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Article ; Online: Effect of antibiotic-administration period on hepatic bile acid profile and expression of pharmacokinetic-related proteins in mouse liver, kidney, and brain capillaries.

Yagi, Ryotaro / Masuda, Takeshi / Ito, Shingo / Ohtsuki, Sumio

2023 Volume 50, Page(s) 100494

Abstract: Antibiotic administration affects pharmacokinetics through changes in the intestinal microbiota, and bile acids are involved in this regulation. The purpose of the present study was to clarify the effect of different periods of antibiotic administration ... ...

Abstract	Antibiotic administration affects pharmacokinetics through changes in the intestinal microbiota, and bile acids are involved in this regulation. The purpose of the present study was to clarify the effect of different periods of antibiotic administration on the hepatic bile acid profile and expression of pharmacokinetic-related proteins in mouse liver, kidney, and brain capillaries. Vancomycin and polymyxin B were orally administered to mice for either 5- or 25-days. The hepatic bile acid profile of the 25-day treatment group was distinct. In the liver, the protein expression of cytochrome P450 (Cyp)3a11 showed the greatest reduction to 11.4% after the 5-day treatment and further reduced to 7.01% after the 25-day treatment. Similar reductions were observed for sulfotransferase 1d1, Cyp2b10, carboxylesterase 2e, UDP-glucuronosyltransferase (Ugt)1a5, and Ugt1a9. In the kidney and brain capillaries, no drug-metabolizing enzymes or drug transporters were changed with >1.5-fold or <0.66-fold statistical significance in either period. These results suggest that bile acids and metabolizing enzymes in the liver are affected in a period-dependent manner by antibiotic treatment, while the blood-brain barrier and kidneys are less affected. Drug-drug interactions of antibiotics via the intestinal microbiota should be considered by changing drug metabolism in the liver.
MeSH term(s)	Mice ; Animals ; Bile Acids and Salts/pharmacology ; Capillaries/metabolism ; Liver/metabolism ; Glucuronosyltransferase/metabolism ; Brain/metabolism ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/metabolism ; Kidney/metabolism
Chemical Substances	Bile Acids and Salts ; Glucuronosyltransferase (EC 2.4.1.17) ; Anti-Bacterial Agents
Language	English
Publishing date	2023-02-09
Publishing country	England
Document type	Journal Article
ZDB-ID	2095748-8
ISSN	1880-0920 ; 1347-4367 ; 0916-1139
ISSN (online)	1880-0920
ISSN	1347-4367 ; 0916-1139
DOI	10.1016/j.dmpk.2023.100494
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Article ; Online: Development of a method for isolating brain capillaries from a single neonatal mouse brain and comparison of proteomic profiles between neonatal and adult brain capillaries.

Hamada, Yudai / Ogata, Seiryo / Masuda, Takeshi / Ito, Shingo / Ohtsuki, Sumio

Fluids and barriers of the CNS

2023 Volume 20, Issue 1, Page(s) 50

Abstract: Background: The functions and protein expressions of the blood-brain barrier are changed throughout brain development following birth. This study aimed to develop a method to isolate brain capillaries from a single frozen neonatal mouse brain and ... ...

Abstract	Background: The functions and protein expressions of the blood-brain barrier are changed throughout brain development following birth. This study aimed to develop a method to isolate brain capillaries from a single frozen neonatal mouse brain and elucidate the enrichment of brain capillaries by quantitative proteomic analysis. We further compared the expression profile of proteins between neonatal and adult brain capillary fractions. Methods: The brain capillary fraction was prepared by the optimized method from a single frozen mouse neonatal brain on postnatal day 7. The brain capillary fractions and brain lysates were digested by trypsin and analyzed by liquid chromatography-mass spectrometry for quantitative proteomics. Results: By optimizing the isolation method, we observed brain capillaries in the fraction prepared from a single neonatal mouse brain (nBC fraction). A protein amount of 31.5 μg, which is enough for proteomic analysis, was recovered from the nBC fraction. By proteomics analysis, the brain capillary selective proteins, including Abcb1a/Mdr1, Slc2a1/Glut1, Claudin-5, and Pecam-1, were found to be concentrated > 13.4-fold more in nBC fractions than in whole brain lysates. The marker proteins for neurons and astrocytes were not concentrated in nBC fractions, while those of pericytes and microglia were concentrated. Compared to adult mouse brain capillary fractions (aBC fractions), the expressions of Abcb1a/Mdr1a, Abcc4/Mrp4, and Slc2a1/Glut1 were significantly lower in nBC fractions than in aBC fractions, whereas those of Slc1a4/Asct1, Slc1a5/Asct2, Slc7a1/Cat1, and Slc16a1/Mct1 were significantly higher. Amino acid transporters, Slc38a5/Snat5, showed the greatest nBC-to-aBC ratio among transporters (9.83-fold). Network analysis of proteins expressed differentially between nBC and aBC fractions revealed that the proteins with terms related to the extracellular matrix were enriched. Conclusions: We succeeded in isolating brain capillaries from a single frozen brain of a neonatal mouse at postnatal day 7. Proteomic analysis revealed the differential expression in brain capillaries between neonatal and adult mice. Specifically, amino acid transporters, including Slc1a5/Asct2 and Slc38a5/Snat5, were found to be induced in neonatal brain capillaries. The present isolation method will promote the study of the function and expression of the neonatal blood-brain barrier.
MeSH term(s)	Mice ; Animals ; Animals, Newborn ; Glucose Transporter Type 1/metabolism ; Capillaries/metabolism ; Proteomics/methods ; Brain/metabolism ; Blood-Brain Barrier/metabolism
Chemical Substances	Glucose Transporter Type 1
Language	English
Publishing date	2023-06-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2595406-4
ISSN	2045-8118 ; 2045-8118
ISSN (online)	2045-8118
ISSN	2045-8118
DOI	10.1186/s12987-023-00449-w
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Article ; Online: Diurnal Changes in Protein Expression at the Blood-Brain Barrier in Mice.

Ogata, Seiryo / Ito, Shingo / Masuda, Takeshi / Ohtsuki, Sumio

Biological & pharmaceutical bulletin

2022 Volume 45, Issue 6, Page(s) 751–756

Abstract: Circadian rhythms influence the transport function of the blood-brain barrier (BBB) and peripheral organs. However, the influence of circadian rhythms on protein expression in the BBB remains to be completely elucidated. Therefore, we aimed to ... ...

Abstract	Circadian rhythms influence the transport function of the blood-brain barrier (BBB) and peripheral organs. However, the influence of circadian rhythms on protein expression in the BBB remains to be completely elucidated. Therefore, we aimed to investigate diurnal changes in protein expression in the mouse BBB using quantitative proteomics. Quantitative proteomics showed that the expression of 67, 10, and 20 proteins in the isolated mouse brain capillary fraction changed significantly at zeitgeber time (ZT) 6, 12, and 18, respectively, compared to ZT0. Among them, the levels of 44 proteins were significantly increased at ZT6 and then returned to the same level as ZT0 at ZT12 and ZT18. Gene ontology analysis indicated that the proteins significantly increased at ZT6 were majorly related to translation. The brain capillary endothelial cell-selective proteins sepiapterin reductase and vascular endothelial growth factor receptor 2 showed diurnal variation. In contrast, the expression of ABC transporters, SLC transporters, and receptors associated with receptor-mediated transcytosis, and tight junction proteins did not change within a day. The present findings demonstrated that protein expression related to transport function and physical barrier at the BBB was maintained throughout the day, although the proteins involved in some biological processes exhibited diurnal variation at the BBB.
MeSH term(s)	ATP-Binding Cassette Transporters/metabolism ; Animals ; Biological Transport ; Blood-Brain Barrier/metabolism ; Circadian Rhythm ; Mice ; Proteomics ; Vascular Endothelial Growth Factor Receptor-2
Chemical Substances	ATP-Binding Cassette Transporters ; Kdr protein, mouse (EC 2.7.10.1) ; Vascular Endothelial Growth Factor Receptor-2 (EC 2.7.10.1)
Language	English
Publishing date	2022-06-01
Publishing country	Japan
Document type	Journal Article
ZDB-ID	1150271-x
ISSN	1347-5215 ; 0918-6158
ISSN (online)	1347-5215
ISSN	0918-6158
DOI	10.1248/bpb.b22-00016
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Article ; Online: Human Hepatic Transporter Signature Peptides for Quantitative Targeted Absolute Proteomics: Selection, Digestion Efficiency, and Peptide Stability.

Mori, Ayano / Masuda, Takeshi / Ito, Shingo / Ohtsuki, Sumio

Pharmaceutical research

2022 Volume 39, Issue 11, Page(s) 2965–2978

Abstract: Purpose: Quantitative targeted absolute proteomics (QTAP) quantifies proteins by measuring the signature peptides produced from target proteins by trypsin digestion. The selection of signature peptides is critical for reliable peptide quantification. ... ...

Abstract	Purpose: Quantitative targeted absolute proteomics (QTAP) quantifies proteins by measuring the signature peptides produced from target proteins by trypsin digestion. The selection of signature peptides is critical for reliable peptide quantification. The purpose of this study was to comprehensively assess the digestion efficiency and stability of tryptic peptides and to identify optimal signature peptides for human hepatic transporters and membrane marker proteins. Methods: The plasma membrane fraction of the human liver was digested at different time points and the peptides were comprehensively quantified using quantitative proteomics. Transporters and membrane markers were quantified using the signature peptides by QTAP. Results: Tryptic peptides were classified into clusters with low digestion efficiency, low stability, and high digestion efficiency and stability. Using the cluster information, we found that a proline residue next to the digestion site or the peptide position in or close to the transmembrane domains lowers digestion efficiency. A peptide containing cysteine at the N-terminus or arginine-glycine lowers peptide stability. Based on this information and the time course of peptide quantification, optimal signature peptides were identified for human hepatic transporters and membrane markers. The quantification of transporters with multiple signature peptides yielded consistent absolute values with less than 30% of coefficient variants in human liver microsomes and homogenates. Conclusions: The signature peptides selected in the present study enabled the reliable quantification of human hepatic transporters. The QTAP protocol using these optimal signature peptides provides quantitative data on hepatic transporters usable for integrated pharmacokinetic studies.
MeSH term(s)	Humans ; Proteomics/methods ; Peptides ; Membrane Transport Proteins/metabolism ; Liver/metabolism ; Membrane Proteins/metabolism ; Digestion ; Trypsin/chemistry
Chemical Substances	Peptides ; Membrane Transport Proteins ; Membrane Proteins ; Trypsin (EC 3.4.21.4)
Language	English
Publishing date	2022-09-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	843063-9
ISSN	1573-904X ; 0724-8741 ; 0739-0742
ISSN (online)	1573-904X
ISSN	0724-8741 ; 0739-0742
DOI	10.1007/s11095-022-03387-8
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Article ; Online: Advances in sample preparation for membrane proteome quantification.

Masuda, Takeshi / Ito, Shingo / Ohtsuki, Sumio

Drug discovery today. Technologies

2021 Volume 39, Page(s) 23–29

Abstract: Membrane proteins mediate various biological processes. Most drugs commercially available target proteins on the cell surface. Therefore, proteomics of plasma membrane proteins provides useful information for drug discovery. However, membrane proteins ... ...

Abstract	Membrane proteins mediate various biological processes. Most drugs commercially available target proteins on the cell surface. Therefore, proteomics of plasma membrane proteins provides useful information for drug discovery. However, membrane proteins are one of the most difficult biological groups to quantify by proteomics because of their hydrophobicity and low protein content. To obtain unbiased quantitative membrane proteomics data, specific strategies should be followed during sample preparation. This review explores the most recent advances in sample preparation for the quantitative analysis of the membrane proteome, including enrichment by subcellular fractionation and trypsin digestion.
MeSH term(s)	Membrane Proteins ; Proteome ; Proteomics
Chemical Substances	Membrane Proteins ; Proteome
Language	English
Publishing date	2021-06-25
Publishing country	England
Document type	Journal Article ; Review
ISSN	1740-6749
ISSN (online)	1740-6749
DOI	10.1016/j.ddtec.2021.06.005
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Article ; Online: Proteomic alterations in the brain and blood-brain barrier during brain Aβ accumulation in an APP knock-in mouse model of Alzheimer's disease.

Ito, Shingo / Yagi, Ryotaro / Ogata, Seiryo / Masuda, Takeshi / Saito, Takashi / Saido, Takaomi / Ohtsuki, Sumio

Fluids and barriers of the CNS

2023 Volume 20, Issue 1, Page(s) 66

Abstract: Background: Blood-brain barrier (BBB) dysfunction is supposed to be an early event in the development of Alzheimer's disease (AD). This study aimed to investigate the relationship between BBB alterations and AD progression in terms of amyloid-β peptide ( ...

Abstract	Background: Blood-brain barrier (BBB) dysfunction is supposed to be an early event in the development of Alzheimer's disease (AD). This study aimed to investigate the relationship between BBB alterations and AD progression in terms of amyloid-β peptide (Aβ) accumulation in the brains of humanized amyloid precursor protein knock-in (APP-KI) mice. Methods: Brain Aβ accumulation was examined using immunohistochemical analysis. Alterations in differentially expressed proteins were determined using sequential window acquisition of all theoretical fragment ion mass spectroscopy (SWATH-MS)-based quantitative proteomics, and Metascape, STRING, Gene Ontology, and KEGG were used for network analyses of altered biological pathways and processes. Statistical significance was determined using the unpaired two-tailed Student's t-test and Welch's t-test for two groups and one-way analysis of variance followed by Tukey's test for more than two groups. Correlations between two groups were determined using Pearson's correlation analysis. Results: Brain Aβ accumulation in APP-KI mice was detectable at 2 months, increased significantly at 5 months, and remained elevated at 12 months of age. The levels of differentially expressed proteins in isolated brain capillaries were higher in younger mice, whereas those in the brain were higher in older mice. Network analyses indicated changes in basement membrane-associated and ribosomal proteins in the brain capillaries. There were no significant changes in key proteins involved in drug or Aβ transport at the BBB. In contrast, solute carrier transporter levels in astrocytes, microglia, and neurons were altered in the brain of older mice. Moreover, the levels of the lipid transporters Apoe and Apoj were upregulated in both the brain and isolated brain capillaries after Aβ accumulation. Conclusions: Our results suggest that changes in the brain occurred after advanced Aβ accumulation, whereas initial Aβ accumulation was sufficient to cause alterations in the BBB. These findings may help elucidate the role of BBB alterations in AD progression and predict the distribution of drugs across the BBB in the brain of patients with AD.
MeSH term(s)	Animals ; Mice ; Blood-Brain Barrier ; Alzheimer Disease/genetics ; Proteomics ; Brain ; Membrane Transport Proteins ; Disease Models, Animal
Chemical Substances	Membrane Transport Proteins
Language	English
Publishing date	2023-09-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2595406-4
ISSN	2045-8118 ; 2045-8118
ISSN (online)	2045-8118
ISSN	2045-8118
DOI	10.1186/s12987-023-00466-9
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Article ; Online: Knockdown of Podocalyxin Post-Transcriptionally Induces the Expression and Activity of ABCB1/MDR1 in Human Brain Microvascular Endothelial Cells.

Nagano, Hinako / Ogata, Seiryo / Ito, Shingo / Masuda, Takeshi / Ohtsuki, Sumio

Journal of pharmaceutical sciences

2022 Volume 111, Issue 6, Page(s) 1812–1819

Abstract: Podocalyxin (PODXL) is a highly sialylated transmembrane protein that is expressed on the luminal membrane of brain microvascular endothelial cells. To clarify the role of PODXL in the blood-brain barrier (BBB), the present study aimed to investigate the ...

Abstract	Podocalyxin (PODXL) is a highly sialylated transmembrane protein that is expressed on the luminal membrane of brain microvascular endothelial cells. To clarify the role of PODXL in the blood-brain barrier (BBB), the present study aimed to investigate the effect of PODXL-knockdown on protein expression, especially the expression of ABCB1/MDR1, in human microvascular endothelial cells (hCMEC/D3). By quantitative proteomics, gene ontology enrichment with differentially expressed proteins showed that PODXL-knockdown influenced the immune response and intracellular trafficking. Among transporters, the protein expression of ABCB1/MDR1 and ABCG2/BCRP was significantly elevated by approximately 2-fold in the PODXL-knockdown cells. In the knockdown cells, the efflux activity of ABCB1/MDR1 was significantly increased, while its mRNA expression was not significantly different from that of the control cells. As receptors and tight junction proteins, levels of low-density lipoprotein receptor-related protein 1 and occludin were significantly increased, while those of transferrin receptor and claudin-11 were significantly decreased in the knockdown cells. The present results suggest that PODXL functions as a modulator of BBB function, including transport, tight junctions, and immune responses. Furthermore, PODXL post-transcriptionally regulates the protein expression and efflux activity of ABCB1/MDR1 at the BBB, which may affect drug distribution in the brain.
MeSH term(s)	ATP Binding Cassette Transporter, Subfamily B/genetics ; ATP Binding Cassette Transporter, Subfamily B/metabolism ; ATP Binding Cassette Transporter, Subfamily G, Member 2/metabolism ; Blood-Brain Barrier/metabolism ; Brain/metabolism ; Endothelial Cells/metabolism ; Humans ; Neoplasm Proteins/metabolism ; Sialoglycoproteins
Chemical Substances	ABCB1 protein, human ; ATP Binding Cassette Transporter, Subfamily B ; ATP Binding Cassette Transporter, Subfamily G, Member 2 ; Neoplasm Proteins ; Sialoglycoproteins ; podocalyxin
Language	English
Publishing date	2022-02-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3151-3
ISSN	1520-6017 ; 0022-3549
ISSN (online)	1520-6017
ISSN	0022-3549
DOI	10.1016/j.xphs.2022.02.006
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Article ; Online: Effect of Insulin Receptor-Knockdown on the Expression Levels of Blood-Brain Barrier Functional Proteins in Human Brain Microvascular Endothelial Cells.

Nagano, Hinako / Ito, Shingo / Masuda, Takeshi / Ohtsuki, Sumio

Pharmaceutical research

2021 Volume 39, Issue 7, Page(s) 1561–1574

Abstract: Purpose: The insulin receptor (INSR) mediates insulin signaling to modulate cellular functions. Although INSR is expressed at the blood-brain barrier (BBB), its role in the modulation of BBB function is poorly understood. Therefore, in this study, we ... ...

Abstract	Purpose: The insulin receptor (INSR) mediates insulin signaling to modulate cellular functions. Although INSR is expressed at the blood-brain barrier (BBB), its role in the modulation of BBB function is poorly understood. Therefore, in this study, we aimed to analyze the effect of INSR knockdown on the expression levels of functional proteins at the BBB. Methods: We established the INSR-knockdown cell line (shINSR) using human cerebral microvascular endothelial cells (hCMEC/D3). The cellular proteome was analyzed using quantitative proteomics. Results: INSR mRNA and protein expressions were decreased in shINSR cells. The suppression of INSR-mediated signaling in shINSR cells was evaluated. The proteins involved in glycolysis and glycogenolysis were suppressed in shINSR cells. As amyloid-β peptide-related proteins, the expressions of presenilin-1 was increased, and those of the insulin-degrading enzyme and neprilysin were decreased. The expressions of BBB transporters, including the ABCB1/MDR1, ABCG2/BCRP, and SLCO2A1/OATP2A1 were significantly decreased by more than 50% in shINSR cells. The efflux activity of ABCB1/MDR1 was also suppressed. The expressions of the low-density lipoprotein receptor-related protein 1 were significantly increased, and those of the transferrin receptor were significantly decreased in shINSR cells. The expression of claudin-5 was also suppressed in shINSR cells. Conclusions: The present study suggests that INSR-mediated signaling is involved in the regulation of functional protein expression at the BBB and contributes to the maintenance of BBB function. Changes in the expressions of amyloid-β peptide-related proteins may contribute to the development of cerebral amyloid angiopathy via the suppression of INSR-mediated signaling.
MeSH term(s)	ATP Binding Cassette Transporter, Subfamily G, Member 2/metabolism ; Amyloid beta-Peptides/metabolism ; Antigens, CD/genetics ; Blood-Brain Barrier/metabolism ; Brain/metabolism ; Endothelial Cells/metabolism ; Humans ; Neoplasm Proteins/metabolism ; Organic Anion Transporters/metabolism ; Receptor, Insulin/genetics
Chemical Substances	ATP Binding Cassette Transporter, Subfamily G, Member 2 ; Amyloid beta-Peptides ; Antigens, CD ; Neoplasm Proteins ; Organic Anion Transporters ; SLCO2A1 protein, human ; INSR protein, human (EC 2.7.10.1) ; Receptor, Insulin (EC 2.7.10.1)
Language	English
Publishing date	2021-11-22
Publishing country	United States
Document type	Editorial
ZDB-ID	843063-9
ISSN	1573-904X ; 0724-8741 ; 0739-0742
ISSN (online)	1573-904X
ISSN	0724-8741 ; 0739-0742
DOI	10.1007/s11095-021-03131-8
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Article: [Novel approach for biochemistry by quantitative targeted proteomics: new protein quantification method without using antibodies].

Ohtsuki, Sumio

Seikagaku. The Journal of Japanese Biochemical Society

2012 Volume 84, Issue 11, Page(s) 911–919

MeSH term(s)	Animals ; Antibodies/immunology ; Biochemistry/methods ; Humans ; Protein Binding ; Proteins/analysis ; Proteins/chemistry ; Proteins/metabolism ; Proteomics/methods ; Reproducibility of Results
Chemical Substances	Antibodies ; Proteins
Language	Japanese
Publishing date	2012-11
Publishing country	Japan
Document type	Journal Article ; Review
ZDB-ID	282319-6
ISSN	0037-1017
ISSN	0037-1017
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Article ; Online: Targeted proteomics for cancer biomarker verification and validation.

Ogata, Seiryo / Masuda, Takeshi / Ito, Shingo / Ohtsuki, Sumio

Cancer biomarkers : section A of Disease markers

2020 Volume 33, Issue 4, Page(s) 427–436

Abstract: Targeted proteomics is a method that measures the amount of target proteins via liquid chromatography-tandem mass spectrometry and is used to verify and validate the candidate cancer biomarker proteins. Compared with antibody-based quantification methods ...

Abstract	Targeted proteomics is a method that measures the amount of target proteins via liquid chromatography-tandem mass spectrometry and is used to verify and validate the candidate cancer biomarker proteins. Compared with antibody-based quantification methods such as ELISA, targeted proteomics enables rapid method development, simultaneous measurement of multiple proteins, and high-specificity detection of modifications. Moreover, by spiking the internal standard peptide, targeted proteomics detects the absolute amounts of marker proteins, which is essential for determining the cut-off values for diagnosis and thus for multi-institutional validation. With these unique features, targeted proteomics can seamlessly transfer cancer biomarker candidate proteins from the discovery phase to the verification and validation phases, thereby resulting in an accelerated cancer biomarker pipeline. Furthermore, understanding the basic principles, advantages, and disadvantages is necessary to effectively utilize targeted proteomics in cancer biomarker pipelines. This review aimed to introduce the technical principles of targeted proteomics for cancer biomarker verification and validation.
MeSH term(s)	Biomarkers, Tumor ; Humans ; Mass Spectrometry/methods ; Neoplasms/diagnosis ; Proteins/analysis ; Proteomics/methods
Chemical Substances	Biomarkers, Tumor ; Proteins
Language	English
Publishing date	2020-08-27
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	2203517-5
ISSN	1875-8592 ; 1574-0153 ; 1875-8592
ISSN (online)	1875-8592 ; 1574-0153
ISSN	1875-8592
DOI	10.3233/CBM-210218
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