TY  - JOUR
A1  - Kline, Rachel A.
A1  - Lößlein, Lena
A1  - Kurian, Dominic
A1  - Aguilar Martí, Judit
A1  - Eaton, Samantha L.
A1  - Court, Felipe A.
A1  - Gillingwater, Thomas H.
A1  - Wishart, Thomas M.
T1  - An optimized comparative proteomic approach as a tool in neurodegenerative disease research
JF  - Cells
N2  - Recent advances in proteomic technologies now allow unparalleled assessment of the molecular composition of a wide range of sample types. However, the application of such technologies and techniques should not be undertaken lightly. Here, we describe why the design of a proteomics experiment itself is only the first step in yielding high-quality, translatable results. Indeed, the effectiveness and/or impact of the majority of contemporary proteomics screens are hindered not by commonly considered technical limitations such as low proteome coverage but rather by insufficient analyses. Proteomic experimentation requires a careful methodological selection to account for variables from sample collection, through to database searches for peptide identification to standardised post-mass spectrometry options directed analysis workflow, which should be adjusted for each study, from determining when and how to filter proteomic data to choosing holistic versus trend-wise analyses for biologically relevant patterns. Finally, we highlight and discuss the difficulties inherent in the modelling and study of the majority of progressive neurodegenerative conditions. We provide evidence (in the context of neurodegenerative research) for the benefit of undertaking a comparative approach through the application of the above considerations in the alignment of publicly available pre-existing data sets to identify potential novel regulators of neuronal stability.
KW  - proteomics
KW  - systems biology
KW  - experimental design
KW  - neurodegeneration
KW  - pathway analysis
KW  - data filtering
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-285912
SN  - 2073-4409
VL  - 11
IS  - 17
ER  - 
TY  - JOUR
A1  - Busch, Albert
A1  - Busch, Martin
A1  - Scholz, Claus-Jürgen
A1  - Kellersmann, Richard
A1  - Otto, Christoph
A1  - Chernogubova, Ekaterina
A1  - Maegdefessel, Lars
A1  - Zernecke, Alma
A1  - Lorenz, Udo
T1  - Aneurysm miRNA Signature Differs, Depending on Disease Localization and Morphology
JF  - International Journal of Molecular Science
N2  - Limited comprehension of aneurysm pathology has led to inconclusive results from clinical trials. miRNAs are key regulators of post-translational gene modification and are useful tools in elucidating key features of aneurysm pathogenesis in distinct entities of abdominal and popliteal aneurysms. Here, surgically harvested specimens from 19 abdominal aortic aneurysm (AAA) and 8 popliteal artery aneurysm (PAA) patients were analyzed for miRNA expression and histologically classified regarding extracellular matrix (ECM) remodeling and inflammation. DIANA-based computational target prediction and pathway enrichment analysis verified our results, as well as previous ones. miRNA-362, -19b-1, -194, -769, -21 and -550 were significantly down-regulated in AAA samples depending on degree of inflammation. Similar or inverse regulation was found for miR-769, 19b-1 and miR-550, -21, whereas miR-194 and -362 were unaltered in PAA. In situ hybridization verified higher expression of miR-550 and -21 in PAA compared to AAA and computational analysis for target genes and pathway enrichment affirmed signal transduction, cell-cell-interaction and cell degradation pathways, in line with previous results. Despite the vague role of miRNAs for potential diagnostic and treatment purposes, the number of candidates from tissue signature studies is increasing. Tissue morphology influences subsequent research, yet comparison of distinct entities of aneurysm disease can unravel core pathways.
KW  - AAA
KW  - miRNA expression
KW  - pathway analysis
KW  - histologic diversity
KW  - popliteal aneurysm
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-146422
SN  - International Journal of Molecular Science
VL  - 17
IS  - 1
ER  -