
@article{biadglegne_mycobacterium_2022,
	title = {Mycobacterium tuberculosis affects protein and lipid content of circulating exosomes in infected patients depending on tuberculosis disease state},
	volume = {10},
	issn = {2227-9059},
	url = {https://www.mdpi.com/2227-9059/10/4/783},
	doi = {10.3390/biomedicines10040783},
	abstract = {Tuberculosis (TB), which is caused by the bacterium Mycobacterium tuberculosis (Mtb), is still one of the deadliest infectious diseases. Understanding how the host and pathogen interact in active TB will have a significant impact on global TB control efforts. Exosomes are increasingly recognized as a means of cell-to-cell contact and exchange of soluble mediators. In the case of TB, exosomes are released from the bacillus and infected cells. In the present study, a comprehensive lipidomics and proteomics analysis of size exclusion chromatography-isolated plasma-derived exosomes from patients with TB lymphadenitis (TBL) and treated as well as untreated pulmonary TB (PTB) was performed to elucidate the possibility to utilize exosomes in diagnostics and knowledge building. According to our findings, exosome-derived lipids and proteins originate from both the host and Mtb in the plasma of active TB patients. Exosomes from all patients are mostly composed of sphingomyelins (SM), phosphatidylcholines, phosphatidylinositols, free fatty acids, triacylglycerols (TAG), and cholesterylesters. Relative proportions of, e.g., SMs and TAGs, vary depending on the disease or treatment state and could be linked to Mtb pathogenesis and dormancy. We identified three proteins of Mtb origin: DNA-directed RNA polymerase subunit beta (RpoC), Diacyglycerol O-acyltransferase (Rv2285), and Formate hydrogenase (HycE), the latter of which was discovered to be differently expressed in TBL patients. Furthermore, we discovered that Mtb infection alters the host protein composition of circulating exosomes, significantly affecting a total of 37 proteins. All TB patients had low levels of apolipoproteins, as well as the antibacterial proteins cathelicidin, Scavenger Receptor Cysteine Rich Family Member (SSC5D), and Ficolin 3 (FCN3). When compared to healthy controls, the protein profiles of PTB and TBL were substantially linked, with 14 proteins being co-regulated. However, adhesion proteins (integrins, Intercellular adhesion molecule 2 (ICAM2), CD151, Proteoglycan 4 (PRG4)) were shown to be more prevalent in PTB patients, while immunoglobulins, Complement component 1r (C1R), and Glutamate receptor-interacting protein 1 (GRIP1) were found to be more abundant in TBL patients, respectively. This study could confirm findings from previous reports and uncover novel molecular profiles not previously in focus of TB research. However, we applied a minimally invasive sampling and analysis of circulating exosomes in TB patients. Based on the findings given here, future studies into host–pathogen interactions could pave the way for the development of new vaccines and therapies.},
	language = {en},
	number = {4},
	urldate = {2024-04-09},
	journal = {Biomedicines},
	author = {Biadglegne, Fantahun and Schmidt, Johannes R. and Engel, Kathrin M. and Lehmann, Jörg and Lehmann, Robert T. and Reinert, Anja and König, Brigitte and Schiller, Jürgen and Kalkhof, Stefan and Sack, Ulrich},
	month = mar,
	year = {2022},
	pages = {783},
}

@article{vehmas_liver_2016,
	title = {Liver lipid metabolism is altered by increased circulating estrogen to androgen ratio in male mouse},
	volume = {133},
	issn = {18743919},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1874391915302086},
	doi = {10.1016/j.jprot.2015.12.009},
	language = {en},
	urldate = {2024-04-09},
	journal = {Journal of Proteomics},
	author = {Vehmas, Anni P. and Adam, Marion and Laajala, Teemu D. and Kastenmüller, Gabi and Prehn, Cornelia and Rozman, Jan and Ohlsson, Claes and Fuchs, Helmut and Hrabě De Angelis, Martin and Gailus-Durner, Valérie and Elo, Laura L. and Aittokallio, Tero and Adamski, Jerzy and Corthals, Garry and Poutanen, Matti and Strauss, Leena},
	month = feb,
	year = {2016},
	pages = {66--75},
}

@article{castellano-escuder_pomashiny:_2021,
	title = {{POMAShiny}: {A} user-friendly web-based workflow for metabolomics and proteomics data analysis},
	volume = {17},
	issn = {1553-7358},
	shorttitle = {Pomashiny},
	url = {https://dx.plos.org/10.1371/journal.pcbi.1009148},
	doi = {10.1371/journal.pcbi.1009148},
	abstract = {Metabolomics and proteomics, like other omics domains, usually face a data mining challenge in providing an understandable output to advance in biomarker discovery and precision medicine. Often, statistical analysis is one of the most difficult challenges and it is critical in the subsequent biological interpretation of the results. Because of this, combined with the computational programming skills needed for this type of analysis, several bioinformatic tools aimed at simplifying metabolomics and proteomics data analysis have emerged. However, sometimes the analysis is still limited to a few hidebound statistical methods and to data sets with limited flexibility. POMAShiny is a web-based tool that provides a structured, flexible and user-friendly workflow for the visualization, exploration and statistical analysis of metabolomics and proteomics data. This tool integrates several statistical methods, some of them widely used in other types of omics, and it is based on the POMA R/Bioconductor package, which increases the reproducibility and flexibility of analyses outside the web environment. POMAShiny and POMA are both freely available at
              https://github.com/nutrimetabolomics/POMAShiny
              and
              https://github.com/nutrimetabolomics/POMA
              , respectively.},
	language = {en},
	number = {7},
	urldate = {2024-04-09},
	journal = {PLOS Computational Biology},
	author = {Castellano-Escuder, Pol and González-Domínguez, Raúl and Carmona-Pontaque, Francesc and Andrés-Lacueva, Cristina and Sánchez-Pla, Alex},
	editor = {Marz, Manja},
	month = jul,
	year = {2021},
	pages = {e1009148},
}

@article{ritchie_limma_2015,
	title = {Limma powers differential expression analyses for rna-sequencing and microarray studies},
	volume = {43},
	issn = {1362-4962, 0305-1048},
	url = {http://academic.oup.com/nar/article/43/7/e47/2414268/limma-powers-differential-expression-analyses-for},
	doi = {10.1093/nar/gkv007},
	language = {en},
	number = {7},
	urldate = {2024-04-09},
	journal = {Nucleic Acids Research},
	author = {Ritchie, Matthew E. and Phipson, Belinda and Wu, Di and Hu, Yifang and Law, Charity W. and Shi, Wei and Smyth, Gordon K.},
	month = apr,
	year = {2015},
	pages = {e47--e47},
}

@article{zhu_deqms:_2020,
	title = {Deqms: a method for accurate variance estimation in differential protein expression analysis},
	volume = {19},
	issn = {15359476},
	shorttitle = {Deqms},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1535947620349975},
	doi = {10.1074/mcp.TIR119.001646},
	language = {en},
	number = {6},
	urldate = {2024-04-09},
	journal = {Molecular \& Cellular Proteomics},
	author = {Zhu, Yafeng and Orre, Lukas M. and Zhou Tran, Yan and Mermelekas, Georgios and Johansson, Henrik J. and Malyutina, Alina and Anders, Simon and Lehtiö, Janne},
	month = jun,
	year = {2020},
	pages = {1047--1057},
}


@article{suomi_rots:_2017,
	title = {{ROTS}: {An} {R} package for reproducibility-optimized statistical testing},
	volume = {13},
	issn = {1553-7358},
	shorttitle = {Rots},
	url = {https://dx.plos.org/10.1371/journal.pcbi.1005562},
	doi = {10.1371/journal.pcbi.1005562},
	language = {en},
	number = {5},
	urldate = {2024-04-09},
	journal = {PLOS Computational Biology},
	author = {Suomi, Tomi and Seyednasrollah, Fatemeh and Jaakkola, Maria K. and Faux, Thomas and Elo, Laura L.},
	editor = {Poisot, Timothée},
	month = may,
	year = {2017},
	pages = {e1005562},
}

@article{cox_accurate_2014,
	title = {Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed maxlfq},
	volume = {13},
	issn = {15359476},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1535947620333107},
	doi = {10.1074/mcp.M113.031591},
	language = {en},
	number = {9},
	urldate = {2024-04-09},
	journal = {Molecular \& Cellular Proteomics},
	author = {Cox, Jürgen and Hein, Marco Y. and Luber, Christian A. and Paron, Igor and Nagaraj, Nagarjuna and Mann, Matthias},
	month = sep,
	year = {2014},
	pages = {2513--2526},
}
