminus antibody. Our results provide experimental evidence to further localize the ligand binding domain and suggest that regions of the N-terminus and C-terminus may be non-covalently associated.

The effect of mersalyl on inositol trisphosphate receptor binding and ion channel function

A number of thiol-reactive agents induce repetitive Ca2+ spiking in cells by a mechanism thought to involve sensitization of the inositol 1,4,5-trisphosphate receptor (IP3R). To further define the basis of this interaction, we have studied the effect of several thiol-reactive agents on [3H]IP3 binding, IP3-gated channel activity, and conformation of the IP3R in membranes from hepatocytes, cultured WB rat liver epithelial cells, and cerebellum microsomes. At 4 degrees C, the organomercurial thiol-reactive agent mersalyl markedly stimulates (3-4fold) [3H]IP3 binding to permeabilized hepatocytes. The closely related molecule, thimerosal, has only a small stimulatory effect under these conditions, and GSSG or N-ethylmaleimide are without effect. The stimulatory effect of mersalyl was associated with a decrease in Kd of the IP3R with no change in Bmax. Mersalyl was without effect on detergent-solubilized hepatocyte binding sites or on the [3H]IP3 binding activity of cerebellum microsomes. In contrast to thimerosal, which potentiates IP3-mediated Ca2+ release, mersalyl blocked IP3-gated Ca2+ channels. Mersalyl pretreatment of WB membranes altered the pattern of immunoreactive receptor fragments generated upon subsequent cleavage of the receptor with proteinase K. This effect was not reproduced by thimerosal and was also not observed in experiments on cerebellum microsomes. We conclude that the WB cell and brain IP3 receptors are differently regulated by modification of thiol groups. Reaction of the WB cell IP3 receptor with mersalyl alters its conformation and modifies the accessibility of sites on the protein that are cleaved by proteinase K. In the presence of mersalyl, the receptor has high affinity for IP3 but is inactive as a Ca2+ channel. This contrasts with the high affinity receptor/active Ca2+ channel induced by thimerosal, suggesting that even closely related thiol agents may interact at different thiol groups.

Rapid restoration of B-cell function in XID mice by intravenous transfer of peritoneal cavity B cells

The primary method employed to correct immune deficiency is bone marrow transfer. Depending upon the exact nature of the immune deficiency, however, alternative cell sources may be used to provide a more rapid reconstitution of immune function. In this report, peritoneal cavity (PerC) B cells are shown to be effective in the rapid emendation of the B-cell defect exhibited by XID mice. Restoration of normal numbers of splenic IgM antibody-secreting cells (ASC) and serum IgM levels were observed 4 and 7 days, respectively, after the i.v. transfer of 3 x 10(6) PerC. This regimen also restored responsiveness to thymus-independent type 2 (TI-2) antigens in XID recipients. Transfer of 30 x 10(6) spleen (SP) cells restored these functions in XID recipients but at a considerably slower rate. The data indicate that introducing a small number of PerC B cells into systemic circulation results in the rapid restoration of serum IgM levels in unirradiated XID mice.

Treatment of stiff-man syndrome with intravenous immune globulin

OBJECTIVE

To evaluate the efficacy of intravenous immune globulin (IVIG) in the treatment of stiff-man syndrome (SMS).

METHODS

An open, unblinded study of 3 patients with active disease and/or disease refractory to treatment with diazepam and/or corticosteroids.

RESULTS

All 3 bedridden patients improved substantially shortly after infusion with IVIG and regained function.

CONCLUSION

IVIG may be useful for the treatment of SMS.

Stability of long-term renal function in heart transplant patients treated with induction therapy and low-dose cyclosporine

Long-term renal function was evaluated in heart transplant recipients who were treated with antilymphocyte globulin induction therapy and low-dose cyclosporine therapy. Although an initial 16% drop in the glomerular filtration rate occurred, long-term follow-up revealed stability of renal function. Four-year patient survival was 77.6%. Use of induction therapy with low-dose cyclosporine may preserve renal function without compromising long-term patient survival.

Efficacy of graded elastic compression in the lower leg

Graded elastic compression stockings on the lower leg were evaluated for their ability to (1) decrease leg volume, (2) decrease circumference, and (3) alleviate discomfort. One hundred three test subjects participated in this study, including 30 normal, asymptomatic control subjects. The conditions of the 73 symptomatic patients were categorized by pain and swelling, varicose veins, venous stasis, lymphedema, and phlebitis, which constituted symptoms in 120 legs. Although total body weight did not change during the week of observation, the volume, circumference, and pain decreased in the symptomatic group. The volume of the stockinged leg decreased in comparison with the nonstockinged control leg in the asymptomatic subjects as well. We conclude that non-custom-made graded elastic stockings with 24 mm Hg of pressure at the ankle are effective in decreasing volume, circumference, and symptoms in the lower leg in patients with minimal problems during a one-week period.