1
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Jovanović B, Temko D, Stevens LE, Seehawer M, Fassl A, Murphy K, Anand J, Garza K, Gulvady A, Qiu X, Harper NW, Daniels VW, Xiao-Yun H, Ge JY, Alečković M, Pyrdol J, Hinohara K, Egri SB, Papanastasiou M, Vadhi R, Font-Tello A, Witwicki R, Peluffo G, Trinh A, Shu S, Diciaccio B, Ekram MB, Subedee A, Herbert ZT, Wucherpfennig KW, Letai AG, Jaffe JD, Sicinski P, Brown M, Dillon D, Long HW, Michor F, Polyak K. Heterogeneity and transcriptional drivers of triple-negative breast cancer. Cell Rep 2023; 42:113564. [PMID: 38100350 PMCID: PMC10842760 DOI: 10.1016/j.celrep.2023.113564] [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: 06/01/2023] [Revised: 10/05/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous disease with limited treatment options. To characterize TNBC heterogeneity, we defined transcriptional, epigenetic, and metabolic subtypes and subtype-driving super-enhancers and transcription factors by combining functional and molecular profiling with computational analyses. Single-cell RNA sequencing revealed relative homogeneity of the major transcriptional subtypes (luminal, basal, and mesenchymal) within samples. We found that mesenchymal TNBCs share features with mesenchymal neuroblastoma and rhabdoid tumors and that the PRRX1 transcription factor is a key driver of these tumors. PRRX1 is sufficient for inducing mesenchymal features in basal but not in luminal TNBC cells via reprogramming super-enhancer landscapes, but it is not required for mesenchymal state maintenance or for cellular viability. Our comprehensive, large-scale, multiplatform, multiomics study of both experimental and clinical TNBC is an important resource for the scientific and clinical research communities and opens venues for future investigation.
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Affiliation(s)
- Bojana Jovanović
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Temko
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Laura E Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Marco Seehawer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine Murphy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jayati Anand
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kodie Garza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Anushree Gulvady
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nicholas W Harper
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Veerle W Daniels
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Huang Xiao-Yun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jennifer Y Ge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Maša Alečković
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jason Pyrdol
- Departments of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Kunihiko Hinohara
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Shawn B Egri
- The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | | | - Raga Vadhi
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alba Font-Tello
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Robert Witwicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Guillermo Peluffo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Anne Trinh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Benedetto Diciaccio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Muhammad B Ekram
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ashim Subedee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zachary T Herbert
- Department of Molecular Biology Core Facility, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kai W Wucherpfennig
- Departments of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Anthony G Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jacob D Jaffe
- The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
| | - Deborah Dillon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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2
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Gentili M, Liu B, Papanastasiou M, Dele-Oni D, Schwartz MA, Carlson RJ, Al'Khafaji AM, Krug K, Brown A, Doench JG, Carr SA, Hacohen N. ESCRT-dependent STING degradation inhibits steady-state and cGAMP-induced signalling. Nat Commun 2023; 14:611. [PMID: 36739287 PMCID: PMC9899276 DOI: 10.1038/s41467-023-36132-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/17/2023] [Indexed: 02/06/2023] Open
Abstract
Stimulator of interferon genes (STING) is an intracellular sensor of cyclic di-nucleotides involved in the innate immune response against pathogen- or self-derived DNA. STING trafficking is tightly linked to its function, and its dysregulation can lead to disease. Here, we systematically characterize genes regulating STING trafficking and examine their impact on STING-mediated responses. Using proximity-ligation proteomics and genetic screens, we demonstrate that an endosomal sorting complex required for transport (ESCRT) complex containing HGS, VPS37A and UBAP1 promotes STING degradation, thereby terminating STING-mediated signaling. Mechanistically, STING oligomerization increases its ubiquitination by UBE2N, forming a platform for ESCRT recruitment at the endosome that terminates STING signaling via sorting in the lysosome. Finally, we show that expression of a UBAP1 mutant identified in patients with hereditary spastic paraplegia and associated with disrupted ESCRT function, increases steady-state STING-dependent type I IFN responses in healthy primary monocyte-derived dendritic cells and fibroblasts. Based on these findings, we propose that STING is subject to a tonic degradative flux and that the ESCRT complex acts as a homeostatic regulator of STING signaling.
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Affiliation(s)
| | - Bingxu Liu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | | | | | - Marc A Schwartz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Rebecca J Carlson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts Institute of Technology, Department of Health Sciences and Technology, Cambridge, MA, USA
| | | | - Karsten Krug
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam Brown
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, 02114, USA.
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3
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Stevens LE, Peluffo G, Qiu X, Temko D, Fassl A, Li Z, Trinh A, Seehawer M, Jovanović B, Alečković M, Wilde CM, Geck RC, Shu S, Kingston NL, Harper NW, Almendro V, Pyke AL, Egri SB, Papanastasiou M, Clement K, Zhou N, Walker S, Salas J, Park SY, Frank DA, Meissner A, Jaffe JD, Sicinski P, Toker A, Michor F, Long HW, Overmoyer BA, Polyak K. JAK-STAT Signaling in Inflammatory Breast Cancer Enables Chemotherapy-Resistant Cell States. Cancer Res 2023; 83:264-284. [PMID: 36409824 PMCID: PMC9845989 DOI: 10.1158/0008-5472.can-22-0423] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 09/23/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022]
Abstract
Inflammatory breast cancer (IBC) is a difficult-to-treat disease with poor clinical outcomes due to high risk of metastasis and resistance to treatment. In breast cancer, CD44+CD24- cells possess stem cell-like features and contribute to disease progression, and we previously described a CD44+CD24-pSTAT3+ breast cancer cell subpopulation that is dependent on JAK2/STAT3 signaling. Here we report that CD44+CD24- cells are the most frequent cell type in IBC and are commonly pSTAT3+. Combination of JAK2/STAT3 inhibition with paclitaxel decreased IBC xenograft growth more than either agent alone. IBC cell lines resistant to paclitaxel and doxorubicin were developed and characterized to mimic therapeutic resistance in patients. Multi-omic profiling of parental and resistant cells revealed enrichment of genes associated with lineage identity and inflammation in chemotherapy-resistant derivatives. Integrated pSTAT3 chromatin immunoprecipitation sequencing and RNA sequencing (RNA-seq) analyses showed pSTAT3 regulates genes related to inflammation and epithelial-to-mesenchymal transition (EMT) in resistant cells, as well as PDE4A, a cAMP-specific phosphodiesterase. Metabolomic characterization identified elevated cAMP signaling and CREB as a candidate therapeutic target in IBC. Investigation of cellular dynamics and heterogeneity at the single cell level during chemotherapy and acquired resistance by CyTOF and single cell RNA-seq identified mechanisms of resistance including a shift from luminal to basal/mesenchymal cell states through selection for rare preexisting subpopulations or an acquired change. Finally, combination treatment with paclitaxel and JAK2/STAT3 inhibition prevented the emergence of the mesenchymal chemo-resistant subpopulation. These results provide mechanistic rational for combination of chemotherapy with inhibition of JAK2/STAT3 signaling as a more effective therapeutic strategy in IBC. SIGNIFICANCE Chemotherapy resistance in inflammatory breast cancer is driven by the JAK2/STAT3 pathway, in part via cAMP/PKA signaling and a cell state switch, which can be overcome using paclitaxel combined with JAK2 inhibitors.
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Affiliation(s)
- Laura E Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Guillermo Peluffo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Daniel Temko
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
| | - Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Anne Trinh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Marco Seehawer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Bojana Jovanović
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Maša Alečković
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Callahan M Wilde
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Renee C Geck
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Natalie L Kingston
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nicholas W Harper
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Vanessa Almendro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Alanna L Pyke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shawn B Egri
- The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | | | - Kendell Clement
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts.,The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Ningxuan Zhou
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sarah Walker
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jacqueline Salas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - So Yeon Park
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - David A Frank
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts.,The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Jacob D Jaffe
- The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
| | - Alex Toker
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts.,The Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts.,The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts.,The Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts.,Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Beth A Overmoyer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.,The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts.,The Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts.,Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, Massachusetts
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4
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DiCiaccio B, Papachristou E, Papanastasiou M, Reiter A, Carroll J, Polyak K. Abstract A023: Sensitivity/resistance mechanisms to KDM5 inhibition in basal breast cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.cancepi22-a023] [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: 12/05/2022]
Abstract
Abstract
We previously described that the KDM5B histone H3 lysine 4 demethylase is amplified and overexpressed in luminal estrogen receptor positive breast cancer, and its activity is associated with resistance to endocrine therapies. We have found that the KDM5A paralog is specifically amplified and overexpressed in basal breast cancer, providing a novel therapeutic opportunity for an aggressive breast cancer subtype. To identify modulators of KDM5 inhibitor sensitivity in KDM5A-amplified basal breast cancer, we performed a genome wide CRISPR viability screen in a KDM5A-amplified basal breast cancer cell line. Our CRISPR screen results and follow up studies implicate Rho-GTPase signaling and the transcriptional repressor ZBTB7A as modulators of cellular response to KDM5 inhibition. We are currently investigating the underlying mechanisms for how these components alter sensitivity/resistance to KDM5 inhibition. Our results suggest potential therapeutic opportunities of inhibiting the KDM5 family of H3K4 demethylases in basal breast cancer.
Citation Format: Benedetto DiCiaccio, Evangelia Papachristou, Malvina Papanastasiou, Andrew Reiter, Jason Carroll, Kornelia Polyak. Sensitivity/resistance mechanisms to KDM5 inhibition in basal breast cancer. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A023.
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Affiliation(s)
| | | | | | | | - Jason Carroll
- 2Cancer Research UK Cambridge Institute, Cambridge, England, United Kingdom,
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5
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Seehawer M, Li Z, Nishida J, Cejas P, Reiter A, Goldman S, Foidart P, Rojas E, Papanastasiou M, Adelman K, Long H, Polyak K. Abstract A020: Histone modification by Kmt2c and Kmt2d regulate metastasis in triple-negative breast cancer in vivo. Cancer Res 2022. [DOI: 10.1158/1538-7445.cancepi22-a020] [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: 12/04/2022]
Abstract
Abstract
Breast cancer is the most common cancer type worldwide accounting for more than 2 million newly diagnosed cases in 2020. Approximately 20% of all breast tumors in the USA is the highly metastatic subtype triple-negative breast cancer (TNBC). Despite recent development of new therapies, disease-free survival rates of TNBC patients are still relatively low. In this study we describe the role of histone modifier lysine methyltransferase 2C and 2D (KMT2C and KMT2D) in metastasis. KMT2C and KMT2D are among the most commonly mutated genes across all cancer types including TNBC. To examine the functional relevance of Kmt2c and Kmt2d mutations in a murine TNBC mouse model, we mutated Kmt2c and Kmt2d using CRISPR/Cas9. In order to minimize confounder effects of constitutive CRISPR/Cas9 expression we utilized a unique strategy of consecutive transient transfections. Mutation of Kmt2c or Kmt2d did not impact tumor growth in vivo, however, Kmt2c and Kmt2d mutant tumors were highly metastatic to multiple organs while no metastases were found in mice with wildtype tumors. To unravel the underlying mechanisms, we first performed histone mass spectrometry. As expected, direct histone modification target of Kmt2cd and Kmt2d, H3K4me1 levels were reduced in mutant cells. Interestingly, we also identified decreased levels of H3K27me3 and increased levels of H3K27ac. To further delineate the impact of these changes we performed ChIP-seq for these three histone modifications. In accordance with the histone mass spectrometry data peak intensities for H3K4me1, H3K27me3, and H3K27ac were increased or decreased, respectively, in mutant cells. Additionally, to examine effects of these changes on chromatin remodeling we performed ATAC sequencing. We identified differencent chromatin structures between wildtype and mutant cells, validating the impact of Kmt2c and Kmt2d perturbation on histone modification and chromatin remodeling. Lastly, we performed RNA-seq and PRO-seq analyses to identify genes and pathways that could explain the increased metastatic capacity of the mutant cells. Gene set enrichment analyses revealed differential regulation of pro-inflammatory pathways in Kmt2c mutant cells correlating with increased number of T-cells in Kmt2c mutant tumors. Kmt2d mutant cells showed alterations in metabolic pathways which we also identified by unbiased metabolomics showing significant changes. This study revealed that mutations in Kmt2c and Kmt2d are sufficient to induce distant metastases and we deciphered underlying mechanism that could be explored as novel strategies to treat or prevent metastasis.
Citation Format: Marco Seehawer, Zheqi Li, Jun Nishida, Paloma Cejas, Andrew Reiter, Seth Goldman, Pierre Foidart, Ernesto Rojas, Malvina Papanastasiou, Karen Adelman, Henry Long, Kornelia Polyak. Histone modification by Kmt2c and Kmt2d regulate metastasis in triple-negative breast cancer in vivo. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A020.
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Affiliation(s)
| | - Zheqi Li
- 1Dana-Farber Cancer Institute, Boston, MA,
| | | | | | | | | | | | | | | | | | - Henry Long
- 1Dana-Farber Cancer Institute, Boston, MA,
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6
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Gross SM, Dane MA, Smith RL, Devlin KL, McLean IC, Derrick DS, Mills CE, Subramanian K, London AB, Torre D, Evangelista JE, Clarke DJB, Xie Z, Erdem C, Lyons N, Natoli T, Pessa S, Lu X, Mullahoo J, Li J, Adam M, Wassie B, Liu M, Kilburn DF, Liby TA, Bucher E, Sanchez-Aguila C, Daily K, Omberg L, Wang Y, Jacobson C, Yapp C, Chung M, Vidovic D, Lu Y, Schurer S, Lee A, Pillai A, Subramanian A, Papanastasiou M, Fraenkel E, Feiler HS, Mills GB, Jaffe JD, Ma’ayan A, Birtwistle MR, Sorger PK, Korkola JE, Gray JW, Heiser LM. A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses. Commun Biol 2022; 5:1066. [PMID: 36207580 PMCID: PMC9546880 DOI: 10.1038/s42003-022-03975-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 08/05/2021] [Accepted: 09/12/2022] [Indexed: 02/01/2023] Open
Abstract
The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix proteins. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understanding of the linkage between molecular and phenotypic changes, we generated a comprehensive dataset that catalogs the transcriptional, proteomic, epigenomic and phenotypic responses of MCF10A mammary epithelial cells after exposure to the ligands EGF, HGF, OSM, IFNG, TGFB and BMP2. Systematic assessment of the molecular and cellular phenotypes induced by these ligands comprise the LINCS Microenvironment (ME) perturbation dataset, which has been curated and made publicly available for community-wide analysis and development of novel computational methods ( synapse.org/LINCS_MCF10A ). In illustrative analyses, we demonstrate how this dataset can be used to discover functionally related molecular features linked to specific cellular phenotypes. Beyond these analyses, this dataset will serve as a resource for the broader scientific community to mine for biological insights, to compare signals carried across distinct molecular modalities, and to develop new computational methods for integrative data analysis.
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Affiliation(s)
- Sean M. Gross
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Mark A. Dane
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Rebecca L. Smith
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Kaylyn L. Devlin
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Ian C. McLean
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Daniel S. Derrick
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Caitlin E. Mills
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Kartik Subramanian
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Alexandra B. London
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Denis Torre
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - John Erol Evangelista
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Daniel J. B. Clarke
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Zhuorui Xie
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Cemal Erdem
- grid.26090.3d0000 0001 0665 0280Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC USA
| | - Nicholas Lyons
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Ted Natoli
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Sarah Pessa
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Xiaodong Lu
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - James Mullahoo
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Jonathan Li
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Miriam Adam
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Brook Wassie
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Moqing Liu
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - David F. Kilburn
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Tiera A. Liby
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Elmar Bucher
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Crystal Sanchez-Aguila
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Kenneth Daily
- grid.430406.50000 0004 6023 5303Sage Bionetworks, Seattle, WA USA
| | - Larsson Omberg
- grid.430406.50000 0004 6023 5303Sage Bionetworks, Seattle, WA USA
| | - Yunguan Wang
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Connor Jacobson
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Clarence Yapp
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Mirra Chung
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Dusica Vidovic
- grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Institute for Data Science & Computing, University of Miami, Miami, FL 33136 USA
| | - Yiling Lu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Stephan Schurer
- grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Institute for Data Science & Computing, University of Miami, Miami, FL 33136 USA
| | - Albert Lee
- grid.94365.3d0000 0001 2297 5165Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, USA
| | - Ajay Pillai
- grid.94365.3d0000 0001 2297 5165Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Aravind Subramanian
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Malvina Papanastasiou
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Ernest Fraenkel
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Heidi S. Feiler
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA
| | - Gordon B. Mills
- grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Division of Oncological Sciences, OHSU, Portland, OR USA
| | - Jake D. Jaffe
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Avi Ma’ayan
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Marc R. Birtwistle
- grid.26090.3d0000 0001 0665 0280Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC USA
| | - Peter K. Sorger
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - James E. Korkola
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA
| | - Joe W. Gray
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA
| | - Laura M. Heiser
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA
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7
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Meharena HS, Marco A, Dileep V, Lockshin ER, Akatsu GY, Mullahoo J, Watson LA, Ko T, Guerin LN, Abdurob F, Rengarajan S, Papanastasiou M, Jaffe JD, Tsai LH. Down-syndrome-induced senescence disrupts the nuclear architecture of neural progenitors. Cell Stem Cell 2022; 29:116-130.e7. [PMID: 34995493 PMCID: PMC8805993 DOI: 10.1016/j.stem.2021.12.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [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: 05/10/2020] [Revised: 08/30/2021] [Accepted: 12/09/2021] [Indexed: 01/09/2023]
Abstract
Down syndrome (DS) is a genetic disorder driven by the triplication of chromosome 21 (T21) and characterized by a wide range of neurodevelopmental and physical disabilities. Transcriptomic analysis of tissue samples from individuals with DS has revealed that T21 induces a genome-wide transcriptional disruption. However, the consequences of T21 on the nuclear architecture and its interplay with the transcriptome remain unknown. In this study, we find that unlike human induced pluripotent stem cells (iPSCs), iPSC-derived neural progenitor cells (NPCs) exhibit genome-wide "chromosomal introversion," disruption of lamina-associated domains, and global chromatin accessibility changes in response to T21, consistent with the transcriptional and nuclear architecture changes characteristic of senescent cells. Treatment of T21-harboring NPCs with senolytic drugs alleviates the transcriptional, molecular, and cellular dysfunctions associated with DS. Our findings provide a mechanistic link between T21 and global transcriptional disruption and indicate that senescence-associated phenotypes may play a key role in the neurodevelopmental pathogenesis of DS.
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Affiliation(s)
- Hiruy S. Meharena
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Correspondence: Hiruy Meharena (), Li-Huei Tsai () – Lead Contact
| | - Asaf Marco
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Vishnu Dileep
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Elana R. Lockshin
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Grace Y. Akatsu
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - James Mullahoo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - L. Ashley Watson
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tak Ko
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lindsey N. Guerin
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Fatema Abdurob
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shruthi Rengarajan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | | | - Jacob D. Jaffe
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Correspondence: Hiruy Meharena (), Li-Huei Tsai () – Lead Contact
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8
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Dele-Oni DO, Christianson KE, Egri SB, Vaca Jacome AS, DeRuff KC, Mullahoo J, Sharma V, Davison D, Ko T, Bula M, Blanchard J, Young JZ, Litichevskiy L, Lu X, Lam D, Asiedu JK, Toder C, Officer A, Peckner R, MacCoss MJ, Tsai LH, Carr SA, Papanastasiou M, Jaffe JD. Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds. Sci Data 2021; 8:226. [PMID: 34433823 PMCID: PMC8387426 DOI: 10.1038/s41597-021-01008-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023] Open
Abstract
While gene expression profiling has traditionally been the method of choice for large-scale perturbational profiling studies, proteomics has emerged as an effective tool in this context for directly monitoring cellular responses to perturbations. We previously reported a pilot library containing 3400 profiles of multiple perturbations across diverse cellular backgrounds in the reduced-representation phosphoproteome (P100) and chromatin space (Global Chromatin Profiling, GCP). Here, we expand our original dataset to include profiles from a new set of cardiotoxic compounds and from astrocytes, an additional neural cell model, totaling 5300 proteomic signatures. We describe filtering criteria and quality control metrics used to assess and validate the technical quality and reproducibility of our data. To demonstrate the power of the library, we present two case studies where data is queried using the concept of "connectivity" to obtain biological insight. All data presented in this study have been deposited to the ProteomeXchange Consortium with identifiers PXD017458 (P100) and PXD017459 (GCP) and can be queried at https://clue.io/proteomics .
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Affiliation(s)
| | | | - Shawn B Egri
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States
| | | | | | - James Mullahoo
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States
| | - Vagisha Sharma
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, United States
| | - Desiree Davison
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States
| | - Tak Ko
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
| | - Michael Bula
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
| | - Joel Blanchard
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
| | - Jennie Z Young
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
| | - Lev Litichevskiy
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States
| | - Xiaodong Lu
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States
| | - Daniel Lam
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States
| | - Jacob K Asiedu
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States
| | - Caidin Toder
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States
| | - Adam Officer
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States
| | - Ryan Peckner
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, United States
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States
| | | | - Jacob D Jaffe
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States.
- Inzen Therapeutics, Cambridge, MA, 02139, United States.
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9
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Rossmann MP, Hoi K, Chan V, Abraham BJ, Yang S, Mullahoo J, Papanastasiou M, Wang Y, Elia I, Perlin JR, Hagedorn EJ, Hetzel S, Weigert R, Vyas S, Nag PP, Sullivan LB, Warren CR, Dorjsuren B, Greig EC, Adatto I, Cowan CA, Schreiber SL, Young RA, Meissner A, Haigis MC, Hekimi S, Carr SA, Zon LI. Cell-specific transcriptional control of mitochondrial metabolism by TIF1γ drives erythropoiesis. Science 2021; 372:716-721. [PMID: 33986176 DOI: 10.1126/science.aaz2740] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 03/29/2021] [Indexed: 12/11/2022]
Abstract
Transcription and metabolism both influence cell function, but dedicated transcriptional control of metabolic pathways that regulate cell fate has rarely been defined. We discovered, using a chemical suppressor screen, that inhibition of the pyrimidine biosynthesis enzyme dihydroorotate dehydrogenase (DHODH) rescues erythroid differentiation in bloodless zebrafish moonshine (mon) mutant embryos defective for transcriptional intermediary factor 1 gamma (tif1γ). This rescue depends on the functional link of DHODH to mitochondrial respiration. The transcription elongation factor TIF1γ directly controls coenzyme Q (CoQ) synthesis gene expression. Upon tif1γ loss, CoQ levels are reduced, and a high succinate/α-ketoglutarate ratio leads to increased histone methylation. A CoQ analog rescues mon's bloodless phenotype. These results demonstrate that mitochondrial metabolism is a key output of a lineage transcription factor that drives cell fate decisions in the early blood lineage.
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Affiliation(s)
- Marlies P Rossmann
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 01238, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karen Hoi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 01238, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Victoria Chan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 01238, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Song Yang
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - James Mullahoo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Ying Wang
- Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada
| | - Ilaria Elia
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Julie R Perlin
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Elliott J Hagedorn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sara Hetzel
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Raha Weigert
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Sejal Vyas
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Partha P Nag
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lucas B Sullivan
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Curtis R Warren
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Bilguujin Dorjsuren
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 01238, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Eugenia Custo Greig
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 01238, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Isaac Adatto
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 01238, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Chad A Cowan
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | | | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 01238, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Marcia C Haigis
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Siegfried Hekimi
- Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Leonard I Zon
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 01238, USA. .,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
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10
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Rossmann MP, Hoi K, Chan V, Abraham BJ, Yang S, Mullahoo J, Papanastasiou M, Elia I, Vyas S, Nag PP, Sullivan LB, Perlin JR, Hagedorn EJ, Hetzel S, Weigert R, Warren CR, Dorjsuren B, Greig EC, Cowan CA, Schreiber SL, Young RA, Meissner A, Haigis M, Carr SA, Zon LI. Abstract PR04: Transcriptional regulation of mitochondrial metabolism by TIF1γ drives erythroid progenitor differentiation. Cancer Res 2020. [DOI: 10.1158/1538-7445.epimetab20-pr04] [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
Understanding in-vivo mechanisms of erythropoiesis is critical for directed differentiation approaches to treat blood disorders such as leukemias. Zebrafish moonshine (mon) mutant embryos defective for the conserved transcriptional intermediary factor 1 gamma (tif1γ) do not specify enough erythroid progenitors due to a transcription elongation block characterized by aberrantly paused RNA polymerase II. To elucidate the TIF1γ-mediated mechanisms in erythroid differentiation, we performed a chemical suppressor screen using 3,100 compounds and identified inhibitors of the essential mitochondrial pyrimidine synthesis enzyme dihydroorotate dehydrogenase (DHODH). Leflunomide as well as the structurally unrelated DHODH inhibitor brequinar rescue the formation of erythroid progenitors in 61% (38/62) and 68% (50/74) of mon embryos, respectively. Beyond changes in nucleotide metabolism, in-vivo metabolic analyses revealed low levels of TCA cycle metabolites which were functionally linked to a reduced oxygen consumption rate. In addition, an increased 2HG/αKG ratio was associated with higher histone methylation states at H3K27, H3K36 and H4K20 as assessed by quantitative targeted mass spectrometry, which may contribute to the erythroid differentiation block upon tif1γ loss. DHODH is the only pyrimidine de novo synthesis enzyme located in mitochondria and its activity is coupled to that of the electron transport chain (ETC) via coenzyme Q (CoQ). Rotenone, a potent ETC complex I inhibitor reversed the rescue by DHODH inhibition in mon embryos. Through parallel genome-wide transcriptome and chromatin immunoprecipitation analyses, we found that genes encoding CoQ metabolic enzymes are direct TIF1γ targets. Treatment with the CoQ analog decylubiquinone rescued erythroid progenitors in 26% (33/126) of mon embryos. These results demonstrate a tight coordination of nucleotide and mitochondrial metabolism as a key function of tif1γ-dependent transcription and reveal that TIF1γ activity regulates a metabolic program that drives cell fate decisions in the early blood lineage. Our work highlights the importance of the plasticity achieved by transcription regulatory processes such as transcription elongation for metabolic processes during lineage differentiation and could have therapeutic potential for blood diseases.
Citation Format: Marlies P. Rossmann, Karen Hoi, Victoria Chan, Brian J. Abraham, Song Yang, James Mullahoo, Malvina Papanastasiou, Ilaria Elia, Sejal Vyas, Partha P. Nag, Lucas B. Sullivan, Julie R. Perlin, Elliott J. Hagedorn, Sara Hetzel, Raha Weigert, Curtis R. Warren, Bilguujin Dorjsuren, Eugenia Custo Greig, Chad A. Cowan, Stuart L. Schreiber, Richard A. Young, Alexander Meissner, Marcia Haigis, Steven A. Carr, Leonard I. Zon. Transcriptional regulation of mitochondrial metabolism by TIF1γ drives erythroid progenitor differentiation [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr PR04.
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Affiliation(s)
- Marlies P. Rossmann
- 1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA,
| | - Karen Hoi
- 1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA,
| | - Victoria Chan
- 1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA,
| | | | - Song Yang
- 3Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA,
| | | | | | - Ilaria Elia
- 5Department of Cell Biology, Harvard Medical School, Boston, MA,
| | - Sejal Vyas
- 5Department of Cell Biology, Harvard Medical School, Boston, MA,
| | | | | | - Julie R. Perlin
- 3Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA,
| | - Elliott J. Hagedorn
- 3Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA,
| | - Sara Hetzel
- 7Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany,
| | - Raha Weigert
- 7Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany,
| | - Curtis R. Warren
- 8Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Bilguujin Dorjsuren
- 1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA,
| | - Eugenia Custo Greig
- 1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA,
| | - Chad A. Cowan
- 8Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | | | | | - Alexander Meissner
- 7Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany,
| | - Marcia Haigis
- 5Department of Cell Biology, Harvard Medical School, Boston, MA,
| | | | - Leonard I. Zon
- 1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA,
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11
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Mullahoo J, Zhang T, Clauser K, Carr SA, Jaffe JD, Papanastasiou M. Dual protease type XIII/pepsin digestion offers superior resolution and overlap for the analysis of histone tails by HX-MS. Methods 2020; 184:135-140. [PMID: 32004545 DOI: 10.1016/j.ymeth.2020.01.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 08/01/2019] [Revised: 01/22/2020] [Accepted: 01/26/2020] [Indexed: 01/26/2023] Open
Abstract
The N-terminal regions of histone proteins (tails) are dynamic elements that protrude from the nucleosome and are involved in many aspects of chromatin organization. Their epigenetic role is well-established, and post-translational modifications (PTMs) present on these regions contribute to transcriptional regulation. While hydrogen/deuterium exchange mass spectrometry (HX-MS) is well-suited for the analysis of dynamic structures, it has seldom been employed to analyze histones due to the poor N-terminal coverage obtained using pepsin. Here, we test the applicability of a dual protease type XIII/pepsin digestion column to this class of proteins. We optimize online digestion conditions using the H4 monomer, and extend the method to the analysis of histones in monomeric states and nucleosome core particles (NCPs). We show that the dual protease column generates many short and overlapping N-terminal peptides. We evaluate our method by performing hydrogen exchange experiments of NCPs for different time points and present full coverage of the tails at excellent resolution. We further employ electron transfer dissociation and showcase an unprecedented degree of overlap across multiple peptides that is several fold higher than previously reported methods. The method we report here may be readily applied to the HX-MS investigation of histone dynamics and to the footprints of histone binding proteins on nucleosomes.
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Affiliation(s)
- James Mullahoo
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Terry Zhang
- Thermo Scientific, San Jose, CA, United States
| | - Karl Clauser
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Jacob D Jaffe
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
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12
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Papanastasiou M, Mullahoo J, DeRuff KC, Bajrami B, Karageorgos I, Johnston SE, Peckner R, Myers SA, Carr SA, Jaffe JD. Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS. Mol Cell Proteomics 2019; 18:2089-2098. [PMID: 31409669 PMCID: PMC6773551 DOI: 10.1074/mcp.ra119.001325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 01/15/2019] [Revised: 07/19/2019] [Indexed: 12/27/2022] Open
Abstract
The N-terminal regions (tails) of histone proteins are dynamic elements that protrude from the nucleosome and are involved in many aspects of chromatin organization. Their epigenetic role is well-established, and post-translational modifications present on these regions contribute to transcriptional regulation. Considering their biological significance, relatively few structural details have been established for histone tails, mainly because of their inherently disordered nature. Although hydrogen/deuterium exchange mass spectrometry (HX-MS) is well-suited for the analysis of dynamic structures, it has seldom been employed in this context, presumably because of the poor N-terminal coverage provided by pepsin. Inspired from histone-clipping events, we profiled the activity of cathepsin-L under HX-MS quench conditions and characterized its specificity employing the four core histones (H2A, H2B, H3 and H4). Cathepsin-L demonstrated cleavage patterns that were substrate- and pH-dependent. Cathepsin-L generated overlapping N-terminal peptides about 20 amino acids long for H2A, H3, and H4 proving its suitability for the analysis of histone tails dynamics. We developed a comprehensive HX-MS method in combination with pepsin and obtained full sequence coverage for all histones. We employed our method to analyze histones H3 and H4. We observe rapid deuterium exchange of the N-terminal tails and cooperative unfolding (EX1 kinetics) in the histone-fold domains of histone monomers in-solution. Overall, this novel strategy opens new avenues for investigating the dynamic properties of histones that are not apparent from the crystal structures, providing insights into the structural basis of the histone code.
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Affiliation(s)
| | | | | | | | - Ioannis Karageorgos
- Biomolecular Measurements Division, National Institute of Standards and Technology, Gaithersburg, MD;; Institute for Bioscience and Biotechnology Research, Rockville, MD
| | | | - Ryan Peckner
- The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Jacob D Jaffe
- The Broad Institute of MIT and Harvard, Cambridge, MA
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13
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Hudgens JW, Gallagher ES, Karageorgos I, Anderson KW, Filliben JJ, Huang RYC, Chen G, Bou-Assaf GM, Espada A, Chalmers MJ, Harguindey E, Zhang HM, Walters BT, Zhang J, Venable J, Steckler C, Park I, Brock A, Lu X, Pandey R, Chandramohan A, Anand GS, Nirudodhi SN, Sperry JB, Rouse JC, Carroll JA, Rand KD, Leurs U, Weis DD, Al-Naqshabandi MA, Hageman TS, Deredge D, Wintrode PL, Papanastasiou M, Lambris JD, Li S, Urata S. Interlaboratory Comparison of Hydrogen-Deuterium Exchange Mass Spectrometry Measurements of the Fab Fragment of NISTmAb. Anal Chem 2019; 91:7336-7345. [PMID: 31045344 DOI: 10.1021/acs.analchem.9b01100] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is an established, powerful tool for investigating protein-ligand interactions, protein folding, and protein dynamics. However, HDX-MS is still an emergent tool for quality control of biopharmaceuticals and for establishing dynamic similarity between a biosimilar and an innovator therapeutic. Because industry will conduct quality control and similarity measurements over a product lifetime and in multiple locations, an understanding of HDX-MS reproducibility is critical. To determine the reproducibility of continuous-labeling, bottom-up HDX-MS measurements, the present interlaboratory comparison project evaluated deuterium uptake data from the Fab fragment of NISTmAb reference material (PDB: 5K8A ) from 15 laboratories. Laboratories reported ∼89 800 centroid measurements for 430 proteolytic peptide sequences of the Fab fragment (∼78 900 centroids), giving ∼100% coverage, and ∼10 900 centroid measurements for 77 peptide sequences of the Fc fragment. Nearly half of peptide sequences are unique to the reporting laboratory, and only two sequences are reported by all laboratories. The majority of the laboratories (87%) exhibited centroid mass laboratory repeatability precisions of ⟨ sLab⟩ ≤ (0.15 ± 0.01) Da (1σx̅). All laboratories achieved ⟨sLab⟩ ≤ 0.4 Da. For immersions of protein at THDX = (3.6 to 25) °C and for D2O exchange times of tHDX = (30 s to 4 h) the reproducibility of back-exchange corrected, deuterium uptake measurements for the 15 laboratories is σreproducibility15 Laboratories( tHDX) = (9.0 ± 0.9) % (1σ). A nine laboratory cohort that immersed samples at THDX = 25 °C exhibited reproducibility of σreproducibility25C cohort( tHDX) = (6.5 ± 0.6) % for back-exchange corrected, deuterium uptake measurements.
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Affiliation(s)
- Jeffrey W Hudgens
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Elyssia S Gallagher
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Ioannis Karageorgos
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Kyle W Anderson
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - James J Filliben
- Statistical Engineering Division , National Institute of Standards and Technology , Gaithersburg , Maryland 20899 , United States
| | - Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Research and Development , Bristol-Myers Squibb Company , Princeton , New Jersey 08540 , United States
| | - Guodong Chen
- Pharmaceutical Candidate Optimization, Research and Development , Bristol-Myers Squibb Company , Princeton , New Jersey 08540 , United States
| | - George M Bou-Assaf
- Analytical Development , Biogen Inc. , 225 Binney Street , Cambridge , Massachusetts 02142 , United States
| | - Alfonso Espada
- Centro de Investigación Lilly S.A. , 28108 Alcobendas , Spain
| | - Michael J Chalmers
- Lilly Research Laboratories , Eli Lilly and Company , Indianapolis , Indiana 46285 , United States
| | | | - Hui-Min Zhang
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Benjamin T Walters
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Jennifer Zhang
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - John Venable
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Caitlin Steckler
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States.,Joint Center for Structural Genomics , La Jolla , California 92037 , United States
| | - Inhee Park
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Ansgar Brock
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Xiaojun Lu
- MedImmune LLC , One MedImmune Way , Gaithersburg , Maryland 20878 , United States
| | - Ratnesh Pandey
- MedImmune LLC , One MedImmune Way , Gaithersburg , Maryland 20878 , United States
| | - Arun Chandramohan
- Department of Biological Sciences , National University of Singapore , 14, Science Drive 4 , Singapore 117543
| | - Ganesh Srinivasan Anand
- Department of Biological Sciences , National University of Singapore , 14, Science Drive 4 , Singapore 117543
| | - Sasidhar N Nirudodhi
- Vaccine R&D , Pfizer Inc. , 401 N Middletown Rd , Pearl River, New York 10965 , United States
| | - Justin B Sperry
- Analytical R&D , Pfizer Inc. , 700 Chesterfield Parkway West , Chesterfield , Missouri 63017 , United States
| | - Jason C Rouse
- Analytical R&D , Pfizer Inc. , 1 Burtt Road , Andover , Massachusetts 01810 , United States
| | - James A Carroll
- Analytical R&D , Pfizer Inc. , 700 Chesterfield Parkway West , Chesterfield , Missouri 63017 , United States
| | - Kasper D Rand
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - Ulrike Leurs
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - David D Weis
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States
| | - Mohammed A Al-Naqshabandi
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States.,Department of General Science , Soran University , Kawa Street , Soran , Kurdistan Region, Iraq
| | - Tyler S Hageman
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States
| | - Daniel Deredge
- Department of Pharmaceutical Sciences , University of Maryland, Baltimore, School of Pharmacy , 20 North Pine Street , Baltimore , Maryland 21201 , United States
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences , University of Maryland, Baltimore, School of Pharmacy , 20 North Pine Street , Baltimore , Maryland 21201 , United States
| | - Malvina Papanastasiou
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Laboratories , University of Pennsylvania , 422 Curie Boulevard , Philadelphia , Pennsylvania 19104 , United States
| | - John D Lambris
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Laboratories , University of Pennsylvania , 422 Curie Boulevard , Philadelphia , Pennsylvania 19104 , United States
| | - Sheng Li
- Department of Medicine , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
| | - Sarah Urata
- Department of Medicine , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
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14
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Hudgens JW, Gallagher ES, Karageorgos I, Anderson KW, Huang RYC, Chen G, Bou-Assaf GM, Espada A, Chalmers MJ, Harguindey E, Zhang HM, Walters BT, Zhang J, Venable J, Steckler C, Park I, Brock A, Lu X, Pandey R, Chandramohan A, Anand GS, Nirudodhi SN, Sperry JB, Rouse JC, Carroll JA, Rand KD, Leurs U, Weis DD, Al-Naqshabandi MA, Hageman TS, Deredge D, Wintrode PL, Papanastasiou M, Lambris JD, Li S, Urata S. Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Centroid Data Measured between 3.6 °C and 25.4 °C for the Fab Fragment of NISTmAb. J Res Natl Inst Stand Technol 2019; 124:1-7. [PMID: 34877153 PMCID: PMC7339623 DOI: 10.6028/jres.124.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/10/2019] [Indexed: 06/13/2023]
Abstract
The spreadsheet file reported herein provides centroid data, descriptive of
deuterium uptake, for the FabFragment of NISTmAb (PDB: 5K8A) reference material, as
measured by the bottom-up hydrogen-deuterium exchange mass spectrometry (HDX-MS)
method. The protein sample was incubated in deuterium-rich solutions under uniform
pH and salt concentrations between 3.6 oC and 25.4 oC for seven intervals ranging
over (0 to 14,400) s plus a ∞pseudo s control. The deuterium content of peptic
peptide fragments were measured by mass spectrometry. These data were reported by
fifteen laboratories, which conducted the measurements using orbitrap and Q-TOF mass
spectrometers. The cohort reported ≈ 78,900 centroids for 430 proteolytic peptide
sequences of the heavy and light chains of NISTmAb, providing nearly 100 % coverage.
In addition, some groups reported ≈ 10,900 centroid measurements for 77 peptide
sequences of the Fc fragment. The instrumentation and physical and chemical
conditions under which these data were acquired are documented.
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Affiliation(s)
- Jeffrey W Hudgens
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurements Division, Gaithersburg, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Elyssia S Gallagher
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurements Division, Gaithersburg, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Ioannis Karageorgos
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurements Division, Gaithersburg, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Kyle W Anderson
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurements Division, Gaithersburg, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Richard Y-C Huang
- Bristol-Myers Squibb Company, Pharmaceutical Candidate Optimization, Research and Development, Princeton, NJ 08540, USA
| | - Guodong Chen
- Bristol-Myers Squibb Company, Pharmaceutical Candidate Optimization, Research and Development, Princeton, NJ 08540, USA
| | - George M Bou-Assaf
- Biogen Inc., Analytical Development, 225 Binney Street, Cambridge, MA 02142, USA
| | - Alfonso Espada
- Centro de Investigación Lilly S.A., 28108-Alcobendas, Spain
| | - Michael J Chalmers
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | | | - Hui-Min Zhang
- Genentech, Inc. Protein Analytical Chemistry, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Benjamin T Walters
- Genentech, Inc. Protein Analytical Chemistry, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jennifer Zhang
- Genentech, Inc. Protein Analytical Chemistry, 1 DNA Way, South San Francisco, CA 94080, USA
| | - John Venable
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Caitlin Steckler
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
- Joint Center for Structural Genomics, La Jolla, CA 92037, USA
| | - Inhee Park
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Ansgar Brock
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Xiaojun Lu
- MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Ratnesh Pandey
- MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Arun Chandramohan
- National University of Singapore, Department of Biological Sciences, 14, Science Drive 4, Singapore 117543
| | - Ganesh Srinivasan Anand
- National University of Singapore, Department of Biological Sciences, 14, Science Drive 4, Singapore 117543
| | | | - Justin B Sperry
- Pfizer Inc., Analytical R&D, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA
| | - Jason C Rouse
- Pfizer Inc., Analytical R&D, 1 Burtt Road, Andover, MA 01810, USA
| | - James A Carroll
- Pfizer Inc., Analytical R&D, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA
| | - Kasper D Rand
- University of Copenhagen, Department of Pharmacy, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Ulrike Leurs
- University of Copenhagen, Department of Pharmacy, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - David D Weis
- University of Kansas, Department of Chemistry, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA
| | - Mohammed A Al-Naqshabandi
- University of Kansas, Department of Chemistry, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA
- Soran University, Department of General Science, Kawa Street, Soran, Kurdistan Region, Iraq
| | - Tyler S Hageman
- University of Kansas, Department of Chemistry, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA
| | - Daniel Deredge
- University of Maryland, Baltimore, School of Pharmacy, Department of Pharmaceutical Sciences, 20 North Pine Street, Baltimore, MD 21201, USA
| | - Patrick L Wintrode
- University of Maryland, Baltimore, School of Pharmacy, Department of Pharmaceutical Sciences, 20 North Pine Street, Baltimore, MD 21201, USA
| | - Malvina Papanastasiou
- University of Pennsylvania, Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Labs, 422 Curie Boulevard, Philadelphia, PA 19104-6100, USA
| | - John D Lambris
- University of Pennsylvania, Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Labs, 422 Curie Boulevard, Philadelphia, PA 19104-6100, USA
| | - Sheng Li
- University of Southern California, Department of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Sarah Urata
- University of Southern California, Department of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
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15
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Hinohara K, Wu HJ, Vigneau S, McDonald TO, Igarashi KJ, Yamamoto KN, Madsen T, Fassl A, Egri SB, Papanastasiou M, Ding L, Peluffo G, Cohen O, Kales SC, Lal-Nag M, Rai G, Maloney DJ, Jadhav A, Simeonov A, Wagle N, Brown M, Meissner A, Sicinski P, Jaffe JD, Jeselsohn R, Gimelbrant AA, Michor F, Polyak K. KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Cancer Cell 2019; 35:330-332. [PMID: 30753830 PMCID: PMC6428693 DOI: 10.1016/j.ccell.2019.01.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Hinohara K, Wu HJ, Vigneau S, McDonald TO, Igarashi KJ, Yamamoto KN, Madsen T, Fassl A, Egri SB, Papanastasiou M, Ding L, Peluffo G, Cohen O, Kales SC, Lal-Nag M, Rai G, Maloney DJ, Jadhav A, Simeonov A, Wagle N, Brown M, Meissner A, Sicinski P, Jaffe JD, Jeselsohn R, Gimelbrant AA, Michor F, Polyak K. KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Cancer Cell 2018; 34:939-953.e9. [PMID: 30472020 PMCID: PMC6310147 DOI: 10.1016/j.ccell.2018.10.014] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 08/17/2018] [Accepted: 10/25/2018] [Indexed: 12/30/2022]
Abstract
Members of the KDM5 histone H3 lysine 4 demethylase family are associated with therapeutic resistance, including endocrine resistance in breast cancer, but the underlying mechanism is poorly defined. Here we show that genetic deletion of KDM5A/B or inhibition of KDM5 activity increases sensitivity to anti-estrogens by modulating estrogen receptor (ER) signaling and by decreasing cellular transcriptomic heterogeneity. Higher KDM5B expression levels are associated with higher transcriptomic heterogeneity and poor prognosis in ER+ breast tumors. Single-cell RNA sequencing, cellular barcoding, and mathematical modeling demonstrate that endocrine resistance is due to selection for pre-existing genetically distinct cells, while KDM5 inhibitor resistance is acquired. Our findings highlight the importance of cellular phenotypic heterogeneity in therapeutic resistance and identify KDM5A/B as key regulators of this process.
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Affiliation(s)
- Kunihiko Hinohara
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Hua-Jun Wu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sébastien Vigneau
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas O McDonald
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kyomi J Igarashi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kimiyo N Yamamoto
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thomas Madsen
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Shawn B Egri
- The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Lina Ding
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Guillermo Peluffo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ofir Cohen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Stephen C Kales
- National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
| | - Madhu Lal-Nag
- National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
| | - David J Maloney
- National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Ludwig Center at Harvard, Boston, MA 02215, USA
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jacob D Jaffe
- The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Rinath Jeselsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander A Gimelbrant
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Ludwig Center at Harvard, Boston, MA 02215, USA.
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Ludwig Center at Harvard, Boston, MA 02215, USA.
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Szymanski D, Papanastasiou M, Pandarinathan L, Zvonok N, Janero DR, Pavlopoulos S, Vouros P, Makriyannis A. Aliphatic Azides as Selective Cysteine Labeling Reagents for Integral Membrane Proteins. J Med Chem 2018; 61:11199-11208. [DOI: 10.1021/acs.jmedchem.8b01302] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Dennis Szymanski
- Center for Drug Discovery, Northeastern University, 116 Mugar Hall, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Malvina Papanastasiou
- Center for Drug Discovery, Northeastern University, 116 Mugar Hall, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Lakshmipathi Pandarinathan
- Center for Drug Discovery, Northeastern University, 116 Mugar Hall, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Nikolai Zvonok
- Center for Drug Discovery, Northeastern University, 116 Mugar Hall, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - David R. Janero
- Center for Drug Discovery, Northeastern University, 116 Mugar Hall, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Spiro Pavlopoulos
- Center for Drug Discovery, Northeastern University, 116 Mugar Hall, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Paul Vouros
- Barnett Institute, Northeastern University, 215 Hurtig Hall, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Alexandros Makriyannis
- Center for Drug Discovery, Northeastern University, 116 Mugar Hall, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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18
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Litichevskiy L, Peckner R, Abelin JG, Asiedu JK, Creech AL, Davis JF, Davison D, Dunning CM, Egertson JD, Egri S, Gould J, Ko T, Johnson SA, Lahr DL, Lam D, Liu Z, Lyons NJ, Lu X, MacLean BX, Mungenast AE, Officer A, Natoli TE, Papanastasiou M, Patel J, Sharma V, Toder C, Tubelli AA, Young JZ, Carr SA, Golub TR, Subramanian A, MacCoss MJ, Tsai LH, Jaffe JD. A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations. Cell Syst 2018; 6:424-443.e7. [PMID: 29655704 PMCID: PMC5951639 DOI: 10.1016/j.cels.2018.03.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/26/2018] [Accepted: 03/14/2018] [Indexed: 01/05/2023]
Abstract
Although the value of proteomics has been demonstrated, cost and scale are typically prohibitive, and gene expression profiling remains dominant for characterizing cellular responses to perturbations. However, high-throughput sentinel assays provide an opportunity for proteomics to contribute at a meaningful scale. We present a systematic library resource (90 drugs × 6 cell lines) of proteomic signatures that measure changes in the reduced-representation phosphoproteome (P100) and changes in epigenetic marks on histones (GCP). A majority of these drugs elicited reproducible signatures, but notable cell line- and assay-specific differences were observed. Using the "connectivity" framework, we compared signatures across cell types and integrated data across assays, including a transcriptional assay (L1000). Consistent connectivity among cell types revealed cellular responses that transcended lineage, and consistent connectivity among assays revealed unexpected associations between drugs. We further leveraged the resource against public data to formulate hypotheses for treatment of multiple myeloma and acute lymphocytic leukemia. This resource is publicly available at https://clue.io/proteomics.
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Affiliation(s)
| | - Ryan Peckner
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | | | - Jacob K Asiedu
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Amanda L Creech
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - John F Davis
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Desiree Davison
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | | | - Jarrett D Egertson
- University of Washington, Department of Genome Sciences, 3720 15th Avenue NE, Seattle, WA 98195, USA
| | - Shawn Egri
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Joshua Gould
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Tak Ko
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Sarah A Johnson
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - David L Lahr
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Daniel Lam
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Zihan Liu
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | | | - Xiaodong Lu
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Brendan X MacLean
- University of Washington, Department of Genome Sciences, 3720 15th Avenue NE, Seattle, WA 98195, USA
| | - Alison E Mungenast
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Adam Officer
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Ted E Natoli
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | | | - Jinal Patel
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Vagisha Sharma
- University of Washington, Department of Genome Sciences, 3720 15th Avenue NE, Seattle, WA 98195, USA
| | - Courtney Toder
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | | | - Jennie Z Young
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Steven A Carr
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Todd R Golub
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | | | - Michael J MacCoss
- University of Washington, Department of Genome Sciences, 3720 15th Avenue NE, Seattle, WA 98195, USA
| | - Li-Huei Tsai
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jacob D Jaffe
- The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA.
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19
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Devaurs D, Papanastasiou M, Antunes DA, Abella JR, Moll M, Ricklin D, Lambris JD, Kavraki LE. Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling. IJCBDD 2018; 11:90-113. [PMID: 30700993 PMCID: PMC6349257 DOI: 10.1504/ijcbdd.2018.090834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen/deuterium exchange detected by mass spectrometry (HDXMS) provides valuable information on protein structure and dynamics. Although HDX-MS data is often interpreted using crystal structures, it was suggested that conformational ensembles produced by molecular dynamics simulations yield more accurate interpretations. In this paper, we analyse the complement protein C3d by performing an HDX-MS experiment, and evaluate several interpretation methodologies using an existing prediction model to derive HDX-MS data from protein structure. To interpret and refine C3d's HDX-MS data, we look for a conformation (or conformational ensemble) of C3d that allows computationally replicating this data. We confirm that crystal structures are not a good choice and suggest that conformational ensembles produced by molecular dynamics simulations might not always be satisfactory either. Finally, we show that coarse-grained conformational sampling of C3d produces a conformation from which its HDX-MS data can be replicated and refined.
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Affiliation(s)
- Didier Devaurs
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Malvina Papanastasiou
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Dinler A Antunes
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Jayvee R Abella
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Mark Moll
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Daniel Ricklin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - John D Lambris
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lydia E Kavraki
- Department of Computer Science, Rice University, Houston, TX, USA
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20
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Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma'ayan A, Stathias V, Terryn R, Cooper D, Forlin M, Koleti A, Vidovic D, Chung C, Schürer SC, Vasiliauskas J, Pilarczyk M, Shamsaei B, Fazel M, Ren Y, Niu W, Clark NA, White S, Mahi N, Zhang L, Kouril M, Reichard JF, Sivaganesan S, Medvedovic M, Meller J, Koch RJ, Birtwistle MR, Iyengar R, Sobie EA, Azeloglu EU, Kaye J, Osterloh J, Haston K, Kalra J, Finkbiener S, Li J, Milani P, Adam M, Escalante-Chong R, Sachs K, Lenail A, Ramamoorthy D, Fraenkel E, Daigle G, Hussain U, Coye A, Rothstein J, Sareen D, Ornelas L, Banuelos M, Mandefro B, Ho R, Svendsen CN, Lim RG, Stocksdale J, Casale MS, Thompson TG, Wu J, Thompson LM, Dardov V, Venkatraman V, Matlock A, Van Eyk JE, Jaffe JD, Papanastasiou M, Subramanian A, Golub TR, Erickson SD, Fallahi-Sichani M, Hafner M, Gray NS, Lin JR, Mills CE, Muhlich JL, Niepel M, Shamu CE, Williams EH, Wrobel D, Sorger PK, Heiser LM, Gray JW, Korkola JE, Mills GB, LaBarge M, Feiler HS, Dane MA, Bucher E, Nederlof M, Sudar D, Gross S, Kilburn DF, Smith R, Devlin K, Margolis R, Derr L, Lee A, Pillai A. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Syst 2018; 6:13-24. [PMID: 29199020 PMCID: PMC5799026 DOI: 10.1016/j.cels.2017.11.001] [Citation(s) in RCA: 241] [Impact Index Per Article: 40.2] [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: 07/27/2017] [Revised: 09/13/2017] [Accepted: 11/01/2017] [Indexed: 12/19/2022]
Abstract
The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and signatures. By assembling an integrated picture of the range of responses of human cells exposed to many perturbations, the LINCS program aims to better understand human disease and to advance the development of new therapies. Perturbations under study include drugs, genetic perturbations, tissue micro-environments, antibodies, and disease-causing mutations. Responses to perturbations are measured by transcript profiling, mass spectrometry, cell imaging, and biochemical methods, among other assays. The LINCS program focuses on cellular physiology shared among tissues and cell types relevant to an array of diseases, including cancer, heart disease, and neurodegenerative disorders. This Perspective describes LINCS technologies, datasets, tools, and approaches to data accessibility and reusability.
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Affiliation(s)
- Alexandra B Keenan
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sherry L Jenkins
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kathleen M Jagodnik
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Simon Koplev
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Edward He
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Denis Torre
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zichen Wang
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anders B Dohlman
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Moshe C Silverstein
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander Lachmann
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maxim V Kuleshov
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avi Ma'ayan
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Vasileios Stathias
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Raymond Terryn
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Daniel Cooper
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Michele Forlin
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Amar Koleti
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Dusica Vidovic
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Caty Chung
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Stephan C Schürer
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Jouzas Vasiliauskas
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Marcin Pilarczyk
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Behrouz Shamsaei
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Mehdi Fazel
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Yan Ren
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Wen Niu
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Nicholas A Clark
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Shana White
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Naim Mahi
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Lixia Zhang
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Michal Kouril
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - John F Reichard
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Siva Sivaganesan
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Mario Medvedovic
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Jaroslaw Meller
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Rick J Koch
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marc R Birtwistle
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ravi Iyengar
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric A Sobie
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Evren U Azeloglu
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Julia Kaye
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jeannette Osterloh
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kelly Haston
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jaslin Kalra
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Steve Finkbiener
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jonathan Li
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Pamela Milani
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Miriam Adam
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | | | - Karen Sachs
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Alex Lenail
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Divya Ramamoorthy
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Ernest Fraenkel
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Gavin Daigle
- NeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Uzma Hussain
- NeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Alyssa Coye
- NeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jeffrey Rothstein
- NeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Dhruv Sareen
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Loren Ornelas
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Maria Banuelos
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Berhan Mandefro
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ritchie Ho
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Clive N Svendsen
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ryan G Lim
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Jennifer Stocksdale
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Malcolm S Casale
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Terri G Thompson
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Jie Wu
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Leslie M Thompson
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Victoria Dardov
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - Andrea Matlock
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - Jacob D Jaffe
- LINCS PCCSE, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Aravind Subramanian
- LINCS Center for Transcriptomics, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Todd R Golub
- LINCS Center for Transcriptomics, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Sean D Erickson
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | | | - Marc Hafner
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | | | - Jia-Ren Lin
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Caitlin E Mills
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | | | - Mario Niepel
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - David Wrobel
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Peter K Sorger
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Laura M Heiser
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joe W Gray
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - James E Korkola
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Gordon B Mills
- MEP-LINCS Center, Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark LaBarge
- MEP-LINCS Center, Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA 91011, USA; MEP-LINCS Center, Center for Cancer Biomarkers Research, University of Bergen, Bergen 5009, Norway
| | - Heidi S Feiler
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Mark A Dane
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Elmar Bucher
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Michel Nederlof
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA; MEP-LINCS Center, Quantitative Imaging Systems LLC, Portland, OR 97239, USA
| | - Damir Sudar
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA; MEP-LINCS Center, Quantitative Imaging Systems LLC, Portland, OR 97239, USA
| | - Sean Gross
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - David F Kilburn
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Rebecca Smith
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kaylyn Devlin
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
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21
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Devaurs D, Antunes DA, Papanastasiou M, Moll M, Ricklin D, Lambris JD, Kavraki LE. Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data. Front Mol Biosci 2017; 4:13. [PMID: 28344973 PMCID: PMC5344923 DOI: 10.3389/fmolb.2017.00013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/24/2017] [Indexed: 11/13/2022] Open
Abstract
Monitoring hydrogen/deuterium exchange (HDX) undergone by a protein in solution produces experimental data that translates into valuable information about the protein's structure. Data produced by HDX experiments is often interpreted using a crystal structure of the protein, when available. However, it has been shown that the correspondence between experimental HDX data and crystal structures is often not satisfactory. This creates difficulties when trying to perform a structural analysis of the HDX data. In this paper, we evaluate several strategies to obtain a conformation providing a good fit to the experimental HDX data, which is a premise of an accurate structural analysis. We show that performing molecular dynamics simulations can be inadequate to obtain such conformations, and we propose a novel methodology involving a coarse-grained conformational sampling approach instead. By extensively exploring the intrinsic flexibility of a protein with this approach, we produce a conformational ensemble from which we extract a single conformation providing a good fit to the experimental HDX data. We successfully demonstrate the applicability of our method to four small and medium-sized proteins.
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Affiliation(s)
- Didier Devaurs
- Department of Computer Science, Rice UniversityHouston, TX, USA
| | | | - Malvina Papanastasiou
- Department of Pathology and Laboratory Medicine, University of PennsylvaniaPhiladelphia, PA, USA
- Broad Institute of MIT & HarvardCambridge, MA, USA
| | - Mark Moll
- Department of Computer Science, Rice UniversityHouston, TX, USA
| | - Daniel Ricklin
- Department of Pathology and Laboratory Medicine, University of PennsylvaniaPhiladelphia, PA, USA
- Department of Pharmaceutical Sciences, University of BaselBasel, Switzerland
| | - John D. Lambris
- Department of Pathology and Laboratory Medicine, University of PennsylvaniaPhiladelphia, PA, USA
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22
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Papanastasiou M, Koutsogiannaki S, Sarigiannis Y, Geisbrecht BV, Ricklin D, Lambris JD. Structural Implications for the Formation and Function of the Complement Effector Protein iC3b. J Immunol 2017; 198:3326-3335. [PMID: 28258193 DOI: 10.4049/jimmunol.1601864] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/10/2017] [Indexed: 01/17/2023]
Abstract
Complement-mediated opsonization, phagocytosis, and immune stimulation are critical processes in host defense and homeostasis, with the complement activation fragment iC3b playing a key effector role. To date, however, there is no high-resolution structure of iC3b, and some aspects of its structure-activity profile remain controversial. Here, we employed hydrogen-deuterium exchange mass spectrometry to describe the structure and dynamics of iC3b at a peptide resolution level in direct comparison with its parent protein C3b. In our hydrogen-deuterium exchange mass spectrometry study, 264 peptides were analyzed for their deuterium content, providing almost complete sequence coverage for this 173-kDa protein. Several peptides in iC3b showed significantly higher deuterium uptake when compared with C3b, revealing more dynamic, solvent-exposed regions. Most of them resided in the CUB domain, which contains the heptadecapeptide C3f that is liberated during the conversion of C3b to iC3b. Our data suggest a highly disordered CUB, which has acquired a state similar to that of intrinsically disordered proteins, resulting in a predominant form of iC3b that features high structural flexibility. The structure was further validated using an anti-iC3b mAb that was shown to target an epitope in the CUB region. The information obtained in this work allows us to elucidate determinants of iC3b specificity and activity and provide functional insights into the protein's recognition pattern with respect to regulators and receptors of the complement system.
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Affiliation(s)
- Malvina Papanastasiou
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
| | - Sophia Koutsogiannaki
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
| | - Yiannis Sarigiannis
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506
| | - Daniel Ricklin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
| | - John D Lambris
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
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Primikyri A, Papanastasiou M, Sarigiannis Y, Koutsogiannaki S, Reis ES, Tuplano JV, Resuello RRG, Nilsson B, Ricklin D, Lambris JD. Method development and validation for the quantitation of the complement inhibitor Cp40 in human and cynomolgus monkey plasma by UPLC-ESI-MS. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1041-1042:19-26. [PMID: 27992787 DOI: 10.1016/j.jchromb.2016.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 07/11/2016] [Revised: 10/10/2016] [Accepted: 12/03/2016] [Indexed: 12/16/2022]
Abstract
Cp40 is a 14-amino acid cyclic analog of the peptidic complement inhibitor compstatin that binds with sub-nanomolar affinity to complement component C3 and has already shown promise in various models of complement-related diseases. The preclinical and clinical development of this compound requires a robust, accurate, and sensitive method for quantitatively monitoring Cp40 in biological samples. In this study, we describe the development and validation of an ultra-high performance liquid chromatography electrospray mass spectrometry method for the quantitation of Cp40 in human and non-human primate (NHP) plasma. Isotope-labeled Cp40 was used as an internal standard, allowing for the accurate and absolute quantitation of Cp40. Labeled and non-labeled Cp40 were extracted from plasma using reversed phase-solid phase extraction, with recovery rates exceeding 80%, indicating minor matrix effects. The triply charged states of Cp40 and isotope-labeled Cp40 were detected at m/z 596.60 and 600.34, respectively, via a Q-TOF mass spectrometer and were used for quantitation. The method was linear in the range of 0.18-3.58μg/mL (r2≥0.99), with precision values below 0.71% in NHP and 0.77% in human plasma. The accuracy of the method ranged from -2.17% to 17.99% in NHP and from -0.26% to 15.75% in human plasma. The method was successfully applied to the quantitation of Cp40 in cynomolgus monkey plasma after an initial intravenous bolus of 2mg/kg followed by repetitive subcutaneous administration at 1mg/kg. The high reproducibility, accuracy, and robustness of the method developed here render it suitable for drug monitoring of Cp40, and potentially other compstatin analogs, in both human and NHP plasma samples during pharmacokinetic and pharmacodynamic studies.
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Affiliation(s)
- Alexandra Primikyri
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, USA
| | - Malvina Papanastasiou
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, USA
| | - Yiannis Sarigiannis
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, USA
| | - Sophia Koutsogiannaki
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, USA
| | - Edimara S Reis
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, USA
| | - Joel V Tuplano
- Simian Conservation Breeding and Research Center (SICONBREC), Makati City, Philippines
| | - Ranillo R G Resuello
- Simian Conservation Breeding and Research Center (SICONBREC), Makati City, Philippines
| | - Bo Nilsson
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | - Daniel Ricklin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, USA.
| | - John D Lambris
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, USA.
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Papanastasiou M, Orfanoudaki G, Kountourakis N, Koukaki M, Sardis MF, Aivaliotis M, Tsolis KC, Karamanou S, Economou A. Rapid label-free quantitative analysis of the E. coli
BL21(DE3) inner membrane proteome. Proteomics 2015; 16:85-97. [DOI: 10.1002/pmic.201500304] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 09/05/2015] [Accepted: 10/12/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Malvina Papanastasiou
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Department Pathology & Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania; Philadelphia USA
| | - Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Department of Biology; University of Crete; Iraklio Greece
| | - Nikos Kountourakis
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
| | - Marina Koukaki
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
| | - Marios Frantzeskos Sardis
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Leuven Belgium
| | - Michalis Aivaliotis
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
| | - Konstantinos C. Tsolis
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Department of Biology; University of Crete; Iraklio Greece
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Leuven Belgium
| | - Spyridoula Karamanou
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Leuven Belgium
| | - Anastassios Economou
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Department of Biology; University of Crete; Iraklio Greece
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Leuven Belgium
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Fichna J, Wood JT, Papanastasiou M, Vadivel SK, Oprocha P, Sałaga M, Sobczak M, Mokrowiecka A, Cygankiewicz AI, Zakrzewski PK, Małecka-Panas E, Krajewska WM, Kościelniak P, Makriyannis A, Storr MA. Endocannabinoid and cannabinoid-like fatty acid amide levels correlate with pain-related symptoms in patients with IBS-D and IBS-C: a pilot study. PLoS One 2013; 8:e85073. [PMID: 24386448 PMCID: PMC3874007 DOI: 10.1371/journal.pone.0085073] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 11/22/2013] [Indexed: 12/04/2022] Open
Abstract
Aims Irritable bowel syndrome (IBS) is a functional gastrointestinal (GI) disorder, associated with alterations of bowel function, abdominal pain and other symptoms related to the GI tract. Recently the endogenous cannabinoid system (ECS) was shown to be involved in the physiological and pathophysiological control of the GI function. The aim of this pilot study was to investigate whether IBS defining symptoms correlate with changes in endocannabinoids or cannabinoid like fatty acid levels in IBS patients. Methods AEA, 2-AG, OEA and PEA plasma levels were determined in diarrhoea-predominant (IBS-D) and constipation-predominant (IBS-C) patients and were compared to healthy subjects, following the establishment of correlations between biolipid contents and disease symptoms. FAAH mRNA levels were evaluated in colonic biopsies from IBS-D and IBS-C patients and matched controls. Results Patients with IBS-D had higher levels of 2AG and lower levels of OEA and PEA. In contrast, patients with IBS-C had higher levels of OEA. Multivariate analysis found that lower PEA levels are associated with cramping abdominal pain. FAAH mRNA levels were lower in patients with IBS-C. Conclusion IBS subtypes and their symptoms show distinct alterations of endocannabinoid and endocannabinoid-like fatty acid levels. These changes may partially result from reduced FAAH expression. The here reported changes support the notion that the ECS is involved in the pathophysiology of IBS and the development of IBS symptoms.
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Affiliation(s)
- Jakub Fichna
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Medicine, Division of Gastroenterology, University of Calgary, Calgary, Alberta, Canada
- Department of Biomolecular Chemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - JodiAnne T. Wood
- Center for Drug Discovery, Northeastern University, Boston, Massachusetts, United States of America
| | - Malvina Papanastasiou
- Center for Drug Discovery, Northeastern University, Boston, Massachusetts, United States of America
| | - Subramanian K. Vadivel
- Center for Drug Discovery, Northeastern University, Boston, Massachusetts, United States of America
| | - Piotr Oprocha
- Faculty of Applied Mathematics, AGH University of Science and Technology, Cracow, Poland
| | - Maciej Sałaga
- Department of Biomolecular Chemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Marta Sobczak
- Department of Biomolecular Chemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Anna Mokrowiecka
- Department of Digestive Tract Diseases, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Adam I. Cygankiewicz
- Department of Cytobiochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Piotr K. Zakrzewski
- Department of Cytobiochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Ewa Małecka-Panas
- Department of Digestive Tract Diseases, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Wanda M. Krajewska
- Department of Cytobiochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Piotr Kościelniak
- Faculty of Mathematics and Computer Science, Jagiellonian University, Cracow, Poland
| | - Alexandros Makriyannis
- Center for Drug Discovery, Northeastern University, Boston, Massachusetts, United States of America
| | - Martin A. Storr
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Medicine, Division of Gastroenterology, University of Calgary, Calgary, Alberta, Canada
- Department of Medicine, Division of Gastroenterology, Ludwig Maximilians University of Munich, Munich, Germany
- * E-mail:
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26
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Papanastasiou M, Orfanoudaki G, Koukaki M, Kountourakis N, Sardis MF, Aivaliotis M, Karamanou S, Economou A. The Escherichia coli peripheral inner membrane proteome. Mol Cell Proteomics 2012; 12:599-610. [PMID: 23230279 DOI: 10.1074/mcp.m112.024711] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Biological membranes are essential for cell viability. Their functional characteristics strongly depend on their protein content, which consists of transmembrane (integral) and peripherally associated membrane proteins. Both integral and peripheral inner membrane proteins mediate a plethora of biological processes. Whereas transmembrane proteins have characteristic hydrophobic stretches and can be predicted using bioinformatics approaches, peripheral inner membrane proteins are hydrophilic, exist in equilibria with soluble pools, and carry no discernible membrane targeting signals. We experimentally determined the cytoplasmic peripheral inner membrane proteome of the model organism Escherichia coli using a multidisciplinary approach. Initially, we extensively re-annotated the theoretical proteome regarding subcellular localization using literature searches, manual curation, and multi-combinatorial bioinformatics searches of the available databases. Next we used sequential biochemical fractionations coupled to direct identification of individual proteins and protein complexes using high resolution mass spectrometry. We determined that the proposed cytoplasmic peripheral inner membrane proteome occupies a previously unsuspected ∼19% of the basic E. coli BL21(DE3) proteome, and the detected peripheral inner membrane proteome occupies ∼25% of the estimated expressed proteome of this cell grown in LB medium to mid-log phase. This value might increase when fleeting interactions, not studied here, are taken into account. Several proteins previously regarded as exclusively cytoplasmic bind membranes avidly. Many of these proteins are organized in functional or/and structural oligomeric complexes that bind to the membrane with multiple interactions. Identified proteins cover the full spectrum of biological activities, and more than half of them are essential. Our data suggest that the cytoplasmic proteome displays remarkably dynamic and extensive communication with biological membrane surfaces that we are only beginning to decipher.
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27
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Szymanski DW, Papanastasiou M, Melchior K, Zvonok N, Mercier RW, Janero DR, Thakur GA, Cha S, Wu B, Karger B, Makriyannis A. Mass spectrometry-based proteomics of human cannabinoid receptor 2: covalent cysteine 6.47(257)-ligand interaction affording megagonist receptor activation. J Proteome Res 2011; 10:4789-98. [PMID: 21861534 DOI: 10.1021/pr2005583] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The lack of experimental characterization of the structures and ligand-binding motifs of therapeutic G-protein coupled receptors (GPCRs) hampers rational drug discovery. The human cannabinoid receptor 2 (hCB2R) is a class-A GPCR and promising therapeutic target for small-molecule cannabinergic agonists as medicines. Prior mutational and modeling data constitute provisional evidence that AM-841, a high-affinity classical cannabinoid, interacts with cysteine C6.47(257) in hCB2R transmembrane helix 6 (TMH6) to afford improved hCB2R selectivity and unprecedented agonist potency. We now apply bottom-up mass spectrometry (MS)-based proteomics to define directly the hCB2R-AM-841 interaction at the amino-acid level. Recombinant hCB2R, overexpressed as an N-terminal FLAG-tagged/C-terminal 6His-tagged protein (FLAG-hCB2R-6His) with a baculovirus system, was solubilized and purified by immunochromatography as functional receptor. A multiplex multiple reaction monitoring (MRM)-MS method was developed that allowed us to observe unambiguously all seven discrete TMH peptides in the tryptic digest of purified FLAG-hCB2R-6His and demonstrate that AM-841 modifies hCB2R TMH6 exclusively. High-resolution mass spectra of the TMH6 tryptic peptide obtained by Q-TOF MS/MS analysis demonstrated that AM-841 covalently and selectively modifies hCB2R at TMH6 cysteine C6.47(257). These data demonstrate how integration of MS-based proteomics into a ligand-assisted protein structure (LAPS) experimental paradigm can offer guidance to structure-enabled GPCR agonist design.
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Affiliation(s)
- Dennis W Szymanski
- Center for Drug Discovery, Department of Chemistry and Chemical Biology, College of Science, Northeastern University , Boston, Massachusetts 02115-5000, United States
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28
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March RE, Papanastasiou M, McMahon AW, Allen NS. An investigation of paint from a mural in the church of Sainte Madeleine, Manas, France. J Mass Spectrom 2011; 46:816-820. [PMID: 21834020 DOI: 10.1002/jms.1950] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The pigment in brown paint samples taken from a church in the Drôme region of France has been shown to be almost pure 6-bromoindigo and 6,6'-dibromoindigo. The composition of the pigment was established by comparison with 6-bromoindigo and 6,6'-dibromoindigo standards using atmospheric pressure photoionization combined with liquid chromatography and tandem mass spectrometry. The brown paint samples were taken from a frieze of ca 20 brown images having symmetric tree-like forms composed of five overlapping filled circles representing foliage. The tree-like images, simple rather than artistic, had a metallic luster. The molar ratio of 6-bromoindigo and 6,6'-dibromoindigo in the brown paint pigment (98:2) is remarkably similar to that of shellfish purple from the Mediterranean Murex brandaris (96.5:3.5) thus, it is possible that the origin of the indigoid compounds in the brown paint pigment is the eastern coast of the Mediterranean Sea. As the production of Tyrian purple ended with the fall of Byzantium in 1453, purple pigment had to have been produced prior to this time. We have conjectured about the circumstances that may account for the use of 'purple' in this manner in the Drôme region and how the pigment was transported there from the eastern coast of the Mediterranean Sea during the time of the Crusades.
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Affiliation(s)
- Raymond E March
- Department of Chemistry, Trent University, Peterborough, ON, Canada K9J 7B8.
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29
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Papanastasiou M, McMahon A, Allen N, Doyle A, Johnson B, Keck-Antoine K. The hydrolysis mechanism of bis(2,4-di-tert-butyl)pentaerythritol diphosphite (Alkanox P24): An atmospheric pressure photoionisation mass spectrometric study. Polym Degrad Stab 2006. [DOI: 10.1016/j.polymdegradstab.2006.04.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ortuoste N, Allen NS, Papanastasiou M, McMahon A, Edge M, Johnson B, Keck-Antoine K. Hydrolytic stability and hydrolysis reaction mechanism of bis(2,4-di-tert-butyl)pentaerythritol diphosphite (Alkanox P-24). Polym Degrad Stab 2006. [DOI: 10.1016/j.polymdegradstab.2005.04.039] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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31
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Done D, Millard V, Pattinson H, Papanastasiou M. The attribution of intentionality, causality and disposition by deluded patients. Eur Psychiatry 1996. [DOI: 10.1016/0924-9338(96)88904-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Sarri C, Baxevanis CN, Côté GB, Reclos GJ, Sarafidou E, Spanos T, Papanastasiou M, Grigoriadou M, Papamichail M. Sister-chromatid exchange in highly purified human CD4+ and CD8+ lymphocytes. Mutat Res 1992; 270:125-33. [PMID: 1383729 DOI: 10.1016/0027-5107(92)90123-j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Sister-chromatid exchange (SCE) frequencies were determined in human peripheral blood CD4+ and CD8+ T lymphocyte subpopulations which were rapidly and highly purified from pooled T lymphocytes by immunological methods. The purified lymphocytes were stimulated with phytohemagglutinin (PHA) for 4 days. CD4+ lymphocytes showed significantly higher SCE frequencies than autologous CD8+ lymphocytes when measured simultaneously after identical bromodeoxyuridine (BrdU) incubation times. Differences in SCE frequencies between CD4+ and CD8+ lymphocytes were also detected when mitomycin C (MMC) was added to the cultures. Higher SCE frequencies in CD4+ lymphocytes were associated with lower proliferating rate indices (PRI) as compared to autologous CD8+ lymphocytes. Abnormalities in CD4+ T lymphocyte function and number in peripheral blood have been observed in several diseases characterized by immunological disorders. Thus, our data may suggest a link between some immunological disturbances and abnormal SCE frequencies in T lymphocyte subsets.
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Affiliation(s)
- C Sarri
- Genetics Division, Agia Sofia Children's Hospital, Athens, Greece
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33
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Frillingos S, Seferiadis K, Papanastasiou M, Baxevanis CN, Frangou-Lazaridis M, Economou M, Papamichail M, Tsolas O. Appearance of thymosin alpha 1 in supernatants of monocytes incubated with prothymosin alpha. Arch Biochem Biophys 1992; 296:256-63. [PMID: 1534980 DOI: 10.1016/0003-9861(92)90570-m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Prothymosin alpha, a polypeptide of 109 to 111 amino acid residues, contains the entire thymosin alpha 1 sequence (residues 1-28) at its amino terminal. Human peripheral blood monocytes incubated with prothymosin alpha release thymosin alpha 1 in the culture supernatants. In addition total RNA is found to increase. The production of thymosin alpha 1 involves de novo protein synthesis as shown by the kinetics of this release and its inhibition by actinomycin D and cycloheximide. Thymosin alpha 1 release, possibly in association with HLA-DR, stimulates the proliferation of the T cell population.
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Affiliation(s)
- S Frillingos
- Laboratory of Biological Chemistry, University of Ioannina Medical School, Greece
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34
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Kosmidis PA, Baxevanis CN, Tsavaris N, Papanastasiou M, Anastasopoulos E, Bacoyiannis C, Mylonakis N, Karvounis N, Bafaloukos D, Karabelis A. The prognostic significance of immune changes in patients with renal cell carcinoma treated with interferon alfa-2b. J Clin Oncol 1992; 10:1153-7. [PMID: 1535102 DOI: 10.1200/jco.1992.10.7.1153] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
PURPOSE To evaluate the response rate and the immunorestorative properties of subcutaneously administered interferon alfa-2b (IFN-A2b) in patients with advanced renal cell carcinoma (RCC) and to correlate the immune status with the clinical responses. PATIENTS AND METHODS Twenty-six patients with advanced RCC were treated with recombinant IFN-A2b. The dose was increased progressively from 5 x 10(6) IU the first week to 10 x 10(6) IU the second week, and thereafter to 15 x 10(6) IU subcutaneously. RESULTS Four patients (15%) achieved partial responses (PRs), and five patients (19%) had stable disease (S), whereas 17 patients (65%) progressed. In all patients, blood was withdrawn before IFN treatment and monthly thereafter. T lymphocytes after isolation from peripheral blood were tested for proliferation in the autologous mixed lymphocyte reaction (autoMLR) and allogeneic mixed lymphocyte reaction (alloMLR), interleukin-2 (IL-2) production, expression of IL-2 receptors during the alloMLR, and the production of interleukin-1 (IL-1) by peripheral-blood monocytes. Twelve patients were assessable, four patients had a PR, one patient had S, and seven patients had progressive disease. Striking increases were demonstrated in all parameters 1 month after treatment with IFN-A2b in the four patients who responded and the patient with S. Namely, the autoMLR responses showed a mean increase of 250%, the IL-2 production 247%, the expression of IL-2-specific receptors 446%, the alloMLR responses 160%, and the production of IL-1 262%. On the contrary, the nonresponders did not show any change in their overall immune status, and in some, deterioration of the already depressed immunologic functions was observed. CONCLUSIONS Administration of IFN-A2b results in a marked potentiation of deficient cellular immune response in vitro in those patients with RCC who respond to the treatment. This may have prognostic significance, and certainly more patients are required to be studied for definite conclusions.
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Affiliation(s)
- P A Kosmidis
- Department of Medical Oncology, Metaxa Cancer Hospital, Piraeus, Greece
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35
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Papanastasiou M, Baxevanis CN, Papamichail M. Promotion of murine antitumor activity by prothymosin alpha treatment: I. Induction of tumoricidal peritoneal cells producing high levels of tumour necrosis factor alpha. Cancer Immunol Immunother 1992; 35:145-50. [PMID: 1596938 PMCID: PMC11038346 DOI: 10.1007/bf01741862] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/1991] [Accepted: 01/15/1992] [Indexed: 12/27/2022]
Abstract
The effect of prothymosin alpha (ProT alpha) on the survival of DBA/2 mice inoculated with syngeneic tumour cells was studied. DBA/2 mice inoculated intraperitoneally (i.p.) with 2 x 10(5) syngeneic leukaemic L1210 cells developed ascites within 8-12 days and died 10-14 days later. Treatment with ProT alpha consistently inhibited the development of ascites in 20% of the treated animals and prolonged the survival of 40%-60% of the animals up to 70 days. The most effective treatment schedule of ProT alpha was 300 ng/mouse given i.p. at 2-day intervals for 3 weeks followed by a rest period of 7 days, prior to tumour cell inoculation. Peritoneal exudate (PE) cells collected from mice treated with the optimal dose of ProT alpha produced, in the absence of exogenous stimulus, six- to eightfold higher levels of tumour necrosis factor alpha (TNF alpha) than PE cells from control mice. Furthermore these cells exhibited cytotoxic activity against several tumour cell lines including the syngeneic L1210, the TNF-insensitive P815 mastocytoma, the human MOLT-4 lymphoblastic leukaemia, as well as the murine TNF-sensitive L929 fibroblast cell line. Kinetic studies revealed that both production of TNF alpha and tumoricidal activity peaked 7 days after the last injection of ProT alpha and were maintained at high levels over a period of 1 month. Injections with 150 ng ProT alpha slightly improved the survival of mice whereas higher (500 ng and 1000 ng) doses of ProT alpha and a wide range of thymosin alpha 1 doses remained without any effect. PE cells collected from these mice produced extremely low levels of TNF alpha and exhibited negligible tumoricidal activity. Our data demonstrate that ProT alpha has a protective effect in vivo against the growth of adoptively transferred tumour cells and suggest that this effect is, at least in part, mediated by ProT alpha-activated PE cells. These cells were demonstrated to produce high levels of TNF alpha in vitro and to exhibit activity against both TNF-sensitive and TNF-resistant cell lines.
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Affiliation(s)
- M Papanastasiou
- Department of Immunology, Hellenic Anticancer Institute, Athens, Greece
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