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| Status |
Public on Jun 20, 2024 |
| Title |
Excavation of biomarker candidates for the diagnosis of Talaromyces marneffei infection via genome-wide prediction and functional annotation of secreted proteins |
| Organism |
Talaromyces marneffei |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Talaromyces marneffei is the third most common infectious pathogen in AIDS patients and leads to the highest death rate in Guangxi, China. The lack of reliable biomarkers is one of the major obstacles in current clinical diagnosis, which largely contributes to this high mortality. Here, we present a study that aimed at identifying diagnostic biomarker candidates through genome-wide prediction and functional annotation of Talaromyces marneffei secreted proteins. A total of 584 secreted proteins then emerged, including 382 classical and 202 non-classical ones. Among them, 87 newly obtained functional annotations in this study. The annotated proteins were further evaluated by combining RNA profiling and homology comparison. Three proteins were ultimately highlighted as biomarker candidates with robust expression and remarkable specificity. The predicted phosphoinositide phospholipase C and the galactomannoprotein were suggested playing an interactive immune game though metabolism of arachidonic acid. And therefore, they hold promises in developing new tools for clinical diagnosis of Talaromyces marneffei, possibly also serve as molecular targets of future therapy.
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| Overall design |
Standard strain of T. marneffei ATCC18224 was obtained from American Type Culture Collection (ATCC) and cultured under yeast condition. In brief, fungus was expanded in 37℃ for 14 days, with 200-220 rpm rotation in RPMI 1640 medium plus 10% FBS (Fetal Bovine Serum). Fungus was then precipitated with centrifuge of 14000 g for 10 minutes60. RNA samples were then extracted and sequenced in GeneChem (China). Three independent biological replicates were set in parallel from culture to profiling. Reads were calculated and normalized for each unique transcript.
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| Contributor(s) |
Wei W |
| Citation missing |
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| Submission date |
May 07, 2024 |
| Last update date |
Jun 20, 2024 |
| Contact name |
jing dan |
| E-mail(s) |
202121409@sr.gxmu.edu.cn
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| Phone |
18113574667
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| Organization name |
guangxi medicial university
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| Street address |
Shuangyong Road, Qingxiu District,Nanning, 530021,China
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| City |
nanning |
| State/province |
Guangxi |
| ZIP/Postal code |
530000 |
| Country |
China |
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| Platforms (1) |
| GPL33968 |
Illumina NovaSeq 6000 (Talaromyces marneffei) |
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| Samples (3) |
| GSM8257652 |
Talaromyces marneffei ATCC18224 Y1(fungus) |
| GSM8257653 |
Talaromyces marneffei ATCC18224 Y2(fungus) |
| GSM8257654 |
Talaromyces marneffei ATCC18224 Y3(fungus) |
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| Relations |
| BioProject |
PRJNA1108869 |
