Region of Interest analysis using mass spectrometry imaging of mitochondrial and sarcomeric proteins in acute cardiac infarction tissue

Yajima, Yuka; Hiratsuka, Toru; Kakimoto, Yu; Ogawa, Shinichiro; Shima, Keisuke; Yamazaki, Y.; Yoshikawa, Kenichi; Tamaki, Keiji; Tsuruyama, Tatsuaki

doi:10.1038/s41598-018-25817-7

Cited by 31 publications

(35 citation statements)

References 42 publications

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“…Heterogeneity in mitochondrial populations likely carries biological significance, especially for those proteins present at very low or even substoichiometric copy numbers. Micromanipulation‐ or MALDI imaging‐based approaches to resolve individual mitochondria may provide an avenue for proteins with larger copy numbers and favourable properties for mass spectrometry analysis (Yajima et al ., ; Zhang et al ., ). Innovative single cell proteomic approaches and single molecule approaches, such as nanopore sequencing of proteins (Budnik et al ., ; Restrepo‐Pérez et al ., ) may open the door to the first single organelle proteomes with quantitative protein coverage.…”

Section: Discussionmentioning

confidence: 99%

Single organelle function and organization as estimated from Arabidopsis mitochondrial proteomics

et al. 2019

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Summary Mitochondria host vital cellular functions, including oxidative phosphorylation and co‐factor biosynthesis, which are reflected in their proteome. At the cellular level plant mitochondria are organized into hundreds of discrete functional entities, which undergo dynamic fission and fusion. It is the individual organelle that operates in the living cell, yet biochemical and physiological assessments have exclusively focused on the characteristics of large populations of mitochondria. Here, we explore the protein composition of an individual average plant mitochondrion to deduce principles of functional and structural organisation. We perform proteomics on purified mitochondria from cultured heterotrophic Arabidopsis cells with intensity‐based absolute quantification and scale the dataset to the single organelle based on criteria that are justified by experimental evidence and theoretical considerations. We estimate that a total of 1.4 million protein molecules make up a single Arabidopsis mitochondrion on average. Copy numbers of the individual proteins span five orders of magnitude, ranging from >40 000 for Voltage‐Dependent Anion Channel 1 to sub‐stoichiometric copy numbers, i.e. less than a single copy per single mitochondrion, for several pentatricopeptide repeat proteins that modify mitochondrial transcripts. For our analysis, we consider the physical and chemical constraints of the single organelle and discuss prominent features of mitochondrial architecture, protein biogenesis, oxidative phosphorylation, metabolism, antioxidant defence, genome maintenance, gene expression, and dynamics. While assessing the limitations of our considerations, we exemplify how our understanding of biochemical function and structural organization of plant mitochondria can be connected in order to obtain global and specific insights into how organelles work.

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Section: Discussionmentioning

confidence: 99%

Single organelle function and organization as estimated from Arabidopsis mitochondrial proteomics

et al. 2019

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“…Tumour (T) and Normal (N) represent intensity. IMS-ROI analysis was performed to test the difference between tumour and normal ROI intensity for each batch of imaging data 12 . When analysis was performed with separate ROIs assigned to the tumour region and the normal region of the brain tissue, molecules specific to the tumour region were detected.…”

Section: Discussionmentioning

confidence: 99%

“…FFPE tissues were deposited on indium tin oxide-coated (ITO) glass slides (Sigma-Aldrich, St. Louis, MO) and were treated in 800 μL of the pre-treatment buffer (0.1 M NH 4 HCO 3 and 30% (v/v) CH 3 CN) in an incubation chamber for the brain tissues 2 . Incubation in pre-treatment buffer, heating, and digestion with trypsin solution including 2.5 mM NH 4 HCO 3 and 10% (v/v) CH 3 CN were added to the chambers as described previously in detail 2,[12][13][14] . By these incubation and steaming procedures (SSP), we succeeded in increasing the ionization efficiency of the protein on the FFPE specimen to approximately 4-5 times of the conventional method, and reducing a nonspecific signal noise 2 .…”

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confidence: 99%

Hierarchical Cluster and Region of Interest Analyses Based on Mass Spectrometry Imaging of Human Brain Tumours

Hiratsuka

Arakawa

Yajima

et al. 2020

Sci Rep

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imaging mass spectrometry (iMS) has been rarely used to examine specimens of human brain tumours. in the current study, high quality brain tumour samples were selected by tissue observation. further, iMS analysis was combined with a new hierarchical cluster analysis (iMS-HcA) and region of interest analysis (iMS-Roi). iMS-HcA was successful in creating groups consisting of similar signal distribution images of glial fibrillary acidic protein (GFAP) and related multiple proteins in primary brain tumours. This clustering data suggested the relation of GFAP and these identified proteins in the brain tumorigenesis. Also, high levels of histone proteins, haemoglobin subunit α, tubulins, and GFAP were identified in a metastatic brain tumour using IMS-ROI. Our results show that IMS-HCA and IMS-ROI are promising techniques for identifying biomarkers using brain tumour samples. Recently, matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry has been used to identify diagnostic markers. MALDI-TOF imaging mass spectrometry (MALDI-IMS) now helps to identify phospholipids 1,2 delivered drugs 3 , and peptides in various tissues 4-7. Breast tumour tissue was used in a recently reported study of MALDI-IMS 8. Reports have also been presented regarding IMS being used in the analysis of gastrointestinal, larynx, and ovarian tumours 9,10 , as well as other diseases 11. In our previous study, we also succeeded in identifying proteins related to important myocardial functions such as ATP synthase in acute myocardial infarction 12-14. In the recent five years, clinical formaldehyde-fixed paraffin-embedded (FFPE) tissue has been made available for IMS studies 2,12,15-17. Formaldehyde reacts with amino acid residues, such as arginine-containing amino groups, by methylene-bridging. The bridge makes it challenging to ionize peptides, and study is therefore difficult when using FFPE for IMS. For this reason, alcohol-based non-crosslinking tissue fixative could be an alternative fixative for multiomics tissue analysis, but its usefulness has not been fully verified 18. Some studies have reported that the use of surfactants improved MS sensitivity using considerable limits on subjects and sample amounts for a stable protocol 14. Angel et al. described the availability of matrix metalloproteinase enzymes to derive a better signal 19. In the current study, glioblastoma was selected as the disease of interest for IMS study using FFPE. Glioblastoma is one of the most aggressive brain tumours 20. Treatment of glioblastoma includes a multidisciplinary approach that provides for maximal surgical resection, radiation therapy 21 , and chemotherapy 22,23. The last two therapies primarily target metastatic carcinoma and malignant lymphoma 24. For better treatment, it is crucial to differentiate glioblastoma from metastatic carcinoma and malignant lymphoma. Moreover, for earlier

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“…MSI is a promising technique for understanding the pathogenesis of lethal acute myocardial infarction (AMI). MSI of cardiac tissue was recently reported by several groups including these authors [21,22].…”

Section: Maldi-msi Of Acute Myocardial Infarction (Ami)mentioning

confidence: 90%

Novel Techniques in Histologic Research: Morphometry and Mass Spectrometry Imaging

Tsuruyama¹,

Hieatsuka²

2019

Histology

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Application of mass spectrometry (MS) has recently been developed for the identification of biomarkers using pathologic samples, whereas its application using formaldehyde-fixed paraffin-embedded (FFPE) tissues remains limited. In this review, we introduce MS imaging (MSI) using FFPE tissue. This method is still challenging for peptide ionization, and various pretreatment techniques have been conducted for enhancing the ionization signal of peptides. A simple chemical pretreatment method involving heating in acetonitrile-containing buffer under pressurized conditions is introduced. Further, two-dimensional MSI data are summarized in a DM for region of interest (ROI) and hierarchical cluster analyses. These techniques enable MALDI-MSI analysis of archived pathological FFPE samples to identify new biomarkers.

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Region of Interest analysis using mass spectrometry imaging of mitochondrial and sarcomeric proteins in acute cardiac infarction tissue

Cited by 31 publications

References 42 publications

Single organelle function and organization as estimated from Arabidopsis mitochondrial proteomics

Single organelle function and organization as estimated from Arabidopsis mitochondrial proteomics

Hierarchical Cluster and Region of Interest Analyses Based on Mass Spectrometry Imaging of Human Brain Tumours

Novel Techniques in Histologic Research: Morphometry and Mass Spectrometry Imaging

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