1
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Segovia D, Adams DW, Hoffman N, Safaric Tepes P, Wee TL, Cifani P, Joshua-Tor L, Krainer AR. SRSF1 interactome determined by proximity labeling reveals direct interaction with spliceosomal RNA helicase DDX23. Proc Natl Acad Sci U S A 2024; 121:e2322974121. [PMID: 38743621 DOI: 10.1073/pnas.2322974121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
SRSF1 is the founding member of the SR protein family. It is required-interchangeably with other SR proteins-for pre-mRNA splicing in vitro, and it regulates various alternative splicing events. Dysregulation of SRSF1 expression contributes to cancer and other pathologies. Here, we characterized SRSF1's interactome using proximity labeling and mass spectrometry. This approach yielded 190 proteins enriched in the SRSF1 samples, independently of the N- or C-terminal location of the biotin-labeling domain. The detected proteins reflect established functions of SRSF1 in pre-mRNA splicing and reveal additional connections to spliceosome proteins, in addition to other recently identified functions. We validated a robust interaction with the spliceosomal RNA helicase DDX23/PRP28 using bimolecular fluorescence complementation and in vitro binding assays. The interaction is mediated by the N-terminal RS-like domain of DDX23 and both RRM1 and the RS domain of SRSF1. During pre-mRNA splicing, DDX23's ATPase activity is essential for the pre-B to B spliceosome complex transition and for release of U1 snRNP from the 5' splice site. We show that the RS-like region of DDX23's N-terminal domain is important for spliceosome incorporation, while larger deletions in this domain alter subnuclear localization. We discuss how the identified interaction of DDX23 with SRSF1 and other SR proteins may be involved in the regulation of these processes.
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Affiliation(s)
- Danilo Segovia
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY 11794
| | - Dexter W Adams
- HHMI, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794
| | | | | | - Tse-Luen Wee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Paolo Cifani
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Leemor Joshua-Tor
- HHMI, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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2
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Yao M, Preall J, Yeh JTH, Pappin D, Cifani P, Zhao Y, Shen S, Moresco P, He B, Patel H, Habowski AN, King DA, Raphael K, Rishi A, Sejpal D, Weiss MJ, Tuveson D, Fearon DT. Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies against self-antigens. JCI Insight 2023; 8:e172449. [PMID: 37751306 PMCID: PMC10721257 DOI: 10.1172/jci.insight.172449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 09/14/2023] [Indexed: 09/27/2023] Open
Abstract
Intratumoral B cell responses are associated with more favorable clinical outcomes in human pancreatic ductal adenocarcinoma (PDAC). However, the antigens driving these B cell responses are largely unknown. We sought to discover these antigens by using single-cell RNA sequencing (scRNA-Seq) and immunoglobulin (Ig) sequencing of tumor-infiltrating immune cells from 7 primary PDAC samples. We identified activated T and B cell responses and evidence of germinal center reactions. Ig sequencing identified plasma cell (PC) clones expressing isotype-switched and hypermutated Igs, suggesting the occurrence of T cell-dependent B cell responses. We assessed the reactivity of 41 recombinant antibodies that represented the products of 235 PCs and 12 B cells toward multiple cell lines and PDAC tissues and observed frequent staining of intracellular self-antigens. Three of these antigens were identified: the filamentous actin (F-actin), the nucleic protein RuvB like AAA ATPase 2 (RUVBL2), and the mitochondrial protein heat shock protein family D (Hsp60) member 1 (HSPD1). Antibody titers against F-actin and HSPD1 were substantially elevated in the plasma of patients with PDAC compared with healthy donors. Thus, PCs in PDAC produce autoantibodies reacting with intracellular self-antigens, which may result from promotion of preexisting, autoreactive B cell responses. These observations indicate the chronic inflammatory microenvironment of PDAC can support the adaptive immune response.
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Affiliation(s)
- Min Yao
- Cold Spring Harbor Laboratory and
| | | | | | | | | | | | - Sophia Shen
- Cold Spring Harbor High School, Cold Spring Harbor, New York, USA
| | - Philip Moresco
- Cold Spring Harbor Laboratory and
- Graduate Program in Genetics, Stony Brook University, Stony Brook, New York, USA
- Medical Scientist Training Program, Stony Brook University Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Brian He
- Cold Spring Harbor Laboratory and
| | | | | | - Daniel A. King
- North Shore University Hospital, Manhasset, New York, USA
| | - Kara Raphael
- North Shore University Hospital, Manhasset, New York, USA
| | - Arvind Rishi
- North Shore University Hospital, Manhasset, New York, USA
| | - Divyesh Sejpal
- North Shore University Hospital, Manhasset, New York, USA
| | | | | | - Douglas T. Fearon
- Cold Spring Harbor Laboratory and
- Weill Cornell Medicine, New York, New York, USA
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3
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Zhang L, Braynen J, Fahey A, Chopra K, Cifani P, Tadesse D, Regulski M, Hu F, van Dam HJJ, Xie M, Ware D, Blaby-Haas CE. Two related families of metal transferases, ZNG1 and ZNG2, are involved in acclimation to poor Zn nutrition in Arabidopsis. Front Plant Sci 2023; 14:1237722. [PMID: 37965006 PMCID: PMC10642216 DOI: 10.3389/fpls.2023.1237722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/02/2023] [Indexed: 11/16/2023]
Abstract
Metal homeostasis has evolved to tightly modulate the availability of metals within the cell, avoiding cytotoxic interactions due to excess and protein inactivity due to deficiency. Even in the presence of homeostatic processes, however, low bioavailability of these essential metal nutrients in soils can negatively impact crop health and yield. While research has largely focused on how plants assimilate metals, acclimation to metal-limited environments requires a suite of strategies that are not necessarily involved in metal transport across membranes. The identification of these mechanisms provides a new opportunity to improve metal-use efficiency and develop plant foodstuffs with increased concentrations of bioavailable metal nutrients. Here, we investigate the function of two distinct subfamilies of the nucleotide-dependent metallochaperones (NMCs), named ZNG1 and ZNG2, that are found in plants, using Arabidopsis thaliana as a reference organism. AtZNG1 (AT1G26520) is an ortholog of human and fungal ZNG1, and like its previously characterized eukaryotic relatives, localizes to the cytosol and physically interacts with methionine aminopeptidase type I (AtMAP1A). Analysis of AtZNG1, AtMAP1A, AtMAP2A, and AtMAP2B transgenic mutants are consistent with the role of Arabidopsis ZNG1 as a Zn transferase for AtMAP1A, as previously described in yeast and zebrafish. Structural modeling reveals a flexible cysteine-rich loop that we hypothesize enables direct transfer of Zn from AtZNG1 to AtMAP1A during GTP hydrolysis. Based on proteomics and transcriptomics, loss of this ancient and conserved mechanism has pleiotropic consequences impacting the expression of hundreds of genes, including those involved in photosynthesis and vesicle transport. Members of the plant-specific family of NMCs, ZNG2A1 (AT1G80480) and ZNG2A2 (AT1G15730), are also required during Zn deficiency, but their target protein(s) remain to be discovered. RNA-seq analyses reveal wide-ranging impacts across the cell when the genes encoding these plastid-localized NMCs are disrupted.
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Affiliation(s)
- Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Janeen Braynen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Audrey Fahey
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Kriti Chopra
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, United States
| | - Paolo Cifani
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Dimiru Tadesse
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Michael Regulski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Fangle Hu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Hubertus J. J. van Dam
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Meng Xie
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY, United States
| | - Crysten E. Blaby-Haas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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4
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Perlee S, Kikuchi S, Nakadai T, Masuda T, Ohtsuki S, Matsumoto M, Rahmutulla B, Fukuyo M, Cifani P, Kentsis A, Roeder RG, Kaneda A, Hoshii T. SETD1A function in leukemia is mediated through interaction with mitotic regulators BuGZ/BUB3. EMBO Rep 2023; 24:e57108. [PMID: 37535603 PMCID: PMC10561176 DOI: 10.15252/embr.202357108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 08/05/2023] Open
Abstract
The H3K4 methyltransferase SETD1A plays a crucial role in leukemia cell survival through its noncatalytic FLOS domain-mediated recruitment of cyclin K and regulation of DNA damage response genes. In this study, we identify a functional nuclear localization signal in and interaction partners of the FLOS domain. Our screen for FLOS domain-binding partners reveals that the SETD1A FLOS domain binds mitosis-associated proteins BuGZ/BUB3. Inhibition of both cyclin K and BuGZ/BUB3-binding motifs in SETD1A shows synergistic antileukemic effects. BuGZ/BUB3 localize to SETD1A-bound promoter-TSS regions and SETD1A-negative H3K4me1-positive enhancer regions adjacent to SETD1A target genes. The GLEBS motif and intrinsically disordered region of BuGZ are required for both SETD1A-binding and leukemia cell proliferation. Cell-cycle-specific SETD1A restoration assays indicate that SETD1A expression at the G1/S phase of the cell cycle promotes both the expression of DNA damage response genes and cell cycle progression in leukemia cells.
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Affiliation(s)
- Sarah Perlee
- Department of Cancer Biology and GeneticsMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Gerstner Graduate School of Biomedical SciencesMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Sota Kikuchi
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Tomoyoshi Nakadai
- Laboratory of Biochemistry and Molecular BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Takeshi Masuda
- Laboratory of Pharmaceutical Microbiology, Faculty of Life SciencesKumamoto UniversityKumamotoJapan
- Institute for Advanced BiosciencesKeio UniversityTsuruokaJapan
| | - Sumio Ohtsuki
- Laboratory of Pharmaceutical Microbiology, Faculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Makoto Matsumoto
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Paolo Cifani
- Molecular Pharmacology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Alex Kentsis
- Molecular Pharmacology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Takayuki Hoshii
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
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5
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Kwok N, Aretz Z, Takao S, Ser Z, Cifani P, Kentsis A. Integrative Proteogenomics Using ProteomeGenerator2. J Proteome Res 2023; 22:2750-2764. [PMID: 37418425 PMCID: PMC10783198 DOI: 10.1021/acs.jproteome.3c00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. Likewise, advances in mass spectrometry proteomics now permit highly sensitive and accurate studies of protein expression at the whole proteome-scale. However, most proteomic studies rely on consensus databases to match spectra to peptide and protein sequences, and thus remain limited to the analysis of canonical protein sequences. Here, we develop ProteomeGenerator2 (PG2), based on the scalable and modular ProteomeGenerator framework. PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as noncanonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. We benchmarked PG2 using synthetic data and genomic, transcriptomic, and proteomic analysis of human leukemia cells. PG2 can be integrated with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms, and is available open-source from https://github.com/kentsisresearchgroup/ProteomeGenerator2.
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Affiliation(s)
- Nathaniel Kwok
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
- Doctor of Medicine Program, Weill Cornell Medicine, New York, NY
- Department of Graduate Medical Education, HCA TriStar-Centennial Medical Center, Nashville, TN
| | - Zita Aretz
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
- Physiology Biophysics and Systems Biology Program, Weill Cornell Graduate School, Cornell University, New York, NY
| | - Sumiko Takao
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY
| | - Zheng Ser
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Medical College, Cornell University, New York, NY
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6
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Herrejon Chavez F, Luo H, Cifani P, Pine A, Chu KL, Joshi S, Barin E, Schurer A, Chan M, Chang K, Han GYQ, Pierson AJ, Xiao M, Yang X, Kuehm LM, Hong Y, Nguyen DTT, Chiosis G, Kentsis A, Leslie C, Vu LP, Kharas MG. RNA binding protein SYNCRIP maintains proteostasis and self-renewal of hematopoietic stem and progenitor cells. Nat Commun 2023; 14:2290. [PMID: 37085479 PMCID: PMC10121618 DOI: 10.1038/s41467-023-38001-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 04/11/2023] [Indexed: 04/23/2023] Open
Abstract
Tissue homeostasis is maintained after stress by engaging and activating the hematopoietic stem and progenitor compartments in the blood. Hematopoietic stem cells (HSCs) are essential for long-term repopulation after secondary transplantation. Here, using a conditional knockout mouse model, we revealed that the RNA-binding protein SYNCRIP is required for maintenance of blood homeostasis especially after regenerative stress due to defects in HSCs and progenitors. Mechanistically, we find that SYNCRIP loss results in a failure to maintain proteome homeostasis that is essential for HSC maintenance. SYNCRIP depletion results in increased protein synthesis, a dysregulated epichaperome, an accumulation of misfolded proteins and induces endoplasmic reticulum stress. Additionally, we find that SYNCRIP is required for translation of CDC42 RHO-GTPase, and loss of SYNCRIP results in defects in polarity, asymmetric segregation, and dilution of unfolded proteins. Forced expression of CDC42 recovers polarity and in vitro replating activities of HSCs. Taken together, we uncovered a post-transcriptional regulatory program that safeguards HSC self-renewal capacity and blood homeostasis.
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Affiliation(s)
- Florisela Herrejon Chavez
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hanzhi Luo
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paolo Cifani
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Alli Pine
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karen L Chu
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell School of Medical Sciences, New York, NY, USA
| | - Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ersilia Barin
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pharmacology Program of the Weill Cornell Graduate School of Medicine Sciences, New York, NY, USA
| | - Alexandra Schurer
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mandy Chan
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathryn Chang
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Grace Y Q Han
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aspen J Pierson
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Xiao
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Xuejing Yang
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yuning Hong
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Diu T T Nguyen
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY, USA
| | - Christina Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ly P Vu
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Terry Fox Laboratory, British Columbia Cancer Research Centre, Vancouver, BC, Canada.
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Michael G Kharas
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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7
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Kwok N, Aretz Z, Takao S, Ser Z, Cifani P, Kentsis A. Integrative proteogenomics using ProteomeGenerator2. bioRxiv 2023:2023.01.04.522774. [PMID: 36711693 PMCID: PMC9882001 DOI: 10.1101/2023.01.04.522774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. Likewise, advances in mass spectrometry proteomics now permit highly sensitive and accurate studies of protein expression at the whole proteome-scale. However, most proteomic studies rely on consensus databases to match spectra to peptide and proteins sequences, and thus remain limited to the analysis of canonical protein sequences. Here, we develop ProteomeGenerator2 (PG2), based on the scalable and modular ProteomeGenerator framework. PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. We benchmarked PG2 using synthetic data and genomic, transcriptomic, and proteomic analysis of human leukemia cells. PG2 can be integrated with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms, and is available open-source from https://github.com/kentsisresearchgroup/ProteomeGenerator2 .
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8
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Cifani P, Kentsis A. Quantitative Cell Proteomic Atlas: Pathway-Scale Targeted Mass Spectrometry for High-Resolution Functional Profiling of Cell Signaling. J Proteome Res 2022; 21:2535-2544. [PMID: 36154077 PMCID: PMC10494574 DOI: 10.1021/acs.jproteome.2c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In spite of extensive studies of cellular signaling, many fundamental processes such as pathway integration, cross-talk, and feedback remain poorly understood. To enable integrated and quantitative measurements of cellular biochemical activities, we have developed the Quantitative Cell Proteomics Atlas (QCPA). QCPA consists of panels of targeted mass spectrometry assays to determine the abundance and stoichiometry of regulatory post-translational modifications of sentinel proteins from most known physiologic and pathogenic signaling pathways in human cells. QCPA currently profiles 1 913 peptides from 469 effectors of cell surface signaling, apoptosis, stress response, gene expression, quiescence, and proliferation. For each protein, QCPA includes triplets of isotopically labeled peptides covering known post-translational regulatory sites to determine their stoichiometries and unmodified protein regions to measure total protein abundance. The QCPA framework incorporates analytes to control for technical variability of sample preparation and mass spectrometric analysis, including TrypQuant, a synthetic substrate for accurate quantification of proteolysis efficiency for proteins containing chemically modified residues. The ability to precisely and accurately quantify most known signaling pathways should enable improved chemoproteomic approaches for the comprehensive analysis of cell signaling and clinical proteomics of diagnostic specimens. QCPA is openly available at https://qcpa.mskcc.org.
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Affiliation(s)
- Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065 USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065 USA
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, NY, 10065 USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, NY, 10065 USA
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9
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Paul S, Cifani P, Pappin D, Spratt T. Unique DNA Polymerase kappa Interactome Suggests Novel Cellular Functions. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.0r478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shilpi Paul
- Biochemistry and Molecular BiologyPenn State University College of MedicineHersheyPA
| | - Paolo Cifani
- Cold Spring Harbor LaboratoryCold Spring HarborNY
| | | | - Thomas Spratt
- Biochemistry and Molecular BiologyPenn State University College of MedicineHersheyPA
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10
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Cifani P, Kentsis A. Automated Multidimensional Nanoscale Chromatography for Ultrasensitive Targeted Mass Spectrometry. Methods Mol Biol 2022; 2393:207-224. [PMID: 34837181 PMCID: PMC10320743 DOI: 10.1007/978-1-0716-1803-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Recent advances in nanoscale separations and high-resolution mass spectrometry permit highly sensitive and accurate analyses of complex protein mixtures. Here, we describe improved methods for nanoscale multidimensional chromatography coupled to targeted mass spectrometry (tMS) to achieve ultrasensitive quantification of peptides in complex proteomes. The presented chromatographic system consists of capillary strong-cation exchange (SCX) chromatography column, from which peptides are eluted directly onto high-resolution reversed-phase (RP) analytical columns and nanoelectrospray ion source. SCX prefractionation is used to separate phosphorylated peptides, permitting their ultrasensitive quantification. Resolution and robustness of this chromatographic system, together with the orthogonality of SCX and RP separations, permit scheduling of large panels of targeted MS assays. This design also enables seamless scaling to three-dimensional separations, thereby enabling large-scale, ultrasensitive quantitative proteomics.
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Affiliation(s)
- Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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11
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Cifani P, Li Z, Luo D, Grivainis M, Intlekofer AM, Fenyö D, Kentsis A. Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics. J Proteome Res 2021; 20:1835-1848. [PMID: 33749263 PMCID: PMC8341206 DOI: 10.1021/acs.jproteome.0c00638] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Recent studies have revealed diverse amino acid, post-translational, and noncanonical modifications of proteins in diverse organisms and tissues. However, their unbiased detection and analysis remain hindered by technical limitations. Here, we present a spectral alignment method for the identification of protein modifications using high-resolution mass spectrometry proteomics. Termed SAMPEI for spectral alignment-based modified peptide identification, this open-source algorithm is designed for the discovery of functional protein and peptide signaling modifications, without prior knowledge of their identities. Using synthetic standards and controlled chemical labeling experiments, we demonstrate its high specificity and sensitivity for the discovery of substoichiometric protein modifications in complex cellular extracts. SAMPEI mapping of mouse macrophage differentiation revealed diverse post-translational protein modifications, including distinct forms of cysteine itaconatylation. SAMPEI's robust parametrization and versatility are expected to facilitate the discovery of biological modifications of diverse macromolecules. SAMPEI is implemented as a Python package and is available open-source from BioConda and GitHub (https://github.com/FenyoLab/SAMPEI).
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Affiliation(s)
- Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10021, United States
| | - Zhi Li
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, United States
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, New York 10016, United States
| | - Danmeng Luo
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10021, United States
| | - Mark Grivainis
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, United States
| | - Andrew M Intlekofer
- Human Oncology & Pathogenesis Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, United States
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, United States
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, New York 10016, United States
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10021, United States
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, and Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, New York, New York 10021, United States
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12
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Takao S, Forbes L, Uni M, Cheng S, Pineda JMB, Tarumoto Y, Cifani P, Minuesa G, Chen C, Kharas MG, Bradley RK, Vakoc CR, Koche RP, Kentsis A. Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemia. eLife 2021; 10:65905. [PMID: 33527899 PMCID: PMC7886351 DOI: 10.7554/elife.65905] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/01/2021] [Indexed: 12/17/2022] Open
Abstract
Dysregulated gene expression contributes to most prevalent features in human cancers. Here, we show that most subtypes of acute myeloid leukemia (AML) depend on the aberrant assembly of MYB transcriptional co-activator complex. By rapid and selective peptidomimetic interference with the binding of CBP/P300 to MYB, but not CREB or MLL1, we find that the leukemic functions of MYB are mediated by CBP/P300 co-activation of a distinct set of transcription factor complexes. These MYB complexes assemble aberrantly with LYL1, E2A, C/EBP family members, LMO2, and SATB1. They are organized convergently in genetically diverse subtypes of AML and are at least in part associated with inappropriate transcription factor co-expression. Peptidomimetic remodeling of oncogenic MYB complexes is accompanied by specific proteolysis and dynamic redistribution of CBP/P300 with alternative transcription factors such as RUNX1 to induce myeloid differentiation and apoptosis. Thus, aberrant assembly and sequestration of MYB:CBP/P300 complexes provide a unifying mechanism of oncogenic gene expression in AML. This work establishes a compelling strategy for their pharmacologic reprogramming and therapeutic targeting for diverse leukemias and possibly other human cancers caused by dysregulated gene control.
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Affiliation(s)
- Sumiko Takao
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Lauren Forbes
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, United States.,Departments of Pharmacology and Physiology & Biophysics, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
| | - Masahiro Uni
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Shuyuan Cheng
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, United States.,Departments of Pharmacology and Physiology & Biophysics, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
| | - Jose Mario Bello Pineda
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Medical Scientist Training Program, University of Washington, Seattle, United States.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Genome Sciences, University of Washington, Seattle, United States
| | - Yusuke Tarumoto
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States.,Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States
| | - Gerard Minuesa
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States
| | - Celine Chen
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States
| | - Michael G Kharas
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Departments of Pharmacology and Physiology & Biophysics, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Genome Sciences, University of Washington, Seattle, United States
| | | | - Richard P Koche
- Center for Epigenetics Research, Sloan Kettering Institute, New York, United States
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, United States.,Departments of Pharmacology and Physiology & Biophysics, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
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13
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Ortiz MV, Ahmed S, Burns M, Henssen AG, Hollmann TJ, MacArthur I, Gunasekera S, Gaewsky L, Bradwin G, Ryan J, Letai A, He Y, Naranjo A, Chi YY, LaQuaglia M, Heaton T, Cifani P, Dome JS, Gadd S, Perlman E, Mullen E, Steen H, Kentsis A. Prohibitin is a prognostic marker and therapeutic target to block chemotherapy resistance in Wilms' tumor. JCI Insight 2019; 4:127098. [PMID: 31391345 DOI: 10.1172/jci.insight.127098] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/09/2019] [Indexed: 01/05/2023] Open
Abstract
Wilms' tumor is the most common type of childhood kidney cancer. To improve risk stratification and identify novel therapeutic targets for patients with Wilms' tumor, we used high-resolution mass spectrometry proteomics to identify urine tumor markers associated with Wilms' tumor relapse. We determined the urine proteomes at diagnosis of 49 patients with Wilms' tumor, non-Wilms' tumor renal tumors, and age-matched controls, leading to the quantitation of 6520 urine proteins. Supervised analysis revealed specific urine markers of renal rhabdoid tumors, kidney clear cell sarcomas, renal cell carcinomas as well as those detected in patients with cured and relapsed Wilms' tumor. In particular, urine prohibitin was significantly elevated at diagnosis in patients with relapsed as compared with cured Wilms' tumor. In a validation cohort of 139 patients, a specific urine prohibitin ELISA demonstrated that prohibitin concentrations greater than 998 ng/mL at diagnosis were significantly associated with ultimate Wilms' tumor relapse. Immunohistochemical analysis revealed that prohibitin was highly expressed in primary Wilms' tumor specimens and associated with disease stage. Using functional genetic experiments, we found that prohibitin was required for the growth and survival of Wilms' tumor cells. Overexpression of prohibitin was sufficient to block intrinsic mitochondrial apoptosis and to cause resistance to diverse chemotherapy drugs, at least in part by dysregulating factors that control apoptotic cytochrome c release from mitochondrial cristae. Thus, urine prohibitin may improve therapy stratification, noninvasive monitoring of treatment response, and early disease detection. In addition, therapeutic targeting of chemotherapy resistance induced by prohibitin dysregulation may offer improved therapies for patients with Wilms' and other relapsed or refractory tumors.
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Affiliation(s)
- Michael V Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Saima Ahmed
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Melissa Burns
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Anton G Henssen
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Travis J Hollmann
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ian MacArthur
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Shehana Gunasekera
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lyvia Gaewsky
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Gary Bradwin
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jeremy Ryan
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Anthony Letai
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ying He
- Children's Oncology Group Statistics and Data Center, Department of Biostatistics, University of Florida, Gainesville, Florida, USA
| | - Arlene Naranjo
- Children's Oncology Group Statistics and Data Center, Department of Biostatistics, University of Florida, Gainesville, Florida, USA
| | - Yueh-Yun Chi
- Children's Oncology Group Statistics and Data Center, Department of Biostatistics, University of Florida, Gainesville, Florida, USA
| | - Michael LaQuaglia
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Todd Heaton
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jeffrey S Dome
- Center for Cancer and Blood Disorders, Children's National Health System, Washington, DC, USA
| | - Samantha Gadd
- Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Elizabeth Perlman
- Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | | | - Hanno Steen
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Alex Kentsis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Medical College, Cornell University, New York, New York, USA
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14
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Antao NV, Marcet-Ortega M, Cifani P, Kentsis A, Foley EA. A Cancer-Associated Missense Mutation in PP2A-Aα Increases Centrosome Clustering during Mitosis. iScience 2019; 19:74-82. [PMID: 31357169 PMCID: PMC6664223 DOI: 10.1016/j.isci.2019.07.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/27/2019] [Accepted: 07/12/2019] [Indexed: 12/21/2022] Open
Abstract
Whole-genome doubling (WGD) is common early in tumorigenesis. WGD doubles ploidy and centrosome number. In the ensuing mitoses, excess centrosomes form a multipolar spindle, resulting in a lethal multipolar cell division. To survive, cells must cluster centrosomes to allow bipolar cell division. Cancer cells are often more proficient at centrosome clustering than untransformed cells, but the mechanism behind increased clustering ability is not well understood. Heterozygous missense mutations in PPP2R1A, which encodes the alpha isoform of the "scaffolding" subunit of PP2A (PP2A-Aα), positively correlate with WGD. We introduced a heterozygous hotspot mutation, P179R, into PPP2R1A in human RPE-1 cells. PP2A-AαP179R decreases PP2A assembly and intracellular targeting in mitosis. Strikingly, PP2A-AαP179R enhances centrosome clustering when centrosome number is increased either by cytokinesis failure or centrosome amplification, likely through PP2A-Aα loss of function. Thus cancer-associated mutations in PP2A-Aα may increase cellular fitness after WGD by enhancing centrosome clustering.
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Affiliation(s)
- Noelle V Antao
- Program in Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology, Weill Cornell Medicine Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA; Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marina Marcet-Ortega
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Paolo Cifani
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Emily A Foley
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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15
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Sher F, Hossain M, Seruggia D, Schoonenberg VAC, Yao Q, Cifani P, Dassama LMK, Cole MA, Ren C, Vinjamur DS, Macias-Trevino C, Luk K, McGuckin C, Schupp PG, Canver MC, Kurita R, Nakamura Y, Fujiwara Y, Wolfe SA, Pinello L, Maeda T, Kentsis A, Orkin SH, Bauer DE. Rational targeting of a NuRD subcomplex guided by comprehensive in situ mutagenesis. Nat Genet 2019; 51:1149-1159. [PMID: 31253978 PMCID: PMC6650275 DOI: 10.1038/s41588-019-0453-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 05/21/2019] [Indexed: 12/26/2022]
Abstract
Developmental silencing of fetal globins serves as both a paradigm of spatiotemporal gene regulation and an opportunity for therapeutic intervention of β-hemoglobinopathy. The nucleosome remodeling and deacetylase (NuRD) chromatin complex participates in γ-globin repression. We used pooled CRISPR screening to disrupt NuRD protein coding sequences comprehensively in human adult erythroid precursors. Essential for fetal hemoglobin (HbF) control is a non-redundant subcomplex of NuRD protein family paralogs, whose composition we corroborated by affinity chromatography and proximity labeling mass spectrometry proteomics. Mapping top functional guide RNAs identified key protein interfaces where in-frame alleles resulted in loss-of-function due to destabilization or altered function of subunits. We ascertained mutations of CHD4 that dissociate its requirement for cell fitness from HbF repression in both primary human erythroid precursors and transgenic mice. Finally we demonstrated that sequestering CHD4 from NuRD phenocopied these mutations. These results indicate a generalizable approach to discover protein complex features amenable to rational biochemical targeting.
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Affiliation(s)
- Falak Sher
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
- Center for Translational & Computational Neuroimmunology, Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University Medical Center, Columbia University, New York, NY, USA
| | - Mir Hossain
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Davide Seruggia
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Vivien A C Schoonenberg
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
- Faculty of Science, Radboud University, Nijmegen, the Netherlands
| | - Qiuming Yao
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
- Molecular Pathology Unit & Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laura M K Dassama
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Mitchel A Cole
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Chunyan Ren
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Divya S Vinjamur
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Claudio Macias-Trevino
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Connor McGuckin
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Patrick G Schupp
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Matthew C Canver
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yuko Fujiwara
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Luca Pinello
- Molecular Pathology Unit & Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Takahiro Maeda
- Center for Cellular and Molecular Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA.
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16
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Abstract
Recent development of mass spectrometer cleavable protein cross-linkers and algorithms for their spectral identification now permits large-scale cross-linking mass spectrometry (XL-MS). Here, we optimized the use of cleavable disuccinimidyl sulfoxide (DSSO) cross-linker for labeling native protein complexes in live human cells. We applied a generalized linear mixture model to calibrate cross-link peptide-spectra matching (CSM) scores to control the sensitivity and specificity of large-scale XL-MS. Using specific CSM score thresholds to control the false discovery rate, we found that higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD) can both be effective for large-scale XL-MS protein interaction mapping. We found that the coverage of protein-protein interaction maps is significantly improved through the use of multiple proteases. In addition, the use of focused sample-specific search databases can be used to improve the specificity of cross-linked peptide spectral matching. Application of this approach to human chromatin labeled in live cells recapitulated known and revealed new protein interactions of nucleosomes and other chromatin-associated complexes in situ. This optimized approach for mapping native protein interactions should be useful for a wide range of biological problems.
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Affiliation(s)
| | | | - Alex Kentsis
- Department of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Medical College , Cornell University , New York , New York 10065 , United States
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17
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Griswold AR, Cifani P, Rao SD, Axelrod AJ, Miele MM, Hendrickson RC, Kentsis A, Bachovchin DA. A Chemical Strategy for Protease Substrate Profiling. Cell Chem Biol 2019; 26:901-907.e6. [PMID: 31006619 DOI: 10.1016/j.chembiol.2019.03.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 02/14/2019] [Accepted: 03/12/2019] [Indexed: 02/06/2023]
Abstract
The dipeptidyl peptidases (DPPs) regulate hormones, cytokines, and neuropeptides by cleaving dipeptides after proline from their amino termini. Due to technical challenges, many DPP substrates remain unknown. Here, we introduce a simple method, termed CHOPS (chemical enrichment of protease substrates), for the discovery of protease substrates. CHOPS exploits a 2-pyridinecarboxaldehyde (2PCA)-biotin probe, which selectively biotinylates protein N-termini except those with proline in the second position. CHOPS can, in theory, discover substrates for any protease, but is particularly well suited to discover canonical DPP substrates, as cleaved but not intact DPP substrates can be identified by gel electrophoresis or mass spectrometry. Using CHOPS, we show that DPP8 and DPP9, enzymes that control the Nlrp1 inflammasome through an unknown mechanism, do not directly cleave Nlrp1. We further show that DPP9 robustly cleaves short peptides but not full-length proteins. More generally, this work delineates a practical technology for identifying protease substrates, which we anticipate will complement available "N-terminomic" approaches.
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Affiliation(s)
- Andrew R Griswold
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA; Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Paolo Cifani
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sahana D Rao
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Abram J Axelrod
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Matthew M Miele
- Proteomics Core Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ronald C Hendrickson
- Proteomics Core Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alex Kentsis
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center and Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Daniel A Bachovchin
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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18
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Hoshii T, Cifani P, Feng Z, Huang CH, Koche R, Chen CW, Delaney CD, Lowe SW, Kentsis A, Armstrong SA. A Non-catalytic Function of SETD1A Regulates Cyclin K and the DNA Damage Response. Cell 2019; 172:1007-1021.e17. [PMID: 29474905 DOI: 10.1016/j.cell.2018.01.032] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 10/30/2017] [Accepted: 01/24/2018] [Indexed: 12/22/2022]
Abstract
MLL/SET methyltransferases catalyze methylation of histone 3 lysine 4 and play critical roles in development and cancer. We assessed MLL/SET proteins and found that SETD1A is required for survival of acute myeloid leukemia (AML) cells. Mutagenesis studies and CRISPR-Cas9 domain screening show the enzymatic SET domain is not necessary for AML cell survival but that a newly identified region termed the "FLOS" (functional location on SETD1A) domain is indispensable. FLOS disruption suppresses DNA damage response genes and induces p53-dependent apoptosis. The FLOS domain acts as a cyclin-K-binding site that is required for chromosomal recruitment of cyclin K and for DNA-repair-associated gene expression in S phase. These data identify a connection between the chromatin regulator SETD1A and the DNA damage response that is independent of histone methylation and suggests that targeting SETD1A and cyclin K complexes may represent a therapeutic opportunity for AML and, potentially, for other cancers.
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Affiliation(s)
- Takayuki Hoshii
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02210, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Paolo Cifani
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Zhaohui Feng
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02210, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chun-Hao Huang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Richard Koche
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02210, USA
| | - Chun-Wei Chen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02210, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher D Delaney
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02210, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02210, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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19
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Pronier E, Cifani P, Merlinsky TR, Berman KB, Somasundara AVH, Rampal RK, LaCava J, Wei KE, Pastore F, Maag JL, Park J, Koche R, Kentsis A, Levine RL. Targeting the CALR interactome in myeloproliferative neoplasms. JCI Insight 2018; 3:122703. [PMID: 30429377 DOI: 10.1172/jci.insight.122703] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 09/19/2018] [Indexed: 02/06/2023] Open
Abstract
Mutations in the ER chaperone calreticulin (CALR) are common in myeloproliferative neoplasm (MPN) patients, activate the thrombopoietin receptor (MPL), and mediate constitutive JAK/STAT signaling. The mechanisms by which CALR mutations cause myeloid transformation are incompletely defined. We used mass spectrometry proteomics to identify CALR-mutant interacting proteins. Mutant CALR caused mislocalization of binding partners and increased recruitment of FLI1, ERP57, and CALR to the MPL promoter to enhance transcription. Consistent with a critical role for CALR-mediated JAK/STAT activation, we confirmed the efficacy of JAK2 inhibition on CALR-mutant cells in vitro and in vivo. Due to the altered interactome induced by CALR mutations, we hypothesized that CALR-mutant MPNs may be vulnerable to disruption of aberrant CALR protein complexes. A synthetic peptide designed to competitively inhibit the carboxy terminal of CALR specifically abrogated MPL/JAK/STAT signaling in cell lines and primary samples and improved the efficacy of JAK kinase inhibitors. These findings reveal what to our knowledge is a novel potential therapeutic approach for patients with CALR-mutant MPN.
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Affiliation(s)
- Elodie Pronier
- Human Oncology and Pathogenesis Program.,Center for Epigenetics Research, and
| | - Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, New York, USA
| | - Tiffany R Merlinsky
- Human Oncology and Pathogenesis Program.,Center for Epigenetics Research, and
| | | | | | - Raajit K Rampal
- Human Oncology and Pathogenesis Program.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Karen E Wei
- Human Oncology and Pathogenesis Program.,Center for Epigenetics Research, and
| | - Friederike Pastore
- Human Oncology and Pathogenesis Program.,Center for Epigenetics Research, and
| | | | - Jane Park
- Center for Epigenetics Research, and
| | | | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, New York, USA.,Department of Pediatrics, Weill Cornell Medical College of Cornell University and Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ross L Levine
- Human Oncology and Pathogenesis Program.,Center for Epigenetics Research, and.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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20
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Cifani P, Dhabaria A, Chen Z, Yoshimi A, Kawaler E, Abdel-Wahab O, Poirier JT, Kentsis A. ProteomeGenerator: A Framework for Comprehensive Proteomics Based on de Novo Transcriptome Assembly and High-Accuracy Peptide Mass Spectral Matching. J Proteome Res 2018; 17:3681-3692. [PMID: 30295032 DOI: 10.1021/acs.jproteome.8b00295] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modern mass spectrometry now permits genome-scale and quantitative measurements of biological proteomes. However, analysis of specific specimens is currently hindered by the incomplete representation of biological variability of protein sequences in canonical reference proteomes and the technical demands for their construction. Here, we report ProteomeGenerator, a framework for de novo and reference-assisted proteogenomic database construction and analysis based on sample-specific transcriptome sequencing and high-accuracy mass spectrometry proteomics. This enables the assembly of proteomes encoded by actively transcribed genes, including sample-specific protein isoforms resulting from non-canonical mRNA transcription, splicing, or editing. To improve the accuracy of protein isoform identification in non-canonical proteomes, ProteomeGenerator relies on statistical target-decoy database matching calibrated using sample-specific controls. Its current implementation includes automatic integration with MaxQuant mass spectrometry proteomics algorithms. We applied this method for the proteogenomic analysis of splicing factor SRSF2 mutant leukemia cells, demonstrating high-confidence identification of non-canonical protein isoforms arising from alternative transcriptional start sites, intron retention, and cryptic exon splicing as well as improved accuracy of genome-scale proteome discovery. Additionally, we report proteogenomic performance metrics for current state-of-the-art implementations of SEQUEST HT, MaxQuant, Byonic, and PEAKS mass spectral analysis algorithms. Finally, ProteomeGenerator is implemented as a Snakemake workflow within a Singularity container for one-step installation in diverse computing environments, thereby enabling open, scalable, and facile discovery of sample-specific, non-canonical, and neomorphic biological proteomes.
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Affiliation(s)
- Paolo Cifani
- Molecular Pharmacology Program , Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York City , New York 10065 , United States
| | - Avantika Dhabaria
- Molecular Pharmacology Program , Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York City , New York 10065 , United States
| | - Zining Chen
- Molecular Pharmacology Program , Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York City , New York 10065 , United States
| | | | | | - Omar Abdel-Wahab
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology , New York University Langone Health , New York City , New York 10016 , United States
| | - John T Poirier
- Molecular Pharmacology Program , Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York City , New York 10065 , United States.,Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology , New York University Langone Health , New York City , New York 10016 , United States
| | - Alex Kentsis
- Molecular Pharmacology Program , Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York City , New York 10065 , United States.,Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Medical College , Cornell University , New York , New York 10065 , United States
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21
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Cifani P, Dogan A, Solit DB, Kentsis A. Abstract 5650: Functional proteomics for precise cancer diagnosis and therapy using the MSK Quantitative Cancer Proteomics Atlas. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The advent of molecular biology and molecular profiling in clinical medicine has transformed our understanding of the molecular basis of human cancer. As a result, we are increasingly improving the classification of human tumors based on their specific genetic and molecular mechanisms of pathogenesis. However, currently only a small number of mutant alleles guide treatment decisions, while most observed mutations remain of unknown pathologic and clinical significance. In addition, even for recently approved drugs, such as those targeting activated kinase signaling, clinical efficacy is highly varied, with no currently satisfactory means to identify molecular markers of response and resistance. To address this need, and broadly enable transformative future advances in precision oncology and patient outcomes, we have now developed the Quantitative Cancer Proteomics Atlas (QCPA). This technology permits highly multiplexed, quantitative analysis of the expression and biochemical activity of hundreds of proteins, covering most recurrently mutated and known pathogenic pathways in cancer cells, and designed to be applied to clinically accessible patient specimens. QCPA enables concomitant measurement of cellular concentration and stoichiometry of regulatory post-translational modification of key proteins mediating aberrant survival and proliferation. The activation status of these proteins is then used as a proxy to infer regulatory status of relevant biochemical pathways. These sentinel proteins include 467 known effectors of kinase regulatory signaling, apoptosis, stress response, and proliferation. QCPA measurements can be made using conventional parallel reaction monitoring mass spectrometry, or using an improved method termed accumulated ion monitoring (Cifani & Kentsis 2017). We established analytical metrics of QCPA assays in cancer cell lines, and demonstrated sensitivity and quantification accuracy amenable to measure endogenous chemically modified proteins from microgram specimens. We then demonstrated the ability of QCPA profiling to detect differential biochemical activities in response to defined stimuli in vitro. Next, we deployed QCPA profiling to reveal functional differences between primary human acute myeloid leukemia specimens and CD34+ myeloid progenitors, measuring specific activation of biochemical pathways in cancer cells. Finally, we tested the clinical utility of functional proteomic profiling by determining molecular markers of response and resistance to ERK pathway inhibitors in patient specimens. Thus, QCPA functional proteomic profiling provides a tool to achieve precise diagnosis and rational targeted cancer therapies.
Citation Format: Paolo Cifani, Ahmet Dogan, David B. Solit, Alex Kentsis. Functional proteomics for precise cancer diagnosis and therapy using the MSK Quantitative Cancer Proteomics Atlas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5650.
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Affiliation(s)
- Paolo Cifani
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Dogan
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Alex Kentsis
- Memorial Sloan Kettering Cancer Center, New York, NY
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22
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Brown FC, Still E, Koche RP, Yim CY, Takao S, Cifani P, Reed C, Gunasekera S, Ficarro SB, Romanienko P, Mark W, McCarthy C, de Stanchina E, Gonen M, Seshan V, Bhola P, O'Donnell C, Spitzer B, Stutzke C, Lavallée VP, Hébert J, Krivtsov AV, Melnick A, Paietta EM, Tallman MS, Letai A, Sauvageau G, Pouliot G, Levine R, Marto JA, Armstrong SA, Kentsis A. MEF2C Phosphorylation Is Required for Chemotherapy Resistance in Acute Myeloid Leukemia. Cancer Discov 2018; 8:478-497. [PMID: 29431698 PMCID: PMC5882571 DOI: 10.1158/2159-8290.cd-17-1271] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/22/2018] [Accepted: 01/30/2018] [Indexed: 11/16/2022]
Abstract
In acute myeloid leukemia (AML), chemotherapy resistance remains prevalent and poorly understood. Using functional proteomics of patient AML specimens, we identified MEF2C S222 phosphorylation as a specific marker of primary chemoresistance. We found that Mef2cS222A/S222A knock-in mutant mice engineered to block MEF2C phosphorylation exhibited normal hematopoiesis, but were resistant to leukemogenesis induced by MLL-AF9 MEF2C phosphorylation was required for leukemia stem cell maintenance and induced by MARK kinases in cells. Treatment with the selective MARK/SIK inhibitor MRT199665 caused apoptosis and conferred chemosensitivity in MEF2C-activated human AML cell lines and primary patient specimens, but not those lacking MEF2C phosphorylation. These findings identify kinase-dependent dysregulation of transcription factor control as a determinant of therapy response in AML, with immediate potential for improved diagnosis and therapy for this disease.Significance: Functional proteomics identifies phosphorylation of MEF2C in the majority of primary chemotherapy-resistant AML. Kinase-dependent dysregulation of this transcription factor confers susceptibility to MARK/SIK kinase inhibition in preclinical models, substantiating its clinical investigation for improved diagnosis and therapy of AML. Cancer Discov; 8(4); 478-97. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 371.
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MESH Headings
- Animals
- Antineoplastic Agents/therapeutic use
- Cell Line
- Drug Resistance, Neoplasm
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- MEF2 Transcription Factors/chemistry
- MEF2 Transcription Factors/metabolism
- Mice
- Mice, Transgenic
- Phosphorylation
- Protein Processing, Post-Translational
- Proteomics
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Affiliation(s)
- Fiona C Brown
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eric Still
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard P Koche
- Center for Epigenetics Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christina Y Yim
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumiko Takao
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Casie Reed
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shehana Gunasekera
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Scott B Ficarro
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Peter Romanienko
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Willie Mark
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Craig McCarthy
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mithat Gonen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Venkatraman Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Patrick Bhola
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Conor O'Donnell
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Barbara Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Vincent-Philippe Lavallée
- The Leucegene Project at Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
- Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
| | - Josée Hébert
- The Leucegene Project at Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
- Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
- Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Andrei V Krivtsov
- Center for Epigenetics Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ari Melnick
- Departments of Pediatrics, Pharmacology, and Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, New York
| | - Elisabeth M Paietta
- Montefiore Medical Center-North Division, Albert Einstein College of Medicine, Bronx, New York, New York
| | - Martin S Tallman
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Guy Sauvageau
- The Leucegene Project at Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
- Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
- Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Gayle Pouliot
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ross Levine
- Center for Epigenetics Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center and Weill Medical College of Cornell University, New York, New York
| | - Jarrod A Marto
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Scott A Armstrong
- Center for Epigenetics Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York.
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Departments of Pediatrics, Pharmacology, and Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, New York
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23
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Cifani P, Kentsis A. High Sensitivity Quantitative Proteomics Using Automated Multidimensional Nano-flow Chromatography and Accumulated Ion Monitoring on Quadrupole-Orbitrap-Linear Ion Trap Mass Spectrometer. Mol Cell Proteomics 2017; 16:2006-2016. [PMID: 28821601 DOI: 10.1074/mcp.ra117.000023] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Indexed: 01/18/2023] Open
Abstract
Quantitative proteomics using high-resolution and accuracy mass spectrometry promises to transform our understanding of biological systems and disease. Recent development of parallel reaction monitoring (PRM) using hybrid instruments substantially improved the specificity of targeted mass spectrometry. Combined with high-efficiency ion trapping, this approach also provided significant improvements in sensitivity. Here, we investigated the effects of ion isolation and accumulation on the sensitivity and quantitative accuracy of targeted proteomics using the recently developed hybrid quadrupole-Orbitrap-linear ion trap mass spectrometer. We leveraged ultrahigh efficiency nano-electrospray ionization under optimized conditions to achieve yoctomolar sensitivity with more than seven orders of linear quantitative accuracy. To enable sensitive and specific targeted mass spectrometry, we implemented an automated, two-dimensional (2D) ion exchange-reversed phase nanoscale chromatography system. We found that automated 2D chromatography improved the sensitivity and accuracy of both PRM and an intact precursor scanning mass spectrometry method, termed accumulated ion monitoring (AIM), by more than 100-fold. Combined with automated 2D nano-scale chromatography, AIM achieved subattomolar limits of detection of endogenous proteins in complex biological proteomes. This allowed quantitation of absolute abundance of the human transcription factor MEF2C at ∼100 molecules/cell, and determination of its phosphorylation stoichiometry from as little as 1 μg of extracts isolated from 10,000 human cells. The combination of automated multidimensional nano-scale chromatography and targeted mass spectrometry should enable ultrasensitive high-accuracy quantitative proteomics of complex biological systems and diseases.
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Affiliation(s)
- Paolo Cifani
- From the ‡Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Alex Kentsis
- From the ‡Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065; .,§Department of Pediatrics, Weill Medical College of Cornell University and Memorial Sloan Kettering Cancer Center, New York, NY 10065
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24
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Ortiz MV, Burns M, Eisenberg A, Ahmed S, Gaewsky L, Bradwin G, Cifani P, Henssen A, Macarthur I, LaQuaglia M, Letai A, Naranjo A, Gadd S, Chi YY, Dome J, Perlman E, Mullen E, Steen H, Kentsis A. Abstract 708: Prohibitin is a prognostic marker of treatment failure and therapeutic target to block chemotherapy resistance in Wilms tumor. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Wilms tumor (WT) is the most common kidney tumor of children. Over the last three decades, clinical trials employing multi-modality therapies have resulted in overall survival of greater than 90% for patients with low-risk disease. In spite of these advances, treatment of patients with advanced, anaplastic, and relapsed Wilms tumors remains challenging, with substantial rates of treatment failure and death. To improve risk stratification and identify novel therapeutic targets, we used high-accuracy mass spectrometry urine proteomics to identify urine tumors markers associated with relapsed WT and non-WT renal tumors. We measured urine proteomes at diagnosis of 54 patients with renal WT, clear cell sarcoma, rhabdoid tumor, and age-matched controls, leading to the quantitation of 6,519 urine proteins. In particular, we identified specific urine WT markers, including those that were enriched in patients with relapsed WT, such as mitochondrial regulators prohibitin and DAD1, β-catenin antagonist DACT2, and DNA repair factor SUN1. Using a specific enzyme-linked immunosorbent assay (ELISA) developed to measure urine prohibitin in an independent cohort of 139 WT and control samples, we found that urine prohibitin concentrations over 1000 ng/mL were significantly associated with the risk of disease relapse, with an odds ratio of relapse of 153 and receiver operating characteristic area under the curve of 0.77 (95% confidence interval of 0.64-0.99). Immunohistochemical tumor analysis revealed that prohibitin was highly expressed in primary Wilms tumor specimens. Importantly, using loss- and gain-of-function genetic experiments, we found that prohibitin was required for the growth and survival of Wilms tumor cells, and its overexpression conferred concomitant resistance to vincristine, doxorubicin and actinomycin D. Consistent with prohibitin’s functions in mitochondria, we are using BH3 profiling to elucidate specific intrinsic apoptotic dependencies in distinct subsets of refractory Wilms tumors, as a prelude to rational combination blockade of chemotherapy resistance, such as blockade of BCL2 dependence using venetoclax. In all, the use of urine prohibitin measurements may improve initial therapy stratification, and enable monitoring of response to therapy and early detection of relapse. In addition, therapeutic targeting of chemotherapy resistance induced by prohibitin overexpression may offer improved therapies for patients with relapsed or refractory Wilms tumors.
Citation Format: Michael Vincent Ortiz, Melissa Burns, Amy Eisenberg, Saima Ahmed, Lyvia Gaewsky, Gary Bradwin, Paolo Cifani, Anton Henssen, Ian Macarthur, Michael LaQuaglia, Anthony Letai, Arlene Naranjo, Samantha Gadd, Yueh-Yun Chi, Jeffrey Dome, Elizabeth Perlman, Elizabeth Mullen, Hanno Steen, Alex Kentsis. Prohibitin is a prognostic marker of treatment failure and therapeutic target to block chemotherapy resistance in Wilms tumor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 708. doi:10.1158/1538-7445.AM2017-708
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25
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Abstract
Background High-accuracy mass spectrometry enables near comprehensive quantification of the components of the cellular proteomes, increasingly including their chemically modified variants. Likewise, large-scale libraries of quantified synthetic peptides are becoming available, enabling absolute quantification of chemically modified proteoforms, and therefore systems-level analyses of changes of their absolute abundance and stoichiometry. Existing computational methods provide advanced tools for mass spectral analysis and statistical inference, but lack integrated functions for quantitative analysis of post-translationally modified proteins and their modification stoichiometry. Results Here, we develop ProteoModlR, a program for quantitative analysis of abundance and stoichiometry of post-translational chemical modifications across temporal and steady-state biological states. While ProteoModlR is intended for the analysis of experiments using isotopically labeled reference peptides for absolute quantitation, it also supports the analysis of labeled and label-free data, acquired in both data-dependent and data-independent modes for relative quantitation. Moreover, ProteoModlR enables functional analysis of sparsely sampled quantitative mass spectrometry experiments by inferring the missing values from the available measurements, without imputation. The implemented architecture includes parsing and normalization functions to control for common sources of technical variation. Finally, ProteoModlR’s modular design and interchangeable format are optimally suited for integration with existing computational proteomics tools, thereby facilitating comprehensive quantitative analysis of cellular signaling. Conclusions ProteoModlR and its documentation are available for download at http://github.com/kentsisresearchgroup/ProteoModlR as a stand-alone R package. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1563-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mojdeh Shakiba
- Physiology, Biophysics and Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Sagar Chhangawala
- Physiology, Biophysics and Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Physiology, Biophysics and Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA. .,Department of Pediatrics and Memorial Sloan Kettering Cancer Center, Weill Medical College of Cornell University, New York, NY, USA.
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26
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Cifani P, Kentsis A. Towards comprehensive and quantitative proteomics for diagnosis and therapy of human disease. Proteomics 2016; 17. [PMID: 27775219 DOI: 10.1002/pmic.201600079] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/06/2016] [Accepted: 10/21/2016] [Indexed: 12/21/2022]
Abstract
Given superior analytical features, MS proteomics is well suited for the basic investigation and clinical diagnosis of human disease. Modern MS enables detailed functional characterization of the pathogenic biochemical processes, as achieved by accurate and comprehensive quantification of proteins and their regulatory chemical modifications. Here, we describe how high-accuracy MS in combination with high-resolution chromatographic separations can be leveraged to meet these analytical requirements in a mechanism-focused manner. We review the quantification methods capable of producing accurate measurements of protein abundance and posttranslational modification stoichiometries. We then discuss how experimental design and chromatographic resolution can be leveraged to achieve comprehensive functional characterization of biochemical processes in complex biological proteomes. Finally, we describe current approaches for quantitative analysis of a common functional protein modification: reversible phosphorylation. In all, current instrumentation and methods of high-resolution chromatography and MS proteomics are poised for immediate translation into improved diagnostic strategies for pediatric and adult diseases.
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Affiliation(s)
- Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pediatrics, Weill Cornell College of Cornell University and Memorial Sloan Kettering Cancer Center, New York, NY, USA
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27
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Brown FC, Cifani P, Drill E, He J, Still E, Zhong S, Balasubramanian S, Pavlick D, Yilmazel B, Knapp KM, Alonzo TA, Meshinchi S, Stone RM, Kornblau SM, Marcucci G, Gamis AS, Byrd JC, Gonen M, Levine RL, Kentsis A. Genomics of primary chemoresistance and remission induction failure in paediatric and adult acute myeloid leukaemia. Br J Haematol 2016; 176:86-91. [PMID: 27766616 DOI: 10.1111/bjh.14413] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/31/2016] [Indexed: 01/17/2023]
Abstract
Cure rates of children and adults with acute myeloid leukaemia (AML) remain unsatisfactory partly due to chemotherapy resistance. We investigated the genetic basis of AML in 107 primary cases by sequencing 670 genes mutated in haematological malignancies. SETBP1, ASXL1 and RELN mutations were significantly associated with primary chemoresistance. We identified genomic alterations not previously described in AML, together with distinct genes that were significantly overexpressed in therapy-resistant AML. Defined gene mutations were sufficient to explain primary induction failure in only a minority of cases. Thus, additional genetic or molecular mechanisms must cause primary chemoresistance in paediatric and adult AML.
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Affiliation(s)
- Fiona C Brown
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Esther Drill
- Department of Biostatistics and Epidemiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jie He
- Foundation Medicine, Cambridge, MA, USA
| | - Eric Still
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | | | - Kristina M Knapp
- Leukemia Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Todd A Alonzo
- Children's Oncology Group, Monrovia, CA, USA.,Department of Biostatistics, University of Southern California, Los Angeles, CA, USA
| | - Soheil Meshinchi
- Children's Oncology Group, Monrovia, CA, USA.,Fred Hutchinson Cancer Research Center and the University of Washington School of Medicine, Seattle, WA, USA
| | - Richard M Stone
- Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas and MD Anderson Cancer Center, Houston, TX, USA
| | - Guido Marcucci
- Gehr Family Leukemia Center, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Alan S Gamis
- Children's Oncology Group, Monrovia, CA, USA.,Division of Hematology-Oncology, Children's Mercy Hospitals and Clinics, Kansas City, MO, USA
| | - John C Byrd
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Mithat Gonen
- Department of Biostatistics and Epidemiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center and Weill Medical College of Cornell University, New York, NY, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pediatrics, Memorial Sloan Kettering Cancer Center and Weill Medical College of Cornell University, New York, NY, USA
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28
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Waldemarson S, Kurbasic E, Krogh M, Cifani P, Berggård T, Borg Å, James P. Proteomic analysis of breast tumors confirms the mRNA intrinsic molecular subtypes using different classifiers: a large-scale analysis of fresh frozen tissue samples. Breast Cancer Res 2016; 18:69. [PMID: 27357824 PMCID: PMC4928264 DOI: 10.1186/s13058-016-0732-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 06/19/2016] [Indexed: 12/11/2022] Open
Abstract
Background Breast cancer is a complex and heterogeneous disease that is usually characterized by histological parameters such as tumor size, cellular arrangements/rearrangments, necrosis, nuclear grade and the mitotic index, leading to a set of around twenty subtypes. Together with clinical markers such as hormone receptor status, this classification has considerable prognostic value but there is a large variation in patient response to therapy. Gene expression profiling has provided molecular profiles characteristic of distinct subtypes of breast cancer that reflect the divergent cellular origins and degree of progression. Methods Here we present a large-scale proteomic and transcriptomic profiling study of 477 sporadic and hereditary breast cancer tumors with matching mRNA expression analysis. Unsupervised hierarchal clustering was performed and selected proteins from large-scale tandem mass spectrometry (MS/MS) analysis were transferred into a highly multiplexed targeted selected reaction monitoring assay to classify tumors using a hierarchal cluster and support vector machine with leave one out cross-validation. Results The subgroups formed upon unsupervised clustering agree very well with groups found at transcriptional level; however, the classifiers (genes or their respective protein products) differ almost entirely between the two datasets. In-depth analysis shows clear differences in pathways unique to each type, which may lie behind their different clinical outcomes. Targeted mass spectrometry analysis and supervised clustering correlate very well with subgroups determined by RNA classification and show convincing agreement with clinical parameters. Conclusions This work demonstrates the merits of protein expression profiling for breast cancer stratification. These findings have important implications for the use of genomics and expression analysis for the prediction of protein expression, such as receptor status and drug target expression. The highly multiplexed MS assay is easily implemented in standard clinical chemistry practice, allowing rapid and cheap characterization of tumor tissue suitable for directing the choice of treatment. Electronic supplementary material The online version of this article (doi:10.1186/s13058-016-0732-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sofia Waldemarson
- Department of Immunotechnology, Lund University, Medicon Village, 223 81, Lund, Sweden
| | - Emila Kurbasic
- Department of Immunotechnology, Lund University, Medicon Village, 223 81, Lund, Sweden
| | - Morten Krogh
- Amber Biosciences AB, Skrivarevägen 9, 226 57, Lund, Sweden
| | - Paolo Cifani
- Department of Immunotechnology, Lund University, Medicon Village, 223 81, Lund, Sweden
| | | | - Åke Borg
- Department of Oncology, Lund University, Medicon Village, 223 81, Lund, Sweden
| | - Peter James
- Department of Immunotechnology, Lund University, Medicon Village, 223 81, Lund, Sweden. .,Turku Centre for Biotechnology, Åbo Akademi University, University of Turku Biocity, Tykistokatu 6, 20520, Turku, Finland.
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29
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Skrbo N, Kirik U, Kristian A, Cifani P, Antberg L, Moestue SA, Engebraaten O, Mælandsmo GM, Andersen K, James P, Sørlie T. Abstract A36: Protein expression analysis of intratumor heterogeneity in a luminal-like breast cancer xenograft. Mol Cancer Res 2016. [DOI: 10.1158/1557-3125.advbc15-a36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Estrogen receptor is a key driver in breast cancer and is expressed in about 75% of breast tumors. ER positive tumors are susceptible to endocrine therapies; however, the major obstacle for curative treatment is recurrence due to resistance to anti-estrogens. Endocrine therapies may induce a selective pressure promoting growth of estrogen independent cell subclones. Our aim was to reveal molecular changes occurring in tumors in response to anti-estrogen treatment, and to identify subpopulations of cells able to withstand anti-estrogen treatment.
A luminal-like estrogen-dependent orthotopically growing xenograft model was treated with fulvestrant, or exposed to estrogen deprivation. The effect of ER-signaling inhibition was analyzed using quantitative mass spectrometry (MS) -based proteomic analysis and high resolution magic angle spinning magnetic resonance spectroscopy (HR MAS MRS). Cell surface marker expression (CD24 and SSEA-4) was monitored by flow cytometry, allowing detailed comparison of protein expression between intratumor cell subpopulations.
We found that both modes of anti-estrogen therapy restrained tumor growth and induced expression of enzymes involved in TCA cycle, oxidative phosphorylation and fatty acid beta-oxidation. This was accompanied by changes in levels of specific metabolites indicative of a possible reprogramming of cell metabolism and utilization of oxidative phosphorylation in preference to aerobic glycolysis (decrease in Warburg effect). Furthermore, anti-estrogen treatment seemed to have selective effects on intratumor cell subpopulations, specified by expression of the markers CD24 and SSEA-4. More specifically, highly tumorigenic CD24low/SSEA-4low (dbl. low) cells were eliminated and the seemingly more benign CD24high/SSEA-4high (dbl. high) cells were enriched in the residual tumor. When comparing the proteome in dbl. low verus dbl. high cells sorted from untreated tumors, metabolism was one of the most differentially enriched processes. Enzymes involved in glycolysis, TCA cycle, respiratory electron transport chain and fatty acid were more abundant in the dbl. high subpopulation.
These results suggest that cancer cells may reprogram their metabolism in response to anti-estrogen therapy to support a less estrogen-dependent phenotype. Moreover, subpopulations of cells with different metabolism may exist within the growing tumor, and these may respond differently to anti-estrogen treatment.
Citation Format: Nirma Skrbo, Ufuk Kirik, Alexandr Kristian, Paolo Cifani, Linn Antberg, Siver A. Moestue, Olav Engebraaten, Gunhild M. Mælandsmo, Kristin Andersen, Peter James, Therese Sørlie. Protein expression analysis of intratumor heterogeneity in a luminal-like breast cancer xenograft. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr A36.
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Affiliation(s)
| | - Ufuk Kirik
- 2CREATE Health, Lund University, Lund, Sweden,
| | | | | | | | - Siver A. Moestue
- 3Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | | | - Peter James
- 2CREATE Health, Lund University, Lund, Sweden,
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30
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Abstract
Recent developments in quantitative high-resolution mass spectrometry have led to significant improvements in the sensitivity and specificity of the biochemical analyses of cellular reactions, protein-protein interactions, and small-molecule-drug discovery. These approaches depend on cellular proteome extraction that preserves native protein activities. Here, we systematically analyzed mechanical methods of cell lysis and physical protein extraction to identify those that maximize the extraction of cellular proteins while minimizing their denaturation. Cells were mechanically disrupted using Potter-Elvehjem homogenization, probe- or adaptive-focused acoustic sonication, and were in the presence of various detergents, including polyoxyethylene ethers and esters, glycosides, and zwitterions. Using fluorescence spectroscopy, biochemical assays, and mass spectrometry proteomics, we identified the combination of adaptive focused acoustic (AFA) sonication in the presence of a binary poloxamer-based mixture of octyl-β-glucoside and Pluronic F-127 to maximize the depth and yield of the proteome extraction while maintaining native protein activity. This binary poloxamer extraction system allowed for native proteome extraction comparable in coverage to the proteomes extracted using denaturing SDS or guanidine-containing buffers, including the efficient extraction of all major cellular organelles. This high-efficiency cellular extraction system should prove useful for a variety of cell biochemical studies, including structural and functional proteomics.
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Affiliation(s)
- Avantika Dhabaria
- Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, New York, NY, USA
| | - Paolo Cifani
- Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, New York, NY, USA
| | - Casie Reed
- Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, New York, NY, USA
| | - Hanno Steen
- Boston Children’s Hospital, Harvard Medical School, Boston, MA
| | - Alex Kentsis
- Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, New York, NY, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center and Weill Medical College of Cornell University, New York, NY
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31
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Henssen A, Eisenberg A, Jiang E, Henaff E, Koche R, Burns M, Carson JR, Nanjangud G, Still E, Gandara J, Cifani P, Dhabaria A, Huang X, de Stanchina E, Mullen E, Steen H, Perlman E, Dome J, Antonescu C, Feschotte C, Mason CE, Kentsis A. Abstract 1103: Human tumorigenesis induced by endogenous DNA transposase. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent cancer genome surveys have revealed extremely low rates of coding gene mutations in distinct tumor subtypes, suggesting that alternative mechanisms must contribute to their pathogenesis. Transposons are mobile genetic elements that are found in all living organisms, including humans where they occupy nearly half of the genome. Their mobilization can cause structural rearrangements in normal and cancer cells. However, it remains unknown whether transposition is a cause of cellular transformation or merely a bystander effect of dysregulated gene expression. Here, we report that PGBD5, a recently characterized human gene related to the piggyBac transposase from the cabbage looper moth, is aberrantly expressed in rhabdoid tumors, medulloblastoma, acute leukemias, and some sarcomas and carcinomas. Ectopic expression of PGBD5 in non-transformed primary human cells is sufficient to induce anchorage independence in vitro and penetrant tumor formation in immunodeficient mice in vivo. PGBD5 expression is sufficient to induce genomic mobilization of engineered DNA transposons in human cells, and purified recombinant PGBD5 exhibits transposase domain-dependent endonuclease activity in vitro. Flanking-sequence exponential anchored PCR and massively parallel sequencing of DNA transposon integrations revealed distinct activity on piggyBac-like inverted terminal repeats, and preference for specific euchromatic human genomic loci. This enables mapping of structural rearrangements of endogenous human transposable elements in primary human tumor genomes, some of which target genes involved in cellular transformation. We find that PGBD5 transposase-induced cell transformation is associated with morphologic de-differentiation, induction of distinct Polycomb gene expression programs and structural chromatin remodeling, consistent with its epigenetic control. These findings reveal an unanticipated mechanism of human tumorigenesis, genomic plasticity and structural alterations of non-coding regulatory genomic loci in human cancer.
Citation Format: Anton Henssen, Amy Eisenberg, Eileen Jiang, Elizabeth Henaff, Richard Koche, Melissa Burns, Julianne R. Carson, Gouri Nanjangud, Eric Still, Jorge Gandara, Paolo Cifani, Avantika Dhabaria, Xiaodong Huang, Elisa de Stanchina, Elizabeth Mullen, Hanno Steen, Elizabeth Perlman, Jeffrey Dome, Cristina Antonescu, Cedric Feschotte, Christopher E. Mason, Alex Kentsis. Human tumorigenesis induced by endogenous DNA transposase. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1103. doi:10.1158/1538-7445.AM2015-1103
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Affiliation(s)
- Anton Henssen
- 1Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Amy Eisenberg
- 1Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eileen Jiang
- 1Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth Henaff
- 2Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
| | - Richard Koche
- 3Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Melissa Burns
- 4Dana Farber Cancer Institute, Harvard University, Boston, MA
| | - Julianne R. Carson
- 1Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Eric Still
- 5Memorial-Sloan Kettering Cancer Center, New York, NY
| | - Jorge Gandara
- 2Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
| | - Paolo Cifani
- 1Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Avantika Dhabaria
- 1Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xiaodong Huang
- 6Antitumor Assessment Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Elisa de Stanchina
- 6Antitumor Assessment Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Hanno Steen
- 7Department of Pathology, Boston Children's Hospital, Boston, MA
| | - Elizabeth Perlman
- 8Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | - Jeffrey Dome
- 9Division of Oncology, Children's National Medical Center, Washington, DC
| | - Cristina Antonescu
- 10Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Cedric Feschotte
- 11Department of Human Genetics University of Utah, Salt Lake City, UT
| | - Christopher E. Mason
- 2Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
| | - Alex Kentsis
- 1Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
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32
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Abstract
Breast-cancer-derived cell lines are an important sample source for cancer proteomics and can be classified on the basis of transcriptomic analysis into subgroups corresponding to the molecular subtypes observed in mammary tumors. This study describes a tridimensional fractionation method that allows high sequence coverage and proteome-wide estimation of protein expression levels. This workflow has been used to conduct an in-depth quantitative proteomic survey of five breast cancer cell lines matching all major cancer subgroups and shows that despite their different classification, these cell lines display a very high level of similarity. A proteome-wide comparison with the RNA levels observed in the same samples showed very little to no correlation. Finally, we demonstrate that the proteomes of in vitro models of breast cancer display surprisingly little overlap with those of clinical samples.
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Affiliation(s)
- Paolo Cifani
- Department of Immunotechnology, CREATE Health, Lund University, House 406, Medicon Village, 223 81 Lund, Sweden
| | - Ufuk Kirik
- Department of Immunotechnology, CREATE Health, Lund University, House 406, Medicon Village, 223 81 Lund, Sweden
| | - Sofia Waldemarson
- Department of Immunotechnology, CREATE Health, Lund University, House 406, Medicon Village, 223 81 Lund, Sweden
| | - Peter James
- Department of Immunotechnology, CREATE Health, Lund University, House 406, Medicon Village, 223 81 Lund, Sweden
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33
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Franchin C, Cesaro L, Salvi M, Millioni R, Iori E, Cifani P, James P, Arrigoni G, Pinna L. Quantitative analysis of a phosphoproteome readily altered by the protein kinase CK2 inhibitor quinalizarin in HEK-293T cells. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2015; 1854:609-23. [DOI: 10.1016/j.bbapap.2014.09.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 09/15/2014] [Accepted: 09/22/2014] [Indexed: 01/06/2023]
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34
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Kirik U, Cifani P, Albrekt AS, Lindstedt M, Heyden A, Levander F. Multimodel Pathway Enrichment Methods for Functional Evaluation of Expression Regulation. J Proteome Res 2012; 11:2955-67. [DOI: 10.1021/pr300038b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ufuk Kirik
- Department of Immunotechnology, Lund University Biomedical Centre D13, SE-221 84 Lund,
Sweden
| | - Paolo Cifani
- Department of Immunotechnology, Lund University Biomedical Centre D13, SE-221 84 Lund,
Sweden
| | - Ann-Sofie Albrekt
- Department of Immunotechnology, Lund University Biomedical Centre D13, SE-221 84 Lund,
Sweden
| | - Malin Lindstedt
- Department of Immunotechnology, Lund University Biomedical Centre D13, SE-221 84 Lund,
Sweden
| | - Anders Heyden
- Centre for Mathematical
Sciences, Lund University Box 118, SE-22100,
Lund, Sweden
| | - Fredrik Levander
- Department of Immunotechnology, Lund University Biomedical Centre D13, SE-221 84 Lund,
Sweden
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35
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Antberg L, Cifani P, Sandin M, Levander F, James P. Critical Comparison of Multidimensional Separation Methods for Increasing Protein Expression Coverage. J Proteome Res 2012; 11:2644-52. [DOI: 10.1021/pr201257y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Linn Antberg
- Protein Technology,
Department of Immunotechnology,
CREATE Health, Lund University, Sweden
| | - Paolo Cifani
- Protein Technology,
Department of Immunotechnology,
CREATE Health, Lund University, Sweden
| | - Marianne Sandin
- Protein Technology,
Department of Immunotechnology,
CREATE Health, Lund University, Sweden
| | - Fredrik Levander
- Protein Technology,
Department of Immunotechnology,
CREATE Health, Lund University, Sweden
| | - Peter James
- Protein Technology,
Department of Immunotechnology,
CREATE Health, Lund University, Sweden
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36
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Stella R, Cifani P, Peggion C, Hansson K, Lazzari C, Bendz M, Levander F, Sorgato MC, Bertoli A, James P. Relative Quantification of Membrane Proteins in Wild-Type and Prion Protein (PrP)-Knockout Cerebellar Granule Neurons. J Proteome Res 2011; 11:523-36. [DOI: 10.1021/pr200759m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Roberto Stella
- Department of Biological Chemistry, University of Padova, Italy
| | - Paolo Cifani
- Department of Immunotechnology and CREATE Health, Lund University, Sweden
| | | | - Karin Hansson
- Department of Immunotechnology and CREATE Health, Lund University, Sweden
| | | | - Maria Bendz
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Fredrik Levander
- Department of Immunotechnology and CREATE Health, Lund University, Sweden
| | | | | | - Peter James
- Department of Immunotechnology and CREATE Health, Lund University, Sweden
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37
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Cifani P, Bendz M, Wårell K, Hansson K, Levander F, Sandin M, Krogh M, Ovenberger M, Fredlund E, Vaapil M, Pietras A, Påhlman S, James P. Hunting for Protein Markers of Hypoxia by Combining Plasma Membrane Enrichment with a New Approach to Membrane Protein Analysis. J Proteome Res 2011; 10:1645-56. [DOI: 10.1021/pr100982j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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