1
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Pop RT, Pisante A, Nagy D, Martin PCN, Mikheeva L, Hayat A, Ficz G, Zabet NR. Identification of mammalian transcription factors that bind to inaccessible chromatin. Nucleic Acids Res 2023; 51:8480-8495. [PMID: 37486787 PMCID: PMC10484684 DOI: 10.1093/nar/gkad614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/11/2023] [Indexed: 07/26/2023] Open
Abstract
Transcription factors (TFs) are proteins that affect gene expression by binding to regulatory regions of DNA in a sequence specific manner. The binding of TFs to DNA is controlled by many factors, including the DNA sequence, concentration of TF, chromatin accessibility and co-factors. Here, we systematically investigated the binding mechanism of hundreds of TFs by analysing ChIP-seq data with our explainable statistical model, ChIPanalyser. This tool uses as inputs the DNA sequence binding motif; the capacity to distinguish between strong and weak binding sites; the concentration of TF; and chromatin accessibility. We found that approximately one third of TFs are predicted to bind the genome in a DNA accessibility independent fashion, which includes TFs that can open the chromatin, their co-factors and TFs with similar motifs. Our model predicted this to be the case when the TF binds to its strongest binding regions in the genome, and only a small number of TFs have the capacity to bind dense chromatin at their weakest binding regions, such as CTCF, USF2 and CEBPB. Our study demonstrated that the binding of hundreds of human and mouse TFs is predicted by ChIPanalyser with high accuracy and showed that many TFs can bind dense chromatin.
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Affiliation(s)
- Romana T Pop
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Alessandra Pisante
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Dorka Nagy
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | | | | | - Ateequllah Hayat
- Institute of Medical and Biomedical Education, St George's, University of London, Cranmer Terrace, Tooting SW17 0RE, London
| | - Gabriella Ficz
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Nicolae Radu Zabet
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
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2
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Cecchin M, Simicevic J, Chaput L, Hernandez Gil M, Girolomoni L, Cazzaniga S, Remacle C, Hoeng J, Ivanov NV, Titz B, Ballottari M. Acclimation strategies of the green alga Chlorella vulgaris to different light regimes revealed by physiological and comparative proteomic analyses. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4540-4558. [PMID: 37155956 DOI: 10.1093/jxb/erad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023]
Abstract
Acclimation to different light regimes is at the basis of survival for photosynthetic organisms, regardless of their evolutionary origin. Previous research efforts largely focused on acclimation events occurring at the level of the photosynthetic apparatus and often highlighted species-specific mechanisms. Here, we investigated the consequences of acclimation to different irradiances in Chlorella vulgaris, a green alga that is one of the most promising species for industrial application, focusing on both photosynthetic and mitochondrial activities. Moreover, proteomic analysis of cells acclimated to high light (HL) or low light (LL) allowed identification of the main targets of acclimation in terms of differentially expressed proteins. The results obtained demonstrate photosynthetic adaptation to HL versus LL that was only partially consistent with previous findings in Chlamydomonas reinhardtii, a model organism for green algae, but in many cases similar to vascular plant acclimation events. Increased mitochondrial respiration measured in HL-acclimated cells mainly relied on alternative oxidative pathway dissipating the excessive reducing power produced due to enhanced carbon flow. Finally, proteins involved in cell metabolism, intracellular transport, gene expression, and signaling-including a heliorhodopsin homolog-were identified as strongly differentially expressed in HL versus LL, suggesting their key roles in acclimation to different light regimes.
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Affiliation(s)
- Michela Cecchin
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Jovan Simicevic
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Louise Chaput
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Manuel Hernandez Gil
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Laura Girolomoni
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Stefano Cazzaniga
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Claire Remacle
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, 4000 Liège, Belgium
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Matteo Ballottari
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
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3
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Mazzocca M, Colombo E, Callegari A, Mazza D. Transcription factor binding kinetics and transcriptional bursting: What do we really know? Curr Opin Struct Biol 2021; 71:239-248. [PMID: 34481381 DOI: 10.1016/j.sbi.2021.08.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 11/18/2022]
Abstract
In eukaryotes, transcription is a discontinuous process with mRNA being generated in bursts, after the binding of transcription factors (TFs) to regulatory elements on the genome. Live-cell single-molecule microscopy has highlighted that transcriptional bursting can be controlled by tuning TF/DNA binding kinetics. Yet the timescales of these two processes seem disconnected with TF/DNA interactions typically lasting orders of magnitude shorter than transcriptional bursts. To test models that could reconcile these discrepancies, reliable measurements of TF binding kinetics are needed, also accounting for the current limitations in performing these single-molecule measurements at specific regulatory elements. Here, we review the recent studies linking TF binding kinetics to transcriptional bursting and outline some current and future challenges that need to be addressed to provide a microscopic description of transcriptional regulation kinetics.
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Affiliation(s)
- Matteo Mazzocca
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Emanuele Colombo
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | | | - Davide Mazza
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy.
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4
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Agelopoulos M, Foutadakis S, Thanos D. The Causes and Consequences of Spatial Organization of the Genome in Regulation of Gene Expression. Front Immunol 2021; 12:682397. [PMID: 34149720 PMCID: PMC8212036 DOI: 10.3389/fimmu.2021.682397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/18/2021] [Indexed: 01/05/2023] Open
Abstract
Regulation of gene expression in time, space and quantity is orchestrated by the functional interplay of cis-acting elements and trans-acting factors. Our current view postulates that transcription factors recognize enhancer DNA and read the transcriptional regulatory code by cooperative DNA binding to specific DNA motifs, thus instructing the recruitment of transcriptional regulatory complexes forming a plethora of higher-ordered multi-protein-DNA and protein-protein complexes. Here, we reviewed the formation of multi-dimensional chromatin assemblies implicated in gene expression with emphasis on the regulatory role of enhancer hubs as coordinators of stochastic gene expression. Enhancer hubs contain many interacting regulatory elements and represent a remarkably dynamic and heterogeneous network of multivalent interactions. A functional consequence of such complex interaction networks could be that individual enhancers function synergistically to ensure coordination, tight control and robustness in regulation of expression of spatially connected genes. In this review, we discuss fundamental paradigms of such inter- and intra- chromosomal associations both in the context of immune-related genes and beyond.
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Affiliation(s)
| | | | - Dimitris Thanos
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
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5
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Abstract
PURPOSE OF REVIEW Erythropoiesis is a hierarchical process by which hematopoietic stem cells give rise to red blood cells through gradual cell fate restriction and maturation. Deciphering this process requires the establishment of dynamic gene regulatory networks (GRNs) that predict the response of hematopoietic cells to signals from the environment. Although GRNs have historically been derived from transcriptomic data, recent proteomic studies have revealed a major role for posttranscriptional mechanisms in regulating gene expression during erythropoiesis. These new findings highlight the need to integrate proteomic data into GRNs for a refined understanding of erythropoiesis. RECENT FINDINGS Here, we review recent proteomic studies that have furthered our understanding of erythropoiesis with a focus on quantitative mass spectrometry approaches to measure the abundance of transcription factors and cofactors during differentiation. Furthermore, we highlight challenges that remain in integrating transcriptomic, proteomic, and other omics data into a predictive model of erythropoiesis, and discuss the future prospect of single-cell proteomics. SUMMARY Recent proteomic studies have considerably expanded our knowledge of erythropoiesis beyond the traditional transcriptomic-centric perspective. These findings have both opened up new avenues of research to increase our understanding of erythroid differentiation, while at the same time presenting new challenges in integrating multiple layers of information into a comprehensive gene regulatory model.
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Affiliation(s)
- Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada
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6
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Auer JMT, Stoddart JJ, Christodoulou I, Lima A, Skouloudaki K, Hall HN, Vukojević V, Papadopoulos DK. Of numbers and movement - understanding transcription factor pathogenesis by advanced microscopy. Dis Model Mech 2020; 13:dmm046516. [PMID: 33433399 PMCID: PMC7790199 DOI: 10.1242/dmm.046516] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Transcription factors (TFs) are life-sustaining and, therefore, the subject of intensive research. By regulating gene expression, TFs control a plethora of developmental and physiological processes, and their abnormal function commonly leads to various developmental defects and diseases in humans. Normal TF function often depends on gene dosage, which can be altered by copy-number variation or loss-of-function mutations. This explains why TF haploinsufficiency (HI) can lead to disease. Since aberrant TF numbers frequently result in pathogenic abnormalities of gene expression, quantitative analyses of TFs are a priority in the field. In vitro single-molecule methodologies have significantly aided the identification of links between TF gene dosage and transcriptional outcomes. Additionally, advances in quantitative microscopy have contributed mechanistic insights into normal and aberrant TF function. However, to understand TF biology, TF-chromatin interactions must be characterised in vivo, in a tissue-specific manner and in the context of both normal and altered TF numbers. Here, we summarise the advanced microscopy methodologies most frequently used to link TF abundance to function and dissect the molecular mechanisms underlying TF HIs. Increased application of advanced single-molecule and super-resolution microscopy modalities will improve our understanding of how TF HIs drive disease.
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Affiliation(s)
- Julia M T Auer
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | - Jack J Stoddart
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | | | - Ana Lima
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | | | - Hildegard N Hall
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | - Vladana Vukojević
- Center for Molecular Medicine (CMM), Department of Clinical Neuroscience, Karolinska Institutet, 17176 Stockholm, Sweden
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7
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Martin PC, Zabet NR. Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. Comput Struct Biotechnol J 2020; 18:3590-3605. [PMID: 33304457 PMCID: PMC7708957 DOI: 10.1016/j.csbj.2020.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 01/22/2023] Open
Abstract
Transcription Factors (TFs) bind to DNA and control activity of target genes. Here, we present ChIPanalyser, a user-friendly, versatile and powerful R/Bioconductor package predicting and modelling the binding of TFs to DNA. ChIPanalyser performs similarly to state-of-the-art tools, but is an explainable model and provides biological insights into binding mechanisms of TFs. We focused on investigating the binding mechanisms of three TFs that are known architectural proteins CTCF, BEAF-32 and su(Hw) in three Drosophila cell lines (BG3, Kc167 and S2). While CTCF preferentially binds only to a subset of high affinity sites located mainly in open chromatin, BEAF-32 binds to most of its high affinity binding sites available in open chromatin. In contrast, su(Hw) binds to both open chromatin and also partially closed chromatin. Most importantly, differences in TF binding profiles between cell lines for these TFs are mainly driven by differences in DNA accessibility and not by differences in TF concentrations between cell lines. Finally, we investigated binding of Hox TFs in Drosophila and found that Ubx binds only in open chromatin, while Abd-B and Dfd are capable to bind in both open and partially closed chromatin. Overall, our results show that TFs display different binding mechanisms and that our model is able to recapitulate their specific binding behaviour.
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Affiliation(s)
- Patrick C.N. Martin
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Nicolae Radu Zabet
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
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8
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Li Y, Schwalie PC, Bast-Habersbrunner A, Mocek S, Russeil J, Fromme T, Deplancke B, Klingenspor M. Systems-Genetics-Based Inference of a Core Regulatory Network Underlying White Fat Browning. Cell Rep 2020; 29:4099-4113.e5. [PMID: 31851936 DOI: 10.1016/j.celrep.2019.11.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 10/02/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023] Open
Abstract
Recruitment of brite/beige cells, known as browning of white adipose tissue (WAT), is an efficient way to turn an energy-storing organ into an energy-dissipating one and may therefore be of therapeutic value in combating obesity. However, a comprehensive understanding of the regulatory mechanisms mediating WAT browning is still lacking. Here, we exploit the large natural variation in WAT browning propensity between inbred mouse strains to gain an inclusive view of the core regulatory network coordinating this cellular process. Combining comparative transcriptomics, perturbation-based validations, and gene network analyses, we present a comprehensive gene regulatory network of inguinal WAT browning, revealing up to four distinct regulatory modules with key roles for uncovered transcriptional factors, while also providing deep insights into the genetic architecture of brite adipogenesis. The presented findings therefore greatly increase our understanding of the molecular drivers mediating the intriguing cellular heterogeneity and plasticity of adipose tissue.
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Affiliation(s)
- Yongguo Li
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Petra C Schwalie
- Institute of Bio-engineering, School of Life Sciences, EPFL and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Andrea Bast-Habersbrunner
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Sabine Mocek
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Julie Russeil
- Institute of Bio-engineering, School of Life Sciences, EPFL and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Tobias Fromme
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Bart Deplancke
- Institute of Bio-engineering, School of Life Sciences, EPFL and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Martin Klingenspor
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany.
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9
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Schmidt A, Farine H, Keller MP, Sebastian A, Kozera L, Welford RWD, Strasser DS. Immunoaffinity Targeted Mass Spectrometry Analysis of Human Plasma Samples Reveals an Imbalance of Active and Inactive CXCL10 in Primary Sjögren's Syndrome Disease Patients. J Proteome Res 2020; 19:4196-4209. [PMID: 32870689 DOI: 10.1021/acs.jproteome.0c00494] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the most important advantages of mass spectrometry is the ability to quantify proteins and their modifications in parallel to obtain a holistic picture of the protein of interest. Here, we present a hybrid immunoaffinity targeted mass spectrometry (MS) method that combines efficient pan-antibody enrichment of a specific protein from plasma with the selectivity of high-resolution targeted MS analysis to quantitate specific proteoforms of interest. We used this approach to quantify plasma levels of the chemokine CXCL10 that has been associated with many immunological disorders such as systemic lupus erythematosus and primary Sjögren's Syndrome (pSS). The hybrid approach enabled sensitive, specific, and simultaneous quantification of total, full-length (active) CXCL101-77 and DPP4-truncated (inactive) CXCL103-77 in human plasma down to the low pg/mL level, reaching ELISA sensitivities. Samples from 30 control subjects and 34 pSS patients (n = 64) were analyzed. The ratio of CXCL101-77 to truncated CXCL103-77 was significantly increased in patients with pSS and provided the highest correlation with pSS disease activity. Therefore, this CXCL10 proteoform ratio represents an interesting exploratory disease activity biomarker to further investigate. As this strategy can be readily adapted to other plasma proteins and proteoforms of interest, we are convinced that it will lead to a more detailed understanding of proteoforms in physiology and pathology yielding more relevant biomarkers and drug targets.
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Affiliation(s)
- Alexander Schmidt
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Hervé Farine
- Idorsia Pharmaceuticals, Ltd, Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Marcel P Keller
- Idorsia Pharmaceuticals, Ltd, Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Agata Sebastian
- Department of Rheumatology and Internal Medicine, Wroclaw Medical University, Borowska 210, 50-556 Wroclaw, Poland
| | - Lukasz Kozera
- Lukasiewicz Research Network - PORT Polish Center for Technology Development, National Biobanking Node, Stablowicka 147, 50-066 Wroclaw, Poland
| | - Richard W D Welford
- Idorsia Pharmaceuticals, Ltd, Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Daniel S Strasser
- Idorsia Pharmaceuticals, Ltd, Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
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10
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Gillespie MA, Palii CG, Sanchez-Taltavull D, Shannon P, Longabaugh WJR, Downes DJ, Sivaraman K, Espinoza HM, Hughes JR, Price ND, Perkins TJ, Ranish JA, Brand M. Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis. Mol Cell 2020; 78:960-974.e11. [PMID: 32330456 PMCID: PMC7344268 DOI: 10.1016/j.molcel.2020.03.031] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/20/2020] [Accepted: 03/25/2020] [Indexed: 12/11/2022]
Abstract
Dynamic cellular processes such as differentiation are driven by changes in the abundances of transcription factors (TFs). However, despite years of studies, our knowledge about the protein copy number of TFs in the nucleus is limited. Here, by determining the absolute abundances of 103 TFs and co-factors during the course of human erythropoiesis, we provide a dynamic and quantitative scale for TFs in the nucleus. Furthermore, we establish the first gene regulatory network of cell fate commitment that integrates temporal protein stoichiometry data with mRNA measurements. The model revealed quantitative imbalances in TFs' cross-antagonistic relationships that underlie lineage determination. Finally, we made the surprising discovery that, in the nucleus, co-repressors are dramatically more abundant than co-activators at the protein level, but not at the RNA level, with profound implications for understanding transcriptional regulation. These analyses provide a unique quantitative framework to understand transcriptional regulation of cell differentiation in a dynamic context.
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Affiliation(s)
| | - Carmen G Palii
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada
| | - Daniel Sanchez-Taltavull
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada; Visceral Surgery and Medicine, Inselspital, Bern University Hospital, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland
| | - Paul Shannon
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Karthi Sivaraman
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada
| | | | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - Theodore J Perkins
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada.
| | - Jeffrey A Ranish
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada.
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11
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Suter DM. Transcription Factors and DNA Play Hide and Seek. Trends Cell Biol 2020; 30:491-500. [PMID: 32413318 DOI: 10.1016/j.tcb.2020.03.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 01/12/2023]
Abstract
Transcription factors (TFs) bind to specific DNA motifs to regulate the expression of target genes. To reach their binding sites, TFs diffuse in 3D and perform local motions such as 1D sliding, hopping, or intersegmental transfer. TF-DNA interactions depend on multiple parameters, such as the chromatin environment, TF partitioning into distinct subcellular regions, and cooperativity with other DNA-binding proteins. In this review, how current understanding of the search process has initially been shaped by prokaryotic studies is discussed, as well as what is known about the parameters regulating TF search efficiency in the context of the complex eukaryotic chromatin landscape.
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Affiliation(s)
- David M Suter
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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12
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Chen Q, Jiang Y, Ren Y, Ying M, Lu B. Peptide Selection for Accurate Targeted Protein Quantification via a Dimethylation High-Resolution Mass Spectrum Strategy with a Peptide Release Kinetic Model. ACS OMEGA 2020; 5:3809-3819. [PMID: 32149207 PMCID: PMC7057324 DOI: 10.1021/acsomega.9b02002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 02/06/2020] [Indexed: 06/10/2023]
Abstract
A crucial step in accurate targeted protein quantification using targeted proteomics is to determine optimal proteotypic peptides representing targeted proteins. In this study, a workflow of peptide selection to determine proteotypic peptides using a dimethylation high-resolution mass spectrum strategy with a peptide release kinetic model was investigated and applied in peptide selection of bovine serum albumin. After specificity, digestibility, recovery, and stability evaluation of tryptic peptides in bovine serum albumin, the optimal proteotypic peptide was selected as LVNELTEFAK. The quantification method using LVNELTEFAK gave a linear range of 1-100 ppm with the coefficient greater than 0.9990, and the detection limit of bovine serum albumin in milk was 0.78 mg/kg. Compared with the proteotypic peptides selected by Skyline, the method showed a better performance in method validation. The workflow exhibited high comprehensiveness and efficiency in peptide selection, facilitating accurate targeted protein quantification in the food matrix, which lack protein standards.
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Affiliation(s)
- Qi Chen
- National
Engineering Laboratory of Intelligent Food Technology and Equipment,
Key Laboratory for Agro-Products Postharvest Handling of Ministry
of Agriculture, Key Laboratory for Agro-Products Nutritional Evaluation
of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food
Processing, Fuli Institute of Food Science, College of Biosystems
Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- Ningbo
Research Institute, Zhejiang University, Ningbo 315100, China
| | - Yirong Jiang
- National
Engineering Laboratory of Intelligent Food Technology and Equipment,
Key Laboratory for Agro-Products Postharvest Handling of Ministry
of Agriculture, Key Laboratory for Agro-Products Nutritional Evaluation
of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food
Processing, Fuli Institute of Food Science, College of Biosystems
Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- Ningbo
Research Institute, Zhejiang University, Ningbo 315100, China
| | - Yiping Ren
- Yangtze
Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Meirong Ying
- Zhejiang
Grain and Oil Product Quality Inspection Center, Hangzhou 310012, China
| | - Baiyi Lu
- National
Engineering Laboratory of Intelligent Food Technology and Equipment,
Key Laboratory for Agro-Products Postharvest Handling of Ministry
of Agriculture, Key Laboratory for Agro-Products Nutritional Evaluation
of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food
Processing, Fuli Institute of Food Science, College of Biosystems
Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- Ningbo
Research Institute, Zhejiang University, Ningbo 315100, China
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13
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Posner R, Laubenbacher R. Connecting the molecular function of microRNAs to cell differentiation dynamics. J R Soc Interface 2019; 16:20190437. [PMID: 31551049 PMCID: PMC6769318 DOI: 10.1098/rsif.2019.0437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs form a class of short, non-coding RNA molecules which are essential for proper development in tissue-based plants and animals. To help explain their role in gene regulation, a number of mathematical and computational studies have demonstrated the potential canalizing effects of microRNAs. However, such studies have typically focused on the effects of microRNAs on only one or a few target genes. Consequently, it remains unclear how these small-scale effects add up to the experimentally observed developmental outcomes resulting from microRNA perturbation at the whole-genome level. To answer this question, we built a general computational model of cell differentiation to study the effect of microRNAs in genome-scale gene regulatory networks. Our experiments show that in large gene regulatory networks, microRNAs can control differentiation time without significantly changing steady-state gene expression profiles. This temporal regulatory role cannot be naturally replicated using protein-based transcription factors alone. While several microRNAs have been shown to regulate differentiation time in vivo, our findings provide a new explanation of how the cumulative molecular actions of individual microRNAs influence genome-scale cellular dynamics. Taken together, these results may help explain why tissue-based organisms exclusively depend on miRNA-mediated regulation, while their more primitive counterparts do not.
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Affiliation(s)
- Russell Posner
- Center for Quantitative Medicine, UConn Health, Farmington, CT, USA
| | - Reinhard Laubenbacher
- Center for Quantitative Medicine, UConn Health, Farmington, CT, USA.,The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
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14
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Novikova SE, Vakhrushev IV, Tsvetkova AV, Shushkova NA, Farafonova TE, Yarygin KN, Zgoda VG. [Proteomics of transcription factors: identification of pool of HL-60 cell line-specific regulatory proteins]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2019; 65:294-305. [PMID: 31436170 DOI: 10.18097/pbmc20196504294] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
HL-60 promyelocytic cells are a widely used as a model for studying induced granulocytic differentiation. Investigation of proteins of the nuclear fraction, particularly transcription factors, is necessary for a better understanding of molecular mechanisms of cell maturation. Mass spectrometry is a powerful tool for analyzing a proteome due to its high sensitivity, specificity and performance. In this paper, using the selected reaction monitoring (SRM) method, we have assessed the levels of RBPJ, STAT1, CEBPB, CASP3, VAV1, PRKDC, PARP1 and UBC9 nuclear proteins isolated using hypertonic buffer, detergents (sodium dodecyl sulfate (SDS), sodium deoxycholate (DOC) and fissionable detergent ProteaseMAX™) and using centrifugation in a sucrose density gradient. The minimum and maximum protein content was 1.13±0.28 and 14.34±1.63 fmol/mkg of total protein for the transcription factor RBPJ and ubiquitin-protein ligase type I UBC9, respectively. According to the results of shotgun mass spectrometric analysis of nuclear fractions, 2356 proteins were identified, of which 106 proteins were annotated as transcription factors. 37 transcription factors were uniquely identified in the fraction obtained by centrifugation in a sucrose density gradient, while only 9 and 8 transcription factors were uniquely identified in the nuclear fractions obtained using hypertonic buffer and detergents, respectively. The transcription factors identified in the HL-60 cell line represent regulatory molecules; their directed profiling under the influence of differentiation inducers, will shed light on the mechanism of granulocyte maturation.
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Affiliation(s)
- S E Novikova
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | | | | | - K N Yarygin
- Institute of Biomedical Chemistry, Moscow, Russia
| | - V G Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
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15
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Nguyen CDL, Malchow S, Reich S, Steltgens S, Shuvaev KV, Loroch S, Lorenz C, Sickmann A, Knobbe-Thomsen CB, Tews B, Medenbach J, Ahrends R. A sensitive and simple targeted proteomics approach to quantify transcription factor and membrane proteins of the unfolded protein response pathway in glioblastoma cells. Sci Rep 2019; 9:8836. [PMID: 31222112 PMCID: PMC6586633 DOI: 10.1038/s41598-019-45237-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/31/2019] [Indexed: 12/27/2022] Open
Abstract
Many cellular events are driven by changes in protein expression, measurable by mass spectrometry or antibody-based assays. However, using conventional technology, the analysis of transcription factor or membrane receptor expression is often limited by an insufficient sensitivity and specificity. To overcome this limitation, we have developed a high-resolution targeted proteomics strategy, which allows quantification down to the lower attomol range in a straightforward way without any prior enrichment or fractionation approaches. The method applies isotope-labeled peptide standards for quantification of the protein of interest. As proof of principle, we applied the improved workflow to proteins of the unfolded protein response (UPR), a signaling pathway of great clinical importance, and could for the first time detect and quantify all major UPR receptors, transducers and effectors that are not readily detectable via antibody-based-, SRM- or conventional PRM assays. As transcription and translation is central to the regulation of UPR, quantification and determination of protein copy numbers in the cell is important for our understanding of the signaling process as well as how pharmacologic modulation of these pathways impacts on the signaling. These questions can be answered using our newly established workflow as exemplified in an experiment using UPR perturbation in a glioblastoma cell lines.
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Affiliation(s)
- Chi D L Nguyen
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Sebastian Malchow
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Stefan Reich
- Translational Control Group, Biochemistry I, University of Regensburg, 93053, Regensburg, Germany
| | - Sascha Steltgens
- Institute of Neuropathology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Konstantin V Shuvaev
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Christin Lorenz
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany.,Medizinische Fakultät, Ruhr-Universität Bochum, Bochum, 44801, Germany.,College of Physical Sciences, University of Aberdeen, Old Aberdeen, AB24 3UE, UK
| | - Christiane B Knobbe-Thomsen
- Institute of Neuropathology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Björn Tews
- Schaller Research Group, University of Heidelberg and DKFZ, 69120, Heidelberg, Germany.,Molecular Mechanisms of Tumor Invasion, DKFZ, 69120, Heidelberg, Germany
| | - Jan Medenbach
- Translational Control Group, Biochemistry I, University of Regensburg, 93053, Regensburg, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany.
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16
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Macossay-Castillo M, Marvelli G, Guharoy M, Jain A, Kihara D, Tompa P, Wodak SJ. The Balancing Act of Intrinsically Disordered Proteins: Enabling Functional Diversity while Minimizing Promiscuity. J Mol Biol 2019; 431:1650-1670. [PMID: 30878482 DOI: 10.1016/j.jmb.2019.03.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/25/2019] [Accepted: 03/03/2019] [Indexed: 10/27/2022]
Abstract
Intrinsically disordered proteins (IDPs) or regions (IDRs) perform diverse cellular functions, but are also prone to forming promiscuous and potentially deleterious interactions. We investigate the extent to which the properties of, and content in, IDRs have adapted to enable functional diversity while limiting interference from promiscuous interactions in the crowded cellular environment. Information on protein sequences, their predicted intrinsic disorder, and 3D structure contents is related to data on protein cellular concentrations, gene co-expression, and protein-protein interactions in the well-studied yeast Saccharomyces cerevisiae. Results reveal that both the protein IDR content and the frequency of "sticky" amino acids in IDRs (those more frequently involved in protein interfaces) decrease with increasing protein cellular concentration. This implies that the IDR content and the amino acid composition of IDRs experience negative selection as the protein concentration increases. In the S. cerevisiae protein-protein interaction network, the higher a protein's IDR content, the more frequently it interacts with IDR-containing partners, and the more functionally diverse the partners are. Employing a clustering analysis of Gene Ontology terms, we newly identify ~600 putative multifunctional proteins in S. cerevisiae. Strikingly, these proteins are enriched in IDRs and contribute significantly to all the observed trends. In particular, IDRs of multi-functional proteins feature more sticky amino acids than IDRs of their non-multifunctional counterparts, or the surfaces of structured yeast proteins. This property likely affords sufficient binding affinity for the functional interactions, commonly mediated by short IDR segments, thereby counterbalancing the loss in overall IDR conformational entropy upon binding.
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Affiliation(s)
- Mauricio Macossay-Castillo
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Giulio Marvelli
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Mainak Guharoy
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Aashish Jain
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA; Department of Biological Sciences, Purdue University, Hockmeyer Structural Biology Building, 249 S. Martin Jischke Dr West Lafayette, IN 47907, USA
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok korutja 2, 1117 Budapest, Hungary
| | - Shoshana J Wodak
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium.
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17
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Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu K, Takahashi K, Dogterom M, Ten Wolde PR. eGFRD in all dimensions. J Chem Phys 2019; 150:054108. [PMID: 30736681 DOI: 10.1063/1.5064867] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Biochemical reactions often occur at low copy numbers but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a prominent tool for understanding how stochasticity at the microscopic level influences the macroscopic behavior of such systems. While particle-based models guarantee the level of detail necessary to accurately describe the microscopic dynamics at very low copy numbers, the algorithms used to simulate them typically imply trade-offs between computational efficiency and biochemical accuracy. eGFRD (enhanced Green's Function Reaction Dynamics) is an exact algorithm that evades such trade-offs by partitioning the N-particle system into M ≤ N analytically tractable one- and two-particle systems; the analytical solutions (Green's functions) then are used to implement an event-driven particle-based scheme that allows particles to make large jumps in time and space while retaining access to their state variables at arbitrary simulation times. Here we present "eGFRD2," a new eGFRD version that implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on 2D planes representing membranes, and on 1D elongated cylinders representative of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion used to model active transport. We find that, for low particle densities, eGFRD2 is up to 6 orders of magnitude faster than conventional Brownian dynamics. We exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1 gradient formation, which involves 3D diffusion, active transport on microtubules, and autophosphorylation on the membrane, confirming recent experimental and theoretical results on this system to hold under genuinely stochastic conditions.
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Affiliation(s)
| | - Joris Paijmans
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Laurens Bossen
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Thomas Miedema
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Martijn Wehrens
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Nils B Becker
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Kazunari Kaizu
- Center for Biosystems Dynamics Research (BDR), RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Koichi Takahashi
- Center for Biosystems Dynamics Research (BDR), RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Marileen Dogterom
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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18
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Li S, Xue T, He F, Liu Z, Ouyang S, Cao D, Wu J. A time-resolved proteomic analysis of transcription factors regulating adipogenesis of human adipose derived stem cells. Biochem Biophys Res Commun 2019; 511:855-861. [PMID: 30850164 DOI: 10.1016/j.bbrc.2019.02.134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 02/25/2019] [Indexed: 12/30/2022]
Abstract
Adipogenesis is one of the key processes during obesity development. Better understanding of this process could advance our knowledge on obesity and its treatment. Transcription factors (TFs) are master regulators during adipogenesis, however, a system-wide analysis of TFs dynamic proteome during adipogenesis is lacking. Here, we profiled 472 TFs and systematically elucidated their roles during the first 7 days of adipogenesis of human adipose-derived stem cells (hADSCs) on proteome scale. We identified two main and four sub-phases during adipogenesis. The commitment phase (0 h-8 h) mainly mediated stem cell proliferation, differentiation and chromatin remodeling, in which proteins of SWI/SNF family are the key centroid nodes. The determination phase (1D-7D) predominately regulated fat cell differentiation and response to lipid and oxygen, which could be associated with terminal differentiation of adipocyte and responsible for maturation. PPARγ, CREB1 and MYC are the centroid nodes of this phase. Remarkably, we identified and verified three TFs (BATF3, MAFF and MXD4) as novel regulators of adipogenesis, whose over-expression could inhibit adipogenesis of hADSCs in vitro. Overall, our study provided a valuable TFs resource to understand the complex process of adipogenesis.
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Affiliation(s)
- Sen Li
- Department of Biochemistry & Immunology, Capital Institute of Pediatrics-Peking University Teaching Hospital, NO. 2, Yabao Road, Chaoyang District, Beijing, 100020, China.
| | - Ting Xue
- Omicsolution Co, Ltd, Shanghai, 201101, China.
| | - Feng He
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, NO. 2, Yabao Road, Chaoyang District, Beijing, 100020, China.
| | - Zhuo Liu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, NO. 2, Yabao Road, Chaoyang District, Beijing, 100020, China.
| | - Shengrong Ouyang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, NO. 2, Yabao Road, Chaoyang District, Beijing, 100020, China.
| | - Dingding Cao
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, NO. 2, Yabao Road, Chaoyang District, Beijing, 100020, China.
| | - Jianxin Wu
- Department of Biochemistry & Immunology, Capital Institute of Pediatrics-Peking University Teaching Hospital, NO. 2, Yabao Road, Chaoyang District, Beijing, 100020, China; Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, NO. 2, Yabao Road, Chaoyang District, Beijing, 100020, China.
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19
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Gibbons BC, Fillmore TL, Gao Y, Moore RJ, Liu T, Nakayasu ES, Metz TO, Payne SH. Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards. J Proteome Res 2018; 18:694-699. [PMID: 30525668 DOI: 10.1021/acs.jproteome.8b00688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Targeted proteomics experiments based on selected reaction monitoring (SRM) have gained wide adoption in the use of clinical biomarkers, cellular modeling, and numerous other biological experiments due to their highly accurate and reproducible quantification. The quantitative accuracy in targeted proteomics experiments is reliant on the stable-isotope, heavy-labeled peptide standards that are spiked into a sample and used as a reference when calculating the abundance of endogenous peptides. Therefore, the quality of measurement for these standards is a critical factor in determining whether data acquisition was successful. With improved mass spectrometry (MS) instrumentation that enables the monitoring of hundreds of peptides in hundreds to thousands of samples, quality assessment is increasingly important and cannot be performed manually. We present Q4SRM, a software tool that rapidly checks the signal from all heavy-labeled peptides and flags those that fail quality-control metrics. Using four metrics, the tool detects problems with both individual SRM transitions and the collective group of transitions that monitor a single peptide. The program's speed and simplicity enable its use at the point of data acquisition and can be ideally run immediately upon the completion of a liquid chromatography-SRM-MS analysis.
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Affiliation(s)
- Bryson C Gibbons
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Thomas L Fillmore
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Yuqian Gao
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Ronald J Moore
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Tao Liu
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Ernesto S Nakayasu
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Thomas O Metz
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Samuel H Payne
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
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20
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Lu R, Rogan PK. Transcription factor binding site clusters identify target genes with similar tissue-wide expression and buffer against mutations. F1000Res 2018; 7:1933. [PMID: 31001412 PMCID: PMC6464064 DOI: 10.12688/f1000research.17363.2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/28/2019] [Indexed: 12/20/2022] Open
Abstract
Background: The distribution and composition of cis-regulatory modules composed of transcription factor (TF) binding site (TFBS) clusters in promoters substantially determine gene expression patterns and TF targets. TF knockdown experiments have revealed that TF binding profiles and gene expression levels are correlated. We use TFBS features within accessible promoter intervals to predict genes with similar tissue-wide expression patterns and TF targets using Machine Learning (ML). Methods: Bray-Curtis Similarity was used to identify genes with correlated expression patterns across 53 tissues. TF targets from knockdown experiments were also analyzed by this approach to set up the ML framework. TFBSs were selected within DNase I-accessible intervals of corresponding promoter sequences using information theory-based position weight matrices (iPWMs) for each TF. Features from information-dense clusters of TFBSs were input to ML classifiers which predict these gene targets along with their accuracy, specificity and sensitivity. Mutations in TFBSs were analyzed in silico to examine their impact on TFBS clustering and predict changes in gene regulation. Results: The glucocorticoid receptor gene ( NR3C1), whose regulation has been extensively studied, was selected to test this approach. SLC25A32 and TANK exhibited the most similar expression patterns to NR3C1. A Decision Tree classifier exhibited the best performance in detecting such genes, based on Area Under the Receiver Operating Characteristic curve (ROC). TF target gene prediction was confirmed using siRNA knockdown, which was more accurate than CRISPR/CAS9 inactivation. TFBS mutation analyses revealed that accurate target gene prediction required at least 1 information-dense TFBS cluster. Conclusions: ML based on TFBS information density, organization, and chromatin accessibility accurately identifies gene targets with comparable tissue-wide expression patterns. Multiple information-dense TFBS clusters in promoters appear to protect promoters from effects of deleterious binding site mutations in a single TFBS that would otherwise alter regulation of these genes.
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Affiliation(s)
- Ruipeng Lu
- Computer Science, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Peter K. Rogan
- Computer Science, University of Western Ontario, London, Ontario, N6A 5B7, Canada
- Biochemistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
- Cytognomix, London, Ontario, N5X 3X5, Canada
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21
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Wiśniewski JR, Wegler C, Artursson P. Multiple-Enzyme-Digestion Strategy Improves Accuracy and Sensitivity of Label- and Standard-Free Absolute Quantification to a Level That Is Achievable by Analysis with Stable Isotope-Labeled Standard Spiking. J Proteome Res 2018; 18:217-224. [PMID: 30336047 DOI: 10.1021/acs.jproteome.8b00549] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Quantification of individual proteins is an essential task in understanding biological processes. For example, determination of concentrations of proteins transporting and metabolizing xenobiotics is a prerequisite for drug disposition predictions in humans based on in vitro data. So far, this task has frequently been accomplished by targeted proteomics. This type of analyses requires preparation of stable isotope labeled standards for each protein of interest. The selection of appropriate standard peptides is usually tedious and the number of proteins that can be studied in a single experiment by these approaches is limited. In addition, incomplete digestion of proteins often affects the accuracy of the quantification. To circumvent these constrains in proteomic protein quantification, label- and standard-free approaches, such as "total protein approach" (TPA) have been proposed. Here we directly compare an approach using stable isotope labeled (SIL) standards and TPA for quantification of transporters and enzymes in human liver samples within the same LC-MS/MS runs. We show that TPA is a convenient alternative to SIL-based methods. Optimization of the sample preparation beyond commonly used single tryptic digestion, by adding consecutive cleavage steps, improves accuracy and reproducibility of the TPA method to a level, which is achievable by analysis using stable isotope-labeled standard spiking.
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Affiliation(s)
- Jacek R Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction , Max-Planck-Institute of Biochemistry , Am Klopferspitz 18 , D-82152 Martinsried , Germany
| | - Christine Wegler
- Department of Pharmacy , Uppsala University , S-751 23 Uppsala , Sweden.,Cardiovascular, Renal and Metabolism , Innovative Medicines and Early Development Biotech Unit , AstraZeneca , Gothenburg , Sweden
| | - Per Artursson
- Department of Pharmacy , Uppsala University , S-751 23 Uppsala , Sweden.,Science for Life Laboratory , Uppsala University , S-751 23 , Uppsala , Sweden
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22
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Vakhrushev IV, Novikova SE, Tsvetkova AV, Karalkin PA, Pyatnitskii MA, Zgoda VG, Yarygin KN. Proteomic Profiling of HL-60 Cells during ATRA-Induced Differentiation. Bull Exp Biol Med 2018; 165:530-543. [PMID: 30121918 PMCID: PMC7087771 DOI: 10.1007/s10517-018-4210-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Indexed: 11/29/2022]
Abstract
Acute promyelocytic leukemia, a form of acute myeloid leukemia, is characterized by cell differentiation arrest at the promyelocyte stage. Current therapeutic options include administration of all trans-retinoic acid (ATRA), but this treatment produces many side effects. ATRA is known to induce differentiation of leukemic cells into granulocytes, but the mechanism of this process is poorly studied. We performed comparative proteomic profiling of HL-60 promyelocytic cells at different stages of ATRA-induced differentiation to identify differentially expressed proteins by high-resolution mass spectrometry and relative quantitative analysis without isotope labels. A total of 1162 proteins identified by at least two unique peptides were analyzed, among them 46 and 172 differentially expressed proteins were identified in the nuclear and cytosol fractions, respectively. These differentially expressed proteins can represent candidate targets for combination therapy of acute promyelocytic leukemia.
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Affiliation(s)
- I V Vakhrushev
- V. N. Orekhovich Research Institute of Biomedical Chemistry, Moscow, Russia.
| | - S E Novikova
- V. N. Orekhovich Research Institute of Biomedical Chemistry, Moscow, Russia
| | - A V Tsvetkova
- V. N. Orekhovich Research Institute of Biomedical Chemistry, Moscow, Russia
| | - P A Karalkin
- V. N. Orekhovich Research Institute of Biomedical Chemistry, Moscow, Russia
| | - M A Pyatnitskii
- V. N. Orekhovich Research Institute of Biomedical Chemistry, Moscow, Russia
| | - V G Zgoda
- V. N. Orekhovich Research Institute of Biomedical Chemistry, Moscow, Russia
| | - K N Yarygin
- V. N. Orekhovich Research Institute of Biomedical Chemistry, Moscow, Russia
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23
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Hakobyan A, Liesack W, Glatter T. Crude-MS Strategy for in-Depth Proteome Analysis of the Methane-Oxidizing Methylocystis sp. strain SC2. J Proteome Res 2018; 17:3086-3103. [DOI: 10.1021/acs.jproteome.8b00216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Werner Liesack
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 16, D-35043 Marburg, Germany
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24
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Vakhrushev IV, Novikova SE, Tsvetkova AV, Pyatnitskiy MA, Yarygin KN. [Comparative proteomic profiling of nuclear and cytosolic fractions from cell lines of different origin]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2018; 64:233-240. [PMID: 29964258 DOI: 10.18097/pbmc20186403233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Proteomic analysis of the nuclear fraction is of great importance, since many cellular processes are initiated in the nucleus. Refinement and choice of experimental procedures for cell lysate fractionation and parameters for mass spectrometric detection and data processing continue to be of current interest. The mass spectrometry analysis presented here was tested on human cell lines derived from different tissues: HL-60 (peripheral blood); HepG2 (liver); EA.hy926 (vascular endothelium). High reproducibility of results and their consistency with biological properties of the objects under study were demonstrated. The use of cells of different types made it possible to reveal a set of 16 proteins whose LFQ-values allow for the discrimination between proteome fractions regardless of cell origin. Also, a set of 16 proteins is suggested which are associated with individual characteristics of cell lines regardless of cell fraction. These protein panels can serve as parameters to verify the proteomic analysis done was of sufficient quality, in particular as indicators of successful fractionation of cell or tissue lysate.
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Affiliation(s)
| | - S E Novikova
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - M A Pyatnitskiy
- Institute of Biomedical Chemistry, Moscow, Russia; National Research University Higher School of Economics, Moscow, Russia
| | - K N Yarygin
- Institute of Biomedical Chemistry, Moscow, Russia
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25
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A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility. Nat Biotechnol 2018; 36:521-529. [DOI: 10.1038/nbt.4138] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/23/2018] [Indexed: 12/29/2022]
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26
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Bottani S, Zabet NR, Wendel JF, Veitia RA. Gene Expression Dominance in Allopolyploids: Hypotheses and Models. TRENDS IN PLANT SCIENCE 2018; 23:393-402. [PMID: 29433919 DOI: 10.1016/j.tplants.2018.01.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/11/2018] [Accepted: 01/15/2018] [Indexed: 05/23/2023]
Abstract
The classical example of nonadditive contributions of the two parents to allopolyploids is nucleolar dominance, which entails silencing of one parental set of ribosomal RNA genes. This has been observed for many other loci. The prevailing explanation for this genome-wide expression disparity is that the two merged genomes differ in their transposable element (TE) complement and in their level of TE-mediated repression of gene expression. Alternatively, and not exclusively, gene expression dominance may arise from mismatches between trans effectors and their targets. Here, we explore quantitative models of regulatory mismatches leading to gene expression dominance. We also suggest that, when pairs of merged genomes are similar from one allopolyploidization event to another, gene-level and genome dominance patterns should also be similar.
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Affiliation(s)
- Samuel Bottani
- Matière et Systèmes Complexes, UMR 7057, Paris 75013, France; Université Paris Diderot-Paris VII, 75205 Paris Cedex 13, France; These authors contributed equally to this work
| | - Nicolae Radu Zabet
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK; These authors contributed equally to this work
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Reiner A Veitia
- Université Paris Diderot-Paris VII, 75205 Paris Cedex 13, France; Institut Jacques Monod, Université Paris Diderot, CNRS UMR7592, Paris 75013, France.
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27
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Narumi R, Masuda K, Tomonaga T, Adachi J, Ueda HR, Shimizu Y. Cell-free synthesis of stable isotope-labeled internal standards for targeted quantitative proteomics. Synth Syst Biotechnol 2018; 3:97-104. [PMID: 29900422 PMCID: PMC5995455 DOI: 10.1016/j.synbio.2018.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/16/2018] [Accepted: 02/18/2018] [Indexed: 01/04/2023] Open
Abstract
High-sensitivity mass spectrometry approaches using selected reaction monitoring (SRM) or multiple reaction monitoring (MRM) methods are powerful tools for targeted quantitative proteomics-based investigation of dynamics in specific biological systems. Both high-sensitivity detection of low-abundance proteins and their quantification using this technique employ stable isotope-labeled peptide internal standards. Currently, there are various ways for preparing standards, including chemical peptide synthesis, cellular protein expression, and cell-free protein or peptide synthesis. Cell-free protein synthesis (CFPS) or in vitro translation (IVT) systems in particular provide high-throughput and low-cost preparation methods, and various cell types and reconstituted forms are now commercially available. Herein, we review the use of such systems for precise and reliable protein quantification.
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Affiliation(s)
- Ryohei Narumi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Satio-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Keiko Masuda
- Laboratory for Single Cell Mass Spectrometry, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Satio-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Satio-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Hiroki R. Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Yoshihiro Shimizu
- Laboratory for Single Cell Mass Spectrometry, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
- Laboratory for Cell-Free Protein Synthesis, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
- Corresponding author. Laboratory for Cell-Free Protein Synthesis, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan.
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28
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Manes NP, Nita-Lazar A. Application of targeted mass spectrometry in bottom-up proteomics for systems biology research. J Proteomics 2018; 189:75-90. [PMID: 29452276 DOI: 10.1016/j.jprot.2018.02.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/25/2018] [Accepted: 02/07/2018] [Indexed: 02/08/2023]
Abstract
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples. Consequently, targeted LC-MS is rapidly advancing biomedical research, especially systems biology research in diverse areas that include proteogenomics, interactomics, kinomics, and biological pathway modeling. With the recent development of targeted LC-MS assays for nearly the entire human proteome, targeted LC-MS is positioned to enable quantitative proteomic profiling of unprecedented quality and accessibility to support fundamental and clinical research. Here we review recent applications of bottom-up proteomics using targeted LC-MS for systems biology research. SIGNIFICANCE: Advances in targeted proteomics are rapidly advancing systems biology research. Recent applications include systems-level investigations focused on posttranslational modifications (such as phosphoproteomics), protein conformation, protein-protein interaction, kinomics, proteogenomics, and metabolic and signaling pathways. Notably, absolute quantification of metabolic and signaling pathway proteins has enabled accurate pathway modeling and engineering. Integration of targeted proteomics with other technologies, such as RNA-seq, has facilitated diverse research such as the identification of hundreds of "missing" human proteins (genes and transcripts that appear to encode proteins but direct experimental evidence was lacking).
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Affiliation(s)
- Nathan P Manes
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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29
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Musa YR, Boller S, Puchalska M, Grosschedl R, Mittler G. Comprehensive Proteomic Investigation of Ebf1 Heterozygosity in Pro-B Lymphocytes Utilizing Data Independent Acquisition. J Proteome Res 2017; 17:76-85. [DOI: 10.1021/acs.jproteome.7b00369] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yaarub R. Musa
- Proteomics
Facility, ‡Department of Molecular and Cellular Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Sören Boller
- Proteomics
Facility, ‡Department of Molecular and Cellular Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Monika Puchalska
- Proteomics
Facility, ‡Department of Molecular and Cellular Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Rudolf Grosschedl
- Proteomics
Facility, ‡Department of Molecular and Cellular Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Gerhard Mittler
- Proteomics
Facility, ‡Department of Molecular and Cellular Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
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30
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Abstract
Most biological mechanisms involve more than one type of biomolecule, and hence operate not solely at the level of either genome, transcriptome, proteome, metabolome or ionome. Datasets resulting from single-omic analysis are rapidly increasing in throughput and quality, rendering multi-omic studies feasible. These should offer a comprehensive, structured and interactive overview of a biological mechanism. However, combining single-omic datasets in a meaningful manner has so far proved challenging, and the discovery of new biological information lags behind expectation. One reason is that experiments conducted in different laboratories can typically not to be combined without restriction. Second, the interpretation of multi-omic datasets represents a significant challenge by nature, as the biological datasets are heterogeneous not only for technical, but also for biological, chemical, and physical reasons. Here, multi-layer network theory and methods of artificial intelligence might contribute to solve these problems. For the efficient application of machine learning however, biological datasets need to become more systematic, more precise - and much larger. We conclude our review with basic guidelines for the successful set-up of a multi-omic experiment.
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31
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Torres S, García-Palmero I, Marín-Vicente C, Bartolomé RA, Calviño E, Fernández-Aceñero MJ, Casal JI. Proteomic Characterization of Transcription and Splicing Factors Associated with a Metastatic Phenotype in Colorectal Cancer. J Proteome Res 2017; 17:252-264. [PMID: 29131639 DOI: 10.1021/acs.jproteome.7b00548] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We investigated new transcription and splicing factors associated with the metastatic phenotype in colorectal cancer. A concatenated tandem array of consensus transcription factor (TF)-response elements was used to pull down nuclear extracts in two different pairs of colorectal cancer cells, KM12SM/KM12C and SW620/480, genetically related but differing in metastatic ability. Proteins were analyzed by label-free LC-MS and quantified with MaxLFQ. We found 240 proteins showing a significant dysregulation in highly metastatic KM12SM cells relative to nonmetastatic KM12C cells and 257 proteins in metastatic SW620 versus SW480. In both cell lines there were similar alterations in genuine TFs and components of the splicing machinery like UPF1, TCF7L2/TCF-4, YBX1, or SRSF3. However, a significant number of alterations were cell-line specific. Functional silencing of MAFG, TFE3, TCF7L2/TCF-4, and SRSF3 in KM12 cells caused alterations in adhesion, survival, proliferation, migration, and liver homing, supporting their role in metastasis. Finally, we investigated the prognostic value of the altered TFs and splicing factors in cancer patients. SRSF3 and SFPQ showed significant prognostic value. We observed that SRSF3 displayed a gradual loss of expression associated with cancer progression. Loss of SRSF3 expression was significantly associated with poor survival and shorter disease-free survival, particularly in early stages, in colorectal cancer.
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Affiliation(s)
- Sofía Torres
- Functional Proteomics, Centro de Investigaciones Biológicas (CIB-CSIC) , Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Irene García-Palmero
- Functional Proteomics, Centro de Investigaciones Biológicas (CIB-CSIC) , Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Consuelo Marín-Vicente
- Functional Proteomics, Centro de Investigaciones Biológicas (CIB-CSIC) , Ramiro de Maeztu 9, Madrid 28040, Spain.,Proteomic Facilities, CIB-CSIC , Madrid 28040, Spain
| | - Rubén A Bartolomé
- Functional Proteomics, Centro de Investigaciones Biológicas (CIB-CSIC) , Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Eva Calviño
- Functional Proteomics, Centro de Investigaciones Biológicas (CIB-CSIC) , Ramiro de Maeztu 9, Madrid 28040, Spain
| | | | - J Ignacio Casal
- Functional Proteomics, Centro de Investigaciones Biológicas (CIB-CSIC) , Ramiro de Maeztu 9, Madrid 28040, Spain
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32
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Stark AL, Madian AG, Williams SW, Chen V, Wing C, Hause RJ, To LA, Gill AL, Myers JL, Gorsic LK, Ciaccio MF, White KP, Jones RB, Dolan ME. Identification of Novel Protein Expression Changes Following Cisplatin Treatment and Application to Combination Therapy. J Proteome Res 2017; 16:4227-4236. [DOI: 10.1021/acs.jproteome.7b00576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Amy L. Stark
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Ashraf G. Madian
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Sawyer W. Williams
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Vincent Chen
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Claudia Wing
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Ronald J. Hause
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Lida Anita To
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Amy L. Gill
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jamie L. Myers
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Lidija K. Gorsic
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Mark F. Ciaccio
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kevin P. White
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Richard B. Jones
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - M. Eileen Dolan
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
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33
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Lee H, Qian K, von Toerne C, Hoerburger L, Claussnitzer M, Hoffmann C, Glunk V, Wahl S, Breier M, Eck F, Jafari L, Molnos S, Grallert H, Dahlman I, Arner P, Brunner C, Hauner H, Hauck SM, Laumen H. Allele-specific quantitative proteomics unravels molecular mechanisms modulated by cis-regulatory PPARG locus variation. Nucleic Acids Res 2017; 45:3266-3279. [PMID: 28334807 PMCID: PMC5389726 DOI: 10.1093/nar/gkx105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 02/07/2017] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies identified numerous disease risk loci. Delineating molecular mechanisms influenced by cis-regulatory variants is essential to understand gene regulation and ultimately disease pathophysiology. Combining bioinformatics and public domain chromatin information with quantitative proteomics supports prediction of cis-regulatory variants and enabled identification of allele-dependent binding of both, transcription factors and coregulators at the type 2 diabetes associated PPARG locus. We found rs7647481A nonrisk allele binding of Yin Yang 1 (YY1), confirmed by allele-specific chromatin immunoprecipitation in primary adipocytes. Quantitative proteomics also found the coregulator RING1 and YY1 binding protein (RYBP) whose mRNA levels correlate with improved insulin sensitivity in primary adipose cells carrying the rs7647481A nonrisk allele. Our findings support a concept with diverse cis-regulatory variants contributing to disease pathophysiology at one locus. Proteome-wide identification of both, transcription factors and coregulators, can profoundly improve understanding of mechanisms underlying genetic associations.
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Affiliation(s)
- Heekyoung Lee
- Else Kroener-Fresenius-Center for Nutritional Medicine, Chair of Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München and Technische Universität München, 85354 Freising-Weihenstephan, Germany.,German Center for Diabetes Research (DZD), Germany
| | - Kun Qian
- Else Kroener-Fresenius-Center for Nutritional Medicine, Chair of Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München and Technische Universität München, 85354 Freising-Weihenstephan, Germany.,German Center for Diabetes Research (DZD), Germany.,Research Unit Protein Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Christine von Toerne
- German Center for Diabetes Research (DZD), Germany.,Research Unit Protein Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Lena Hoerburger
- ZIEL - Institute for Food & Health, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Else Kroener-Fresenius-Center for Nutritional Medicine, Paediatric Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany
| | - Melina Claussnitzer
- Else Kroener-Fresenius-Center for Nutritional Medicine, Chair of Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München and Technische Universität München, 85354 Freising-Weihenstephan, Germany.,German Center for Diabetes Research (DZD), Germany.,Hebrew SeniorLife Institute for Aging Research, Harvard Medical School, Boston, MA 02131, USA
| | - Christoph Hoffmann
- ZIEL - Institute for Food & Health, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Else Kroener-Fresenius-Center for Nutritional Medicine, Chair of Molecular Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany
| | - Viktoria Glunk
- Else Kroener-Fresenius-Center for Nutritional Medicine, Chair of Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München and Technische Universität München, 85354 Freising-Weihenstephan, Germany.,German Center for Diabetes Research (DZD), Germany
| | - Simone Wahl
- German Center for Diabetes Research (DZD), Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michaela Breier
- German Center for Diabetes Research (DZD), Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Franziska Eck
- Research Unit Protein Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Leili Jafari
- Research Unit Protein Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Sophie Molnos
- German Center for Diabetes Research (DZD), Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Harald Grallert
- Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München and Technische Universität München, 85354 Freising-Weihenstephan, Germany.,German Center for Diabetes Research (DZD), Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ingrid Dahlman
- Department of Medicine, Huddinge, Karolinska Institutet, SE-141 86 Stockholm, Sweden
| | - Peter Arner
- Department of Medicine, Huddinge, Karolinska Institutet, SE-141 86 Stockholm, Sweden
| | - Cornelia Brunner
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinik Ulm, 89075 Ulm, Germany
| | - Hans Hauner
- Else Kroener-Fresenius-Center for Nutritional Medicine, Chair of Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München and Technische Universität München, 85354 Freising-Weihenstephan, Germany.,German Center for Diabetes Research (DZD), Germany.,Else Kroener-Fresenius-Center for Nutritional Medicine, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Stefanie M Hauck
- German Center for Diabetes Research (DZD), Germany.,Research Unit Protein Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Helmut Laumen
- Else Kroener-Fresenius-Center for Nutritional Medicine, Chair of Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München and Technische Universität München, 85354 Freising-Weihenstephan, Germany.,German Center for Diabetes Research (DZD), Germany.,Research Unit Protein Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Else Kroener-Fresenius-Center for Nutritional Medicine, Paediatric Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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34
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Wesseling H, Elgersma Y, Bahn S. A brain proteomic investigation of rapamycin effects in the Tsc1+/- mouse model. Mol Autism 2017; 8:41. [PMID: 28775826 PMCID: PMC5540199 DOI: 10.1186/s13229-017-0151-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 06/14/2017] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Tuberous sclerosis complex (TSC) is a rare monogenic disorder characterized by benign tumors in multiple organs as well as a high prevalence of epilepsy, intellectual disability and autism. TSC is caused by inactivating mutations in the TSC1 or TSC2 genes. Heterozygocity induces hyperactivation of mTOR which can be inhibited by mTOR inhibitors, such as rapamycin, which have proven efficacy in the treatment of TSC-associated symptoms. The aim of the present study was (1) to identify molecular changes associated with social and cognitive deficits in the brain tissue of Tsc1+/- mice and (2) to investigate the molecular effects of rapamycin treatment, which has been shown to ameliorate genotype-related behavioural deficits. METHODS Molecular alterations in the frontal cortex and hippocampus of Tsc1+/- and control mice, with or without rapamycin treatment, were investigated. A quantitative mass spectrometry-based shotgun proteomic approach (LC-MSE) was employed as an unbiased method to detect changes in protein levels. Changes identified in the initial profiling stage were validated using selected reaction monitoring (SRM). Protein Set Enrichment Analysis was employed to identify dysregulated pathways. RESULTS LC-MSE analysis of Tsc1+/- mice and controls (n = 30) identified 51 proteins changed in frontal cortex and 108 in the hippocampus. Bioinformatic analysis combined with targeted proteomic validation revealed several dysregulated molecular pathways. Using targeted assays, proteomic alterations in the hippocampus validated the pathways "myelination", "dendrite," and "oxidative stress", an upregulation of ribosomal proteins and the mTOR kinase. LC-MSE analysis was also employed on Tsc1+/- and wildtype mice (n = 34) treated with rapamycin or vehicle. Rapamycin treatment exerted a stronger proteomic effect in Tsc1+/- mice with significant changes (mainly decreased expression) in 231 and 106 proteins, respectively. The cellular pathways "oxidative stress" and "apoptosis" were found to be affected in Tsc1+/- mice and the cellular compartments "myelin sheet" and "neurofilaments" were affected by rapamycin treatment. Thirty-three proteins which were altered in Tsc1+/- mice were normalized following rapamycin treatment, amongst them oxidative stress related proteins, myelin-specific and ribosomal proteins. CONCLUSIONS Molecular changes in the Tsc1+/- mouse brain were more prominent in the hippocampus compared to the frontal cortex. Pathways linked to myelination and oxidative stress response were prominently affected and, at least in part, normalized following rapamycin treatment. The results could aid in the identification of novel drug targets for the treatment of cognitive, social and psychiatric symptoms in autism spectrum disorders. Similar pathways have also been implicated in other psychiatric and neurodegenerative disorders and could imply similar disease processes. Thus, the potential efficacy of mTOR inhibitors warrants further investigation not only for autism spectrum disorders but also for other neuropsychiatric and neurodegenerative diseases.
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Affiliation(s)
- Hendrik Wesseling
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT UK
| | - Ype Elgersma
- Department of Neuroscience, Erasmus Medical Center, Rotterdam, 3000 CA The Netherlands
| | - Sabine Bahn
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT UK
- Department of Neuroscience, Erasmus Medical Center, Rotterdam, 3000 CA The Netherlands
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35
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Grossman SR, Zhang X, Wang L, Engreitz J, Melnikov A, Rogov P, Tewhey R, Isakova A, Deplancke B, Bernstein BE, Mikkelsen TS, Lander ES. Systematic dissection of genomic features determining transcription factor binding and enhancer function. Proc Natl Acad Sci U S A 2017; 114:E1291-E1300. [PMID: 28137873 PMCID: PMC5321001 DOI: 10.1073/pnas.1621150114] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Enhancers regulate gene expression through the binding of sequence-specific transcription factors (TFs) to cognate motifs. Various features influence TF binding and enhancer function-including the chromatin state of the genomic locus, the affinities of the binding site, the activity of the bound TFs, and interactions among TFs. However, the precise nature and relative contributions of these features remain unclear. Here, we used massively parallel reporter assays (MPRAs) involving 32,115 natural and synthetic enhancers, together with high-throughput in vivo binding assays, to systematically dissect the contribution of each of these features to the binding and activity of genomic regulatory elements that contain motifs for PPARγ, a TF that serves as a key regulator of adipogenesis. We show that distinct sets of features govern PPARγ binding vs. enhancer activity. PPARγ binding is largely governed by the affinity of the specific motif site and higher-order features of the larger genomic locus, such as chromatin accessibility. In contrast, the enhancer activity of PPARγ binding sites depends on varying contributions from dozens of TFs in the immediate vicinity, including interactions between combinations of these TFs. Different pairs of motifs follow different interaction rules, including subadditive, additive, and superadditive interactions among specific classes of TFs, with both spatially constrained and flexible grammars. Our results provide a paradigm for the systematic characterization of the genomic features underlying regulatory elements, applicable to the design of synthetic regulatory elements or the interpretation of human genetic variation.
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Affiliation(s)
- Sharon R Grossman
- Broad Institute, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Health Sciences and Technology, Harvard Medical School, Boston, MA 02215
| | | | - Li Wang
- Broad Institute, Cambridge, MA 02142
| | - Jesse Engreitz
- Broad Institute, Cambridge, MA 02142
- Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | | | - Ryan Tewhey
- Broad Institute, Cambridge, MA 02142
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Alina Isakova
- Institute of Bioengineering, CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Bart Deplancke
- Institute of Bioengineering, CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Bradley E Bernstein
- Broad Institute, Cambridge, MA 02142
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Tarjei S Mikkelsen
- Broad Institute, Cambridge, MA 02142
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138
| | - Eric S Lander
- Broad Institute, Cambridge, MA 02142;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Systems Biology, Harvard Medical School, Boston, MA 02215
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36
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Millius A, Ueda HR. Systems Biology-Derived Discoveries of Intrinsic Clocks. Front Neurol 2017; 8:25. [PMID: 28220104 PMCID: PMC5292584 DOI: 10.3389/fneur.2017.00025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/17/2017] [Indexed: 12/19/2022] Open
Abstract
A systems approach to studying biology uses a variety of mathematical, computational, and engineering tools to holistically understand and model properties of cells, tissues, and organisms. Building from early biochemical, genetic, and physiological studies, systems biology became established through the development of genome-wide methods, high-throughput procedures, modern computational processing power, and bioinformatics. Here, we highlight a variety of systems approaches to the study of biological rhythms that occur with a 24-h period-circadian rhythms. We review how systems methods have helped to elucidate complex behaviors of the circadian clock including temperature compensation, rhythmicity, and robustness. Finally, we explain the contribution of systems biology to the transcription-translation feedback loop and posttranslational oscillator models of circadian rhythms and describe new technologies and "-omics" approaches to understand circadian timekeeping and neurophysiology.
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Affiliation(s)
- Arthur Millius
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka, Japan
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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37
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Simicevic J, Deplancke B. Transcription factor proteomics-Tools, applications, and challenges. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600317] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/18/2016] [Accepted: 11/11/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Jovan Simicevic
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences; Ecole Polytechnique Fédérale de Lausanne (EPFL), and Swiss Institute of Bioinformatics; Lausanne Switzerland
- LimmaTech Biologics AG; Schlieren Switzerland
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences; Ecole Polytechnique Fédérale de Lausanne (EPFL), and Swiss Institute of Bioinformatics; Lausanne Switzerland
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38
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Deplancke B, Alpern D, Gardeux V. The Genetics of Transcription Factor DNA Binding Variation. Cell 2016; 166:538-554. [PMID: 27471964 DOI: 10.1016/j.cell.2016.07.012] [Citation(s) in RCA: 236] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Indexed: 12/23/2022]
Abstract
Most complex trait-associated variants are located in non-coding regulatory regions of the genome, where they have been shown to disrupt transcription factor (TF)-DNA binding motifs. Variable TF-DNA interactions are therefore increasingly considered as key drivers of phenotypic variation. However, recent genome-wide studies revealed that the majority of variable TF-DNA binding events are not driven by sequence alterations in the motif of the studied TF. This observation implies that the molecular mechanisms underlying TF-DNA binding variation and, by extrapolation, inter-individual phenotypic variation are more complex than originally anticipated. Here, we summarize the findings that led to this important paradigm shift and review proposed mechanisms for local, proximal, or distal genetic variation-driven variable TF-DNA binding. In addition, we discuss the biomedical implications of these findings for our ability to dissect the molecular role(s) of non-coding genetic variants in complex traits, including disease susceptibility.
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Affiliation(s)
- Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Daniel Alpern
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Vincent Gardeux
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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39
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Bauer M, Cubizolles F, Schmidt A, Nigg EA. Quantitative analysis of human centrosome architecture by targeted proteomics and fluorescence imaging. EMBO J 2016; 35:2152-2166. [PMID: 27539480 PMCID: PMC5048348 DOI: 10.15252/embj.201694462] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/25/2016] [Indexed: 12/14/2022] Open
Abstract
Centrioles are essential for the formation of centrosomes and cilia. While numerical and/or structural centrosomes aberrations are implicated in cancer, mutations in centriolar and centrosomal proteins are genetically linked to ciliopathies, microcephaly, and dwarfism. The evolutionarily conserved mechanisms underlying centrosome biogenesis are centered on a set of key proteins, including Plk4, Sas-6, and STIL, whose exact levels are critical to ensure accurate reproduction of centrioles during cell cycle progression. However, neither the intracellular levels of centrosomal proteins nor their stoichiometry within centrosomes is presently known. Here, we have used two complementary approaches, targeted proteomics and EGFP-tagging of centrosomal proteins at endogenous loci, to measure protein abundance in cultured human cells and purified centrosomes. Our results provide a first assessment of the absolute and relative amounts of major components of the human centrosome. Specifically, they predict that human centriolar cartwheels comprise up to 16 stacked hubs and 1 molecule of STIL for every dimer of Sas-6. This type of quantitative information will help guide future studies of the molecular basis of centrosome assembly and function.
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Affiliation(s)
- Manuel Bauer
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Erich A Nigg
- Biozentrum, University of Basel, Basel, Switzerland
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40
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Shi T, Song E, Nie S, Rodland KD, Liu T, Qian WJ, Smith RD. Advances in targeted proteomics and applications to biomedical research. Proteomics 2016; 16:2160-82. [PMID: 27302376 PMCID: PMC5051956 DOI: 10.1002/pmic.201500449] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 05/09/2016] [Accepted: 06/10/2016] [Indexed: 12/17/2022]
Abstract
Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity (Shi et al., Proteomics, 12, 1074-1092, 2012) herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ehwang Song
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Song Nie
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karin D Rodland
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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41
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de Franciscis S, Caravagna G, Mauri G, d’Onofrio A. Gene switching rate determines response to extrinsic perturbations in the self-activation transcriptional network motif. Sci Rep 2016; 6:26980. [PMID: 27256916 PMCID: PMC4891709 DOI: 10.1038/srep26980] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 05/11/2016] [Indexed: 01/01/2023] Open
Abstract
Gene switching dynamics is a major source of randomness in genetic networks, also in the case of large concentrations of the transcription factors. In this work, we consider a common network motif - the positive feedback of a transcription factor on its own synthesis - and assess its response to extrinsic noises perturbing gene deactivation in a variety of settings where the network might operate. These settings are representative of distinct cellular types, abundance of transcription factors and ratio between gene switching and protein synthesis rates. By investigating noise-induced transitions among the different network operative states, our results suggest that gene switching rates are key parameters to shape network response to external perturbations, and that such response depends on the particular biological setting, i.e. the characteristic time scales and protein abundance. These results might have implications on our understanding of irreversible transitions for noise-related phenomena such as cellular differentiation. In addition these evidences suggest to adopt the appropriate mathematical model of the network in order to analyze the system consistently to the reference biological setting.
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Affiliation(s)
| | - Giulio Caravagna
- Università degli Studi di Milano-Bicocca, Dipartimento di Informatica, Sistemistica e Comunicazione, Milano, Italy
- School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Giancarlo Mauri
- Università degli Studi di Milano-Bicocca, Dipartimento di Informatica, Sistemistica e Comunicazione, Milano, Italy
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42
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Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins. Proc Natl Acad Sci U S A 2016; 113:E3461-7. [PMID: 27247408 DOI: 10.1073/pnas.1603799113] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Absolute values of protein expression levels in cells are crucial information for understanding cellular biological systems. Precise quantification of proteins can be achieved by liquid chromatography (LC)-mass spectrometry (MS) analysis of enzymatic digests of proteins in the presence of isotope-labeled internal standards. Thus, development of a simple and easy way for the preparation of internal standards is advantageous for the analyses of multiple target proteins, which will allow systems-level studies. Here we describe a method, termed MS-based Quantification By isotope-labeled Cell-free products (MS-QBiC), which provides the simple and high-throughput preparation of internal standards by using a reconstituted cell-free protein synthesis system, and thereby facilitates both multiplexed and sensitive quantification of absolute amounts of target proteins. This method was applied to a systems-level dynamic analysis of mammalian circadian clock proteins, which consist of transcription factors and protein kinases that govern central and peripheral circadian clocks in mammals. Sixteen proteins from 20 selected circadian clock proteins were successfully quantified from mouse liver over a 24-h time series, and 14 proteins had circadian variations. Quantified values were applied to detect internal body time using a previously developed molecular timetable method. The analyses showed that single time-point data from wild-type mice can predict the endogenous state of the circadian clock, whereas data from clock mutant mice are not applicable because of the disappearance of circadian variation.
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43
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Isakova A, Berset Y, Hatzimanikatis V, Deplancke B. Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models. J Biol Chem 2016; 291:10293-306. [PMID: 26912662 PMCID: PMC4858977 DOI: 10.1074/jbc.m115.691154] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 02/18/2016] [Indexed: 12/31/2022] Open
Abstract
Many transcription factors (TFs) have the ability to cooperate on DNA elements as heterodimers. Despite the significance of TF heterodimerization for gene regulation, a quantitative understanding of cooperativity between various TF dimer partners and its impact on heterodimer DNA binding specificity models is still lacking. Here, we used a novel integrative approach, combining microfluidics-steered measurements of dimer-DNA assembly with mechanistic modeling of the implicated protein-protein-DNA interactions to quantitatively interrogate the cooperative DNA binding behavior of the adipogenic peroxisome proliferator-activated receptor γ (PPARγ):retinoid X receptor α (RXRα) heterodimer. Using the high throughput MITOMI (mechanically induced trapping of molecular interactions) platform, we derived equilibrium DNA binding data for PPARγ, RXRα, as well as the PPARγ:RXRα heterodimer to more than 300 target DNA sites and variants thereof. We then quantified cooperativity underlying heterodimer-DNA binding and derived an integrative heterodimer DNA binding constant. Using this cooperativity-inclusive constant, we were able to build a heterodimer-DNA binding specificity model that has superior predictive power than the one based on a regular one-site equilibrium. Our data further revealed that individual nucleotide substitutions within the target site affect the extent of cooperativity in PPARγ:RXRα-DNA binding. Our study therefore emphasizes the importance of assessing cooperativity when generating DNA binding specificity models for heterodimers.
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Affiliation(s)
- Alina Isakova
- From the Institute of Bioengineering, Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
| | - Yves Berset
- From the Institute of Bioengineering, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, and Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, and Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
| | - Bart Deplancke
- From the Institute of Bioengineering, Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
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44
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Potts GK, Voigt EA, Bailey DJ, Rose CM, Westphall MS, Hebert AS, Yin J, Coon JJ. Neucode Labels for Multiplexed, Absolute Protein Quantification. Anal Chem 2016; 88:3295-303. [PMID: 26882330 PMCID: PMC5141612 DOI: 10.1021/acs.analchem.5b04773] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We describe a new method to accomplish multiplexed, absolute protein quantification in a targeted fashion. The approach draws upon the recently developed neutron encoding (NeuCode) metabolic labeling strategy and parallel reaction monitoring (PRM). Since PRM scanning relies upon high-resolution tandem mass spectra for targeted protein quantification, incorporation of multiple NeuCode labeled peptides permits high levels of multiplexing that can be accessed from high-resolution tandem mass spectra. Here we demonstrate this approach in cultured cells by monitoring a viral infection and the corresponding viral protein production over many infection time points in a single experiment. In this context the NeuCode PRM combination affords up to 30 channels of quantitative information in a single MS experiment.
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Affiliation(s)
- Gregory K Potts
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Emily A Voigt
- Department of Chemical and Biological Engineering, University of Wisconsin , Madison, Wisconsin 53706, United States
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Derek J Bailey
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Christopher M Rose
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Michael S Westphall
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Alexander S Hebert
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - John Yin
- Department of Chemical and Biological Engineering, University of Wisconsin , Madison, Wisconsin 53706, United States
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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Catabolism of Branched Chain Amino Acids Contributes Significantly to Synthesis of Odd-Chain and Even-Chain Fatty Acids in 3T3-L1 Adipocytes. PLoS One 2015; 10:e0145850. [PMID: 26710334 PMCID: PMC4692509 DOI: 10.1371/journal.pone.0145850] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/09/2015] [Indexed: 12/21/2022] Open
Abstract
The branched chain amino acids (BCAA) valine, leucine and isoleucine have been implicated in a number of diseases including obesity, insulin resistance, and type 2 diabetes mellitus, although the mechanisms are still poorly understood. Adipose tissue plays an important role in BCAA homeostasis by actively metabolizing circulating BCAA. In this work, we have investigated the link between BCAA catabolism and fatty acid synthesis in 3T3-L1 adipocytes using parallel 13C-labeling experiments, mass spectrometry and model-based isotopomer data analysis. Specifically, we performed parallel labeling experiments with four fully 13C-labeled tracers, [U-13C]valine, [U-13C]leucine, [U-13C]isoleucine and [U-13C]glutamine. We measured mass isotopomer distributions of fatty acids and intracellular metabolites by GC-MS and analyzed the data using the isotopomer spectral analysis (ISA) framework. We demonstrate that 3T3-L1 adipocytes accumulate significant amounts of even chain length (C14:0, C16:0 and C18:0) and odd chain length (C15:0 and C17:0) fatty acids under standard cell culture conditions. Using a novel GC-MS method, we demonstrate that propionyl-CoA acts as the primer on fatty acid synthase for the production of odd chain fatty acids. BCAA contributed significantly to the production of all fatty acids. Leucine and isoleucine contributed at least 25% to lipogenic acetyl-CoA pool, and valine and isoleucine contributed 100% to lipogenic propionyl-CoA pool. Our results further suggest that low activity of methylmalonyl-CoA mutase and mass action kinetics of propionyl-CoA on fatty acid synthase result in high rates of odd chain fatty acid synthesis in 3T3-L1 cells. Overall, this work provides important new insights into the connection between BCAA catabolism and fatty acid synthesis in adipocytes and underscores the high capacity of adipocytes for metabolizing BCAA.
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Glatter T, Ahrné E, Schmidt A. Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells. J Proteome Res 2015; 14:4472-85. [PMID: 26412744 DOI: 10.1021/acs.jproteome.5b00654] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We evaluated different in-solution and FASP-based sample preparation strategies for absolute protein quantification. Label-free quantification (LFQ) was employed to compare different sample preparation strategies in the bacterium Pseudomonas aeruginosa and human embryonic kidney cells (HEK), and organismal-specific differences in general performance and enrichment of specific protein classes were noted. The original FASP protocol globally enriched for most proteins in the bacterial sample, whereas the sodium deoxycholate in-solution strategy was more efficient with HEK cells. Although detergents were found to be highly suited for global proteome analysis, higher intensities were obtained for high-abundant nucleic acid-associated protein complexes, like the ribosome and histone proteins, using guanidine hydrochloride. Importantly, we show for the first time that the observable total proteome mass of a sample strongly depends on the sample preparation protocol, with some protocols resulting in a significant underestimation of protein mass due to incomplete protein extraction of biased protein groups. Furthermore, we demonstrate that some of the observed abundance biases can be overcome by incorporating a nuclease treatment step or, alternatively, a correction factor for complementary sample preparation approaches.
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Affiliation(s)
- Timo Glatter
- Proteomics Core Facility, Biozentrum, University of Basel , 4056 Basel, Switzerland
| | - Erik Ahrné
- Proteomics Core Facility, Biozentrum, University of Basel , 4056 Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel , 4056 Basel, Switzerland
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47
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Papadopoulos DK, Krmpot AJ, Nikolić SN, Krautz R, Terenius L, Tomancak P, Rigler R, Gehring WJ, Vukojević V. Probing the kinetic landscape of Hox transcription factor-DNA binding in live cells by massively parallel Fluorescence Correlation Spectroscopy. Mech Dev 2015; 138 Pt 2:218-225. [PMID: 26428533 DOI: 10.1016/j.mod.2015.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 09/23/2015] [Accepted: 09/24/2015] [Indexed: 11/25/2022]
Abstract
Hox genes encode transcription factors that control the formation of body structures, segment-specifically along the anterior-posterior axis of metazoans. Hox transcription factors bind nuclear DNA pervasively and regulate a plethora of target genes, deploying various molecular mechanisms that depend on the developmental and cellular context. To analyze quantitatively the dynamics of their DNA-binding behavior we have used confocal laser scanning microscopy (CLSM), single-point fluorescence correlation spectroscopy (FCS), fluorescence cross-correlation spectroscopy (FCCS) and bimolecular fluorescence complementation (BiFC). We show that the Hox transcription factor Sex combs reduced (Scr) forms dimers that strongly associate with its specific fork head binding site (fkh250) in live salivary gland cell nuclei. In contrast, dimers of a constitutively inactive, phospho-mimicking variant of Scr show weak, non-specific DNA-binding. Our studies reveal that nuclear dynamics of Scr is complex, exhibiting a changing landscape of interactions that is difficult to characterize by probing one point at a time. Therefore, we also provide mechanistic evidence using massively parallel FCS (mpFCS). We found that Scr dimers are predominantly formed on the DNA and are equally abundant at the chromosomes and an introduced multimeric fkh250 binding-site, indicating different mobilities, presumably reflecting transient binding with different affinities on the DNA. Our proof-of-principle results emphasize the advantages of mpFCS for quantitative characterization of fast dynamic processes in live cells.
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Affiliation(s)
| | - Aleksandar J Krmpot
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden; Institute of Physics, University of Belgrade, 11080 Belgrade, Serbia
| | - Stanko N Nikolić
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden; Institute of Physics, University of Belgrade, 11080 Belgrade, Serbia
| | - Robert Krautz
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Lars Terenius
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden
| | - Pavel Tomancak
- Max-Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Rudolf Rigler
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; Laboratory of Biomedical Optics, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland
| | - Walter J Gehring
- Department of Cell Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Vladana Vukojević
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden.
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48
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Normanno D, Boudarène L, Dugast-Darzacq C, Chen J, Richter C, Proux F, Bénichou O, Voituriez R, Darzacq X, Dahan M. Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher. Nat Commun 2015; 6:7357. [PMID: 26151127 PMCID: PMC4507003 DOI: 10.1038/ncomms8357] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 04/30/2015] [Indexed: 12/17/2022] Open
Abstract
Many cellular functions rely on DNA-binding proteins finding and associating to specific sites in the genome. Yet the mechanisms underlying the target search remain poorly understood, especially in the case of the highly organized mammalian cell nucleus. Using as a model Tet repressors (TetRs) searching for a multi-array locus, we quantitatively analyse the search process in human cells with single-molecule tracking and single-cell protein–DNA association measurements. We find that TetRs explore the nucleus and reach their target by 3D diffusion interspersed with transient interactions with non-cognate sites, consistent with the facilitated diffusion model. Remarkably, nonspecific binding times are broadly distributed, underlining a lack of clear delimitation between specific and nonspecific interactions. However, the search kinetics is not determined by diffusive transport but by the low association rate to nonspecific sites. Altogether, our results provide a comprehensive view of the recruitment dynamics of proteins at specific loci in mammalian cells. During transcription, replication and repair, DNA-binding proteins must find specific interaction sites hidden within a vast excess of genomic DNA. Here the authors use single-molecule tracking to quantitatively determine the contributions of the different processes that underlie target search in human cells.
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Affiliation(s)
- Davide Normanno
- Laboratoire Kastler Brossel, CNRS UMR 8552, École normale supérieure, Université Pierre et Marie Curie, Paris 6, 46 rue d'Ulm, 75005 Paris, France.,Functional Imaging of Transcription, CNRS UMR 8197, École normale supérieure, Institut de Biologie de l'ENS, IBENS, 46 rue d'Ulm, 75005 Paris, France.,Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA.,Physico-Chimie Curie, Institut Curie, CNRS UMR 168, Université Pierre et Marie Curie, Paris 6, 26 rue d'Ulm, 75005 Paris, France
| | - Lydia Boudarène
- Laboratoire Kastler Brossel, CNRS UMR 8552, École normale supérieure, Université Pierre et Marie Curie, Paris 6, 46 rue d'Ulm, 75005 Paris, France.,Functional Imaging of Transcription, CNRS UMR 8197, École normale supérieure, Institut de Biologie de l'ENS, IBENS, 46 rue d'Ulm, 75005 Paris, France
| | - Claire Dugast-Darzacq
- Functional Imaging of Transcription, CNRS UMR 8197, École normale supérieure, Institut de Biologie de l'ENS, IBENS, 46 rue d'Ulm, 75005 Paris, France.,Université Paris-Diderot, Paris 7, 5 rue Thomas Mann, 75013 Paris, France
| | - Jiji Chen
- Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - Christian Richter
- Laboratoire Kastler Brossel, CNRS UMR 8552, École normale supérieure, Université Pierre et Marie Curie, Paris 6, 46 rue d'Ulm, 75005 Paris, France
| | - Florence Proux
- Functional Imaging of Transcription, CNRS UMR 8197, École normale supérieure, Institut de Biologie de l'ENS, IBENS, 46 rue d'Ulm, 75005 Paris, France
| | - Olivier Bénichou
- Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Paris 6, 4 place Jussieu, 75005 Paris, France
| | - Raphaël Voituriez
- Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Paris 6, 4 place Jussieu, 75005 Paris, France
| | - Xavier Darzacq
- Functional Imaging of Transcription, CNRS UMR 8197, École normale supérieure, Institut de Biologie de l'ENS, IBENS, 46 rue d'Ulm, 75005 Paris, France.,Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - Maxime Dahan
- Laboratoire Kastler Brossel, CNRS UMR 8552, École normale supérieure, Université Pierre et Marie Curie, Paris 6, 46 rue d'Ulm, 75005 Paris, France.,Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA.,Physico-Chimie Curie, Institut Curie, CNRS UMR 168, Université Pierre et Marie Curie, Paris 6, 26 rue d'Ulm, 75005 Paris, France
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49
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Cabanski M, Fields B, Boue S, Boukharov N, DeLeon H, Dror N, Geertz M, Guedj E, Iskandar A, Kogel U, Merg C, Peck MJ, Poussin C, Schlage WK, Talikka M, Ivanov NV, Hoeng J, Peitsch MC. Transcriptional profiling and targeted proteomics reveals common molecular changes associated with cigarette smoke-induced lung emphysema development in five susceptible mouse strains. Inflamm Res 2015; 64:471-86. [PMID: 25962837 PMCID: PMC4464601 DOI: 10.1007/s00011-015-0820-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 03/15/2015] [Accepted: 04/11/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Mouse models are useful for studying cigarette smoke (CS)-induced chronic pulmonary pathologies such as lung emphysema. To enhance translation of large-scale omics data from mechanistic studies into pathophysiological changes, we have developed computational tools based on reverse causal reasoning (RCR). OBJECTIVE In the present study we applied a systems biology approach leveraging RCR to identify molecular mechanistic explanations of pathophysiological changes associated with CS-induced lung emphysema in susceptible mice. METHODS The lung transcriptomes of five mouse models (C57BL/6, ApoE (-/-) , A/J, CD1, and Nrf2 (-/-) ) were analyzed following 5-7 months of CS exposure. RESULTS We predicted 39 molecular changes mostly related to inflammatory processes including known key emphysema drivers such as NF-κB and TLR4 signaling, and increased levels of TNF-α, CSF2, and several interleukins. More importantly, RCR predicted potential molecular mechanisms that are less well-established, including increased transcriptional activity of PU.1, STAT1, C/EBP, FOXM1, YY1, and N-COR, and reduced protein abundance of ITGB6 and CFTR. We corroborated several predictions using targeted proteomic approaches, demonstrating increased abundance of CSF2, C/EBPα, C/EBPβ, PU.1, BRCA1, and STAT1. CONCLUSION These systems biology-derived candidate mechanisms common to susceptible mouse models may enhance understanding of CS-induced molecular processes underlying emphysema development in mice and their relevancy for human chronic obstructive pulmonary disease.
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Affiliation(s)
- Maciej Cabanski
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
- />Novartis Pharma AG, Novartis Institutes for Biomedical Research (NIBR), 4002 Basel, Switzerland
| | - Brett Fields
- />Selventa, One Alewife Center, Cambridge, MA 02140 USA
| | - Stephanie Boue
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | | | - Hector DeLeon
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Natalie Dror
- />Selventa, One Alewife Center, Cambridge, MA 02140 USA
| | - Marcel Geertz
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
- />Bayer Technology Services GmbH, 51368 Leverkusen, Germany
| | - Emmanuel Guedj
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Anita Iskandar
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Ulrike Kogel
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Celine Merg
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Michael J. Peck
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Carine Poussin
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Walter K. Schlage
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Marja Talikka
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Nikolai V. Ivanov
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Julia Hoeng
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Manuel C. Peitsch
- />Philip Morris International Research and Development, Philip Morris Products S.A, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
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50
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Schreiner D, Simicevic J, Ahrné E, Schmidt A, Scheiffele P. Quantitative isoform-profiling of highly diversified recognition molecules. eLife 2015; 4:e07794. [PMID: 25985086 PMCID: PMC4489214 DOI: 10.7554/elife.07794] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/14/2015] [Indexed: 12/28/2022] Open
Abstract
Complex biological systems rely on cell surface cues that govern cellular self-recognition and selective interactions with appropriate partners. Molecular diversification of cell surface recognition molecules through DNA recombination and complex alternative splicing has emerged as an important principle for encoding such interactions. However, the lack of tools to specifically detect and quantify receptor protein isoforms is a major impediment to functional studies. We here developed a workflow for targeted mass spectrometry by selected reaction monitoring that permits quantitative assessment of highly diversified protein families. We apply this workflow to dissecting the molecular diversity of the neuronal neurexin receptors and uncover an alternative splicing-dependent recognition code for synaptic ligands. DOI:http://dx.doi.org/10.7554/eLife.07794.001 To create a protein, a gene is first copied to form an RNA molecule that contains regions known as introns and exons. Splicing removes the introns and joins the exons together to form a molecule of ‘messenger RNA’, which is translated into a protein. Over the course of evolution, many groups—or families—of proteins have expanded and diversified their roles. One way in which this can occur is through a process known as alternative splicing, in which different exons can be included or excluded to generate the final messenger RNA. In this way, a single gene can produce a number of different proteins. These closely related proteins are known as isoforms. The brain contains billions of neurons that communicate with one another across connections known as synapses. A family of proteins called neurexins helps neurons to form these synapses. Humans have three neurexin genes, which undergo extensive alternative splicing to produce thousands of protein isoforms. However, it is not known whether all of these isoforms are produced in neurons, as existing experimental techniques were not sensitive enough to easily distinguish one isoform from another. A technique known as ‘selected reaction monitoring’ (or SRM for short) has recently emerged as a promising way to identify proteins. This allows proteins containing specific sequences to be separated out for analysis, in contrast to existing techniques that test randomly selected protein samples, which will result in most isoforms being missed. Schreiner, Simicevic et al. have now developed SRM further and show that this technique can detect the identity and amount of the neurexin isoforms present at synapses, including those that are only produced in very small quantities. Using SRM, Schreiner, Simicevic et al. demonstrate that neurexin isoforms differ in how they interact with synaptic receptors. Thus, alternative splicing of neurexins underlies a ‘recognition code’ at neuronal synapses. In the future, this newly developed SRM method could be used to investigate isoforms in other protein families and tissues, and so may prove valuable for understanding how a wide range of cellular recognition processes work. DOI:http://dx.doi.org/10.7554/eLife.07794.002
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Affiliation(s)
| | | | - Erik Ahrné
- Biozentrum, University of Basel, Basel, Switzerland
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