Table 1.

Gene expression studies on C. albicans biofilm and drug resistance.

Methodology/Platform	Biological Issue Studied	Major Findings	Reference
Microarrays with probes for C. albicans genes/Eurogentec (Seraing, Belgium)	Transcription profiles of biofilm cells vs. planktonic cells under different conditions of flow, oxygenation, and glucose concentration	Gcn4p, a regulator of amino acid metabolism, is required for biofilm growth	[63]
Microarrays/Eurogentec SA (Ivoz-Ramet, Belgium) in collaboration with European Galar Fungail Consortium (www.pasteur.fr)	Genome-wide expression profile of C. albicans to polyene, pyrimidine, azole, and echinocandin antifungal agents	Different expression profile signatures obtained in exposure to different classes of antifungals with various genes overexpressed	[64]
Oligonucleotide microarray (Agilent Technologies, Santa Clara, CA, USA) with C. albicans Assembly 21 genome (http://www.candidagenome.org/), Full Genome Chromatin Immunoprecipitation Tiling Microarray (ChIP-chip), RNA Sequencing (RNA-seq)	Comparative transcriptional analysis of C. albicans biofilm and planktonic cells, with C. albicans transcription regulator (TR) deletion mutants that are deficient in biofilm formation	Six master regulators Bcr1, Tec1, Efg1, Ndt80, Rob1, and Brg1 are essential for biofilm formation.	[25]
NanoString expression profiling and nCounter platform (NanoString Technologies, Inc., Seattle, US) with ~150 probes from cell wall-related genes, ~50 host-pathogen interaction genes, ~100 genes highly regulated during hypha development or biofilm formation, oxidative or osmotic stress	Expression profiling of genes involved in C. albicans adherence to substrate (silicone), an early step in medical device-related infections	Biofilm regulators Bcr1 and Ace2 have a role in adherence. A large regulatory network of 11 adherence regulators, the zinc-response regulator Zap1, and approximately 25% of the predicted cell surface protein genes known as Cell Surface Targets of Adherence Regulators (CSTARs) are involved in adherence.	[27]
RNA-sequencing (mRNA-Seq 8, Illumina) and Genome Analyzer (Illumina Inc.)	Transcriptome analysis of a Candida Drug Resistance (CDR) strain against its isogenic drug susceptible counterpart	Identified ∼50 genes overexpressed in CDR strain: CZF1 which is involved in transcription regulation of white/opaque switching and hypha formation is upregulated with CDR1 and CDR2, 5’UTR region of TAC1	[45]
Gene expression microarrays (Agilent Technologies), Chromatin immunoprecipitation quantitative real-time PCR (ChIP-qPCR)	Genome-wide expression analysis of biofilm formation at different intervals, immediately after adherence, at 8, 24 and 48 h	Identified Flo8, Gal4, and Rfx2 to be involved in different time points of biofilm formation	[26]
High-throughput next-generation sequencing/Hi-Seq 2500 platform (Illumina)	Use pooled Gene Replacement and Conditional Expression (GRACE) library conditional expression strains to identify novel regulators of cell-to-surface adherence	Novel functional relationship between the Arp2/3 complex and Rho1 important for modulating actin cytoskeleton, endocytosis and cell wall remodeling,	[28]
RNA-seq with TruSeq RNA v2 kit/HiSeq2500 platform (Illumina)	Transcriptomic profiling of 124 mutant C. albicans strains in 10 in vitro conditions for filamentation ability	Genes encoding cell wall/membrane proteins, adhesins, alcohol dehydrogenases, and iron uptake and utilization genes were common genes upregulated across different conditions	[65]
Candida genome microarray (CapitalBio Corp., Beijing, China) with C. albicans genome database (http://www.candidagenome.org/)/CapitalBio BioMixer II hybridization station	Gene expression profiling of fluconazole-resistant C. albicans strain treated with osthole (a natural coumarin) in synergy with fluconazole	Genes in oxidation-reduction process (e.g., catalase encoded by CAT1 and mitochondrial glycosylase encoded by OGG1); CTN1 (carnitine acetyltransferase) and ICL1 (isocitrate lyase) were upregulated	[66]
RNA-seq with BIOO Scientific NEXTflex Directional RNA-seq kit/HiSeq2000 platform (Illumina)	To decipher transcriptional gene expression patterns of dispersal cells versus core biofilm cells and planktonic cells	Transcription pattern of dispersal cells mostly similar to parent biofilm, YWP1 expression ~2-fold higher in dispersal > biofilm > planktonic cells; ~33% of dispersal yeast cells express HWP1	[23]