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Khalid A, Yi W, Yoo S, Abbas S, Si J, Hou X, Hou J. Single-chirality of single-walled carbon nanotubes (SWCNTs) through chromatography and its potential biological applications. NEW J CHEM 2023. [DOI: 10.1039/d2nj04056e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Gel chromatography is used to separate single-chirality and selective-diameter SWCNTs. We also explore the use of photothermal therapy and biosensor applications based on single-chirality, selected-diameter, and unique geometric shape.
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Affiliation(s)
- Asif Khalid
- Key Laboratory for Information Photonic Technology of Shaanxi & Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronics Science and Engineering, Faculty of Electronics and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China
| | - Wenhui Yi
- Key Laboratory for Information Photonic Technology of Shaanxi & Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronics Science and Engineering, Faculty of Electronics and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China
| | - Sweejiang Yoo
- Key Laboratory for Information Photonic Technology of Shaanxi & Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronics Science and Engineering, Faculty of Electronics and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China
| | - Shakeel Abbas
- Key Laboratory for Information Photonic Technology of Shaanxi & Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronics Science and Engineering, Faculty of Electronics and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China
| | - Jinhai Si
- Key Laboratory for Information Photonic Technology of Shaanxi & Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronics Science and Engineering, Faculty of Electronics and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China
| | - Xun Hou
- Key Laboratory for Information Photonic Technology of Shaanxi & Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronics Science and Engineering, Faculty of Electronics and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China
| | - Jin Hou
- Department of Pharmacology, School of Basic Medical Science, Xi’an Medical University, Xi’an, Shaanxi, 710021, China
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2
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Proteogenomic analysis of lung adenocarcinoma reveals tumor heterogeneity, survival determinants, and therapeutically relevant pathways. Cell Rep Med 2022; 3:100819. [PMID: 36384096 PMCID: PMC9729884 DOI: 10.1016/j.xcrm.2022.100819] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/09/2022] [Accepted: 10/18/2022] [Indexed: 11/17/2022]
Abstract
We present a deep proteogenomic profiling study of 87 lung adenocarcinoma (LUAD) tumors from the United States, integrating whole-genome sequencing, transcriptome sequencing, proteomics and phosphoproteomics by mass spectrometry, and reverse-phase protein arrays. We identify three subtypes from somatic genome signature analysis, including a transition-high subtype enriched with never smokers, a transversion-high subtype enriched with current smokers, and a structurally altered subtype enriched with former smokers, TP53 alterations, and genome-wide structural alterations. We show that within-tumor correlations of RNA and protein expression associate with tumor purity and immune cell profiles. We detect and independently validate expression signatures of RNA and protein that predict patient survival. Additionally, among co-measured genes, we found that protein expression is more often associated with patient survival than RNA. Finally, integrative analysis characterizes three expression subtypes with divergent mutations, proteomic regulatory networks, and therapeutic vulnerabilities. This proteogenomic characterization provides a foundation for molecularly informed medicine in LUAD.
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3
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Al-Majdoub ZM, Scotcher D, Achour B, Barber J, Galetin A, Rostami-Hodjegan A. Quantitative Proteomic Map of Enzymes and Transporters in the Human Kidney: Stepping Closer to Mechanistic Kidney Models to Define Local Kinetics. Clin Pharmacol Ther 2021; 110:1389-1400. [PMID: 34390491 DOI: 10.1002/cpt.2396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/03/2021] [Indexed: 12/20/2022]
Abstract
The applications of translational modeling of local drug concentrations in various organs had a sharp increase over the last decade. These are part of the model-informed drug development initiative, adopted by the pharmaceutical industry and promoted by drug regulatory agencies. With respect to the kidney, the models serve as a bridge for understanding animal vs. human observations related to renal drug disposition and any consequential adverse effects. However, quantitative data on key drug-metabolizing enzymes and transporters relevant for predicting renal drug disposition are limited. Using targeted and global quantitative proteomics, we determined the abundance of multiple enzymes and transporters in 20 human kidney cortex samples. Nine enzymes and 22 transporters were quantified (8 for the first time in the kidneys). In addition, > 4,000 proteins were identified and used to form an open database. CYP2B6, CYP3A5, and CYP4F2 showed comparable, but generally low expression, whereas UGT1A9 and UGT2B7 levels were the highest. Significant correlation between abundance and activity (measured by mycophenolic acid clearance) was observed for UGT1A9 (Rs = 0.65, P = 0.004) and UGT2B7 (Rs = 0.70, P = 0.023). Expression of P-gp ≈ MATE-1 and OATP4C1 transporters were high. Strong intercorrelations were observed between several transporters (P-gp/MRP4, MRP2/OAT3, and OAT3/OAT4); no correlation in expression was apparent for functionally related transporters (OCT2/MATEs). This study extends our knowledge of pharmacologically relevant proteins in the kidney cortex, with implications on more prudent use of mechanistic kidney models under the general framework of quantitative systems pharmacology and toxicology.
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Affiliation(s)
- Zubida M Al-Majdoub
- Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, UK
| | - Daniel Scotcher
- Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, UK
| | - Brahim Achour
- Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, UK
| | - Jill Barber
- Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, UK
| | - Aleksandra Galetin
- Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, UK
| | - Amin Rostami-Hodjegan
- Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, UK.,Certara UK (Simcyp Division), Sheffield, UK
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4
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Tu A, Said N, Muddiman DC. Spatially resolved metabolomic characterization of muscle invasive bladder cancer by mass spectrometry imaging. Metabolomics 2021; 17:70. [PMID: 34287708 PMCID: PMC8893274 DOI: 10.1007/s11306-021-01819-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 07/09/2021] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Muscle invasive bladder cancer (MIBC) is an advanced stage of bladder cancer which poses a severe threat to life. Cancer development is usually accompanied by remarkable alterations in cell metabolism, and hence deep insights into MIBC at the metabolomic level can facilitate the understanding of the biochemical mechanisms involved in the cancer development and progression. METHODS In this proof-of-concept study, the optimal cutting temperature (OCT)-embedded MIBC samples were first washed with pure water to remove the polymer compounds which could cause severe signal suppression during mass spectrometry. Further, the tissue sections were analyzed by infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging (IR-MALDESI MSI), providing an overview on the spatially resolved metabolomic profiles. RESULTS The MSI data enabled the discrimination between not only the cancerous and normal tissues, but also the subregions within a tissue section associated with different disease states. Using t-Distributed Stochastic Neighbor Embedding (t-SNE), the hyperdimensional MSI data was mapped into a two-dimensional space to visualize the spectral similarity, providing evidence that metabolomic alterations might have occurred outside the histopathological tumor border. Least absolute shrinkage and selection operator (LASSO) was further employed to classify sample pathology in a pixel-wise manner, yielding excellent prediction sensitivity and specificity up to 96% based on the statistically characteristic spectral features. CONCLUSION The results demonstrate great promise of IR-MALDESI MSI to identify molecular changes derived from cancer and unveil tumor heterogeneity, which can potentially promote the discovery of clinically relevant biomarkers and allow for applications in precision medicine.
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Affiliation(s)
- Anqi Tu
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Neveen Said
- Departments of Cancer Biology, Pathology, and Urology, Wake Forest University School of Medicine, Wake Forest Baptist Comprehensive Cancer Center, Winston Salem, NC, 27157, USA
| | - David C Muddiman
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA.
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC, 27695, USA.
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Xu X, Wei T, Zhong W, Ang R, Lei Y, Zhang H, Li Q. Down-regulation of cylindromatosis protein phosphorylation by BTK inhibitor promotes apoptosis of non-GCB-diffuse large B-cell lymphoma. Cancer Cell Int 2021; 21:195. [PMID: 33827598 PMCID: PMC8025353 DOI: 10.1186/s12935-021-01891-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Non-germinal center B-cell-like diffuse large B-cell lymphoma (non-GCB-DLBCL) has worse clinical outcome than GCB-DLBCL, and some relapsed/refractory non-GCB-DLBCL (R/R non-GCB-DLBCL) are even resistant to CD20 monoclonal antibody (rituximab). Bruton's tyrosine kinase inhibitors (BTKis) are new drugs for B-cell lymphoma. BTKis can promote apoptosis of DLBCL by inactivating nuclear transcription factor κB (NFκB) signaling pathway. Cylindromatosis (CYLD) is a tumor suppressor and ubiquitinase. CYLD can inactivate NFκB signaling pathway through ubiquitination and regulate the apoptosis of hematological tumors. The ubiquitination of CYLD can be regulated by phosphorylation, suggesting that the regulation of CYLD phosphorylation can be a potential mechanism to promote the apoptosis of hematological tumors. Therefore, we hypothesized that BTKis could promote the apoptosis of non-GCB-DLBCL by regulating the phosphorylation of CYLD, especially in rituximab resistant cases, and we proved this hypothesis through both in vivo and in vitro experiments. METHODS The baseline expression levels of CYLD phosphorylation in non-GCB-DLBCL patients and cell lines were detected by Western Blotting. The non-GCB-DLBCL cell lines were treated with BTKis, and apoptosis induced by BTKis treatment was detected by Western blotting, cell viability assay and Annexin V assay. To verify whether the effect of BTKis on apoptosis in non-GCN-DLBCL cells is CYLD dependent, the expression of CYLD was knocked down by lentiviral shRNAs. To verify the effect of BTKis on the phosphorylation of CYLD and the apoptosis in vivo and in rituximab resistant non-GCB-DLBCL, the xeograft model and rituximab resistant non-GCB-DLBCL cells were generated by tumor cell inoculation and escalation of drug concentrations, respectively. RESULTS BTKis induced apoptosis by down-regulating CYLD phosphorylationin in non GCB-DLBCL, xenograft mouse model, and rituximab-resistant cells, and this effect could be enhanced by rituximab. Knocking-down CYLD reversed apoptosis which was induced by BTKis. BTKis induced CYLD-dependent apoptosis in non-GCB-DLBCL including in rituximab-resistant cells. CONCLUSIONS The present results indicated that CYLD phosphorylation is a potential clinical therapeutic target for non-GCB-DLBCL, especially for rituximab-resistant relapsed/refractory cases.
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Affiliation(s)
- Xin Xu
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong, 510630, People's Republic of China.,Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 511458, People's Republic of China
| | - Ting Wei
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People's Republic of China
| | - Weijie Zhong
- Department of Geriatrics, Hematology and Oncology Ward, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, People's Republic of China
| | - Rosalind Ang
- Precision Immunology Institute, Mount Sinai School of Medicine, New York, NY, 10029, USA
| | - Ye Lei
- Precision Immunology Institute, Mount Sinai School of Medicine, New York, NY, 10029, USA
| | - Hui Zhang
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jinan, Shandong, 272067, People's Republic of China
| | - Qingshan Li
- Department of Hematology, Guangzhou Red Cross Hospital, Jinan University, No. 396 Tongfuzhong Road, Haizhu District, 510220, Guangzhou, Guangdong, People's Republic of China.
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Sturtz LA, Wang G, Shah P, Searfoss R, Raj-Kumar PK, Hooke JA, Fantacone-Campbell JL, Deyarmin B, Cutler ML, Sarangarajan R, Narain NR, Hu H, Kiebish MA, Kovatich AJ, Shriver CD. Comparative analysis of differentially abundant proteins quantified by LC-MS/MS between flash frozen and laser microdissected OCT-embedded breast tumor samples. Clin Proteomics 2020; 17:40. [PMID: 33292179 PMCID: PMC7648272 DOI: 10.1186/s12014-020-09300-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/05/2020] [Indexed: 12/21/2022] Open
Abstract
Background Proteomic studies are typically conducted using flash-frozen (FF) samples utilizing tandem mass spectrometry (MS). However, FF specimens are comprised of multiple cell types, making it difficult to ascertain the proteomic profiles of specific cells. Conversely, OCT-embedded (Optimal Cutting Temperature compound) specimens can undergo laser microdissection (LMD) to capture and study specific cell types separately from the cell mixture. In the current study, we compared proteomic data obtained from FF and OCT samples to determine if samples that are stored and processed differently produce comparable results. Methods Proteins were extracted from FF and OCT-embedded invasive breast tumors from 5 female patients. FF specimens were lysed via homogenization (FF/HOM) while OCT-embedded specimens underwent LMD to collect only tumor cells (OCT/LMD-T) or both tumor and stromal cells (OCT/LMD-TS) followed by incubation at 37 °C. Proteins were extracted using the illustra triplePrep kit and then trypsin-digested, TMT-labeled, and processed by two-dimensional liquid chromatography-tandem mass spectrometry (2D LC–MS/MS). Proteins were identified and quantified with Proteome Discoverer v1.4 and comparative analyses performed to identify proteins that were significantly differentially expressed amongst the different processing methods. Results Among the 4,950 proteins consistently quantified across all samples, 216 and 171 proteins were significantly differentially expressed (adjusted p-value < 0.05; |log2 FC|> 1) between FF/HOM vs. OCT/LMD-T and FF/HOM vs. OCT/LMD-TS, respectively, with most proteins being more highly abundant in the FF/HOM samples. PCA and unsupervised hierarchical clustering analysis with these 216 and 171 proteins were able to distinguish FF/HOM from OCT/LMD-T and OCT/LMD-TS samples, respectively. Similar analyses using significantly differentially enriched GO terms also discriminated FF/HOM from OCT/LMD samples. No significantly differentially expressed proteins were detected between the OCT/LMD-T and OCT/LMD-TS samples but trended differences were detected. Conclusions The proteomic profiles of the OCT/LMD-TS samples were more similar to those from OCT/LMD-T samples than FF/HOM samples, suggesting a strong influence from the sample processing methods. These results indicate that in LC–MS/MS proteomic studies, FF/HOM samples exhibit different protein expression profiles from OCT/LMD samples and thus, results from these two different methods cannot be directly compared.
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Affiliation(s)
- Lori A Sturtz
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Guisong Wang
- Murtha Cancer Center/Research Program, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | | | | | | | - Jeffrey A Hooke
- Murtha Cancer Center/Research Program, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - J Leigh Fantacone-Campbell
- Murtha Cancer Center/Research Program, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Brenda Deyarmin
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Mary Lou Cutler
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | | | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA.
| | | | - Albert J Kovatich
- Murtha Cancer Center/Research Program, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA. .,Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA. .,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
| | - Craig D Shriver
- Murtha Cancer Center/Research Program, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA. .,Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
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7
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Rohrbach TD, Boyd AE, Grizzard PJ, Spiegel S, Allegood J, Lima S. A simple method for sphingolipid analysis of tissues embedded in optimal cutting temperature compound. J Lipid Res 2020; 61:953-967. [PMID: 32341007 PMCID: PMC7269760 DOI: 10.1194/jlr.d120000809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/23/2020] [Indexed: 02/06/2023] Open
Abstract
MS-assisted lipidomic tissue analysis is a valuable tool to assess sphingolipid metabolism dysfunction in disease. These analyses can reveal potential pharmacological targets or direct mechanistic studies to better understand the molecular underpinnings and influence of sphingolipid metabolism alterations on disease etiology. But procuring sufficient human tissues for adequately powered studies can be challenging. Therefore, biorepositories, which hold large collections of cryopreserved human tissues, are an ideal retrospective source of specimens. However, this resource has been vastly underutilized by lipid biologists, as the components of OCT compound used in cryopreservation are incompatible with MS analyses. Here, we report results indicating that OCT compound also interferes with protein quantification assays, and that the presence of OCT compound impacts the quantification of extracted sphingolipids by LC-ESI-MS/MS. We developed and validated a simple and inexpensive method that removes OCT compound from OCT compound-embedded tissues. Our results indicate that removal of OCT compound from cryopreserved tissues does not significantly affect the accuracy of sphingolipid measurements with LC-ESI-MS/MS. We used the validated method to analyze sphingolipid alterations in tumors compared with normal adjacent uninvolved lung tissues from individuals with lung cancer and to determine the long-term stability of sphingolipids in OCT compound-cryopreserved normal lung tissues. We show that lung cancer tumors have significantly altered sphingolipid profiles and that sphingolipids are stable for up to 16 years in OCT compound-cryopreserved normal lung tissues. This validated sphingolipidomic OCT compound-removal protocol should be a valuable addition to the lipid biologist's toolbox.
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Affiliation(s)
- Timothy D Rohrbach
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298
| | - April E Boyd
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284
| | | | - Sarah Spiegel
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298
| | - Jeremy Allegood
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298; Virginia Commonwealth University Lipidomics/Metabolomics Shared Resource, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
| | - Santiago Lima
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284; Virginia Commonwealth University Massey Cancer Center, Richmond, VA 23298. mailto:
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Snijders MLH, Zajec M, Walter LAJ, de Louw RMAA, Oomen MHA, Arshad S, van den Bosch TPP, Dekker LJM, Doukas M, Luider TM, Riegman PHJ, van Kemenade FJ, Clahsen-van Groningen MC. Cryo-Gel embedding compound for renal biopsy biobanking. Sci Rep 2019; 9:15250. [PMID: 31649317 PMCID: PMC6813323 DOI: 10.1038/s41598-019-51962-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 10/09/2019] [Indexed: 01/01/2023] Open
Abstract
Optimal preservation and biobanking of renal tissue is vital for good diagnostics and subsequent research. Optimal cutting temperature (OCT) compound is a commonly used embedding medium for freezing tissue samples. However, due to interfering polymers in OCT, analysis as mass spectrometry (MS) is difficult. We investigated if the replacement of OCT with Cryo-Gel as embedding compound for renal biopsies would enable proteomics and not disturb other common techniques used in tissue diagnostics and research. For the present study, fresh renal samples were snap-frozen using Cryo-Gel, OCT and without embedding compound and evaluated using different techniques. In addition, tissue samples from normal spleen, skin, liver and colon were analyzed. Cryo-Gel embedded tissues showed good morphological preservation and no interference in immunohistochemical or immunofluorescent investigations. The quality of extracted RNA and DNA was good. The number of proteins identified using MS was similar between Cryo-Gel embedded samples, samples without embedding compound and OCT embedded samples. However, polymers in the OCT disturbed the signal in the MS, while this was not observed in the Cryo-Gel embedded samples. We conclude that embedding of renal biopsies in Cryo-Gel is an excellent and preferable alternative for OCT compound for both diagnostic and research purposes, especially in those cases where proteomic analysis might be necessary.
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Affiliation(s)
| | - Marina Zajec
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
- Department of Clinical Chemistry, Erasmus MC, Rotterdam, The Netherlands
| | | | | | | | - Shazia Arshad
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | | | | | - Michail Doukas
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
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9
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Jorge S, Capelo JL, LaFramboise W, Dhir R, Lodeiro C, Santos HM. Development of a Robust Ultrasonic-Based Sample Treatment To Unravel the Proteome of OCT-Embedded Solid Tumor Biopsies. J Proteome Res 2019; 18:2979-2986. [PMID: 31173681 DOI: 10.1021/acs.jproteome.9b00248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
An effective three-step proteomics workflow is proposed to overcome the pitfalls caused by polymers present in optimum cutting temperature (OCT)-embedded tissue during its preparation for mass spectrometry analysis. First, the OCT-embedded tissue biopsies are cleaned using ethanol and water in a sequential series of ultrasonic washes in an ultrasound bath (35 kHz ultrasonic frequency, 100% ultrasonic amplitude, 2 min of ultrasonic duty time). Second, a fast ultrasonic-assisted extraction of proteins is done using an ultrasonic probe (30 kHz ultrasonic frequency, 50% ultrasonic amplitude, 2 min of ultrasonic duty time, 1 mm diameter tip). Third, a rapid ultrasonic digestion of complex proteomes is performed using a microplate horn assembly device (20 kHz ultrasonic frequency, 25% ultrasonic amplitude, 4 min of ultrasonic duty time). As a proof of concept, the new workflow was applied to human normal and tumor kidney biopsies including chromophobe renal cell carcinomas (chRCCs) and renal oncocytomas (ROs). A successful cluster of proteomics profiles was obtained comprising 511 and 172 unique proteins found in chRCC and RO samples, respectively. The new method provides high sample throughput and comprehensive protein recovery from OCT samples.
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Affiliation(s)
- Susana Jorge
- BIOSCOPE Research Group, LAQV, REQUIMTE, Department of Chemistry, Faculdade de Ciências e Tecnologia , Universidade NOVA de Lisboa , 2829-516 Caparica , Portugal.,PROTEOMASS Scientific Society , Madan Park, Rua dos Inventores , 2825-152 Caparica , Portugal
| | - José L Capelo
- BIOSCOPE Research Group, LAQV, REQUIMTE, Department of Chemistry, Faculdade de Ciências e Tecnologia , Universidade NOVA de Lisboa , 2829-516 Caparica , Portugal.,PROTEOMASS Scientific Society , Madan Park, Rua dos Inventores , 2825-152 Caparica , Portugal
| | - William LaFramboise
- Department of Pathology , University of Pittsburgh Medical Center , Pittsburgh , Pennsylvania 15261 , United States
| | - Rajiv Dhir
- Department of Pathology , University of Pittsburgh Medical Center , Pittsburgh , Pennsylvania 15261 , United States
| | - Carlos Lodeiro
- BIOSCOPE Research Group, LAQV, REQUIMTE, Department of Chemistry, Faculdade de Ciências e Tecnologia , Universidade NOVA de Lisboa , 2829-516 Caparica , Portugal.,PROTEOMASS Scientific Society , Madan Park, Rua dos Inventores , 2825-152 Caparica , Portugal
| | - Hugo M Santos
- BIOSCOPE Research Group, LAQV, REQUIMTE, Department of Chemistry, Faculdade de Ciências e Tecnologia , Universidade NOVA de Lisboa , 2829-516 Caparica , Portugal.,PROTEOMASS Scientific Society , Madan Park, Rua dos Inventores , 2825-152 Caparica , Portugal
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10
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Hoyer KJR, Dittrich S, Bartram MP, Rinschen MM. Quantification of molecular heterogeneity in kidney tissue by targeted proteomics. J Proteomics 2019. [DOI: 10.1016/j.jprot.2018.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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11
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Jones SM, Mann A, Conrad K, Saum K, Hall DE, McKinney LM, Robbins N, Thompson J, Peairs AD, Camerer E, Rayner KJ, Tranter M, Mackman N, Owens AP. PAR2 (Protease-Activated Receptor 2) Deficiency Attenuates Atherosclerosis in Mice. Arterioscler Thromb Vasc Biol 2018; 38:1271-1282. [PMID: 29599135 PMCID: PMC6324171 DOI: 10.1161/atvbaha.117.310082] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 03/15/2018] [Indexed: 12/25/2022]
Abstract
OBJECTIVE PAR2 (protease-activated receptor 2)-dependent signaling results in augmented inflammation and has been implicated in the pathogenesis of several autoimmune conditions. The objective of this study was to determine the effect of PAR2 deficiency on the development of atherosclerosis. APPROACH AND RESULTS PAR2 mRNA and protein expression is increased in human carotid artery and mouse aortic arch atheroma versus control carotid and aortic arch arteries, respectively. To determine the effect of PAR2 deficiency on atherosclerosis, male and female low-density lipoprotein receptor-deficient (Ldlr-/-) mice (8-12 weeks old) that were Par2+/+ or Par2-/- were fed a fat- and cholesterol-enriched diet for 12 or 24 weeks. PAR2 deficiency attenuated atherosclerosis in the aortic sinus and aortic root after 12 and 24 weeks. PAR2 deficiency did not alter total plasma cholesterol concentrations or lipoprotein distributions. Bone marrow transplantation showed that PAR2 on nonhematopoietic cells contributed to atherosclerosis. PAR2 deficiency significantly attenuated levels of the chemokines Ccl2 and Cxcl1 in the circulation and macrophage content in atherosclerotic lesions. Mechanistic studies using isolated primary vascular smooth muscle cells showed that PAR2 deficiency is associated with reduced Ccl2 and Cxcl1 mRNA expression and protein release into the supernatant resulting in less monocyte migration. CONCLUSIONS Our results indicate that PAR2 deficiency is associated with attenuation of atherosclerosis and may reduce lesion progression by blunting Ccl2- and Cxcl1-induced monocyte infiltration.
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MESH Headings
- Animals
- Aorta, Thoracic/metabolism
- Aorta, Thoracic/pathology
- Aortic Diseases/genetics
- Aortic Diseases/metabolism
- Aortic Diseases/pathology
- Aortic Diseases/prevention & control
- Atherosclerosis/genetics
- Atherosclerosis/metabolism
- Atherosclerosis/pathology
- Atherosclerosis/prevention & control
- Carotid Artery Diseases/genetics
- Carotid Artery Diseases/metabolism
- Carotid Artery Diseases/pathology
- Cell Movement
- Cells, Cultured
- Chemokine CCL2/genetics
- Chemokine CCL2/metabolism
- Chemokine CXCL1/genetics
- Chemokine CXCL1/metabolism
- Disease Models, Animal
- Female
- Genetic Predisposition to Disease
- Humans
- Lipids/blood
- Macrophages/metabolism
- Macrophages/pathology
- Male
- Mice, Knockout
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Phenotype
- Plaque, Atherosclerotic
- Receptor, PAR-1/deficiency
- Receptor, PAR-1/genetics
- Receptor, PAR-2/deficiency
- Receptor, PAR-2/genetics
- Receptors, G-Protein-Coupled/deficiency
- Receptors, G-Protein-Coupled/genetics
- Receptors, LDL/deficiency
- Receptors, LDL/genetics
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Affiliation(s)
- Shannon M Jones
- From the Division of Cardiovascular Health and Disease (S.M.J., A.M., K.C., K.S., L.M.M., N.R., M.T., A.P.O.)
| | - Adrien Mann
- From the Division of Cardiovascular Health and Disease (S.M.J., A.M., K.C., K.S., L.M.M., N.R., M.T., A.P.O.)
| | - Kelsey Conrad
- From the Division of Cardiovascular Health and Disease (S.M.J., A.M., K.C., K.S., L.M.M., N.R., M.T., A.P.O.)
- Pathobiology and Molecular Medicine Program (K.C., M.T., A.P.O.)
| | - Keith Saum
- From the Division of Cardiovascular Health and Disease (S.M.J., A.M., K.C., K.S., L.M.M., N.R., M.T., A.P.O.)
- University of Cincinnati Medical Scientist Training Program (K.S.)
| | - David E Hall
- Department of Nutritional Sciences, College of Allied Health (D.E.H., A.D.P.)
- Department of Internal Medicine (D.E.H., A.D.P.), University of Cincinnati College of Medicine, OH
| | - Lisa M McKinney
- From the Division of Cardiovascular Health and Disease (S.M.J., A.M., K.C., K.S., L.M.M., N.R., M.T., A.P.O.)
| | - Nathan Robbins
- From the Division of Cardiovascular Health and Disease (S.M.J., A.M., K.C., K.S., L.M.M., N.R., M.T., A.P.O.)
| | - Joel Thompson
- Division of Endocrinology and Molecular Medicine, Department of Internal Medicine, University of Kentucky, Lexington (J.T.)
| | - Abigail D Peairs
- Department of Nutritional Sciences, College of Allied Health (D.E.H., A.D.P.)
- Department of Internal Medicine (D.E.H., A.D.P.), University of Cincinnati College of Medicine, OH
| | - Eric Camerer
- INSERM U970, Paris Cardiovascular Research Centre, France (E.C.)
| | - Katey J Rayner
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa Heart Institute, Ontario, Canada (K.J.R.)
| | - Michael Tranter
- From the Division of Cardiovascular Health and Disease (S.M.J., A.M., K.C., K.S., L.M.M., N.R., M.T., A.P.O.)
- Pathobiology and Molecular Medicine Program (K.C., M.T., A.P.O.)
| | - Nigel Mackman
- Division of Hematology and Oncology, Department of Medicine, UNC McAllister Heart Institute, University of North Carolina at Chapel Hill (N.M.)
| | - A Phillip Owens
- From the Division of Cardiovascular Health and Disease (S.M.J., A.M., K.C., K.S., L.M.M., N.R., M.T., A.P.O.)
- Pathobiology and Molecular Medicine Program (K.C., M.T., A.P.O.)
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12
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Holfeld A, Valdés A, Malmström PU, Segersten U, Lind SB. Parallel Proteomic Workflow for Mass Spectrometric Analysis of Tissue Samples Preserved by Different Methods. Anal Chem 2018; 90:5841-5849. [PMID: 29624047 DOI: 10.1021/acs.analchem.8b00379] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Formalin-fixed and paraffin-embedded (FFPE) and optimal cutting temperature (OCT)-embedded and frozen tissue specimens in biobanks are highly valuable in clinical studies but proteomic and post-translational modification (PTM) studies using mass spectrometry (MS) have been limited due to structural arrangement of proteins and contaminations from embedding material. This study aims to develop a parallel proteomic workflow for FFPE and OCT/frozen samples that allows for large-scale, quick, reproducible, qualitative, and quantitative high-resolution MS analysis. The optimized protocol gives details on removal of embedding material, protein extraction, and multienzyme digestion using filter-aided sample preparation method. The method was evaluated by investigating the protein expression levels in nonmuscle-invasive and muscle-invasive bladder cancer samples in two cohorts and MS spectra were carefully reviewed for contaminations. More than 2000 and 3000 proteins in FFPE and OCT/frozen samples, respectively, were identified, and samples could be clustered in different tumor stages based on their protein expression. Furthermore, more than 250 and 400 phosphopeptides could be identified from specific patient samples of FFPE and OCT/frozen, respectively, using titanium dioxide enrichment. The paper presents unique data describing the similarities and differences observed in FFPE and OCT/frozen samples and shows the feasibility to detect proteins and site-specific phosphorylation even after long-term storage of clinical samples.
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13
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Arni S, de Wijn R, Garcia–Villegas R, Bitanihirwe BK, Caviezel C, Weder W, Hillinger S. A strategy to analyse activity-based profiling of tyrosine kinase substrates in OCT-embedded lung cancer tissue. Anal Biochem 2018; 547:77-83. [DOI: 10.1016/j.ab.2018.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 01/11/2023]
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