Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

Wang, Shengbo; García-Seisdedos, David; Prakash, Ananth; Kundu, Deepti Jaiswal; Collins, Andrew; George, Nancy; Fexová, Silvie; Moreno, Pablo; Papatheodorou, Irene; Jones, Andrew R.; Vizcaíno, Juan Antonio

doi:10.1101/2021.12.20.473413

Cited by 4 publications

(3 citation statements)

References 58 publications

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“…Of the 168 identified core matrisome proteins in this study, 95 (56.5%) were shared between all tissues, while only 2 (NTN1 and VWA2) were unique to a single tissue sample (Figure 2B). This contrasts with a recent review of primarily cellular proteomic datasets across 8 mouse organs, which found that 46.9% of identified protein groups were unique to a single organ and only 0.16% of protein groups were identified in all organs 36 . For comparison, 44% of identified proteins were identified in all tissues within the dataset generated by the Human Protein Atlas (HUPA) project 37 .…”

Section: Resultscontrasting

confidence: 84%

A mass spectrometry-based atlas of extracellular matrix proteins across 25 mouse organs

McCabe

Saviola

Hansen

2022

Preprint

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The extracellular matrix is a critical non-cellular component of multi-cellular organisms containing a variety of proteins, glycoproteins, and proteoglycans which has been implicated in a wide variety of essential biological processes, including development, wound healing, and aging. Due to low solubility, many ECM proteins have been underrepresented in previous proteomics datasets. Using an optimized 3-step decellularization and ECM extraction method involving chaotrope extraction and digestion via hydroxylamine hydrochloride, we have generated coverage of the matrisome across 25 organs. We observe that the top 100 most abundant proteins from the ECM fractions of all tissues are generally present in all tissues, indicating that tissue matrices are principally composed of a shared set of ECM proteins. However, these proteins vary up to 4,000-fold between tissues, resulting in highly unique matrix profiles even with the same primary set of proteins. A data reduction approach was used to reveal related networks of expressed ECM proteins across varying tissues, including basement membrane and collagen subtypes.

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Section: Resultscontrasting

confidence: 84%

A mass spectrometry-based atlas of extracellular matrix proteins across 25 mouse organs

McCabe

Saviola

Hansen

2022

Preprint

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“…The Expression Atlas (EA) ‘bulk’ database has two sections: baseline and differential, and already integrates some proteomics data. This data has been generated from reanalysis of human, mouse, rat and cell-line public datasets, all of which have been derived from Data Dependent Acquisition (DDA) 9–11 . The availability of such results in EA therefore supports the integration of proteomics with transcriptomics information.…”

Section: Introductionmentioning

confidence: 99%

Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas

Walzer

García-Seisdedos

Prakash

et al. 2021

Preprint

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Rising numbers of mass spectrometry proteomics datasets available in the public domain, increasingly include volumes generated from Data Independent Acquisition approaches, SWATH-MS in particular. Unlike Data Dependent Acquisition datasets, their re-use is limited, partially due to challenges in combination and use of free software for analysis in the non-specialist laboratory. We introduce a (re-)analysis pipeline for SWATH-MS data available in the PRIDE database, which includes a harmonised combination of metadata annotation protocols, automated workflows for MS data, statistical analysis and results integration into the resource Expression Atlas. Automation is orchestrated with Nextflow, using containerised open analysis software tools, rendering the pipeline readily available, reproducible and easy to update. To demonstrate its utility, we reanalysed 10 public DIA datasets, 1,278 individual SWATH-MS runs, stored in PRIDE. The robustness of the analysis was evaluated and compared to the results obtained in the original publications. The final results were exported into Expression Atlas, making quantitative results from SWATH-MS experiments more widely available and integrated with results from other reanalysed proteomics and transcriptomics datasets.

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“…Comparison analyses were performed to evaluate changes in the z-score for each function over time and across species and reveal biological pathways underlying toxicity-specific phenotypes. Since the mouse and rat SWATH datasets were analysed separately, log 2 transformed normalised protein expression values of orthologous proteins from the 0 h control animals (untreated) were ranked and grouped into 10 bins within each dataset for comparison of basal protein abundances across species (30). Proteins with the lowest protein abundance values were assigned to bin 1, whereas those with the highest abundance values were assigned to bin 10.…”

Section: Methodsmentioning

confidence: 99%

A systems approach reveals species differences in hepatic stress response capacity

Russomanno

Sison-Young

Livoti

et al. 2022

Preprint

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In order to minimise the occurrence of unexpected toxicities as a new medicine transitions from the preclinical to clinical phases of development, it is vital to understand fundamental similarities and differences between preclinical species and humans. The well-known difference in sensitivity of mice and rats to acetaminophen (APAP) liver injury has been related to differences in the fraction that is bioactivated to the reactive metabolite N-acetyl-p-benzoquinoneimine (NAPQI). We have used physiologically-based pharmacokinetic modelling to identify doses of APAP (300 and 1000 mg/kg in mice and rats, respectively) yielding similar hepatic burdens of NAPQI to enable the comparison of temporal liver tissue responses under conditions of equivalent chemical insult. Despite pharmacokinetic and biochemical verification of the equivalent NAPQI insult, serum biomarker and tissue histopathology analyses revealed that mice still exhibited a greater degree of liver injury than rats. Transcriptomic and proteomic analyses highlighted the stronger activation of stress response pathways (including the Nrf2 oxidative stress response and autophagy) in the livers of rats, indicative of a more robust transcriptional adaptation to the equivalent insult. Using RNA-Seq data, we also found that genes associated with these stress responses are expressed at a higher basal level in the livers of rats compared with both mice and humans. Taken together, these data indicate that rats possess a greater basal and adaptive capacity for hepatic stress responses than mice and humans. This has important implications for species selection in preclinical safety testing of drugs associated with reactive metabolite formation and other forms of chemical stress.

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Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

Cited by 4 publications

References 58 publications

A mass spectrometry-based atlas of extracellular matrix proteins across 25 mouse organs

A mass spectrometry-based atlas of extracellular matrix proteins across 25 mouse organs

Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas

A systems approach reveals species differences in hepatic stress response capacity

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