1
|
Gassaway BM, Huttlin EL, Huntsman EM, Yaron-Barir TM, Johnson JL, Kurmi K, Cantley LC, Paulo JA, Ringel AE, Gygi SP, Haigis MC. Profiling Proteins and Phosphorylation Sites During T Cell Activation Using an Integrated Thermal Shift Assay. Mol Cell Proteomics 2024:100801. [PMID: 38880243 DOI: 10.1016/j.mcpro.2024.100801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 05/24/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024] Open
Abstract
T cell activation is a complex biological process of naïve cells maturing into effector cells. Proteomic and phospho-proteomic approaches have provided critical insights into this process, yet it is not always clear how changes in individual proteins or phosphorylation sites have functional significance. Here, we developed the Phosphorylation Integrated Thermal Shift Assay (PITSA) that combines the measurement of protein or phosphorylation site abundance and thermal stability into a single TMT experiment and apply this method to study T cell activation. We quantified the abundance and thermal stability of over 7,500 proteins and 5,000 phosphorylation sites, and identified significant differences in chromatin-related, TCR signaling, DNA repair, and proliferative phosphoproteins. PITSA may be applied to a wide range of biological contexts to generate hypotheses as to which proteins or phosphorylation sites are functionally regulated in a given system, as well as the mechanisms by which this regulation may occur.
Collapse
Affiliation(s)
- Brandon M Gassaway
- Department of Cell Biology, Harvard Medical School; Boston, MA; Department of Chemistry and Biochemistry, Brigham Young University; Provo, UT
| | | | - Emily M Huntsman
- Meyer Cancer Center and Department of Medicine, Weill Cornell Medicine; New York, NY
| | - Tomer M Yaron-Barir
- Meyer Cancer Center and Department of Medicine, Weill Cornell Medicine; New York, NY; Columbia University Vagelos College of Physicians and Surgeons; New York, NY
| | - Jared L Johnson
- Department of Cell Biology, Harvard Medical School; Boston, MA; Dana Farber Cancer Institute; Boston, MA
| | - Kiran Kurmi
- Department of Cell Biology, Harvard Medical School; Boston, MA
| | - Lewis C Cantley
- Department of Cell Biology, Harvard Medical School; Boston, MA; Dana Farber Cancer Institute; Boston, MA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School; Boston, MA
| | - Alison E Ringel
- Department of Cell Biology, Harvard Medical School; Boston, MA; Ragon Institute of Mass General, MIT, and Harvard; Cambridge, MA; Department of Biology, Massachusetts Institute of Technology; Cambridge, MA; Koch Institute for Integrative Cancer Research; Cambridge, MA.
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School; Boston, MA.
| | - Marcia C Haigis
- Department of Cell Biology, Harvard Medical School; Boston, MA.
| |
Collapse
|
2
|
Sinha NK, McKenney C, Yeow ZY, Li JJ, Nam KH, Yaron-Barir TM, Johnson JL, Huntsman EM, Cantley LC, Ordureau A, Regot S, Green R. The ribotoxic stress response drives UV-mediated cell death. Cell 2024:S0092-8674(24)00527-0. [PMID: 38843833 DOI: 10.1016/j.cell.2024.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 03/03/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024]
Abstract
While ultraviolet (UV) radiation damages DNA, eliciting the DNA damage response (DDR), it also damages RNA, triggering transcriptome-wide ribosomal collisions and eliciting a ribotoxic stress response (RSR). However, the relative contributions, timing, and regulation of these pathways in determining cell fate is unclear. Here we use time-resolved phosphoproteomic, chemical-genetic, single-cell imaging, and biochemical approaches to create a chronological atlas of signaling events activated in cells responding to UV damage. We discover that UV-induced apoptosis is mediated by the RSR kinase ZAK and not through the DDR. We identify two negative-feedback modules that regulate ZAK-mediated apoptosis: (1) GCN2 activation limits ribosomal collisions and attenuates ZAK-mediated RSR and (2) ZAK activity leads to phosphodegron autophosphorylation and its subsequent degradation. These events tune ZAK's activity to collision levels to establish regimes of homeostasis, tolerance, and death, revealing its key role as the cellular sentinel for nucleic acid damage.
Collapse
Affiliation(s)
- Niladri K Sinha
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Connor McKenney
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhong Y Yeow
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeffrey J Li
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ki Hong Nam
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tomer M Yaron-Barir
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Emily M Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Sergi Regot
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| |
Collapse
|
3
|
Allen MC, Karplus PA, Mehl RA, Cooley RB. Genetic Encoding of Phosphorylated Amino Acids into Proteins. Chem Rev 2024; 124:6592-6642. [PMID: 38691379 DOI: 10.1021/acs.chemrev.4c00110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.
Collapse
Affiliation(s)
- Michael C Allen
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| |
Collapse
|
4
|
Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
5
|
Shuken SR, Yu Q, Gygi SP. Inserting Pre-analytical Chromatographic Priming Runs Significantly Improves Targeted Pathway Proteomics with Sample Multiplexing. J Proteome Res 2024; 23:1834-1843. [PMID: 38594897 PMCID: PMC11068481 DOI: 10.1021/acs.jproteome.4c00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
GoDig, a platform for targeted pathway proteomics without the need for manual assay scheduling or synthetic standards, is a powerful, flexible, and easy-to-use method that uses tandem mass tags to increase sample throughput up to 18-fold relative to label-free methods. Though the protein-level success rates of GoDig are high, the peptide-level success rates are more limited, hampering assays of harder-to-quantify proteins and site-specific phenomena. To guide the optimization of GoDig assays as well as improvements to the GoDig platform, we created GoDigViewer, a new stand-alone software that provides detailed visualizations of GoDig runs. GoDigViewer guided the implementation of "priming runs," an acquisition mode with significantly higher success rates. In this mode, two or more chromatographic priming runs are automatically performed to improve the accuracy and precision of target elution orders, followed by analytical runs which quantify targets. Using priming runs, success rates exceeded 97% for a list of 400 peptide targets and 95% for a list of 200 targets that are usually not quantified using untargeted mass spectrometry. We used priming runs to establish a quantitative assay of 125 macroautophagy proteins that had a >95% success rate and revealed differences in macroautophagy expression profiles across four human cell lines.
Collapse
Affiliation(s)
- Steven R Shuken
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| |
Collapse
|
6
|
Joyce AW, Searle BC. Computational approaches to identify sites of phosphorylation. Proteomics 2024; 24:e2300088. [PMID: 37897210 DOI: 10.1002/pmic.202300088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Due to their oftentimes ambiguous nature, phosphopeptide positional isomers can present challenges in bottom-up mass spectrometry-based workflows as search engine scores alone are often not enough to confidently distinguish them. Additional scoring algorithms can remedy this by providing confidence metrics in addition to these search results, reducing ambiguity. Here we describe challenges to interpreting phosphoproteomics data and review several different approaches to determine sites of phosphorylation for both data-dependent and data-independent acquisition-based workflows. Finally, we discuss open questions regarding neutral losses, gas-phase rearrangement, and false localization rate estimation experienced by both types of acquisition workflows and best practices for managing ambiguity in phosphosite determination.
Collapse
Affiliation(s)
- Alex W Joyce
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Brian C Searle
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
7
|
Yang K, Whitehouse RL, Dawson SL, Zhang L, Martin JG, Johnson DS, Paulo JA, Gygi SP, Yu Q. Accelerating multiplexed profiling of protein-ligand interactions: High-throughput plate-based reactive cysteine profiling with minimal input. Cell Chem Biol 2024; 31:565-576.e4. [PMID: 38118439 PMCID: PMC10960705 DOI: 10.1016/j.chembiol.2023.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/07/2023] [Accepted: 11/28/2023] [Indexed: 12/22/2023]
Abstract
Chemoproteomics has made significant progress in investigating small-molecule-protein interactions. However, the proteome-wide profiling of cysteine ligandability remains challenging to adapt for high-throughput applications, primarily due to a lack of platforms capable of achieving the desired depth using low input in 96- or 384-well plates. Here, we introduce a revamped, plate-based platform which enables routine interrogation of either ∼18,000 or ∼24,000 reactive cysteines based on starting amounts of 10 or 20 μg, respectively. This represents a 5-10X reduction in input and 2-3X improved coverage. We applied the platform to screen 192 electrophiles in the native HEK293T proteome, mapping the ligandability of 38,450 reactive cysteines from 8,274 human proteins. We further applied the platform to characterize new cellular targets of established drugs, uncovering that ARS-1620, a KRASG12C inhibitor, binds to and inhibits an off-target adenosine kinase ADK. The platform represents a major step forward to high-throughput proteome-wide evaluation of reactive cysteines.
Collapse
Affiliation(s)
- Ka Yang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Shane L Dawson
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Lu Zhang
- Biogen, Cambridge, MA 02142, USA
| | | | | | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
8
|
Shuken SR, Yu Q, Gygi SP. Inserting Pre-Analytical Chromatographic Priming Runs Significantly Improves Targeted Pathway Proteomics With Sample Multiplexing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.08.579551. [PMID: 38370708 PMCID: PMC10871336 DOI: 10.1101/2024.02.08.579551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
GoDig, a recent platform for targeted pathway proteomics without the need for manual assay scheduling or synthetic standard peptides, is a relatively flexible and easy-to-use method that uses tandem mass tags (TMT) to increase sample throughput up to 18-fold relative to label-free targeted proteomics. Though the protein quantification success rate of GoDig is generally high, the peptide-level success rate is more limited, hampering the extension of GoDig to assays of harder-to-quantify proteins and site-specific phenomena. In order to guide the optimization of GoDig assays as well as improvements to the GoDig platform, we created GoDigViewer, a new stand-alone software that provides detailed visualizations of GoDig runs. GoDigViewer guided the implementation of "priming runs," an acquisition mode with significantly higher success rates due to improved elution order calibration. In this mode, one or more chromatographic priming runs are automatically performed to determine accurate and precise target elution orders, followed by analytical runs which quantify targets. Using priming runs, peptide-level quantification success rates exceeded 97% for a list of 400 peptide targets and 95% for a list of 200 targets that are usually not quantified using untargeted mass spectrometry. We used priming runs to establish a quantitative assay of 125 macroautophagy proteins that had a >95% success rate and revealed differences in macroautophagy protein expression profiles across four human cell lines.
Collapse
Affiliation(s)
- Steven R. Shuken
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
| |
Collapse
|
9
|
Paul S, Sarraf SA, Nam KH, Zavar L, DeFoor N, Biswas SR, Fritsch LE, Yaron TM, Johnson JL, Huntsman EM, Cantley LC, Ordureau A, Pickrell AM. NAK-associated protein 1/NAP1 activates TBK1 to ensure accurate mitosis and cytokinesis. J Cell Biol 2024; 223:e202303082. [PMID: 38059900 PMCID: PMC10702366 DOI: 10.1083/jcb.202303082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 10/03/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023] Open
Abstract
Subcellular location and activation of Tank Binding Kinase 1 (TBK1) govern precise progression through mitosis. Either loss of activated TBK1 or its sequestration from the centrosomes causes errors in mitosis and growth defects. Yet, what regulates its recruitment and activation on the centrosomes is unknown. We identified that NAK-associated protein 1 (NAP1) is essential for mitosis, binding to and activating TBK1, which both localize to centrosomes. Loss of NAP1 causes several mitotic and cytokinetic defects due to inactivation of TBK1. Our quantitative phosphoproteomics identified numerous TBK1 substrates that are not only confined to the centrosomes but are also associated with microtubules. Substrate motifs analysis indicates that TBK1 acts upstream of other essential cell cycle kinases like Aurora and PAK kinases. We also identified NAP1 as a TBK1 substrate phosphorylating NAP1 at S318 to promote its degradation by the ubiquitin proteasomal system. These data uncover an important distinct function for the NAP1-TBK1 complex during cell division.
Collapse
Affiliation(s)
- Swagatika Paul
- Graduate Program in Biomedical and Veterinary Sciences, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
| | - Shireen A. Sarraf
- Biochemistry Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Ki Hong Nam
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leila Zavar
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Nicole DeFoor
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Sahitya Ranjan Biswas
- Translational Biology, Medicine, and Health Graduate Program, Virginia Polytechnic Institute and State University, Roanoke, VA, USA
| | - Lauren E. Fritsch
- Translational Biology, Medicine, and Health Graduate Program, Virginia Polytechnic Institute and State University, Roanoke, VA, USA
| | - Tomer M. Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Emily M. Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Lewis C. Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alicia M. Pickrell
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| |
Collapse
|
10
|
McHenry MW, Shi P, Camara CM, Cohen DT, Rettenmaier TJ, Adhikary U, Gygi MA, Yang K, Gygi SP, Wales TE, Engen JR, Wells JA, Walensky LD. Covalent inhibition of pro-apoptotic BAX. Nat Chem Biol 2024:10.1038/s41589-023-01537-6. [PMID: 38233584 DOI: 10.1038/s41589-023-01537-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024]
Abstract
BCL-2-associated X protein (BAX) is a promising therapeutic target for activating or restraining apoptosis in diseases of pathologic cell survival or cell death, respectively. In response to cellular stress, BAX transforms from a quiescent cytosolic monomer into a toxic oligomer that permeabilizes the mitochondria, releasing key apoptogenic factors. The mitochondrial lipid trans-2-hexadecenal (t-2-hex) sensitizes BAX activation by covalent derivatization of cysteine 126 (C126). In this study, we performed a disulfide tethering screen to discover C126-reactive molecules that modulate BAX activity. We identified covalent BAX inhibitor 1 (CBI1) as a compound that selectively derivatizes BAX at C126 and inhibits BAX activation by triggering ligands or point mutagenesis. Biochemical and structural analyses revealed that CBI1 can inhibit BAX by a dual mechanism of action: conformational constraint and competitive blockade of lipidation. These data inform a pharmacologic strategy for suppressing apoptosis in diseases of unwanted cell death by covalent targeting of BAX C126.
Collapse
Affiliation(s)
- Matthew W McHenry
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Peiwen Shi
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christina M Camara
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Daniel T Cohen
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - T Justin Rettenmaier
- Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Utsarga Adhikary
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Micah A Gygi
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ka Yang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - James A Wells
- Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Loren D Walensky
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| |
Collapse
|
11
|
Pino JC, Posso C, Joshi SK, Nestor M, Moon J, Hansen JR, Hutchinson-Bunch C, Gritsenko MA, Weitz KK, Watanabe-Smith K, Long N, McDermott JE, Druker BJ, Liu T, Tyner JW, Agarwal A, Traer E, Piehowski PD, Tognon CE, Rodland KD, Gosline SJC. Mapping the proteogenomic landscape enables prediction of drug response in acute myeloid leukemia. Cell Rep Med 2024; 5:101359. [PMID: 38232702 PMCID: PMC10829797 DOI: 10.1016/j.xcrm.2023.101359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/20/2023] [Accepted: 12/10/2023] [Indexed: 01/19/2024]
Abstract
Acute myeloid leukemia is a poor-prognosis cancer commonly stratified by genetic aberrations, but these mutations are often heterogeneous and fail to consistently predict therapeutic response. Here, we combine transcriptomic, proteomic, and phosphoproteomic datasets with ex vivo drug sensitivity data to help understand the underlying pathophysiology of AML beyond mutations. We measure the proteome and phosphoproteome of 210 patients and combine them with genomic and transcriptomic measurements to identify four proteogenomic subtypes that complement existing genetic subtypes. We build a predictor to classify samples into subtypes and map them to a "landscape" that identifies specific drug response patterns. We then build a drug response prediction model to identify drugs that target distinct subtypes and validate our findings on cell lines representing various stages of quizartinib resistance. Our results show how multiomics data together with drug sensitivity data can inform therapy stratification and drug combinations in AML.
Collapse
Affiliation(s)
- James C Pino
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Camilo Posso
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sunil K Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Michael Nestor
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jamie Moon
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Joshua R Hansen
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chelsea Hutchinson-Bunch
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marina A Gritsenko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karl K Weitz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kevin Watanabe-Smith
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Nicola Long
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Jason E McDermott
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA; Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Tao Liu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Paul D Piehowski
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Karin D Rodland
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA.
| | - Sara J C Gosline
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| |
Collapse
|
12
|
Brown KA, Morris R, Eckhardt SJ, Ge Y, Gellman SH. Phosphorylation Sites of the Gastric Inhibitory Polypeptide Receptor (GIPR) Revealed by Trapped-Ion-Mobility Spectrometry Coupled to Time-of-Flight Mass Spectrometry (TIMS-TOF MS). J Am Chem Soc 2023; 145:28030-28037. [PMID: 38091482 PMCID: PMC10842860 DOI: 10.1021/jacs.3c09078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The gastric inhibitory polypeptide receptor (GIPR), a G protein-coupled receptor (GPCR) that regulates glucose metabolism and insulin secretion, is a target for the development of therapeutic agents to address type 2 diabetes and obesity. Signal transduction processes mediated by GPCR activation typically result in receptor phosphorylation, but very little is known about GIPR phosphorylation. Mass spectrometry (MS) is a powerful tool for detecting phosphorylation and other post-translational modifications of proteins and for identifying modification sites. However, applying MS methods to GPCRs is challenging because the native expression levels are low and the hydrophobicity of these proteins complicates isolation and enrichment. Here we use a widely available technique, trapped-ion-mobility spectrometry coupled to time-of-flight mass spectrometry (TIMS-TOF MS), to characterize the phosphorylation status of the GIPR. We identified eight serine residues that are phosphorylated, one in an intracellular loop and the remainder in the C-terminal domain. Stimulation with the native agonist GIP enhanced phosphorylation at four of these sites. For comparison, we evaluated tirzepatide (TZP), a dual agonist of the glucagon-like peptide-1 (GLP-1) receptor and the GIPR that has recently been approved for the treatment of type 2 diabetes. Stimulation with TZP enhanced phosphorylation at the same four sites that were enhanced with GIP; however, TZP also enhanced phosphorylation at a fifth site that is unique to this synthetic agonist. This work establishes an important and accessible tool for the characterization of signal transduction via the GIPR and reveals an unanticipated functional difference between GIP and TZP.
Collapse
Affiliation(s)
- Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Rylie Morris
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Samantha J. Eckhardt
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| |
Collapse
|
13
|
Ledvin L, Gassaway BM, Tawil J, Urso O, Pizzo D, Welsh KA, Bolhuis DL, Fisher D, Bonni A, Gygi SP, Brown NG, Ferguson CJ. The anaphase-promoting complex controls a ubiquitination-phosphoprotein axis in chromatin during neurodevelopment. Dev Cell 2023; 58:2666-2683.e9. [PMID: 37875116 PMCID: PMC10872926 DOI: 10.1016/j.devcel.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 08/07/2023] [Accepted: 10/03/2023] [Indexed: 10/26/2023]
Abstract
Mutations in the degradative ubiquitin ligase anaphase-promoting complex (APC) alter neurodevelopment by impairing proteasomal protein clearance, but our understanding of their molecular and cellular pathogenesis remains limited. Here, we employ the proteomic-based discovery of APC substrates in APC mutant mouse brain and human cell lines and identify the chromosome-passenger complex (CPC), topoisomerase 2a (Top2a), and Ki-67 as major chromatin factors targeted by the APC during neuronal differentiation. These substrates accumulate in phosphorylated form, suggesting that they fail to be eliminated after mitosis during terminal differentiation. The accumulation of the CPC kinase Aurora B within constitutive heterochromatin and hyperphosphorylation of its target histone 3 are corrected in the mutant brain by pharmacologic Aurora B inhibition. Surprisingly, the reduction of Ki-67, but not H3S10ph, rescued the function of constitutive heterochromatin in APC mutant neurons. These results expand our understanding of how ubiquitin signaling regulates chromatin during neurodevelopment and identify potential therapeutic targets in APC-related disorders.
Collapse
Affiliation(s)
- Leya Ledvin
- Pathology Department, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brandon M Gassaway
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Tawil
- Pathology Department, University of California, San Diego, La Jolla, CA 92093, USA
| | - Olivia Urso
- Pathology Department, University of California, San Diego, La Jolla, CA 92093, USA
| | - Donald Pizzo
- Pathology Department, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kaeli A Welsh
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | | | - Azad Bonni
- Neuroscience Department, Washington University, St. Louis, MO 63110, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas G Brown
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Cole J Ferguson
- Pathology Department, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
14
|
Searle BC, Chien A, Koller A, Hawke D, Herren AW, Kim Kim J, Lee KA, Leib RD, Nelson AJ, Patel P, Ren JM, Stemmer PM, Zhu Y, Neely BA, Patel B. A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development. Mol Cell Proteomics 2023; 22:100639. [PMID: 37657519 PMCID: PMC10561125 DOI: 10.1016/j.mcpro.2023.100639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023] Open
Abstract
Recent advances in methodology have made phosphopeptide analysis a tractable problem for many proteomics researchers. There are now a wide variety of robust and accessible enrichment strategies to generate phosphoproteomes while free or inexpensive software tools for quantitation and site localization have simplified phosphoproteome analysis workflow tremendously. As a research group under the Association for Biomolecular Resource Facilities umbrella, the Proteomics Standards Research Group has worked to develop a multipathway phosphopeptide standard based on a mixture of heavy-labeled phosphopeptides designed to enable researchers to rapidly develop assays. This mixture contains 131 mass spectrometry vetted phosphopeptides specifically chosen to cover as many known biologically interesting phosphosites as possible from seven different signaling networks: AMPK signaling, death and apoptosis signaling, ErbB signaling, insulin/insulin-like growth factor-1 signaling, mTOR signaling, PI3K/AKT signaling, and stress (p38/SAPK/JNK) signaling. Here, we describe a characterization of this mixture spiked into a HeLa tryptic digest stimulated with both epidermal growth factor and insulin-like growth factor-1 to activate the MAPK and PI3K/AKT/mTOR pathways. We further demonstrate a comparison of phosphoproteomic profiling of HeLa performed independently in five labs using this phosphopeptide mixture with data-independent acquisition. Despite different experimental and instrumentation processes, we found that labs could produce reproducible, harmonized datasets by reporting measurements as ratios to the standard, while intensity measurements showed lower consistency between labs even after normalization. Our results suggest that widely available, biologically relevant phosphopeptide standards can act as a quantitative "yardstick" across laboratories and sample preparations enabling experimental designs larger than a single laboratory can perform. Raw data files are publicly available in the MassIVE dataset MSV000090564.
Collapse
Affiliation(s)
- Brian C Searle
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA.
| | - Allis Chien
- Mass Spectrometry Center, Stanford University, Stanford, California, USA
| | | | | | - Anthony W Herren
- UC Davis Genome Center, Proteomics Core, University of California Davis, Davis California, USA
| | - Jenny Kim Kim
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| | - Kimberly A Lee
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Ryan D Leib
- Mass Spectrometry Center, Stanford University, Stanford, California, USA
| | | | - Purvi Patel
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| | - Jian Min Ren
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Paul M Stemmer
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| | - Yiying Zhu
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Benjamin A Neely
- National Institute of Standards and Technology, Charleston, South Carolina, USA
| | - Bhavin Patel
- Thermo Fisher Scientific, Rockford, Illinois, USA
| |
Collapse
|
15
|
Zong Y, Wang Y, Yang Y, Zhao D, Wang X, Shen C, Qiao L. DeepFLR facilitates false localization rate control in phosphoproteomics. Nat Commun 2023; 14:2269. [PMID: 37080984 PMCID: PMC10119288 DOI: 10.1038/s41467-023-38035-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 04/06/2023] [Indexed: 04/22/2023] Open
Abstract
Protein phosphorylation is a post-translational modification crucial for many cellular processes and protein functions. Accurate identification and quantification of protein phosphosites at the proteome-wide level are challenging, not least because efficient tools for protein phosphosite false localization rate (FLR) control are lacking. Here, we propose DeepFLR, a deep learning-based framework for controlling the FLR in phosphoproteomics. DeepFLR includes a phosphopeptide tandem mass spectrum (MS/MS) prediction module based on deep learning and an FLR assessment module based on a target-decoy approach. DeepFLR improves the accuracy of phosphopeptide MS/MS prediction compared to existing tools. Furthermore, DeepFLR estimates FLR accurately for both synthetic and biological datasets, and localizes more phosphosites than probability-based methods. DeepFLR is compatible with data from different organisms, instruments types, and both data-dependent and data-independent acquisition approaches, thus enabling FLR estimation for a broad range of phosphoproteomics experiments.
Collapse
Affiliation(s)
- Yu Zong
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Yuxin Wang
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, China
- Department of Computer Science, and Institute of Modern Languages and Linguistics, Fudan University, Shanghai, China
| | - Yi Yang
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Dan Zhao
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | | | | | - Liang Qiao
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, China.
| |
Collapse
|
16
|
Abu Sammour D, Cairns JL, Boskamp T, Marsching C, Kessler T, Ramallo Guevara C, Panitz V, Sadik A, Cordes J, Schmidt S, Mohammed SA, Rittel MF, Friedrich M, Platten M, Wolf I, von Deimling A, Opitz CA, Wick W, Hopf C. Spatial probabilistic mapping of metabolite ensembles in mass spectrometry imaging. Nat Commun 2023; 14:1823. [PMID: 37005414 PMCID: PMC10067847 DOI: 10.1038/s41467-023-37394-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 03/13/2023] [Indexed: 04/04/2023] Open
Abstract
Mass spectrometry imaging vows to enable simultaneous spatially resolved investigation of hundreds of metabolites in tissues, but it primarily relies on traditional ion images for non-data-driven metabolite visualization and analysis. The rendering and interpretation of ion images neither considers nonlinearities in the resolving power of mass spectrometers nor does it yet evaluate the statistical significance of differential spatial metabolite abundance. Here, we outline the computational framework moleculaR ( https://github.com/CeMOS-Mannheim/moleculaR ) that is expected to improve signal reliability by data-dependent Gaussian-weighting of ion intensities and that introduces probabilistic molecular mapping of statistically significant nonrandom patterns of relative spatial abundance of metabolites-of-interest in tissue. moleculaR also enables cross-tissue statistical comparisons and collective molecular projections of entire biomolecular ensembles followed by their spatial statistical significance evaluation on a single tissue plane. It thereby fosters the spatially resolved investigation of ion milieus, lipid remodeling pathways, or complex scores like the adenylate energy charge within the same image.
Collapse
Affiliation(s)
- Denis Abu Sammour
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
- Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - James L Cairns
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Tobias Boskamp
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
- Center for Industrial Mathematics, University of Bremen, Bremen, Germany
| | - Christian Marsching
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | - Tobias Kessler
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
- DKTK Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carina Ramallo Guevara
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
| | - Verena Panitz
- DKTK Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Ahmed Sadik
- DKTK Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Bioscience, Heidelberg University, Heidelberg, Germany
| | - Jonas Cordes
- Faculty of Computer Science, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Stefan Schmidt
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
| | - Shad A Mohammed
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
- Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Miriam F Rittel
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
- Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Mirco Friedrich
- Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- DKTK Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Platten
- Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- DKTK Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ivo Wolf
- Faculty of Computer Science, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- DKTK Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christiane A Opitz
- DKTK Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
- DKTK Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany.
- Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany.
| |
Collapse
|
17
|
Liu X, Rossio V, Paulo JA. Spin column-based peptide fractionation alternatives for streamlined tandem mass tag (SL-TMT) sample processing. J Proteomics 2023; 276:104839. [PMID: 36758854 PMCID: PMC9990130 DOI: 10.1016/j.jprot.2023.104839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/20/2023] [Accepted: 01/29/2023] [Indexed: 02/10/2023]
Abstract
Fractionation is essential to achieving deep proteome coverage for sample multiplexing experiments where currently up to 18 samples can be analyzed concurrently. However, peptide fractionation (i.e., upstream of LC-MS/MS analysis) with a liquid chromatography system constrains sample processing as only a single sample can be fractionated at once. Here, we highlight the use of spin column-based methods which permit multiple multiplexed samples to be fractionated simultaneously. These methods require only a centrifuge and eliminate the need for a dedicated liquid chromatography system. We investigate peptide fractionation with strong anion exchange (SAX) and high-pH reversed phase (HPRP) spin columns, as well as a combination of both. In two separate experiments, we acquired deep proteome coverage (>8000 quantified proteins), while starting with <25 μg of protein per channel. Our datasets showcase the proteome alterations in two human cell lines resulting from treatment with inhibitors acting on the ubiquitin-proteasome system. We recommend this spin column-based peptide fractionation strategy for high-throughput screening applications or whenever a liquid chromatograph is not readily available. SIGNIFICANCE: Fractionation is a means to achieve deep proteome coverage for global proteomics analysis. Typical liquid chromatography systems may be a prohibitive expense for many laboratories. Here, we investigate prefractionation with strong anion exchange (SAX) and high-pH reversed phase (HPRP) spin columns, as well as a combination of both, as peptide fractionation methods. These spin columns have advantages over liquid chromatography systems, which include relative affordability, higher throughput capability, no carry over, and fewer potential instrument-related malfunctions. In two separate experiments, we acquired deep proteome coverage (>8000 quantified proteins), thereby showing the utility of each or a combination of both spin columns for global proteome analysis.
Collapse
Affiliation(s)
- Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Valentina Rossio
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States.
| |
Collapse
|
18
|
Harada T, Kalfon J, Perez MW, Eagle K, Braes FD, Batley R, Heshmati Y, Ferrucio JX, Ewers J, Mehta S, Kossenkov A, Ellegast JM, Bowker A, Wickramasinghe J, Nabet B, Paralkar VR, Dharia NV, Stegmaier K, Orkin SH, Pimkin M. Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532438. [PMID: 36993171 PMCID: PMC10054969 DOI: 10.1101/2023.03.13.532438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Lineage-defining transcription factors form densely interconnected circuits in chromatin occupancy assays, but the functional significance of these networks remains underexplored. We reconstructed the functional topology of a leukemia cell transcription network from the direct gene-regulatory programs of eight core transcriptional regulators established in pre-steady state assays coupling targeted protein degradation with nascent transcriptomics. The core regulators displayed narrow, largely non-overlapping direct transcriptional programs, forming a sparsely interconnected functional hierarchy stabilized by incoherent feed-forward loops. BET bromodomain and CDK7 inhibitors disrupted the core regulators' direct programs, acting as mixed agonists/antagonists. The network is predictive of dynamic gene expression behaviors in time-resolved assays and clinically relevant pathway activity in patient populations.
Collapse
Affiliation(s)
- Taku Harada
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Jérémie Kalfon
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| | - Monika W. Perez
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Kenneth Eagle
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Ken Eagle Consulting, Houston, TX, 77494, USA
| | - Flora Dievenich Braes
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Rashad Batley
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Yaser Heshmati
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Juliana Xavier Ferrucio
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Jazmin Ewers
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Stuti Mehta
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | | | - Jana M. Ellegast
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| | - Allyson Bowker
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | | | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Vikram R. Paralkar
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Neekesh V. Dharia
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| | - Kimberly Stegmaier
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| | - Stuart H. Orkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Maxim Pimkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA
| |
Collapse
|
19
|
Yi X, Wen B, Ji S, Saltzman A, Jaehnig EJ, Lei JT, Gao Q, Zhang B. Deep learning prediction boosts phosphoproteomics-based discoveries through improved phosphopeptide identification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523329. [PMID: 36711982 PMCID: PMC9882090 DOI: 10.1101/2023.01.11.523329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Shotgun phosphoproteomics enables high-throughput analysis of phosphopeptides in biological samples, but low phosphopeptide identification rate in data analysis limits the potential of this technology. Here we present DeepRescore2, a computational workflow that leverages deep learning-based retention time and fragment ion intensity predictions to improve phosphopeptide identification and phosphosite localization. Using a state-of-the-art computational workflow as a benchmark, DeepRescore2 increases the number of correctly identified peptide-spectrum matches by 17% in a synthetic dataset and identifies 19%-46% more phosphopeptides in biological datasets. In a liver cancer dataset, 30% of the significantly altered phosphosites between tumor and normal tissues and 60% of the prognosis-associated phosphosites identified from DeepRescore2-processed data could not be identified based on the state-of-the-art workflow. Notably, DeepRescore2-processed data uniquely identifies EGFR hyperactivation as a new target in poor-prognosis liver cancer, which is validated experimentally. Integration of deep learning prediction in DeepRescore2 improves phosphopeptide identification and facilitates biological discoveries.
Collapse
|