Abstract
Mycoses are infectious diseases caused by fungi, which incidence has increased in recent decades due to the increasing number of immunocompromised patients and improved diagnostic tests. As eukaryotes, fungi share many similarities with human cells, making it difficult to design drugs without side effects. Commercially available drugs act on a limited number of targets and have been reported fungal resistance to commonly used antifungal drugs. Therefore, elucidating the pathogenesis of fungal infections, the fungal strategies to overcome the hostile environment of the host, and the action of antifungal drugs is essential for develo** new therapeutic approaches and diagnostic tests. Large-scale transcriptional analyses using microarrays and RNA sequencing (RNA-seq), combined with improvements in molecular biology techniques, have improved the study of fungal pathogenicity. Such techniques have provided insights into the infective process by identifying molecular strategies used by the host and pathogen during the course of human mycoses. This chapter will explore the latest discoveries regarding the transcriptome of major human fungal pathogens. Further we will highlight genes essential for host–pathogen interactions, immune response, invasion, infection, antifungal drug response, and resistance. Finally, we will discuss their importance to the discovery of new molecular targets for antifungal drugs.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Aimanianda V, Bayry J, Bozza S, Kniemeyer O, Perruccio K, Elluru SR, Clavaud C, Paris S, Brakhage AA, Kaveri SV, Romani L, Latge JP (2009) Surface hydrophobin prevents immune recognition of airborne fungal spores. Nature 460(7259):1117–1121
Alanio A, Delliere S, Fodil S, Bretagne S, Megarbane B (2020) Prevalence of putative invasive pulmonary aspergillosis in critically ill patients with COVID-19. Lancet Respir Med 8(6):e48–e49
Amich J, Vicentefranqueira R, Leal F, Calera JA (2010) Aspergillus fumigatus survival in alkaline and extreme zinc-limiting environments relies on the induction of a zinc homeostasis system encoded by the zrfC and aspf2 genes. Eukaryot Cell 9 (3):424–437
Ballou ER, Avelar GM, Childers DS, Mackie J, Bain JM, Wagener J, Kastora SL, Panea MD, Hardison SE, Walker LA, Erwig LP, Munro CA, Gow NA, Brown GD, MacCallum DM, Brown AJ (2016) Lactate signalling regulates fungal beta-glucan masking and immune evasion. Nat Microbiol 2:16238
Barelle CJ, Priest CL, Maccallum DM, Gow NA, Odds FC, Brown AJ (2006) Niche-specific regulation of central metabolic pathways in a fungal pathogen. Cell Microbiol 8(6):961–971
Barker KS, Park H, Phan QT, Xu L, Homayouni R, Rogers PD, Filler SG (2008) Transcriptome profile of the vascular endothelial cell response to Candida albicans. J Infect Dis 198(2):193–202
Bedoya SK, Lam B, Lau K, Larkin J 3rd (2013) Th17 cells in immunity and autoimmunity. Clin Dev Immunol 2013:986789
Bielska E, May RC (2019) Extracellular vesicles of human pathogenic fungi. Curr Opin Microbiol 52:90–99
Billmyre RB, Applen Clancey S, Li LX, Doering TL, Heitman J (2020) 5-fluorocytosine resistance is associated with hypermutation and alterations in capsule biosynthesis in Cryptococcus. Nat Commun 11(1):127
Biondo C, Midiri A, Gambuzza M, Gerace E, Falduto M, Galbo R, Bellantoni A, Beninati C, Teti G, Leanderson T, Mancuso G (2008) IFN-alpha/beta signaling is required for polarization of cytokine responses toward a protective type 1 pattern during experimental cryptococcosis. J Immunol 181(1):566–573
Biondo C, Signorino G, Costa A, Midiri A, Gerace E, Galbo R, Bellantoni A, Malara A, Beninati C, Teti G, Mancuso G (2011) Recognition of yeast nucleic acids triggers a host-protective type I interferon response. Eur J Immunol 41(7):1969–1979
Bitencourt TA, Macedo C, Franco ME, Assis AF, Komoto TT, Stehling EG, Beleboni RO, Malavazi I, Marins M, Fachin AL (2016) Transcription profile of Trichophyton rubrum conidia grown on keratin reveals the induction of an adhesin-like protein gene with a tandem repeat pattern. BMC Genomics 17:249
Bitencourt TA, Rezende CP, Quaresemin NR, Moreno P, Hatanaka O, Rossi A, Martinez-Rossi NM, Almeida F (2018) Extracellular vesicles from the dermatophyte Trichophyton interdigitale modulate macrophage and keratinocyte functions. Front Immunol 9:2343
Bitencourt TA, Macedo C, Franco ME, Rocha MC, Moreli IS, Cantelli BAM, Sanches PR, Beleboni RO, Malavazi I, Passos GA, Marins M, Fachin AL (2019a) Trans-chalcone activity against Trichophyton rubrum relies on an interplay between signaling pathways related to cell wall integrity and fatty acid metabolism. BMC Genomics 20(1):411
Bitencourt TA, Oliveira FB, Sanches PR, Rossi A, Martinez-Rossi NM (2019b) The prp4 kinase gene and related spliceosome factor genes in Trichophyton rubrum respond to nutrients and antifungals. J Med Microbiol 68(4):591–599
Bitencourt TA, Lang EAS, Sanches PR, Peres NTA, Oliveira VM, Fachin AL, Rossi A, Martinez-Rossi NM (2020) HacA governs virulence traits and adaptive stress responses in Trichophyton rubrum. Front Microbiol 11:193
Bosch R, Garcia-Valdes E, Moore ER (2000) Complete nucleotide sequence and evolutionary significance of a chromosomally encoded naphthalene-degradation lower pathway from Pseudomonas stutzeri AN10. Gene 245(1):65–74
Brock M (2009) Fungal metabolism in host niches. Curr Opin Microbiol 12(4):371–376
Brown AJ, Haynes K, Quinn J (2009) Nitrosative and oxidative stress responses in fungal pathogenicity. Curr Opin Microbiol 12(4):384–391
Brown GD, Denning DW, Gow NA, Levitz SM, Netea MG, White TC (2012) Hidden killers: human fungal infections. Sci Transl Med 4(165):165rv113
Brown AJ, Budge S, Kaloriti D, Tillmann A, Jacobsen MD, Yin Z, Ene IV, Bohovych I, Sandai D, Kastora S, Potrykus J, Ballou ER, Childers DS, Shahana S, Leach MD (2014) Stress adaptation in a pathogenic fungus. J Exp Biol 217(Pt 1):144–155
Bruno M, Kersten S, Bain JM, Jaeger M, Rosati D, Kruppa MD, Lowman DW, Rice PJ, Graves B, Ma Z, Jiao YN, Chowdhary A, Renieris G, van de Veerdonk FL, Kullberg BJ, Giamarellos-Bourboulis EJ, Hoischen A, Gow NAR, Brown AJP, Meis JF, Williams DL, Netea MG (2020) Transcriptional and functional insights into the host immune response against the emerging fungal pathogen Candida auris. Nat Microbiol 5(12):1516–1531
Burmester A, Shelest E, Glockner G, Heddergott C, Schindler S, Staib P, Heidel A, Felder M, Petzold A, Szafranski K, Feuermann M, Pedruzzi I, Priebe S, Groth M, Winkler R, Li W, Kniemeyer O, Schroeckh V, Hertweck C, Hube B, White TC, Platzer M, Guthke R, Heitman J, Wostemeyer J, Zipfel PF, Monod M, Brakhage AA (2011) Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi. Genome Biol 12(1):R7
Burstein VL, Beccacece I, Guasconi L, Mena CJ, Cervi L, Chiapello LS (2020) Skin immunity to dermatophytes: from experimental infection models to human disease. Front Immunol 11:605644
Cairns T, Minuzzi F, Bignell E (2010) The host-infecting fungal transcriptome. FEMS Microbiol Lett 307(1):1–11
Cambier L, Weatherspoon A, Defaweux V, Bagut ET, Heinen MP, Antoine N, Mignon B (2014) Assessment of the cutaneous immune response during Arthroderma benhamiae and A. vanbreuseghemii infection using an experimental mouse model. Br J Dermatol 170(3):625–633
Cavalheiro M, Teixeira MC (2018) Candida biofilms: threats, challenges, and promising strategies. Front Med (Lausanne) 5:28
Cervelatti EP, Fachin AL, Ferreira-Nozawa MS, Martinez-Rossi NM (2006) Molecular cloning and characterization of a novel ABC transporter gene in the human pathogen Trichophyton rubrum. Med Mycol 44(2):141–147
Chen Y, Toffaletti DL, Tenor JL, Litvintseva AP, Fang C, Mitchell TG, McDonald TR, Nielsen K, Boulware DR, Bicanic T, Perfect JR (2014) The Cryptococcus neoformans transcriptome at the site of human meningitis. MBio 5(1):e01087–e01013
Citiulo F, Jacobsen ID, Miramón P, Schild L, Brunke S, Zipfel P, Brock M, Hube B, Wilson D (2012) Candida albicans Scavenges Host Zinc via Pra1 during Endothelial Invasion. Plos Pathogens 8(6):e1002777. https://doi.org/10.1371/journal.ppat.1002777
Cornet M, Gaillardin C (2014) pH signaling in human fungal pathogens: a new target for antifungal strategies. Eukaryot Cell 13(3):342–352
Cortez KJ, Lyman CA, Kottilil S, Kim HS, Roilides E, Yang J, Fullmer B, Lempicki R, Walsh TJ (2006) Functional genomics of innate host defense molecules in normal human monocytes in response to Aspergillus fumigatus. Infect Immun 74(4):2353–2365
Costa C, Ponte A, Pais P, Santos R, Cavalheiro M, Yaguchi T, Chibana H, Teixeira MC (2015) New mechanisms of flucytosine resistance in C. glabrata unveiled by a chemogenomics analysis in S. cerevisiae. PLoS One 10(8):e0135110
Coste AT, Karababa M, Ischer F, Bille J, Sanglard D (2004) TAC1, transcriptional activator of CDR genes, is a new transcription factor involved in the regulation of Candida albicans ABC transporters CDR1 and CDR2. Eukaryot Cell 3(6):1639–1652
Cowen LE (2009) Hsp90 orchestrates stress response signaling governing fungal drug resistance. PLoS Pathog 5(8):e1000471
da Silva Ferreira ME, Malavazi I, Savoldi M, Brakhage AA, Goldman MH, Kim HS, Nierman WC, Goldman GH (2006) Transcriptome analysis of Aspergillus fumigatus exposed to voriconazole. Curr Genet 50(1):32–44
da Silva LG, Martins MP, Sanches PR, Peres NTA, Martinez-Rossi NM, Rossi A (2020) Saline stress affects the pH-dependent regulation of the transcription factor PacC in the dermatophyte Trichophyton interdigitale. Braz J Microbiol 51(4):1585–1591
de Jesus-Berrios M, Liu L, Nussbaum JC, Cox GM, Stamler JS, Heitman J (2003) Enzymes that counteract nitrosative stress promote fungal virulence. Curr Biol 13(22):1963–1968
d’Enfert C, Kaune AK, Alaban LR, Chakraborty S, Cole N, Delavy M, Kosmala D, Marsaux B, Frois-Martins R, Morelli M, Rosati D, Valentine M, **e Z, Emritloll Y, Warn PA, Bequet F, Bougnoux ME, Bornes S, Gresnigt MS, Hube B, Jacobsen ID, Legrand M, Leibundgut-Landmann S, Manichanh C, Munro CA, Netea MG, Queiroz K, Roget K, Thomas V, Thoral C, Van den Abbeele P, Walker AW, Brown AJP (2020) The impact of the fungus-host-microbiota interplay upon Candida albicans infections: current knowledge and new perspectives. FEMS Microbiol Rev 45
Deng W, Liang P, Zheng Y, Su Z, Gong Z, Chen J, Feng P, Chen J (2020) Differential gene expression in HaCaT cells may account for the various clinical presentation caused by anthropophilic and geophilic dermatophytes infections. Mycoses 63(1):21–29
de-Souza-Silva CM, Hurtado FA, Tavares AH, de Oliveira GP Jr, Raiol T, Nishibe C, Agustinho DP, Almeida NF, Walter M, Nicola AM, Bocca AL, Albuquerque P, Silva-Pereira I (2020) Transcriptional remodeling patterns in murine dendritic cells infected with Paracoccidioides brasiliensis: more is not necessarily better. J Fungi (Basel) 6(4)
Dhamgaye S, Bernard M, Lelandais G, Sismeiro O, Lemoine S, Coppee JY, Le Crom S, Prasad R, Devaux F (2012) RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans. BMC Genomics 13:396
Diao YJ, Zhao R, Deng XM, Leng WC, Peng JP, ** Q (2009) Transcriptional profiles of Trichophyton rubrum in response to itraconazole. Med Mycol 47(3):237–247
Du H, Bing J, Hu T, Ennis CL, Nobile CJ, Huang G (2020) Candida auris: epidemiology, biology, antifungal resistance, and virulence. PLoS Pathog 16(10):e1008921
Fachin AL, Maffei CM, Martinez-Rossi NM (1996) In vitro susceptibility of Trichophyton rubrum isolates to griseofulvin and tioconazole. Induction and isolation of a resistant mutant to both antimycotic drugs. Mutant of Trichophyton rubrum resistant to griseofulvin and tioconazole. Mycopathologia 135(3):141–143
Fachin AL, Contel EP, Martinez-Rossi NM (2001) Effect of sub-MICs of antimycotics on expression of intracellular esterase of Trichophyton rubrum. Med Mycol 39(1):129–133
Fachin AL, Ferreira-Nozawa MS, Maccheroni W, Martinez-Rossi NM (2006) Role of the ABC transporter TruMDR2 in terbinafine, 4-nitroquinoline N-oxide and ethidium bromide susceptibility in Trichophyton rubrum. J Med Microbiol 55(Pt 8):1093–1099
Fan W, Kraus PR, Boily MJ, Heitman J (2005) Cryptococcus neoformans gene expression during murine macrophage infection. Eukaryot Cell 4 (8):1420–1433
Ferreira-Nozawa MS, Silveira HCS, Ono CJ, Fachin AL, Rossi A, Martinez-Rossi NM (2006) The pH signaling transcription factor PacC mediates the growth of Trichophyton rubrum on human nail in vitro. Med Mycol 44(7):641–645
Firat YH, Simanski M, Rademacher F, Schroder L, Brasch J, Harder J (2014) Infection of keratinocytes with Trichophytum rubrum induces epidermal growth factor-dependent RNase 7 and human beta-defensin-3 expression. PLoS One 9(4):e93941
Fradin C, Kretschmar M, Nichterlein T, Gaillardin C, d'Enfert C, Hube B (2003) Stage-specific gene expression of Candida albicans in human blood. Mol Microbiol 47(6):1523–1543
Fradin C, De Groot P, MacCallum D, Schaller M, Klis F, Odds FC, Hube B (2005) Granulocytes govern the transcriptional response, morphology and proliferation of Candida albicans in human blood. Mol Microbiol 56(2):397–415
Fradin C, Mavor AL, Weindl G, Schaller M, Hanke K, Kaufmann SH, Mollenkopf H, Hube B (2007) The early transcriptional response of human granulocytes to infection with Candida albicans is not essential for killing but reflects cellular communications. Infect Immun 75(3):1493–1501
Frazzitta AE, Vora H, Price MS, Tenor JL, Betancourt-Quiroz M, Toffaletti DL, Cheng N, Perfect JR (2013) Nitrogen source-dependent capsule induction in human-pathogenic cryptococcus species. Eukaryot Cell 12(11):1439–1450
Gautam P, Shankar J, Madan T, Sirdeshmukh R, Sundaram CS, Gade WN, Basir SF, Sarma PU (2008) Proteomic and transcriptomic analysis of Aspergillus fumigatus on exposure to amphotericin B. Antimicrob Agents Chemother 52(12):4220–4227
Gibbons JG, Beauvais A, Beau R, McGary KL, Latge JP, Rokas A (2012) Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus. Eukaryot Cell 11(1):68–78
Gomez P, Hackett TL, Moore MM, Knight DA, Tebbutt SJ (2011) Functional genomics of human bronchial epithelial cells directly interacting with conidia of Aspergillus fumigatus. BMC Genomics 11:358
Gonzalez Segura G, Cantelli BA, Peronni K, Rodrigo Sanches P, Komoto TT, Rizzi E, Beleboni RO, Junior W, Martinez-Rossi NM, Marins M, Fachin AL (2020) Cellular and molecular response of macrophages THP-1 during co-culture with inactive Trichophyton rubrum Conidia. J Fungi (Basel) 6(4)
Graminha MA, Rocha EM, Prade RA, Martinez-Rossi NM (2004) Terbinafine resistance mediated by salicylate 1-monooxygenase in Aspergillus nidulans. Antimicrob Agents Chemother 48(9):3530–3535
Gupta AK, Mays RR, Versteeg SG, Piraccini BM, Shear NH, Piguet V, Tosti A, Friedlander SF (2018) Tinea capitis in children: a systematic review of management. J Eur Acad Dermatol Venereol 32(12):2264–2274
Heddergott C, Bruns S, Nietzsche S, Leonhardt I, Kurzai O, Kniemeyer O, Brakhage AA (2012) The Arthroderma benhamiae hydrophobin HypA mediates hydrophobicity and influences recognition by human immune effector cells. Eukaryot Cell 11(5):673–682
Hu G, Cheng PY, Sham A, Perfect JR, Kronstad JW (2008) Metabolic adaptation in Cryptococcus neoformans during early murine pulmonary infection. Mol Microbiol 69(6):1456–1475
Huang MY, Woolford CA, May G, McManus CJ, Mitchell AP (2019) Circuit diversification in a biofilm regulatory network. PLoS Pathog 15(5):e1007787
Ibrahim-Granet O, Dubourdeau M, Latge JP, Ave P, Huerre M, Brakhage AA, Brock M (2008) Methylcitrate synthase from Aspergillus fumigatus is essential for manifestation of invasive aspergillosis. Cell Microbiol 10(1):134–148
Idnurm A, Giles SS, Perfect JR, Heitman J (2007) Peroxisome function regulates growth on glucose in the basidiomycete fungus Cryptococcus neoformans. Eukaryot Cell 6(1):60–72
Imtiaz T, Lee KK, Munro CA, MacCallum DM, Shankland GS, Johnson EM, MacGregor MS, Bal AM (2012) Echinocandin resistance due to simultaneous FKS mutation and increased cell wall chitin in a Candida albicans bloodstream isolate following brief exposure to caspofungin. J Med Microbiol 61(Pt 9):1330–1334
Inglis DO, Berkes CA, Hocking Murray DR, Sil A (2010) Conidia but not yeast cells of the fungal pathogen Histoplasma capsulatum trigger a type I interferon innate immune response in murine macrophages. Infect Immun 78(9):3871–3882
Jacob TR, Peres NT, Martins MP, Lang EA, Sanches PR, Rossi A, Martinez-Rossi NM (2015) Heat shock protein 90 (Hsp90) as a molecular target for the development of novel drugs against the dermatophyte Trichophyton rubrum. Front Microbiol 6:1241
Johns LE, Goldman GH, Ries LNA, Brown NA (2021) Nutrient sensing and acquisition in fungi: mechanisms promoting pathogenesis in plant and human hosts. Fungal Biol Rev 36:1–14
Kalem MC, Subbiah H, Leipheimer J, Glazier VE, Panepinto JC (2021) Puf4 mediates post-transcriptional regulation of cell wall biosynthesis and caspofungin resistance in Cryptococcus neoformans. MBio 12(1)
Kano R (2021) ATP-binding Cassette (ABC) transporter proteins in highly terbinafine-resistant strains of Trichophyton indotineae (Former species name: Trichophyton interdigitale). Med Mycol J 62(1):21–25
Kean R, Delaney C, Sherry L, Borman A, Johnson EM, Richardson MD, Rautemaa-Richardson R, Williams C, Ramage G (2018) Transcriptome assembly and profiling of Candida auris reveals novel insights into biofilm-mediated resistance. mSphere 3(4)
Kim HS, Choi EH, Khan J, Roilides E, Francesconi A, Kasai M, Sein T, Schaufele RL, Sakurai K, Son CG, Greer BT, Chanock S, Lyman CA, Walsh TJ (2005) Expression of genes encoding innate host defense molecules in normal human monocytes in response to Candida albicans. Infect Immun 73(6):3714–3724
Kretschmer M, Wang J, Kronstad JW (2012) Peroxisomal and mitochondrial beta-oxidation pathways influence the virulence of the pathogenic fungus Cryptococcus neoformans. Eukaryot Cell 11(8):1042–1054
Krober A, Etzrodt S, Bach M, Monod M, Kniemeyer O, Staib P, Brakhage AA (2017) The transcriptional regulators SteA and StuA contribute to keratin degradation and sexual reproduction of the dermatophyte Arthroderma benhamiae. Curr Genet 63(1):103–116
Lambou K, Lamarre C, Beau R, Dufour N, Latge JP (2010) Functional analysis of the superoxide dismutase family in Aspergillus fumigatus. Mol Microbiol 75(4):910–923
Lang EAS, Bitencourt TA, Peres NTA, Lopes L, Silva LG, Cazzaniga RA, Rossi A, Martinez-Rossi NM (2020) The stuA gene controls development, adaptation, stress tolerance, and virulence of the dermatophyte Trichophyton rubrum. Microbiol Res 241:126592
Li H, Li Y, Sun T, Du W, Li C, Suo C, Meng Y, Liang Q, Lan T, Zhong M, Yang S, Niu C, Li D, Ding C (2019) Unveil the transcriptional landscape at the Cryptococcus-host axis in mice and nonhuman primates. PLoS Negl Trop Dis 13(7):e0007566
Li P, Seneviratne CJ, Luan Q, ** L (2021) Proteomic analysis of caspofungin-induced responses in planktonic cells and biofilms of Candida albicans. Front Microbiol 12:639123
Lim CS, Rosli R, Seow HF, Chong PP (2011) Transcriptome profiling of endothelial cells during infections with high and low densities of C. albicans cells. Int J Med Microbiol 301(6):536–546
Liu TT, Lee RE, Barker KS, Lee RE, Wei L, Homayouni R, Rogers PD (2005) Genome-wide expression profiling of the response to azole, polyene, echinocandin, and pyrimidine antifungal agents in Candida albicans. Antimicrob Agents Chemother 49(6):2226–2236
Liu TT, Znaidi S, Barker KS, Xu L, Homayouni R, Saidane S, Morschhauser J, Nantel A, Raymond M, Rogers PD (2007) Genome-wide expression and location analyses of the Candida albicans Tac1p regulon. Eukaryot Cell 6(11):2122–2138
Liu H, Xu W, Bruno VM, Phan QT, Solis NV, Woolford CA, Ehrlich RL, Shetty AC, McCraken C, Lin J, Bromley MJ, Mitchell AP, Filler SG (2021) Determining Aspergillus fumigatus transcription factor expression and function during invasion of the mammalian lung. PLoS Pathog 17(3):e1009235
Livonesi MC, Souto JT, Campanelli AP, Maffei CM, Martinez R, Rossi MA, Da Silva JS (2008) Deficiency of IL-12p40 subunit determines severe paracoccidioidomycosis in mice. Med Mycol 46(7):637–646
Lopes L, Bitencourt TA, Lang EAS, Sanches PR, Peres NTA, Rossi A, Martinez-Rossi NM (2019) Genes coding for LysM domains in the dermatophyte Trichophyton rubrum: a transcription analysis. Med Mycol 58(3):372–379
Lorenz MC, Fink GR (2001) The glyoxylate cycle is required for fungal virulence. Nature 412(6842):83–86
Lorenz MC, Bender JA, Fink GR (2004) Transcriptional response of Candida albicans upon internalization by macrophages. Eukaryot Cell 3(5):1076–1087
Luberto C, Martinez-Marino B, Taraskiewicz D, Bolanos B, Chitano P, Toffaletti DL, Cox GM, Perfect JR, Hannun YA, Balish E, Del Poeta M (2003) Identification of App1 as a regulator of phagocytosis and virulence of Cryptococcus neoformans. J Clin Invest 112(7):1080–1094
Lupo P, Chang YC, Kelsall BL, Farber JM, Pietrella D, Vecchiarelli A, Leon F, Kwon-Chung KJ (2008) The presence of capsule in Cryptococcus neoformans influences the gene expression profile in dendritic cells during interaction with the fungus. Infect Immun 76(4):1581–1589
Mamouei Z, Singh S, Lemire B, Gu Y, Alqarihi A, Nabeela S, Li D, Ibrahim A, Uppuluri P (2021) An evolutionarily diverged mitochondrial protein controls biofilm growth and virulence in Candida albicans. PLoS Biol 19(3):e3000957
Maranhão FCA, Paião FG, Martinez-Rossi NM (2007) Isolation of transcripts over-expressed in human pathogen Trichophyton rubrum during growth in keratin. Microb Pathog 43(4):166–172
Martinez-Rossi NM, Peres NT, Rossi A (2008) Antifungal resistance mechanisms in dermatophytes. Mycopathologia 166(5-6):369–383
Martinez-Rossi NM, Persinoti GF, Peres NTA, Rossi A (2012) Role of pH in the pathogenesis of dermatophytoses. Mycoses 55(5):381–387
Martinez-Rossi NM, Jacob TR, Sanches PR, Peres NT, Lang EA, Martins MP, Rossi A (2016) Heat shock proteins in dermatophytes: current advances and perspectives. Curr Genomics 17(2):99–111
Martinez-Rossi NM, Peres NT, Rossi A (2017) Pathogenesis of dermatophytosis: sensing the host tissue. Mycopathologia 182(1-2):215–227
Martinez-Rossi NM, Bitencourt TA, Peres NTA, Lang EAS, Gomes EV, Quaresemin NR, Martins MP, Lopes L, Rossi A (2018) Dermatophyte resistance to antifungal drugs: mechanisms and prospectus. Front Microbiol 9:1108
Martins MP, Franceschini ACC, Jacob TR, Rossi A, Martinez-Rossi NM (2016) Compensatory expression of multidrug-resistance genes encoding ABC transporters in dermatophytes. J Med Microbiol 65(7):605–610
Martins MP, Rossi A, Sanches PR, Martinez-Rossi NM (2019) Differential expression of multidrug-resistance genes in Trichophyton rubrum. J I OMICS 9(2):65–69
Martins MP, Martinez-Rossi NM, Sanches PR, Rossi A (2020a) The PAC-3 transcription factor critically regulates phenotype-associated genes in Neurospora crassa. Genet Mol Biol 43(3):e20190374
Martins MP, Rossi A, Sanches PR, Bortolossi JC, Martinez-Rossi NM (2020b) Comprehensive analysis of the dermatophyte Trichophyton rubrum transcriptional profile reveals dynamic metabolic modulation. Biochem J 477(5):873–885
McDonagh A, Fedorova ND, Crabtree J, Yu Y, Kim S, Chen D, Loss O, Cairns T, Goldman G, Armstrong-James D, Haynes K, Haas H, Schrettl M, May G, Nierman WC, Bignell E (2008) Sub-telomere directed gene expression during initiation of invasive aspergillosis. PLoS Pathog 4(9):e1000154
Mendes NS, Silva PM, Silva-Rocha R, Martinez-Rossi NM, Rossi A (2016) Pre-mRNA splicing is modulated by antifungal drugs in the filamentous fungus Neurospora crassa. FEBS Open Bio 6(4):358–368
Mendes NS, Bitencourt TA, Sanches PR, Silva-Rocha R, Martinez-Rossi NM, Rossi A (2018) Transcriptome-wide survey of gene expression changes and alternative splicing in Trichophyton rubrum in response to undecanoic acid. Sci Rep 8(1):2520
Missall TA, Lodge JK, McEwen JE (2004) Mechanisms of resistance to oxidative and nitrosative stress: implications for fungal survival in mammalian hosts. Eukaryot Cell 3(4):835–846
Mittal J, Ponce MG, Gendlina I, Nosanchuk JD (2019) Histoplasma capsulatum: mechanisms for pathogenesis. Curr Top Microbiol Immunol 422:157–191
Monod M (2008) Secreted proteases from dermatophytes. Mycopathologia 166(5–6):285–294
Morschhauser J, Barker KS, Liu TT, Bla BWJ, Homayouni R, Rogers PD (2007) The transcription factor Mrr1p controls expression of the MDR1 efflux pump and mediates multidrug resistance in Candida albicans. PLoS Pathog 3(11):e164
Morton CO, Varga JJ, Hornbach A, Mezger M, Sennefelder H, Kneitz S, Kurzai O, Krappmann S, Einsele H, Nierman WC, Rogers TR, Loeffler J (2011) The temporal dynamics of differential gene expression in Aspergillus fumigatus interacting with human immature dendritic cells in vitro. PLoS One 6(1):e16016
Muller V, Viemann D, Schmidt M, Endres N, Ludwig S, Leverkus M, Roth J, Goebeler M (2007) Candida albicans triggers activation of distinct signaling pathways to establish a proinflammatory gene expression program in primary human endothelial cells. J Immunol 179(12):8435–8445
Mullick A, Elias M, Harakidas P, Marcil A, Whiteway M, Ge B, Hudson TJ, Caron AW, Bourget L, Picard S, Jovcevski O, Massie B, Thomas DY (2004) Gene expression in HL60 granulocytoids and human polymorphonuclear leukocytes exposed to Candida albicans. Infect Immun 72(1):414–429
Munoz JF, Gade L, Chow NA, Loparev VN, Juieng P, Berkow EL, Farrer RA, Litvintseva AP, Cuomo CA (2018) Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species. Nat Commun 9(1):5346
Munoz JF, Delorey T, Ford CB, Li BY, Thompson DA, Rao RP, Cuomo CA (2019) Coordinated host-pathogen transcriptional dynamics revealed using sorted subpopulations and single macrophages infected with Candida albicans. Nat Commun 10(1):1607
Neves-da-Rocha J, Bitencourt TA, Oliveira VM, Sanches PR, Rossi A, Martinez-Rossi NM (2019) Alternative splicing in heat shock protein transcripts as a mechanism of cell adaptation in Trichophyton rubrum. Cell 8(10)
Nobile CJ, Fox EP, Nett JE, Sorrells TR, Mitrovich QM, Hernday AD, Tuch BB, Andes DR, Johnson AD (2012) A recently evolved transcriptional network controls biofilm development in Candida albicans. Cell 148(1–2):126–138
O’Meara TR, Xu W, Selvig KM, O’Meara MJ, Mitchell AP, Alspaugh JA (2013) The Cryptococcus neoformans Rim101 transcription factor directly regulates genes required for adaptation to the host. Mol Cell Biol 34(4):673–684
Oosthuizen JL, Gomez P, Ruan J, Hackett TL, Moore MM, Knight DA, Tebbutt SJ (2011) Dual organism transcriptomics of airway epithelial cells interacting with conidia of Aspergillus fumigatus. PLoS One 6(5):e20527
Osborne CS, Leitner I, Favre B, Ryder NS (2005) Amino acid substitution in Trichophyton rubrum squalene epoxidase associated with resistance to terbinafine. Antimicrob Agents Chemother 49(7):2840–2844
Osborne CS, Leitner I, Hofbauer B, Fielding CA, Favre B, Ryder NS (2006) Biological, biochemical, and molecular characterization of a new clinical Trichophyton rubrum isolate resistant to terbinafine. Antimicrob Agents Chemother 50(6):2234–2236
Paiao FG, Segato F, Cursino-Santos JR, Peres NT, Martinez-Rossi NM (2007) Analysis of Trichophyton rubrum gene expression in response to cytotoxic drugs. FEMS Microbiol Lett 271(2):180–186
Pathakumari B, Liang G, Liu W (2020) Immune defence to invasive fungal infections: a comprehensive review. Biomed Pharmacother 130:110550
Peres NTA, Maranhao FCA, Rossi A, Martinez-Rossi NM (2010a) Dermatophytes: host-pathogen interaction and antifungal resistance. An Bras Dermatol 85(5):657–667
Peres NTA, Sanches PR, Falcão JP, Silveira HCS, Paião FG, Maranhão FCA, Gras DE, Segato F, Cazzaniga RA, Mazucato M, Cursino-Santos JR, Aquino-Ferreira R, Rossi A, Martinez-Rossi NM (2010b) Transcriptional profiling reveals the expression of novel genes in response to various stimuli in the human dermatophyte Trichophyton rubrum. BMC Microbiol 10:39–48
Peres NT, Silva LG, Santos Rda S, Jacob TR, Persinoti GF, Rocha LB, Falcao JP, Rossi A, Martinez-Rossi NM (2016) In vitro and ex vivo infection models help assess the molecular aspects of the interaction of Trichophyton rubrum with the host milieu. Med Mycol 54(4):420–427
Perlin DS (2015) Mechanisms of echinocandin antifungal drug resistance. Ann N Y Acad Sci 1354:1–11
Persinoti GF, de Aguiar Peres NT, Jacob TR, Rossi A, Vencio RZ, Martinez-Rossi NM (2014) RNA-sequencing analysis of Trichophyton rubrum transcriptome in response to sublethal doses of acriflavine. BMC Genomics 15(Suppl 7):S1
Petrucelli MF, Peronni K, Sanches PR, Komoto TT, Matsuda JB, Silva Junior WAD, Beleboni RO, Martinez-Rossi NM, Marins M, Fachin AL (2018) Dual RNA-Seq analysis of Trichophyton rubrum and HaCat keratinocyte co-culture highlights important genes for fungal-host interaction. Genes (Basel) 9(7)
Petrucelli MF, Matsuda JB, Peroni K, Sanches PR, Silva WA Jr, Beleboni RO, Martinez-Rossi NM, Marins M, Fachin AL (2019) The transcriptional profile of Trichophyton rubrum co-cultured with human keratinocytes shows new insights about gene modulation by terbinafine. Pathogens 8(4)
Ramirez MA, Lorenz MC (2007) Mutations in alternative carbon utilization pathways in Candida albicans attenuate virulence and confer pleiotropic phenotypes. Eukaryot Cell 6(2):280–290
Richie DL, Hartl L, Aimanianda V, Winters MS, Fuller KK, Miley MD, White S, McCarthy JW, Latge JP, Feldmesser M, Rhodes JC, Askew DS (2009) A role for the unfolded protein response (UPR) in virulence and antifungal susceptibility in Aspergillus fumigatus. PLoS Pathog 5(1):e1000258
Rocha EM, Gardiner RE, Park S, Martinez-Rossi NM, Perlin DS (2006) A Phe389Leu substitution in ergA confers terbinafine resistance in Aspergillus fumigatus. Antimicrob Agents Chemother 50(7):2533–2536
Rodrigues ML, Nosanchuk JD (2020) Fungal diseases as neglected pathogens: a wake-up call to public health officials. PLoS Negl Trop Dis 14(2):e0007964
Romani L (2011) Immunity to fungal infections. Nat Rev Immunol 11(4):275–288
Rosam K, Monk BC, Lackner M (2020) Sterol 14alpha-demethylase ligand-binding pocket-mediated acquired and intrinsic azole resistance in fungal pathogens. J Fungi (Basel) 7(1)
Rossi A, Cruz AHS, Santos RS, Silva PM, Silva EM, Mendes NS, Martinez-Rossi NM (2013) Ambient pH sensing in filamentous fungi: pitfalls in elucidating regulatory hierarchical signaling networks. IUBMB Life 65(11):930–935
Rossi A, Martins MP, Bitencourt TA, Peres NTA, Rocha CHL, Rocha FMG, Neves-da-Rocha J, Lopes MER, Sanches PR, Bortolossi JC, Martinez-Rossi NM (2021) Reassessing the use of undecanoic acid as a therapeutic strategy for treating fungal infections. Mycopathologia
Rude TH, Toffaletti DL, Cox GM, Perfect JR (2002) Relationship of the glyoxylate pathway to the pathogenesis of Cryptococcus neoformans. Infect Immun 70(10):5684–5694
Sagatova AA (2021) Strategies to better target fungal squalene monooxygenase. J Fungi (Basel) 7(1)
Sanguinetti M, Posteraro B, Fiori B, Ranno S, Torelli R, Fadda G (2005) Mechanisms of azole resistance in clinical isolates of Candida glabrata collected during a hospital survey of antifungal resistance. Antimicrob Agents Chemother 49(2):668–679
Santos HL, Lang EAS, Segato F, Rossi A, Martinez-Rossi NM (2018) Terbinafine resistance conferred by multiple copies of the salicylate 1-monooxygenase gene in Trichophyton rubrum. Med Mycol 56(3):378–381
Schobel F, Ibrahim-Granet O, Ave P, Latge JP, Brakhage AA, Brock M (2007) Aspergillus fumigatus does not require fatty acid metabolism via isocitrate lyase for development of invasive aspergillosis. Infect Immun 75(3):1237–1244
Seelbinder B, Wallstabe J, Marischen L, Weiss E, Wurster S, Page L, Loffler C, Bussemer L, Schmitt AL, Wolf T, Linde J, Cicin-Sain L, Becker J, Kalinke U, Vogel J, Panagiotou G, Einsele H, Westermann AJ, Schauble S, Loeffler J (2020) Triple RNA-Seq reveals synergy in a human virus-fungus co-infection model. Cell Rep 33(7):108389
Segato F, Nozawa SR, Rossi A, Martinez-Rossi NM (2008) Over-expression of genes coding for proline oxidase, riboflavin kinase, cytochrome c oxidase and an MFS transporter induced by acriflavin in Trichophyton rubrum. Med Mycol 46(2):135–139
Shapiro RS, Robbins N, Cowen LE (2011) Regulatory circuitry governing fungal development, drug resistance, and disease. Microbiol Mol Biol Rev 75(2):213–267
Shiraki Y, Ishibashi Y, Hiruma M, Nishikawa A, Ikeda S (2006) Cytokine secretion profiles of human keratinocytes during Trichophyton tonsurans and Arthroderma benhamiae infections. J Med Microbiol 55(Pt 9):1175–1185
Silva SS, Tavares AHFP, Passos-Silva DG, Fachin AL, Teixeira SMR, Soares CMA, Carvalho MJA, Bocca AL, Silva-Pereira I, Passos GAS, Felipe MSS (2008) Transcriptional response of murine macrophages upon infection with opsonized Paracoccidioides brasiliensis yeast cells. Microbes Infect 10(1):12–20
Silva DL, Lima CM, Magalhaes VCR, Baltazar LM, Peres NTA, Caligiorne RB, Moura AS, Fereguetti T, Martins JC, Rabelo LF, Abrahao JS, Lyon AC, Johann S, Santos DA (2021) Fungal and bacterial coinfections increase mortality of severely ill COVID-19 patients. J Hosp Infect
Silva MG, Schrank A, Bailão EFLC, Bailão AM, Borges CL, Staats CC, Parente JA, Pereira M, Salem-Izacc SM, Mendes-Giannini MJS, Oliveira RMZ, Rosa e Silva LK, Nosanchuk JD, Vainstein MH and Soares CMA (2011) The homeostasis of iron, copper, and zinc in Paracoccidioides brasiliensis, Cryptococcus neoformans var. grubii, and Cryptococcus gattii: a comparative analysis. Front Microbiol 2:49. https://doi.org/10.3389/fmicb.2011.00049
Silveira HCS, Gras DE, Cazzaniga RA, Sanches PR, Rossi A, Martinez-Rossi NM (2010) Transcriptional profiling reveals genes in the human pathogen Trichophyton rubrum that are expressed in response to pH signaling. Microb Pathog 48(2):91–96
Souto JT, Figueiredo F, Furlanetto A, Pfeffer K, Rossi MA, Silva JS (2000) Interferon-gamma and tumor necrosis factor-alpha determine resistance to Paracoccidioides brasiliensis infection in mice. Am J Pathol 156(5):1811–1820
Staib P, Zaugg C, Mignon B, Weber J, Grumbt M, Pradervand S, Harshman K, Monod M (2010) Differential gene expression in the pathogenic dermatophyte Arthroderma benhamiae in vitro versus during infection. Microbiology 156(Pt 3):884–895
Stark R, Grzelak M, Hadfield J (2019) RNA sequencing: the teenage years. Nat Rev Genet 20(11):631–656
Subramani A, Griggs P, Frantzen N, Mendez J, Tucker J, Murriel J, Sircy LM, Millican GE, McClelland EE, Seipelt-Thiemann RL, Nelson DE (2020) Intracellular Cryptococcus neoformans disrupts the transcriptome profile of M1- and M2-polarized host macrophages. PLoS One 15(8):e0233818
Sugui JA, Kim HS, Zarember KA, Chang YC, Gallin JI, Nierman WC, Kwon-Chung KJ (2008) Genes differentially expressed in conidia and hyphae of Aspergillus fumigatus upon exposure to human neutrophils. PLoS One 3(7):e2655
Sun N, Fonzi W, Chen H, She X, Zhang L, Calderone R (2013) Azole susceptibility and transcriptome profiling in Candida albicans mitochondrial electron transport chain complex I mutants. Antimicrob Agents Chemother 57(1):532–542
Tavares AH, Derengowski LS, Ferreira KS, Silva SS, Macedo C, Bocca AL, Passos GA, Almeida SR, Silva-Pereira I (2012) Murine dendritic cells transcriptional modulation upon Paracoccidioides brasiliensis infection. PLoS Negl Trop Dis 6(1):e1459
Thewes S, Kretschmar M, Park H, Schaller M, Filler SG, Hube B (2007) In vivo and ex vivo comparative transcriptional profiling of invasive and non-invasive Candida albicans isolates identifies genes associated with tissue invasion. Mol Microbiol 63(6):1606–1628
Tierney L, Linde J, Muller S, Brunke S, Molina JC, Hube B, Schock U, Guthke R, Kuchler K (2012) An interspecies regulatory network inferred from simultaneous RNA-seq of Candida albicans invading innate immune cells. Front Microbiol 3:85
Upadhya R, Kim H, Jung KW, Park G, Lam W, Lodge JK, Bahn YS (2013) Sulphiredoxin plays peroxiredoxin-dependent and -independent roles via the HOG signalling pathway in Cryptococcus neoformans and contributes to fungal virulence. Mol Microbiol 90(3):630–648
Vediyappan G, Rossignol T, d'Enfert C (2010) Interaction of Candida albicans biofilms with antifungals: transcriptional response and binding of antifungals to beta-glucans. Antimicrob Agents Chemother 54(5):2096–2111
Vermes A, Guchelaar HJ, Dankert J (2000) Flucytosine: a review of its pharmacology, clinical indications, pharmacokinetics, toxicity and drug interactions. J Antimicrob Chemother 46(2):171–179
Wachtler B, Wilson D, Haedicke K, Dalle F, Hube B (2011) From attachment to damage: defined genes of Candida albicans mediate adhesion, invasion and damage during interaction with oral epithelial cells. PLoS One 6(2):e17046
Walker LA, Maccallum DM, Bertram G, Gow NA, Odds FC, Brown AJ (2009) Genome-wide analysis of Candida albicans gene expression patterns during infection of the mammalian kidney. Fungal Genet Biol 46(2):210–219
Wang M, Zhao Y, Cao L, Luo S, Ni B, Zhang Y, Chen Z (2021) Transcriptome sequencing revealed the inhibitory mechanism of ketoconazole on clinical Microsporum canis. J Vet Sci 22(1):e4
Westermann AJ, Barquist L, Vogel J (2017) Resolving host-pathogen interactions by dual RNA-seq. PLoS Pathog 13(2):e1006033
White TC, Holleman S, Dy F, Mirels LF, Stevens DA (2002) Resistance mechanisms in clinical isolates of Candida albicans. Antimicrob Agents Chemother 46(6):1704–1713
Woodfolk JA, Platts-Mills TA (1998) The immune response to dermatophytes. Res Immunol 149(4–5):436–445; discussion 522-433
Yamada T, Maeda M, Alshahni MM, Tanaka R, Yaguchi T, Bontems O, Salamin K, Fratti M, Monod M (2017) Terbinafine resistance of Trichophyton clinical isolates caused by specific point mutations in the squalene epoxidase gene. Antimicrob Agents Chemother 61(7)
Yu L, Zhang W, Liu T, Wang X, Peng J, Li S, ** Q (2007a) Global gene expression of Trichophyton rubrum in response to PH11B, a novel fatty acid synthase inhibitor. J Appl Microbiol 103(6):2346–2352
Yu L, Zhang W, Wang L, Yang J, Liu T, Peng J, Leng W, Chen L, Li R, ** Q (2007b) Transcriptional profiles of the response to ketoconazole and amphotericin B in Trichophyton rubrum. Antimicrob Agents Chemother 51(1):144–153
Yu CH, Chen Y, Desjardins CA, Tenor JL, Toffaletti DL, Giamberardino C, Litvintseva A, Perfect JR, Cuomo CA (2020) Landscape of gene expression variation of natural isolates of Cryptococcus neoformans in response to biologically relevant stresses. Microb Genom 6(1)
Zakikhany K, Naglik JR, Schmidt-Westhausen A, Holland G, Schaller M, Hube B (2007) In vivo transcript profiling of Candida albicans identifies a gene essential for interepithelial dissemination. Cell Microbiol 9(12):2938–2954
Zamith-Miranda D, Amatuzzi RF, Martins ST, Vieira AZ, da Rocha IM, Rodrigues ML, Trentin G, Almeida F, Nakayasu ES, Nosanchuk JD, Alves LR (2020) Integrated transcriptional analysis of the cellular and extracellular vesicle RNA content of Candida auris in response to caspofungin. bioRxiv. https://doi.org/10.1101/2020.12.04.411843
Zhang W, Yu L, Yang J, Wang L, Peng J, ** Q (2009) Transcriptional profiles of response to terbinafine in Trichophyton rubrum. Appl Microbiol Biotechnol 82(6):1123–1130
Zhu X, Ge Y, Wu T, Zhao K, Chen Y, Wu B, Zhu F, Zhu B, Cui L (2020) Co-infection with respiratory pathogens among COVID-2019 cases. Virus Res 285:198005
Acknowledgments
This work was supported by grants from Brazilian funding agencies FAPESP (Grant No. 2019/22596-9), National Council for Scientific and Technological Development (CNPq) (Grants No. 305797/2017-4 and 304989/2017-7); Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) – Finance Code 001; and Fundação de Apoio ao Ensino, Pesquisa e Assistência (FAEPA).
FAPESP supported the postdoctoral fellowships to N.P. (2009/08411-4), T.B. (2015/23435-8), G.P. (2012/22232-8 and 2013/19195-6), and E.L. (2011/08424-9).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG
About this chapter
Cite this chapter
Peres, N.T.A., Bitencourt, T.A., Persinoti, G.F., Lang, E.A.S., Rossi, A., Martinez-Rossi, N.M. (2022). Transcriptome in Human Mycoses. In: Passos, G.A. (eds) Transcriptomics in Health and Disease. Springer, Cham. https://doi.org/10.1007/978-3-030-87821-4_17
Download citation
DOI: https://doi.org/10.1007/978-3-030-87821-4_17
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-87820-7
Online ISBN: 978-3-030-87821-4
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)