Long Non-Coding RNAs in Cryptococcus neoformans: Insights Into Fungal Pathogenesis

Kalem, Murat C.; Panepinto, John C.

doi:10.3389/fcimb.2022.858317

Cited by 13 publications

(12 citation statements)

References 66 publications

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“…Although many fungal lncRNAs are intergenic [31, 35, 37], evidence from several fungal pathogens suggests that a large proportion of their lncRNAs could be antisense to protein-coding genes [35, 38, 111]. Surprisingly, only two antisense lncRNAs were identified using our approach.…”

Section: Discussionmentioning

confidence: 99%

“…Importantly, recent discoveries show that lncRNAs in fungal pathogens can have direct effects on virulence, for example through the regulation of enzymatic activity. Including in Trichoderma reesei, natural variants in the lncRNA HAX1 influence cellulase production [ 36 ], and in Verticilium dahliae , three lncRNAs were found to regulate the expression of cell-wall-degrading enzymes, with mutants resulting in decreased virulence on cotton [ 37 ] In Cryptococcus neoformans, lncRNAs were found in extracellular vesicles containing virulence factors known to modulate the host immune response [ 38 ], and in Fusarium graminearum , the lncRNA lncRsp1 influences virulence on wheat by regulating Fgsp1 , which is required for normal ascospore discharge [ 39 ]. These examples illustrate the multitude of roles lncRNAs can play in pathogenicity-associated processes of filamentous fungi.…”

Section: Introductionmentioning

confidence: 99%

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The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici

Glad,

Tralamazza,

Croll

2023

Microbial Genomics

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Long non-coding RNAs (lncRNAs) are regulatory molecules interacting in a wide array of biological processes. lncRNAs in fungal pathogens can be responsive to stress and play roles in regulating growth and nutrient acquisition. Recent evidence suggests that lncRNAs may also play roles in virulence, such as regulating pathogenicity-associated enzymes and on-host reproductive cycles. Despite the importance of lncRNAs, only a few model fungi have well-documented inventories of lncRNA. In this study, we apply a recent computational pipeline to predict high-confidence lncRNA candidates in Zymoseptoria tritici, an important global pathogen of wheat impacting global food production. We analyse genomic features of lncRNAs and the most likely associated processes through analyses of expression over a host infection cycle. We find that lncRNAs are frequently expressed during early infection, before the switch to necrotrophic growth. They are mostly located in facultative heterochromatic regions, which are known to contain many genes associated with pathogenicity. Furthermore, we find that lncRNAs are frequently co-expressed with genes that may be involved in responding to host defence signals, such as oxidative stress. Finally, we assess pangenome features of lncRNAs using four additional reference-quality genomes. We find evidence that the repertoire of expressed lncRNAs varies substantially between individuals, even though lncRNA loci tend to be shared at the genomic level. Overall, this study provides a repertoire and putative functions of lncRNAs in Z. tritici enabling future molecular genetics and functional analyses in an important pathogen.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici

Glad,

Tralamazza,

Croll

2023

Microbial Genomics

View full text Add to dashboard Cite

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“…2016; Gröhs Ferrareze et al . 2021; Kalem and Panepinto 2022). However, even though the study of extracellular transcriptome has become a hot topic in number of organisms including microbes (Hulstaert et al .…”

Section: Discussionmentioning

confidence: 99%

“…Our results allow us to complete the characterization of the Cryptococus snoRNAome (Canzler et al . 2018; Kalem and Panepinto 2022). Yet, we did not observe a specific enrichment in EV extract for the two snoRNAs we checked by RT-qPCR.…”

Section: Discussionmentioning

confidence: 99%

TheCryptococcusextracellular vesicle transcriptome

Taheraly,

Maufrais,

Moyrand

et al. 2023

Preprint

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Extracellular vesicles (EVs) are now recognized as key players in the biology of numerous organisms, including pathogenic fungi. However, studying EVs in these organisms remains challenging. The recent implementation of new protocols to purify EVs in the pathogenic yeastCryptococcus neoformanshas resulted in a more detailed description of their structure and protein composition. Although a few publications describing RNA molecules associated with EVs have already been published, we reasoned that these new protocols would be beneficial for gaining a deeper understanding of the EV transcriptome. We thus purified EVs and confirmed that some RNAs were associated with these EV extracts. Iodixanol gradient analyses also revealed that these RNAs co-sedimented with EVs. We then sequenced these RNAs in parallel with RNAs extracted from the very cells producing these EVs using different types of sequencing libraries. Our data confirm the presence of siRNAs and tRFs associated with EVs, some of which are enriched. We also identified some snoRNAs, which inCryptococcus are mostly borne by coding gene or lncRNA introns.

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“…LncRNAs are a class of noncoding RNAs that do not encode proteins and are longer than 200 nucleotides. As the largest and most extensively studied class of noncoding RNAs, lncRNAs have become a research hotspot in biomedicine over the past decade ( Mercer, Dinger & Mattick, 2009 ; Kalem & Panepinto, 2022 ; Peng et al, 2023 ; Zhang et al, 2023 ). They exert their biological functions through cell cycle regulation, gene imprinting, mRNA degradation, chromatin remodeling, and splicing and translation regulation.…”

Section: Introductionmentioning

confidence: 99%

Cuproptosis-related lncRNA SNHG16 as a biomarker for the diagnosis and prognosis of head and neck squamous cell carcinoma

Han,

Li,

Huang

et al. 2023

PeerJ

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Background We aim to investigate the potential value of cuproptosis-related lncRNA signaling in predicting clinical prognosis and immunotherapy and its relationship with drug sensitivity in head and neck squamous cell carcinoma (HNSCC). Methods We first identified the lncRNAs associated with cuproptosis genes in HNSCC and then conducted a series of analytical studies to investigate the expression and prognostic significance of these lncRNAs. Finally, we used RT-qPCR to validate our findings in a laryngeal squamous cell carcinoma cell line and 12 pairs of laryngeal squamous cell carcinoma and adjacent normal tissues. Results We identified 11 differentially expressed lncRNAs that were associated with cuproptosis genes in HNSCC and also served as prognostic markers for this cancer. Enrichment analysis revealed that these lncRNAs were related to immune-related functions that were suppressed in patients with oncogene mutations in the high-risk group. The patients with a high tumor mutation burden exhibited poor overall survival (OS). We used the tumor immune dysfunction and exclusion model to show that the patients in the high-risk group had great potential for immune evasion and less effective immunotherapy. We also identified several drugs that could be effective in treating HNSCC. Experimental validation showed that AC090587.1 and AC012184.3 exhibited differential expression between the TU686 and HBE cell lines, and SNHG16 showed differential expression among the TU686, TU212, and control HBE cells. Among the 12 pairs of cancer and adjacent tissues collected in the clinic, only SNHG16 showed differential expression. Targeted therapy against SNHG16 holds promise as a prospective novel strategy for the clinical management of HNSCC.

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Long Non-Coding RNAs in Cryptococcus neoformans: Insights Into Fungal Pathogenesis

Cited by 13 publications

References 66 publications

The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici

The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici

TheCryptococcusextracellular vesicle transcriptome

Cuproptosis-related lncRNA SNHG16 as a biomarker for the diagnosis and prognosis of head and neck squamous cell carcinoma

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