Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans

Abstract

The fungus Cryptococcus neoformans is a leading cause of mortality and morbidity among HIV-infected individuals. We utilized the completed genome sequence and optimized methods for homologous DNA replacement using high-velocity particle bombardment to engineer 1201 gene knockout mutants. We screened this resource in vivo for proliferation in murine lung tissue and in vitro for three well-recognized virulence attributes-polysaccharide capsule formation, melanization, and growth at body temperature. We identified dozens of previously uncharacterized genes that affect these known attributes as well as 40 infectivity mutants without obvious defects in these traits. The latter mutants affect predicted regulatory factors, secreted proteins, and immune-related factors, and represent powerful tools for elucidating novel virulence mechanisms. In particular, we describe a GATA family transcription factor that inhibits phagocytosis by murine macrophages independently of the capsule, indicating a previously unknown mechanism of innate immune modulation.

Figures

Figure 1

Schematic overview of systematic phenotypic profiling strategy utilized in this work.

Figure 2. In vivo signature-tagged mutagenesis (STM) analysis of gene deletions

(A) Mutants were pooled in groups of 48 and used to intranasally infect three mice. Quantitative PCR with signature tag-specific primers was used to calculate an STM score for each mutant. Red-dotted lines indicate cutoffs used to identify STM phenotypes of interest. (B) 104 mutants assayed by STM were sorted into new pools containing different competitors and retested. Original STM scores show a strong correlation with repooled STM scores. (C) The frequencies of STM scores observed in this screen were plotted for both the deletion collection and the sxi1Δ control strains. Red-dotted lines indicate cutoffs used to identify STM phenotypes of interest. Indicated below are the STM scores of gene knockouts in the collection previously reported to have (red) or not to have (black) virulence defects. (D–E) Survival curve analyses of mice infected with individual strains demonstrate the correlation between STM phenotypes and virulence phenotypes. Both hypovirulent and hypervirulent strains were accurately identified by STM. P-values indicate the significance of the virulence phenotype. (F) Shown is the distribution of in vivo and in vitro phenotypes in the deletion collection. Significant overlaps were seen between mutants with defects in the three virulence attributes and mutants with in vivo infectivity defects.

Figure 3. Proteins identified in this work that regulate capsule formation, melanization, and/or infectivity

Factors previously reported to affect these phenotypes and factors that affect growth in YNB are not included. Proteins predicted to encode signal peptides are outlined in red. The relationships between melanization, dissemination, and lung infectivity are discussed in the text.

Figure 4. Gat201 is a regulator of multiple virulence pathways

(A) gat201Δ mutant strains (two independent knockout strains) were avirulent during monotypic infection and a GAT201 overexpression strain was hypervirulent. (B) gat201Δ mutant strains did not induce an observable capsule by India ink staining in capsule-inducing conditions, though capsule polysaccharide on the cell surface was detected by antibody staining (Figure 5B). GAT201 overexpression resulted in ectopic capsule formation in normally non-inducing conditions. Quantification of capsule size is shown in Figure S11. (C) gat201Δ mutants strains showed increased melanization while a GAT201 overexpression strain showed decreased melanization. (D) Transcriptional profiles of pRPL2b::GAT201 and wild-type grown at 37°C in minimal medium were compared using whole-genome microarrays. Values represent the average of four microarrays.

Figure 5. Gat201 inhibits phagocytosis independent of capsule

(A–B) Phagocytosis of untreated wild-type (WT) and gat201Δ cells by RAW264.7 macrophages was measured in both WT and capsule-deficient backgrounds. The percentage of macrophages containing internalized C. neoformans cells was determined after 24 hours of co-incubation. Data are represented as mean +/− SD from triplicate well s. (C) GXM can be detected on the cell surface of gat201Δ cells, but not in single and double mutants containing deletions of CAP genes. (D) Model of GAT201 regulation of phagocytosis. “X” represents a novel capsule-independent mechanism for inhibiting phagocytosis by macrophages.