1
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Yang Z, Chen L, Huang Y, Dong J, Yan Q, Li Y, Qiu J, Li H, Zhao D, Liu F, Tang D, Dai Y. Proteomic profiling of laser capture microdissection kidneys from diabetic nephropathy patients. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1243:124231. [PMID: 38996754 DOI: 10.1016/j.jchromb.2024.124231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/23/2024] [Accepted: 07/01/2024] [Indexed: 07/14/2024]
Abstract
Diabetic nephropathy (DN) remains the primary cause of end-stage renal disease (ESRD), warranting equal attention and separate analysis of glomerular, tubular, and interstitial lesions in its diagnosis and intervention. This study aims to identify the specific proteomics characteristics of DN, and assess changes in the biological processes associated with DN. 5 patients with DN and 5 healthy kidney transplant donor control individuals were selected for analysis. The proteomic characteristics of glomeruli, renal tubules, and renal interstitial tissue obtained through laser capture microscopy (LCM) were studied using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). Significantly, the expression of multiple heat shock proteins (HSPs), tubulins, and heterogeneous nuclear ribonucleoproteins (hnRNPs) in glomeruli and tubules was significantly reduced. Differentially expressed proteins (DEPs) in the glomerulus showed significant enrichment in pathways related to cell junctions and cell movement, including the regulation of actin cytoskeleton and tight junction. DEPs in renal tubules were significantly enriched in glucose metabolism-related pathways, such as glucose metabolism, glycolysis/gluconeogenesis, and the citric acid cycle. Moreover, the glycolysis/gluconeogenesis pathway was a co-enrichment pathway in both DN glomeruli and tubules. Notably, ACTB emerged as the most crucial protein in the protein-protein interaction (PPI) analysis of DEPs in both glomeruli and renal tubules. In this study, we delve into the unique proteomic characteristics of each sub-region of renal tissue. This enhances our understanding of the potential pathophysiological changes in DN, particularly the potential involvement of glycolysis metabolic disorder, glomerular cytoskeleton and cell junctions. These insights are crucial for further research into the identification of disease biomarkers and the pathogenesis of DN.
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Affiliation(s)
- Zhiqian Yang
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China; Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Liangmei Chen
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Yingxin Huang
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China; Department of Nephrology, Xiaolan People's Hospital of Zhongshan, 528400, China
| | - Jingjing Dong
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China; Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Qiang Yan
- Department of Organ Transplantation, 924 Hospital, Guilin 541002, China
| | - Ya Li
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China
| | - Jing Qiu
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China
| | - Haitao Li
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China
| | - Da Zhao
- The First Affiliated Hospital, School of Medicine, Anhui University of Science and Technology, Huainan 232001, Anhui, China
| | - Fanna Liu
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China.
| | - Donge Tang
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China.
| | - Yong Dai
- Comprehensive Health Industry Research Center, Taizhou Research Institute, Southern University of Science and Technology, Taizhou 317000, China; The First Affiliated Hospital, School of Medicine, Anhui University of Science and Technology, Huainan 232001, Anhui, China.
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2
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Pencik J, Philippe C, Schlederer M, Atas E, Pecoraro M, Grund-Gröschke S, Li WJ, Tracz A, Heidegger I, Lagger S, Trachtová K, Oberhuber M, Heitzer E, Aksoy O, Neubauer HA, Wingelhofer B, Orlova A, Witzeneder N, Dillinger T, Redl E, Greiner G, D'Andrea D, Östman JR, Tangermann S, Hermanova I, Schäfer G, Sternberg F, Pohl EE, Sternberg C, Varady A, Horvath J, Stoiber D, Malcolm TI, Turner SD, Parkes EE, Hantusch B, Egger G, Rose-John S, Poli V, Jain S, Armstrong CWD, Hoermann G, Goffin V, Aberger F, Moriggl R, Carracedo A, McKinney C, Kennedy RD, Klocker H, Speicher MR, Tang DG, Moazzami AA, Heery DM, Hacker M, Kenner L. STAT3/LKB1 controls metastatic prostate cancer by regulating mTORC1/CREB pathway. Mol Cancer 2023; 22:133. [PMID: 37573301 PMCID: PMC10422794 DOI: 10.1186/s12943-023-01825-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/14/2023] [Indexed: 08/14/2023] Open
Abstract
Prostate cancer (PCa) is a common and fatal type of cancer in men. Metastatic PCa (mPCa) is a major factor contributing to its lethality, although the mechanisms remain poorly understood. PTEN is one of the most frequently deleted genes in mPCa. Here we show a frequent genomic co-deletion of PTEN and STAT3 in liquid biopsies of patients with mPCa. Loss of Stat3 in a Pten-null mouse prostate model leads to a reduction of LKB1/pAMPK with simultaneous activation of mTOR/CREB, resulting in metastatic disease. However, constitutive activation of Stat3 led to high LKB1/pAMPK levels and suppressed mTORC1/CREB pathway, preventing mPCa development. Metformin, one of the most widely prescribed therapeutics against type 2 diabetes, inhibits mTORC1 in liver and requires LKB1 to mediate glucose homeostasis. We find that metformin treatment of STAT3/AR-expressing PCa xenografts resulted in significantly reduced tumor growth accompanied by diminished mTORC1/CREB, AR and PSA levels. PCa xenografts with deletion of STAT3/AR nearly completely abrogated mTORC1/CREB inhibition mediated by metformin. Moreover, metformin treatment of PCa patients with high Gleason grade and type 2 diabetes resulted in undetectable mTORC1 levels and upregulated STAT3 expression. Furthermore, PCa patients with high CREB expression have worse clinical outcomes and a significantly increased risk of PCa relapse and metastatic recurrence. In summary, we have shown that STAT3 controls mPCa via LKB1/pAMPK/mTORC1/CREB signaling, which we have identified as a promising novel downstream target for the treatment of lethal mPCa.
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Affiliation(s)
- Jan Pencik
- Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria.
- Center for Biomarker Research in Medicine, 8010, Graz, Austria.
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090, Vienna, Austria.
| | - Cecile Philippe
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090, Vienna, Austria
| | - Michaela Schlederer
- Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria
| | - Emine Atas
- Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria
| | - Matteo Pecoraro
- Institute for Research in Biomedicine, Università Della Svizzera Italiana, 6500, Bellinzona, Switzerland
| | - Sandra Grund-Gröschke
- Department of Biosciences and Medical Biology, Cancer Cluster Salzburg, Paris-Lodron University of Salzburg, 5020, Salzburg, Austria
| | - Wen Jess Li
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Experimental Therapeutics Graduate Program, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Amanda Tracz
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Isabel Heidegger
- Department of Urology, Medical University Innsbruck, 6020, Innsbruck, Austria
| | - Sabine Lagger
- Unit for Pathology of Laboratory Animals, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Karolína Trachtová
- Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria
- Central European Institute of Technology, Masaryk University, 60177, Brno, Czech Republic
- Christian Doppler Laboratory for Applied Metabolomics (CDL-AM), Medical University of Vienna, 1090, Vienna, Austria
| | | | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, 8010, Graz, Austria
| | - Osman Aksoy
- Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria
- Department for Basic and Translational Oncology and Hematology, Division Molecular Oncology and Hematology, Karl Landsteiner University of Health Sciences, 3500, Krems, Austria
| | - Heidi A Neubauer
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Bettina Wingelhofer
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Anna Orlova
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Nadine Witzeneder
- Department of Laboratory Medicine, Medical University of Vienna, 1090, Vienna, Austria
| | - Thomas Dillinger
- Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria
| | - Elisa Redl
- Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria
| | - Georg Greiner
- Department of Laboratory Medicine, Medical University of Vienna, 1090, Vienna, Austria
| | - David D'Andrea
- Department of Urology, Medical University of Vienna, 1090, Vienna, Austria
| | - Johnny R Östman
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Simone Tangermann
- Unit for Pathology of Laboratory Animals, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Ivana Hermanova
- Center for Cooperative Research in Biosciences, Basque Research and Technology Alliance (BRTA), 20850, Derio, Spain
| | - Georg Schäfer
- Department of Pathology, Medical University Innsbruck, 6020, Innsbruck, Austria
| | - Felix Sternberg
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Elena E Pohl
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Christina Sternberg
- Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria
- Unit for Pathology of Laboratory Animals, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
- Biochemical Institute, University of Kiel, 24098, Kiel, Germany
| | - Adam Varady
- Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria
| | - Jaqueline Horvath
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Dagmar Stoiber
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, 3500, Krems, Austria
| | - Tim I Malcolm
- Department of Pathology, University of Cambridge, Cambridge, CB20QQ, UK
| | - Suzanne D Turner
- Department of Pathology, University of Cambridge, Cambridge, CB20QQ, UK
- Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Eileen E Parkes
- Department of Oncology, University of Oxford, Oxford, OX37DQ, UK
| | - Brigitte Hantusch
- Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria
| | - Gerda Egger
- Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria
- Ludwig Boltzmann Institute Applied Diagnostics, 1090, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090, Vienna, Austria
| | | | - Valeria Poli
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Turin, 10126, Turin, Italy
| | - Suneil Jain
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT71NN, UK
| | - Chris W D Armstrong
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT71NN, UK
| | | | - Vincent Goffin
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, 75015, Paris, France
| | - Fritz Aberger
- Department of Biosciences and Medical Biology, Cancer Cluster Salzburg, Paris-Lodron University of Salzburg, 5020, Salzburg, Austria
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Arkaitz Carracedo
- Center for Cooperative Research in Biosciences, Basque Research and Technology Alliance (BRTA), 20850, Derio, Spain
| | - Cathal McKinney
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT71NN, UK
- Almac Diagnostics, Craigavon, BT63 5QD, UK
| | - Richard D Kennedy
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT71NN, UK
- Almac Diagnostics, Craigavon, BT63 5QD, UK
| | - Helmut Klocker
- Department of Urology, Medical University Innsbruck, 6020, Innsbruck, Austria
| | - Michael R Speicher
- Institute of Human Genetics, Medical University of Graz, 8010, Graz, Austria
| | - Dean G Tang
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Experimental Therapeutics Graduate Program, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Ali A Moazzami
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - David M Heery
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Marcus Hacker
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090, Vienna, Austria
| | - Lukas Kenner
- Department of Pathology, Medical University of Vienna, 1090, Vienna, Austria.
- Center for Biomarker Research in Medicine, 8010, Graz, Austria.
- Unit for Pathology of Laboratory Animals, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
- Christian Doppler Laboratory for Applied Metabolomics (CDL-AM), Medical University of Vienna, 1090, Vienna, Austria.
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3
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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4
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Dong C, Richardson LT, Solouki T, Murray KK. Infrared Laser Ablation Microsampling with a Reflective Objective. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:463-470. [PMID: 35104132 PMCID: PMC8895455 DOI: 10.1021/jasms.1c00306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
A Schwarzschild reflective objective with a numerical aperture of 0.3 and working distance of 10 cm was used for laser ablation sampling of tissue for off-line mass spectrometry. The objective focused the laser to a diameter of 5 μm and produced 10 μm ablation spots on thin ink films and tissue sections. Rat brain tissue sections 50 μm thick were ablated in transmission geometry, and the ablated material was captured in a microcentrifuge tube containing solvent. Proteins from ablated tissue sections were quantified with a Bradford assay, which indicated that approximately 300 ng of protein was captured from a 1 mm2 area of ablated tissue. Areas of tissue ranging from 0.01 to 1 mm2 were ablated and captured for bottom-up proteomics. Proteins were extracted from the captured tissue and digested for liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis for peptide and protein identification.
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Affiliation(s)
- Chao Dong
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Luke T. Richardson
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Touradj Solouki
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Kermit K. Murray
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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5
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Rai NK, Singh V, Li L, Willard B, Tripathi A, Dutta R. Comparative Proteomic Profiling Identifies Reciprocal Expression of Mitochondrial Proteins Between White and Gray Matter Lesions From Multiple Sclerosis Brains. Front Neurol 2022; 12:779003. [PMID: 35002930 PMCID: PMC8740228 DOI: 10.3389/fneur.2021.779003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/29/2021] [Indexed: 12/27/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic inflammatory and demyelinating disease of the central nervous system, where ongoing demyelination and remyelination failure are the major factors for progressive neurological disability. In this report, we employed a comprehensive proteomic approach and immunohistochemical validation to gain insight into the pathobiological mechanisms that may be associated with the progressive phase of MS. Isolated proteins from myelinated regions, demyelinated white-matter lesions (WMLs), and gray-matter lesions (GMLs) from well-characterized progressive MS brain tissues were subjected to label-free quantitative mass spectrometry. Using a system-biology approach, we detected increased expression of proteins belonging to mitochondrial electron transport complexes and oxidative phosphorylation pathway in WMLs. Intriguingly, many of these proteins and pathways had opposite expression patterns and were downregulated in GMLs of progressive MS brains. A comparison to the human MitoCarta database mapped the mitochondrial proteins to mitochondrial subunits in both WMLs and GMLs. Taken together, we provide evidence of opposite expression of mitochondrial proteins in response to demyelination of white- and gray-matter regions in progressive MS brain.
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Affiliation(s)
- Nagendra Kumar Rai
- Department of Neurosciences, Cleveland Clinic, Cleveland, OH, United States
| | - Vaibhav Singh
- Department of Neurosciences, Cleveland Clinic, Cleveland, OH, United States
| | - Ling Li
- Proteomic Core Facility, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Belinda Willard
- Proteomic Core Facility, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States.,Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH, United States
| | - Ajai Tripathi
- Department of Neurosciences, Cleveland Clinic, Cleveland, OH, United States
| | - Ranjan Dutta
- Department of Neurosciences, Cleveland Clinic, Cleveland, OH, United States.,Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH, United States
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Abstract
The tumor microenvironment forms a complex pro-tumorigenic milieu constituted by extracellular matrix, surrounding stroma, infiltrating cell populations, and signaling molecules. Proteomic studies have the potential to reveal how individual cell populations within the tumor tissue modulate the microenvironment through protein secretion and consequently alter their protein expression and localization to adapt to this milieu. As a result, proteomic approaches have uncovered how these dynamic components communicate and promote tumor development and progression. The characterization of these mechanisms is relevant for the identification of clinically targetable pathways and for the development of diagnostic tools. Here we describe a method based on the isolation of individual cell compartments and the chromatographic fractionation of intact proteins, followed by enzymatic digestion of individual fractions, and mass-spectrometry analysis, for the profiling of tumor microenvironment cell populations.
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Affiliation(s)
- Michela Capello
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hiroyuki Katayama
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Samir M Hanash
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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7
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Lawal RO, Richardson LT, Dong C, Donnarumma F, Solouki T, Murray KK. Deep-ultraviolet laser ablation sampling for proteomic analysis of tissue. Anal Chim Acta 2021; 1184:339021. [PMID: 34625253 DOI: 10.1016/j.aca.2021.339021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/29/2021] [Accepted: 08/30/2021] [Indexed: 01/22/2023]
Abstract
Deep-ultraviolet laser ablation with a pulsed 193 nm ArF excimer laser was used to remove localized regions from tissue sections from which proteins were extracted for spatially resolved proteomic analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). The ability to capture intact proteins by ablation at 193 nm wavelength was verified by matrix-assisted laser desorption ionization (MALDI) of the protein standard bovine serum albumin (BSA), which showed that BSA was ablated and captured without fragmentation. A Bradford assay of the ablated and captured proteins indicated 90% efficiency for transfer of the intact protein at a laser fluence of 3 kJ/m2. Rat brain tissue sections mounted on quartz microscope slides and ablated in transmission mode yielded 2 μg protein per mm2 as quantified by the Bradford assay. Tissue areas ranging from 0.06 mm2 to 1 mm2 were ablated and the ejected material was collected for proteomic analysis. Extracted proteins were digested and the resulting peptides were analyzed by LC-MS/MS. The proteins extracted from the ablated areas were identified and the average number of identified proteins ranged from 85 in the 0.06 mm2 area to 2400 in the 1 mm2 area of a 50 μm thick tissue. In comparison to infrared laser ablation of equivalent sampled areas, both the protein mass and number of proteins identified using DUV laser ablation sampling were approximately four times larger.
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Affiliation(s)
- Remilekun O Lawal
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Luke T Richardson
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Chao Dong
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
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8
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Kostas JC, Greguš M, Schejbal J, Ray S, Ivanov AR. Simple and Efficient Microsolid-Phase Extraction Tip-Based Sample Preparation Workflow to Enable Sensitive Proteomic Profiling of Limited Samples (200 to 10,000 Cells). J Proteome Res 2021; 20:1676-1688. [PMID: 33625864 PMCID: PMC7954648 DOI: 10.1021/acs.jproteome.0c00890] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In-depth LC-MS-based proteomic profiling of limited biological and clinical samples, such as rare cells or tissue sections from laser capture microdissection or microneedle biopsies, has been problematic due, in large, to the inefficiency of sample preparation and attendant sample losses. To address this issue, we developed on-microsolid-phase extraction tip (OmSET)-based sample preparation for limited biological samples. OmSET is simple, efficient, reproducible, and scalable and is a widely accessible method for processing ∼200 to 10,000 cells. The developed method benefits from minimal sample processing volumes (1-3 μL) and conducting all sample processing steps on-membrane within a single microreactor. We first assessed the feasibility of using micro-SPE tips for nanogram-level amounts of tryptic peptides, minimized the number of required sample handling steps, and reduced the hands-on time. We then evaluated the capability of OmSET for quantitative analysis of low numbers of human monocytes. Reliable and reproducible label-free quantitation results were obtained with excellent correlations between protein abundances and the amounts of starting material (R2 = 0.93) and pairwise correlations between sample processing replicates (R2 = 0.95) along with the identification of approximately 300, 1800, and 2000 protein groups from injected ∼10, 100, and 500 cell equivalents, resulting from processing approximately 200, 2000, and 10,000 cells, respectively.
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Affiliation(s)
- James C Kostas
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Michal Greguš
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Jan Schejbal
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Somak Ray
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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9
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Alexovič M, Sabo J, Longuespée R. Microproteomic sample preparation. Proteomics 2021; 21:e2000318. [PMID: 33547857 DOI: 10.1002/pmic.202000318] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/11/2022]
Abstract
Multiple applications of proteomics in life and health science, pathology and pharmacology, require handling size-limited cell and tissue samples. During proteomic sample preparation, analyte loss in these samples arises when standard procedures are used. Thus, specific considerations have to be taken into account for processing, that are summarised under the term microproteomics (μPs). Microproteomic workflows include: sampling (e.g., flow cytometry, laser capture microdissection), sample preparation (possible disruption of cells or tissue pieces via lysis, protein extraction, digestion in bottom-up approaches, and sample clean-up) and analysis (chromatographic or electrophoretic separation, mass spectrometric measurements and statistical/bioinformatic evaluation). All these steps must be optimised to reach wide protein dynamic ranges and high numbers of identifications. Under optimal conditions, sampling is adapted to the studied sample types and nature, sample preparation isolates and enriches the whole protein content, clean-up removes salts and other interferences such as detergents or chaotropes, and analysis identifies as many analytes as the instrumental throughput and sensitivity allow. In the suggested review, we present and discuss the current state in μP applications for processing of small number of cells (cell μPs) and microscopic tissue regions (tissue μPs).
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Affiliation(s)
- Michal Alexovič
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, Košice, Slovakia
| | - Ján Sabo
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, Košice, Slovakia
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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10
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Oberhuber M, Pecoraro M, Rusz M, Oberhuber G, Wieselberg M, Haslinger P, Gurnhofer E, Schlederer M, Limberger T, Lagger S, Pencik J, Kodajova P, Högler S, Stockmaier G, Grund‐Gröschke S, Aberger F, Bolis M, Theurillat J, Wiebringhaus R, Weiss T, Haitel A, Brehme M, Wadsak W, Griss J, Mohr T, Hofer A, Jäger A, Pollheimer J, Egger G, Koellensperger G, Mann M, Hantusch B, Kenner L. STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer. Mol Syst Biol 2020; 16:e9247. [PMID: 32323921 PMCID: PMC7178451 DOI: 10.15252/msb.20199247] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 01/05/2023] Open
Abstract
Prostate cancer (PCa) has a broad spectrum of clinical behavior; hence, biomarkers are urgently needed for risk stratification. Here, we aim to find potential biomarkers for risk stratification, by utilizing a gene co-expression network of transcriptomics data in addition to laser-microdissected proteomics from human and murine prostate FFPE samples. We show up-regulation of oxidative phosphorylation (OXPHOS) in PCa on the transcriptomic level and up-regulation of the TCA cycle/OXPHOS on the proteomic level, which is inversely correlated to STAT3 expression. We hereby identify gene expression of pyruvate dehydrogenase kinase 4 (PDK4), a key regulator of the TCA cycle, as a promising independent prognostic marker in PCa. PDK4 predicts disease recurrence independent of diagnostic risk factors such as grading, staging, and PSA level. Therefore, low PDK4 is a promising marker for PCa with dismal prognosis.
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11
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Eckert MA, Coscia F, Chryplewicz A, Chang JW, Hernandez KM, Pan S, Tienda SM, Nahotko DA, Li G, Blaženović I, Lastra RR, Curtis M, Yamada SD, Perets R, McGregor SM, Andrade J, Fiehn O, Moellering RE, Mann M, Lengyel E. Proteomics reveals NNMT as a master metabolic regulator of cancer-associated fibroblasts. Nature 2019; 569:723-728. [PMID: 31043742 PMCID: PMC6690743 DOI: 10.1038/s41586-019-1173-8] [Citation(s) in RCA: 277] [Impact Index Per Article: 55.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 03/27/2019] [Indexed: 12/23/2022]
Abstract
High-grade serous carcinoma has a poor prognosis, owing primarily to its early dissemination throughout the abdominal cavity. Genomic and proteomic approaches have provided snapshots of the proteogenomics of ovarian cancer1,2, but a systematic examination of both the tumour and stromal compartments is critical in understanding ovarian cancer metastasis. Here we develop a label-free proteomic workflow to analyse as few as 5,000 formalin-fixed, paraffin-embedded cells microdissected from each compartment. The tumour proteome was stable during progression from in situ lesions to metastatic disease; however, the metastasis-associated stroma was characterized by a highly conserved proteomic signature, prominently including the methyltransferase nicotinamide N-methyltransferase (NNMT) and several of the proteins that it regulates. Stromal NNMT expression was necessary and sufficient for functional aspects of the cancer-associated fibroblast (CAF) phenotype, including the expression of CAF markers and the secretion of cytokines and oncogenic extracellular matrix. Stromal NNMT expression supported ovarian cancer migration, proliferation and in vivo growth and metastasis. Expression of NNMT in CAFs led to depletion of S-adenosyl methionine and reduction in histone methylation associated with widespread gene expression changes in the tumour stroma. This work supports the use of ultra-low-input proteomics to identify candidate drivers of disease phenotypes. NNMT is a central, metabolic regulator of CAF differentiation and cancer progression in the stroma that may be therapeutically targeted.
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Affiliation(s)
- Mark A Eckert
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Fabian Coscia
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Agnieszka Chryplewicz
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Jae Won Chang
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Kyle M Hernandez
- Center for Research Informatics, University of Chicago, Chicago, IL, USA
| | - Shawn Pan
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Samantha M Tienda
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Dominik A Nahotko
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Gang Li
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Ivana Blaženović
- West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA, USA
| | - Ricardo R Lastra
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Marion Curtis
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - S Diane Yamada
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Ruth Perets
- Division of Oncology, Clinical Research Institute at Rambam, Rambam Health Care Campus, Haifa, Israel
| | | | - Jorge Andrade
- Center for Research Informatics, University of Chicago, Chicago, IL, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA, USA
| | | | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ernst Lengyel
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA.
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12
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Jágr M, Ergang P, Pataridis S, Kolrosová M, Bartoš M, Mikšík I. Proteomic analysis of dentin-enamel junction and adjacent protein-containing enamel matrix layer of healthy human molar teeth. Eur J Oral Sci 2018; 127:112-121. [DOI: 10.1111/eos.12594] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Michal Jágr
- Institute of Physiology; The Czech Academy of Sciences; Prague Czech Republic
- Quality of Plant Products; Crop Research Institute; Prague Czech Republic
| | - Peter Ergang
- Institute of Physiology; The Czech Academy of Sciences; Prague Czech Republic
| | - Statis Pataridis
- Institute of Physiology; The Czech Academy of Sciences; Prague Czech Republic
| | - Marta Kolrosová
- Department of Analytical Chemistry; Faculty of Science; Charles University; Prague Czech Republic
| | - Martin Bartoš
- Institute of Dental Medicine; First Faculty of Medicine; Charles University and General University Hospital; Prague Czech Republic
| | - Ivan Mikšík
- Institute of Physiology; The Czech Academy of Sciences; Prague Czech Republic
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13
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Duran-Ortiz S, Brittain AL, Kopchick JJ. The impact of growth hormone on proteomic profiles: a review of mouse and adult human studies. Clin Proteomics 2017; 14:24. [PMID: 28670222 PMCID: PMC5492507 DOI: 10.1186/s12014-017-9160-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/20/2017] [Indexed: 12/17/2022] Open
Abstract
Growth hormone (GH) is a protein that is known to stimulate postnatal growth, counter regulate insulin's action and induce expression of insulin-like growth factor-1. GH exerts anabolic or catabolic effects depending upon on the targeted tissue. For instance, GH increases skeletal muscle and decreases adipose tissue mass. Our laboratory has spent the past two decades studying these effects, including the effects of GH excess and depletion, on the proteome of several mouse and human tissues. This review first discusses proteomic techniques that are commonly used for these types of studies. We then examine the proteomic differences found in mice with excess circulating GH (bGH mice) or mice with disruption of the GH receptor gene (GHR-/-). We also describe the effects of increased and decreased GH action on the proteome of adult patients with either acromegaly, GH deficiency or patients after short-term GH treatment. Finally, we explain how these proteomic studies resulted in the discovery of potential biomarkers for GH action, particularly those related with the effects of GH on aging, glucose metabolism and body composition.
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Affiliation(s)
- Silvana Duran-Ortiz
- Edison Biotechnology Institute, Ohio University, Athens, OH USA.,Department of Biological Sciences, College of Arts and Sciences, Ohio University, Athens, OH USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH USA
| | - Alison L Brittain
- Edison Biotechnology Institute, Ohio University, Athens, OH USA.,Department of Biological Sciences, College of Arts and Sciences, Ohio University, Athens, OH USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH USA.,Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
| | - John J Kopchick
- Edison Biotechnology Institute, Ohio University, Athens, OH USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH USA.,Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
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14
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Lazar C, Gatto L, Ferro M, Bruley C, Burger T. Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies. J Proteome Res 2016; 15:1116-25. [DOI: 10.1021/acs.jproteome.5b00981] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Cosmin Lazar
- Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
| | - Laurent Gatto
- Computational Proteomics Unit, Cambridge CB2 1GA, United Kingdom
- Cambridge Center for Proteomics, Cambridge CB2 1GA, United Kingdom
| | - Myriam Ferro
- Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
| | - Christophe Bruley
- Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
| | - Thomas Burger
- Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CNRS, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
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15
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Pfenning AR, Hara E, Whitney O, Rivas MV, Wang R, Roulhac PL, Howard JT, Wirthlin M, Lovell PV, Ganapathy G, Mouncastle J, Moseley MA, Thompson JW, Soderblom EJ, Iriki A, Kato M, Gilbert MTP, Zhang G, Bakken T, Bongaarts A, Bernard A, Lein E, Mello CV, Hartemink AJ, Jarvis ED. Convergent transcriptional specializations in the brains of humans and song-learning birds. Science 2014; 346:1256846. [PMID: 25504733 DOI: 10.1126/science.1256846] [Citation(s) in RCA: 285] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Song-learning birds and humans share independently evolved similarities in brain pathways for vocal learning that are essential for song and speech and are not found in most other species. Comparisons of brain transcriptomes of song-learning birds and humans relative to vocal nonlearners identified convergent gene expression specializations in specific song and speech brain regions of avian vocal learners and humans. The strongest shared profiles relate bird motor and striatal song-learning nuclei, respectively, with human laryngeal motor cortex and parts of the striatum that control speech production and learning. Most of the associated genes function in motor control and brain connectivity. Thus, convergent behavior and neural connectivity for a complex trait are associated with convergent specialized expression of multiple genes.
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Affiliation(s)
- Andreas R Pfenning
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA.
| | - Erina Hara
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Osceola Whitney
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Miriam V Rivas
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Rui Wang
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Petra L Roulhac
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Jason T Howard
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Morgan Wirthlin
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ganeshkumar Ganapathy
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Jacquelyn Mouncastle
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - M Arthur Moseley
- Duke Proteomics and Metabolomics Core Facility, Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - J Will Thompson
- Duke Proteomics and Metabolomics Core Facility, Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Erik J Soderblom
- Duke Proteomics and Metabolomics Core Facility, Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Atsushi Iriki
- Laboratory for Symbolic Cognitive Development, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Masaki Kato
- Laboratory for Symbolic Cognitive Development, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Trygve Bakken
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | | | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA
| | | | - Erich D Jarvis
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA.
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16
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Whitney O, Pfenning AR, Howard JT, Blatti CA, Liu F, Ward JM, Wang R, Audet JN, Kellis M, Mukherjee S, Sinha S, Hartemink AJ, West AE, Jarvis ED. Core and region-enriched networks of behaviorally regulated genes and the singing genome. Science 2014; 346:1256780. [PMID: 25504732 DOI: 10.1126/science.1256780] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Songbirds represent an important model organism for elucidating molecular mechanisms that link genes with complex behaviors, in part because they have discrete vocal learning circuits that have parallels with those that mediate human speech. We found that ~10% of the genes in the avian genome were regulated by singing, and we found a striking regional diversity of both basal and singing-induced programs in the four key song nuclei of the zebra finch, a vocal learning songbird. The region-enriched patterns were a result of distinct combinations of region-enriched transcription factors (TFs), their binding motifs, and presinging acetylation of histone 3 at lysine 27 (H3K27ac) enhancer activity in the regulatory regions of the associated genes. RNA interference manipulations validated the role of the calcium-response transcription factor (CaRF) in regulating genes preferentially expressed in specific song nuclei in response to singing. Thus, differential combinatorial binding of a small group of activity-regulated TFs and predefined epigenetic enhancer activity influences the anatomical diversity of behaviorally regulated gene networks.
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Affiliation(s)
- Osceola Whitney
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA.
| | - Andreas R Pfenning
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA. Computer Science and Artificial Intelligence Laboratory and the Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Jason T Howard
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Charles A Blatti
- Department of Computer Science, University of Illinois, Urbana-Champaign, IL, USA
| | - Fang Liu
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - James M Ward
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Rui Wang
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Jean-Nicoles Audet
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory and the Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Saurabh Sinha
- Department of Computer Science, University of Illinois, Urbana-Champaign, IL, USA
| | | | - Anne E West
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Erich D Jarvis
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA.
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17
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Proteomic analysis of chicken eggshell cuticle membrane layer. Anal Bioanal Chem 2014; 406:7633-40. [DOI: 10.1007/s00216-014-8213-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/17/2014] [Accepted: 09/22/2014] [Indexed: 12/17/2022]
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18
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Mesri M. Advances in Proteomic Technologies and Its Contribution to the Field of Cancer. Adv Med 2014; 2014:238045. [PMID: 26556407 PMCID: PMC4590950 DOI: 10.1155/2014/238045] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 06/30/2014] [Indexed: 12/12/2022] Open
Abstract
Systematic studies of the cancer genome have generated a wealth of knowledge in recent years. These studies have uncovered a number of new cancer genes not previously known to be causal targets in cancer. Genetic markers can be used to determine predisposition to tumor development, but molecularly targeted treatment strategies are not widely available for most cancers. Precision care plans still must be developed by understanding and implementing basic science research into clinical treatment. Proteomics is continuing to make major strides in the discovery of fundamental biological processes as well as more recent transition into an assay platform capable of measuring hundreds of proteins in any biological system. As such, proteomics can translate basic science discoveries into the clinical practice of precision medicine. The proteomic field has progressed at a fast rate over the past five years in technology, breadth and depth of applications in all areas of the bioscience. Some of the previously experimental technical approaches are considered the gold standard today, and the community is now trying to come to terms with the volume and complexity of the data generated. Here I describe contribution of proteomics in general and biological mass spectrometry in particular to cancer research, as well as related major technical and conceptual developments in the field.
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Affiliation(s)
- Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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19
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Mäbert K, Cojoc M, Peitzsch C, Kurth I, Souchelnytskyi S, Dubrovska A. Cancer biomarker discovery: current status and future perspectives. Int J Radiat Biol 2014; 90:659-77. [PMID: 24524284 DOI: 10.3109/09553002.2014.892229] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PURPOSE Cancer is a multigene disease which arises as a result of mutational and epigenetic changes coupled with activation of complex signaling networks. The use of biomarkers for early cancer detection, staging and individualization of therapy might improve patient care. A few fundamental issues such as tumor heterogeneity, a highly dynamic nature of the intrinsic and extrinsic determinants of radio- and chemoresistance, along with the plasticity and diversity of cancer stem cells (CSC) make biomarker development a challenging task. In this review we outline the preclinical strategies of cancer biomarker discovery including genomic, proteomic, metabolomic and microRNomic profiling, comparative genome hybridization (CGH), single nucleotide polymorphism (SNP) analysis, high throughput screening (HTS) and next generation sequencing (NGS). Other promising approaches such as assessment of circulating tumor cells (CTC), analysis of CSC-specific markers and cell-free circulating tumor DNA (ctDNA) are also discussed. CONCLUSIONS The emergence of powerful proteomic and genomic technologies in conjunction with advanced bioinformatic tools allows the simultaneous analysis of thousands of biological molecules. These techniques yield the discovery of new tumor signatures, which are sensitive and specific enough for early cancer detection, for monitoring disease progression and for proper treatment selection, paving the way to individualized cancer treatment.
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Affiliation(s)
- Katrin Mäbert
- OncoRay-National Center for Radiation Research in Oncology, Medical Faculty Dresden Carl Gustav Carus , TU Dresden , Germany
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20
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Can T, Faas L, Ashford DA, Dowle A, Thomas J, O'Toole P, Blanco G. Proteomic analysis of laser capture microscopy purified myotendinous junction regions from muscle sections. Proteome Sci 2014; 12:25. [PMID: 25071420 PMCID: PMC4113200 DOI: 10.1186/1477-5956-12-25] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 04/25/2014] [Indexed: 12/14/2022] Open
Abstract
The myotendinous junction is a specialized structure of the muscle fibre enriched in mechanosensing complexes, including costameric proteins and core elements of the z-disc. Here, laser capture microdissection was applied to purify membrane regions from the myotendinous junctions of mouse skeletal muscles, which were then processed for proteomic analysis. Sarcolemma sections from the longitudinal axis of the muscle fibre were used as control for the specificity of the junctional preparation. Gene ontology term analysis of the combined lists indicated a statistically significant enrichment in membrane-associated proteins. The myotendinous junction preparation contained previously uncharacterized proteins, a number of z-disc costameric ligands (e.g., actinins, capZ, αB cristallin, filamin C, cypher, calsarcin, desmin, FHL1, telethonin, nebulin, titin and an enigma-like protein) and other proposed players of sarcomeric stretch sensing and signalling, such as myotilin and the three myomesin homologs. A subset were confirmed by immunofluorescence analysis as enriched at the myotendinous junction, suggesting that laser capture microdissection from muscle sections is a valid approach to identify novel myotendinous junction players potentially involved in mechanotransduction pathways.
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Affiliation(s)
- Tugba Can
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Laura Faas
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - David A Ashford
- Bioscience Technology Facility, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Adam Dowle
- Bioscience Technology Facility, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Jerry Thomas
- Bioscience Technology Facility, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Peter O'Toole
- Bioscience Technology Facility, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Gonzalo Blanco
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
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21
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Josset L, Tisoncik-Go J, Katze MG. Moving H5N1 studies into the era of systems biology. Virus Res 2013; 178:151-67. [PMID: 23499671 PMCID: PMC3834220 DOI: 10.1016/j.virusres.2013.02.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 02/24/2013] [Indexed: 12/20/2022]
Abstract
The dynamics of H5N1 influenza virus pathogenesis are multifaceted and can be seen as an emergent property that cannot be comprehended without looking at the system as a whole. In past years, most of the high-throughput studies on H5N1-host interactions have focused on the host transcriptomic response, at the cellular or the lung tissue level. These studies pointed out that the dynamics and magnitude of the innate immune response and immune cell infiltration is critical to H5N1 pathogenesis. However, viral-host interactions are multidimensional and advances in technologies are creating new possibilities to systematically measure additional levels of 'omic data (e.g. proteomic, metabolomic, and RNA profiling) at each temporal and spatial scale (from the single cell to the organism) of the host response. Natural host genetic variation represents another dimension of the host response that determines pathogenesis. Systems biology models of H5N1 disease aim at understanding and predicting pathogenesis through integration of these different dimensions by using intensive computational modeling. In this review, we describe the importance of 'omic studies for providing a more comprehensive view of infection and mathematical models that are being developed to integrate these data. This review provides a roadmap for what needs to be done in the future and what computational strategies should be used to build a global model of H5N1 pathogenesis. It is time for systems biology of H5N1 pathogenesis to take center stage as the field moves toward a more comprehensive view of virus-host interactions.
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Affiliation(s)
- Laurence Josset
- Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 98195, United States
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22
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Tappenden DM, Hwang HJ, Yang L, Thomas RS, LaPres JJ. The Aryl-Hydrocarbon Receptor Protein Interaction Network (AHR-PIN) as Identified by Tandem Affinity Purification (TAP) and Mass Spectrometry. J Toxicol 2013; 2013:279829. [PMID: 24454361 PMCID: PMC3870133 DOI: 10.1155/2013/279829] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/09/2013] [Accepted: 10/14/2013] [Indexed: 12/28/2022] Open
Abstract
The aryl-hydrocarbon receptor (AHR), a ligand activated PAS superfamily transcription factor, mediates most, if not all, of the toxicity induced upon exposure to various dioxins, dibenzofurans, and planar polyhalogenated biphenyls. While AHR-mediated gene regulation plays a central role in the toxic response to dioxin exposure, a comprehensive understanding of AHR biology remains elusive. AHR-mediated signaling starts in the cytoplasm, where the receptor can be found in a complex with the heat shock protein of 90 kDa (Hsp90) and the immunophilin-like protein, aryl-hydrocarbon receptor-interacting protein (AIP). The role these chaperones and other putative interactors of the AHR play in the toxic response is not known. To more comprehensively define the AHR-protein interaction network (AHR-PIN) and identify other potential pathways involved in the toxic response, a proteomic approach was undertaken. Using tandem affinity purification (TAP) and mass spectrometry we have identified several novel protein interactions with the AHR. These interactions physically link the AHR to proteins involved in the immune and cellular stress responses, gene regulation not mediated directly via the traditional AHR:ARNT heterodimer, and mitochondrial function. This new insight into the AHR signaling network identifies possible secondary signaling pathways involved in xenobiotic-induced toxicity.
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Affiliation(s)
- Dorothy M. Tappenden
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA
- Center for Integrative Toxicology, Michigan State University, East Lansing, MI 48824-1319, USA
| | - Hye Jin Hwang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA
- Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI 48824-1319, USA
| | - Longlong Yang
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC 27709, USA
| | - Russell S. Thomas
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC 27709, USA
| | - John J. LaPres
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA
- Center for Integrative Toxicology, Michigan State University, East Lansing, MI 48824-1319, USA
- Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI 48824-1319, USA
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Thompson JW, Robeson A, Andersen JL. Identification of deacetylase substrates with the biotin switch approach. Methods Mol Biol 2013; 1077:133-148. [PMID: 24014404 DOI: 10.1007/978-1-62703-637-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The identification of lysine-acetylated proteins and deacetylase substrates has primarily relied on protein immune-affinity techniques with antibodies that recognize acetylated lysine residues (Kac antibodies). While these antibody-based techniques are continuously improving, they can be limited by the narrow and many times unknown epitope specificity of Kac antibodies. An alternative approach is the biotin switch capture of deacetylated proteins. Similar in part to other biotin switch methodologies, this technique relies on the blocking of native lysine residues and removal of the modification of interest in vitro, after which the newly deacetylated proteins can be captured and identified by mass spectrometry (MS). In this chapter, we cover the essential steps of the procedure, highlight key points in the assay to reduce false positive protein identification, and discuss the quantitative MS methods useful for identifying the captured deacetylase substrates. We also discuss potential strategies and future improvements to overcome current limitations of the assay.
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Affiliation(s)
- J Will Thompson
- Duke Proteomics Core Facility, Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, NC, USA
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24
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Scharff C, Adam I. Neurogenetics of birdsong. Curr Opin Neurobiol 2012; 23:29-36. [PMID: 23102970 DOI: 10.1016/j.conb.2012.10.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Revised: 10/02/2012] [Accepted: 10/08/2012] [Indexed: 11/29/2022]
Abstract
Songbirds are a productive model organism to study the neural basis of auditory-guided vocal motor learning. Like human babies, juvenile songbirds learn many of their vocalizations by imitating an adult conspecific. This process is a product of genetic predispositions and the individual's life experience and has been investigated mainly by neuroanatomical, physiological and behavioral methods. Results have revealed general principles governing vertebrate motor behavior, sensitive periods, sexual dimorphism, social behavior regulation and adult neurogenesis. More recently, the emerging field of birdsong neurogenetics has advanced the way we think about genetic contributions to communication, mechanistically and conceptually.
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Affiliation(s)
- Constance Scharff
- Freie Universität Berlin, Institute of Biology, Takustraße 6, 14195 Berlin, Germany.
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25
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Solid-phase capture for the detection and relative quantification of S-nitrosoproteins by mass spectrometry. Methods 2012; 62:130-7. [PMID: 23064468 DOI: 10.1016/j.ymeth.2012.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 04/04/2012] [Accepted: 10/02/2012] [Indexed: 01/18/2023] Open
Abstract
The proteomic analysis of S-nitrosylated protein (SNO-proteins) has long depended on the biotin switch technique (BST), which requires blocking of free thiols, ascorbate-based denitrosylation of SNO-Cys, biotinylation of nascent thiol and avidin-based affinity isolation. A more recent development is resin assisted-capture of SNO-proteins (SNO-RAC), which substitutes thiopropyl Sepharose (TPS) for biotin-avidin, thus reducing the number of steps required for enrichment of S-nitrosylated proteins. In addition, SNO-RAC facilitates on-resin proteolytic digestion following SNO-protein capture, greatly simplifying the purification of peptides containing sites of S-nitrosylation ("SNO-sites"). This resin-based approach has also now been applied to detection of alternative Cys-based modifications, including S-palmitoylation (Acyl-RAC) and S-oxidation (Ox-RAC). Here, we review the important steps to minimize false-positive identification of SNO-proteins, give detailed methods for processing of protein-bound TPS for mass spectrometry (MS) based analysis, and discuss the various quantitative MS methods that are compatible with SNO-RAC. We also discuss strategies to overcome the current limitations surrounding MS-based SNO-site localization in peptides containing more than one potential target Cys residue. This article therefore serves as a starting point and guide for the MS-focused exploration of SNO-proteomes by SNO-RAC.
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Hara E, Rivas MV, Ward JM, Okanoya K, Jarvis ED. Convergent differential regulation of parvalbumin in the brains of vocal learners. PLoS One 2012; 7:e29457. [PMID: 22238614 PMCID: PMC3253077 DOI: 10.1371/journal.pone.0029457] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 11/29/2011] [Indexed: 11/19/2022] Open
Abstract
Spoken language and learned song are complex communication behaviors found in only a few species, including humans and three groups of distantly related birds – songbirds, parrots, and hummingbirds. Despite their large phylogenetic distances, these vocal learners show convergent behaviors and associated brain pathways for vocal communication. However, it is not clear whether this behavioral and anatomical convergence is associated with molecular convergence. Here we used oligo microarrays to screen for genes differentially regulated in brain nuclei necessary for producing learned vocalizations relative to adjacent brain areas that control other behaviors in avian vocal learners versus vocal non-learners. A top candidate gene in our screen was a calcium-binding protein, parvalbumin (PV). In situ hybridization verification revealed that PV was expressed significantly higher throughout the song motor pathway, including brainstem vocal motor neurons relative to the surrounding brain regions of all distantly related avian vocal learners. This differential expression was specific to PV and vocal learners, as it was not found in avian vocal non-learners nor for control genes in learners and non-learners. Similar to the vocal learning birds, higher PV up-regulation was found in the brainstem tongue motor neurons used for speech production in humans relative to a non-human primate, macaques. These results suggest repeated convergent evolution of differential PV up-regulation in the brains of vocal learners separated by more than 65–300 million years from a common ancestor and that the specialized behaviors of learned song and speech may require extra calcium buffering and signaling.
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Affiliation(s)
- Erina Hara
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Graduate School of Advanced Integration Science, Chiba University, Chiba, Japan
- * E-mail: (EH); (EDJ)
| | - Miriam V. Rivas
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - James M. Ward
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kazuo Okanoya
- Graduate School of Advanced Integration Science, Chiba University, Chiba, Japan
- Laboratory for Biolinguistics, RIKEN BSI, Saitama, Japan
| | - Erich D. Jarvis
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail: (EH); (EDJ)
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