Metaproteomic Analysis of an Oral Squamous Cell Carcinoma Dataset Suggests Diagnostic Potential of the Mycobiome
Abstract
:1. Introduction
2. Results
2.1. An Increased Overall Microbial Species Diversity Is Observed in OSCC Conditions
2.2. Identification of Differentially Abundant Fungal Proteins
2.3. Hierarchical Clustering Reveals Diagnostic Potential of Fungal Microbiome
3. Discussion
3.1. Enrichment of Nucleocytoplasmic Large DNA Viruses in the Oral Virome
3.2. Periodontal Pathogens and Opportunistic Bacteria Are Enriched in OSCC
3.3. An Unexpected Fungal Diversity Is Observed in the OSCC Patient Samples
3.4. Fungal Proteins Implicate Pathogens Capable of Soft Tissue Damage
3.5. Clustering of the Mycobiome Protein Profile Shows Diagnostic Potential
4. Methods
4.1. Data Collection
4.2. Trans-Proteomic Pipeline Analysis
4.3. Secondary Analysis and Visualisation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Accession | Protein Description | Fungal Species | Log2 Fold Change | Adjusted p-Value |
---|---|---|---|---|
A0A4Q4V9G8 | HET domain-containing protein | Monosporascus sp. MG133 | 1.41 | 1.17 × 10−19 |
A0A0M8MZV6 | Tubulin beta chain | Escovopsis weberi | 1.13 | 3.94 × 10−18 |
A0A0C9X1M1 | Unplaced genomic scaffold K443scaffold_229, whole genome shotgun sequence | Laccaria amethystina | 1.22 | 1.49 × 10−15 |
A0A098VNG2 | Tubulin beta chain | Mitosporidium daphniae | 0.98 | 5.31 × 10−15 |
W6MU27 | ERF-3 | Kuraishia capsulata | 1.19 | 3.16 × 10−12 |
A0A1E3Q4C5 | Tubulin beta chain | Lipomyces starkeyi | 1.14 | 4.80 × 10−12 |
A0A0D2A2I2 | Endoplasmic reticulum chaperone BiP | Verruconis gallopava | 1.16 | 1.66 × 10−11 |
A0A261Y4X6 | Adenine phosphoribosyltransferase | Bifiguratus adelaidae | 1.68 | 3.66 × 10−10 |
A0A0B2UG97 | Tubulin beta chain | Ordospora colligata | 0.95 | 5.10 × 10−10 |
A0A4Y7TST9 | Actin-1 | Coprinellus micaceus | −1.70 | 2.45 × 10−09 |
A0A1J5XBD0 | Actin | Amphiamblys sp. WSBS2006 | 3.00 | 2.57 × 10−09 |
A0A512U7H9 | Uncharacterized protein | Metschnikowia sp. JCM 33374 | 2.27 | 5.62 × 10−09 |
K1WHF7 | DNA-directed RNA polymerase subunit | Marssonina brunnea f. sp. multigermtubi | 1.17 | 1.42 × 10−08 |
A0A4P9YSZ5 | Glyceraldehyde-3-phosphate dehydrogenase | Syncephalis pseudoplumigaleata | −0.80 | 1.42 × 10−08 |
A0A168NSS0 | SAM_MT_RSMB_NOP domain-containing protein | Absidia glauca | 1.71 | 7.38 × 10−08 |
A0A0A0HRG7 | Actin | Paracoccidioides brasiliensis | 1.46 | 1.25 × 10−07 |
A0A167QHP6 | Uncharacterized protein | Phycomyces blakesleeanus | 0.70 | 8.77 × 10−07 |
R4XE35 | DNA-directed RNA polymerase subunit | Taphrina deformans | 1.84 | 9.27 × 10−07 |
A0A1X2H166 | Eukaryotic peptide chain release factor subunit 1 | Syncephalastrum racemosum | 1.60 | 1.32 × 10−06 |
A0A395SGK8 | Non-ribosomal peptide synthetase | Fusarium longipes | 1.44 | 1.32 × 10−06 |
K5X852 | WD_REPEATS_REGION domain-containing protein | Phanerochaete carnosa | 2.60 | 3.48 × 10−06 |
M5E4N2 | Tryptophanyl-tRNA synthetase | Malassezia sympodialis | 1.64 | 3.48 × 10−06 |
A0A1Y1WUH8 | Beta-glucosidase | Anaeromyces robustus | 1.34 | 4.96 × 10−06 |
A0A068RIK2 | Phosphoglycerate kinase | Lichtheimia corymbifera | 1.89 | 6.27 × 10−06 |
A0A4Q0A1Y4 | 14-3-3 domain-containing protein | Dimargaris cristalligena | 2.06 | 7.94 × 10−06 |
A0A5M6C8D5 | ADP-ribosylation factor | Kwoniella shandongensis | 1.82 | 9.64 × 10−06 |
A0A3N4K760 | Tubulin alpha chain | Morchella conica | 1.41 | 1.10 × 10−05 |
A0A1Y1WHV7 | Dynein heavy chain, cytoplasmic | Linderina pennispora | 1.37 | 1.27 × 10−05 |
A0A3M2T8I6 | Uncharacterized protein | Aspergillus sp. HF37 | 1.62 | 1.63 × 10−05 |
R9PCI5 | Tubulin beta chain | Pseudozyma hubeiensis | 0.78 | 1.90 × 10−05 |
Organism Type | No. of Reference Proteomes | No. of Protein Entries | Size (GB) | URL/Directory |
---|---|---|---|---|
Virus | 10,062 | 517,610 | 0.18 | https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Viruses/ (release no. 2021_3; accessed on 2 June 2021) |
Fungi | 784 | 8,370,376 | 4.61 | https://www.uniprot.org/uniprot/?query=proteome%3a(taxonomy%3a%22Fungi+%5b4751%5d%22+AND+reference%3ayes) (release no. 2021_3; accessed on 2 June 2021) |
Bacteria | 2087 | 5,044,213 | 1.89 | http://homd.org/ftp/genomes/PROKKA/current/faa/ (ver 9.1.4: accessed on 9 September 2020) |
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He, S.; Chakraborty, R.; Ranganathan, S. Metaproteomic Analysis of an Oral Squamous Cell Carcinoma Dataset Suggests Diagnostic Potential of the Mycobiome. Int. J. Mol. Sci. 2023, 24, 1050. https://doi.org/10.3390/ijms24021050
He S, Chakraborty R, Ranganathan S. Metaproteomic Analysis of an Oral Squamous Cell Carcinoma Dataset Suggests Diagnostic Potential of the Mycobiome. International Journal of Molecular Sciences. 2023; 24(2):1050. https://doi.org/10.3390/ijms24021050
Chicago/Turabian StyleHe, Steven, Rajdeep Chakraborty, and Shoba Ranganathan. 2023. "Metaproteomic Analysis of an Oral Squamous Cell Carcinoma Dataset Suggests Diagnostic Potential of the Mycobiome" International Journal of Molecular Sciences 24, no. 2: 1050. https://doi.org/10.3390/ijms24021050