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Green BL, Gamble LA, Diggs LP, Nousome D, Patterson JC, Joughin BA, Gasmi B, Lux SC, Samaranayake SG, Miettinen M, Quezado M, Hernandez JM, Yaffe MB, Davis JL. Early Immune Changes Support Signet Ring Cell Dormancy in CDH1-Driven Hereditary Diffuse Gastric Carcinogenesis. Mol Cancer Res 2023; 21:1356-1365. [PMID: 37707375 PMCID: PMC10840796 DOI: 10.1158/1541-7786.mcr-23-0122] [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: 02/24/2023] [Revised: 08/07/2023] [Accepted: 09/11/2023] [Indexed: 09/15/2023]
Abstract
Stage IA gastric adenocarcinoma, characterized by foci of intramucosal signet ring cells (SRC), is found in nearly all asymptomatic patients with germline pathogenic CDH1 variants and hereditary diffuse gastric cancer syndrome (HDGC). The molecular steps involved in initiating malignant transformation and promoting SRC dormancy in HDGC are unknown. Here, whole-exome bulk RNA sequencing (RNA-seq) of SRCs and adjacent non-SRC epithelium (NEP) was performed on laser-capture microdissected (LCM) regions of interest found in risk-reducing total gastrectomy specimens from patients with HDGC (Clinicaltrials.gov ID: NCT03030404). In total, 20 patients (6 male, 14 female) with confirmed HDGC were identified. Analysis of differentially expressed genes (DEG) demonstrated upregulation of certain individual EMT and proliferation genes. However, no oncogenic pathways were found to be upregulated in SRCs. Rather, SRC regions had significant enrichment in pathways involved in T-cell signaling. CIBERSORTx predicted significant increases in the presence of regulatory T cells (Treg) specific to SRC regions. IHC confirmed an increase in FOXP3+ cells in SRC foci, as well as elevations in CD4+ T cells and HLA-DR staining. In summary, the tumor immune microenvironment is microscopically inseparable from stage IA gastric SRCs using a granular isolation technique. An elevation in CD4+ T cells within SRC regions correlates with clinically observed SRC dormancy, while Treg upregulation represents a potential immune escape mechanism. IMPLICATIONS Characterization of the tumor-immune microenvironment in HDGC underscores the potential for the immune system to shape the transcriptional profile of the earliest tumors, which suggests immune-directed therapy as a potential cancer interception strategy in diffuse-type gastric cancer.
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Affiliation(s)
- Benjamin L. Green
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lauren A. Gamble
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laurence P. Diggs
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Darryl Nousome
- Biomedical Informatics and Data Science, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Jesse C. Patterson
- Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian A. Joughin
- Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Billel Gasmi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephanie C. Lux
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sarah G. Samaranayake
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Markku Miettinen
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Martha Quezado
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan M. Hernandez
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael B. Yaffe
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeremy L. Davis
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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van de Kooij B, van der Wal FJ, Rother MB, Creixell P, Stout M, Wiegant W, Joughin BA, Vornberger J, van Vugt MA, Altmeyer M, Yaffe MB, van Attikum H. The Fanconi anemia core complex promotes CtIP-dependent end-resection to drive homologous recombination at DNA double-strand breaks. bioRxiv 2023:2023.09.05.556391. [PMID: 37732274 PMCID: PMC10508776 DOI: 10.1101/2023.09.05.556391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Homologous Recombination (HR) is a high-fidelity repair mechanism of DNA Double-Strand Breaks (DSBs), which are induced by irradiation, genotoxic chemicals or physiological DNA damaging processes. DSBs are also generated as intermediates during the repair of interstrand crosslinks (ICLs). In this context, the Fanconi anemia (FA) core complex, which is effectively recruited to ICLs, promotes HR-mediated DSB-repair. However, whether the FA core complex also promotes HR at ICL-independent DSBs remains controversial. Here, we identified the FA core complex members FANCL and Ube2T as HR-promoting factors in a CRISPR/Cas9-based screen with cells carrying the DSB-repair reporter DSB-Spectrum. Using isogenic cell-line models, we validated the HR-function of FANCL and Ube2T, and demonstrated a similar function for their ubiquitination-substrate FANCD2. We further show that FANCL and Ube2T are directly recruited to DSBs and are required for the accumulation of FANCD2 at these break sites. Mechanistically, we demonstrate that FANCL ubiquitin ligase activity is required for the accumulation of the nuclease CtIP at DSBs, and consequently for optimal end-resection and Rad51 loading. CtIP overexpression rescues HR in FANCL-deficient cells, validating that FANCL primarily regulates HR by promoting CtIP recruitment. Together, these data demonstrate that the FA core complex and FANCD2 have a dual genome maintenance function by promoting repair of DSBs as well as the repair of ICLs.
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Affiliation(s)
- Bert van de Kooij
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Current address: Department of Medical Oncology, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Fenna J. van der Wal
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Magdalena B. Rother
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Pau Creixell
- Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Current address: CRUK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Merula Stout
- Department of Molecular Mechanisms of Disease, University of Zurich (UZH), Zurich, Switzerland
| | - Wouter Wiegant
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Brian A. Joughin
- Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Julia Vornberger
- Department of Molecular Mechanisms of Disease, University of Zurich (UZH), Zurich, Switzerland
| | - Marcel A.T.M. van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich (UZH), Zurich, Switzerland
| | - Michael B. Yaffe
- Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Surgery, Beth Israel Deaconess Medical Center, Divisions of Acute Care Surgery, Trauma, and Critical Care and Surgical Oncology, Harvard Medical School, Boston
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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3
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Netterfield TS, Ostheimer GJ, Tentner AR, Joughin BA, Dakoyannis AM, Sharma CD, Sorger PK, Janes KA, Lauffenburger DA, Yaffe MB. Biphasic JNK-Erk signaling separates the induction and maintenance of cell senescence after DNA damage induced by topoisomerase II inhibition. Cell Syst 2023; 14:582-604.e10. [PMID: 37473730 PMCID: PMC10627503 DOI: 10.1016/j.cels.2023.06.005] [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: 06/14/2022] [Revised: 03/24/2023] [Accepted: 06/13/2023] [Indexed: 07/22/2023]
Abstract
Genotoxic stress in mammalian cells, including those caused by anti-cancer chemotherapy, can induce temporary cell-cycle arrest, DNA damage-induced senescence (DDIS), or apoptotic cell death. Despite obvious clinical importance, it is unclear how the signals emerging from DNA damage are integrated together with other cellular signaling pathways monitoring the cell's environment and/or internal state to control different cell fates. Using single-cell-based signaling measurements combined with tensor partial least square regression (t-PLSR)/principal component analysis (PCA) analysis, we show that JNK and Erk MAPK signaling regulates the initiation of cell senescence through the transcription factor AP-1 at early times after doxorubicin-induced DNA damage and the senescence-associated secretory phenotype (SASP) at late times after damage. These results identify temporally distinct roles for signaling pathways beyond the classic DNA damage response (DDR) that control the cell senescence decision and modulate the tumor microenvironment and reveal fundamental similarities between signaling pathways responsible for oncogene-induced senescence (OIS) and senescence caused by topoisomerase II inhibition. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Tatiana S Netterfield
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gerard J Ostheimer
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andrea R Tentner
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian A Joughin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexandra M Dakoyannis
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Charvi D Sharma
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Computer Science and Molecular Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin A Janes
- Department of Biomedical Engineering and Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael B Yaffe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Division of Acute Care Surgery, Trauma, and Surgical Critical Care, and Division of Surgical Oncology, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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Gordon KS, Kyung T, Perez CR, Holec PV, Ramos A, Zhang AQ, Agarwal Y, Liu Y, Koch CE, Starchenko A, Joughin BA, Lauffenburger DA, Irvine DJ, Hemann MT, Birnbaum ME. Author Correction: Screening for CD19-specific chimaeric antigen receptors with enhanced signalling via a barcoded library of intracellular domains. Nat Biomed Eng 2023; 7:599-602. [PMID: 36737667 DOI: 10.1038/s41551-023-01006-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Khloe S Gordon
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Singapore-MIT Alliance for Research and Technology Centre, Singapore, Singapore
| | - Taeyoon Kyung
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Caleb R Perez
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Patrick V Holec
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Azucena Ramos
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Angela Q Zhang
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Health, Science, and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yash Agarwal
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yunpeng Liu
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Catherine E Koch
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alina Starchenko
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian A Joughin
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MIT, MGH and Harvard, Cambridge, MA, USA
| | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MIT, MGH and Harvard, Cambridge, MA, USA
| | - Michael T Hemann
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael E Birnbaum
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Singapore-MIT Alliance for Research and Technology Centre, Singapore, Singapore.
- Ragon Institute of MIT, MGH and Harvard, Cambridge, MA, USA.
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Riça IG, Joughin BA, Teke ME, Emmons TR, Griffith A, Cahill LA, Banner-Goodspeed V, Robson SC, Hernandez JM, Segal BH, Otterbein LE, Hauser CJ, Lederer JA, Yaffe MB. Neutrophil heterogeneity and emergence of a distinct population of CD11b/CD18-activated low-density neutrophils after trauma. J Trauma Acute Care Surg 2023; 94:187-196. [PMID: 36694330 PMCID: PMC9881754 DOI: 10.1097/ta.0000000000003823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
INTRODUCTION Multiple large clinical trauma trials have documented an increased susceptibility to infection after injury. Although neutrophils (polymorphonuclear leukocytes [PMNs]) were historically considered a homogeneous cell type, we hypothesized that injury could alter neutrophil heterogeneity and predispose to dysfunction. To explore whether trauma modifies PMN heterogeneity, we performed an observational mass-spectrometry-based cytometry study on total leukocytes and low-density PMNs found in the peripheral blood mononuclear cell fraction of leukocytes from healthy controls and trauma patients. METHODS A total of 74 samples from 12 trauma patients, each sampled at 1 or more time points, and matched controls were fractionated and profiled by mass-spectrometry-based cytometry using a panel of 44 distinct markers. After deconvolution and conservative gating on neutrophils, data were analyzed using Seurat, followed by clustering of principal components. RESULTS Eleven distinct neutrophil populations were resolved in control and trauma neutrophils based on differential protein surface marker expression. Trauma markedly altered the basal heterogeneity of neutrophil subgroups seen in the control samples, with loss of a dominant population of resting neutrophils marked by high expression of C3AR and low levels of CD63, CD64, and CD177 (cluster 1), and expansion of two alternative neutrophil populations, one of which is marked by high expression of CD177 with suppression of CD10, CD16, C3AR, CD63, and CD64 (cluster 6). Remarkably, following trauma, a substantially larger percentage of neutrophils sediment in the monocyte fraction. These low-density neutrophils bear markers of functional exhaustion and form a unique trauma-induced population (cluster 9) with markedly upregulated expression of active surface adhesion molecules (activated CD11b/CD18), with suppression of nearly all other surface markers, including receptors for formyl peptides, leukotrienes, chemokines, and complement. CONCLUSION Circulating neutrophils demonstrate considerable evidence of functional heterogeneity that is markedly altered by trauma. Trauma induces evolution of a novel, exhausted, low-density neutrophil population with immunosuppressive features.
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Affiliation(s)
- Ingred Goretti Riça
- Departments of Biological Engineering and Biology, David H. Koch Institute for Integrative Cancer Research, and Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian A. Joughin
- Departments of Biological Engineering and Biology, David H. Koch Institute for Integrative Cancer Research, and Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Martha E. Teke
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tiffany R. Emmons
- Departments of Biological Engineering and Biology, David H. Koch Institute for Integrative Cancer Research, and Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alec Griffith
- Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Laura A. Cahill
- Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Valerie Banner-Goodspeed
- Department of Anesthesia, Critical Care, and Pain Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115 USA
| | - Simon C. Robson
- Department of Anesthesia, Critical Care, and Pain Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115 USA
| | - Jonathan M. Hernandez
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Brahm H. Segal
- Department of Medicine, Roswell Park Comprehensive Cancer Center, University of Buffalo School of Medicine, Buffalo, NY14263 USA
| | - Leo E. Otterbein
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115 USA
| | - Carl J. Hauser
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115 USA
| | - James A. Lederer
- Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Michael B. Yaffe
- Departments of Biological Engineering and Biology, David H. Koch Institute for Integrative Cancer Research, and Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115 USA
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6
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Gordon KS, Kyung T, Perez CR, Holec PV, Ramos A, Zhang AQ, Agarwal Y, Liu Y, Koch C, Starchenko A, Joughin BA, Lauffenburger DA, Irvine DJ, Hemann MT, Birnbaum ME. Screening for CD19-specific chimaeric antigen receptors with enhanced signalling via a barcoded library of intracellular domains. Nat Biomed Eng 2022; 6:855-866. [PMID: 35710755 PMCID: PMC9389442 DOI: 10.1038/s41551-022-00896-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 05/03/2022] [Indexed: 02/06/2023]
Abstract
The immunostimulatory intracellular domains (ICDs) of chimaeric antigen receptors (CARs) are essential for converting antigen recognition into antitumoural function. Although there are many possible combinations of ICDs, almost all current CARs rely on combinations of CD3𝛇, CD28 and 4-1BB. Here we show that a barcoded library of 700,000 unique CD19-specific CARs with diverse ICDs cloned into lentiviral vectors and transduced into Jurkat T cells can be screened at high throughput via cell sorting and next-generation sequencing to optimize CAR signalling for antitumoural functions. By using this screening approach, we identified CARs with new ICD combinations that, compared with clinically available CARs, endowed human primary T cells with comparable tumour control in mice and with improved proliferation, persistence, exhaustion and cytotoxicity after tumour rechallenge in vitro. The screening strategy can be adapted to other disease models, cell types and selection conditions, and could be used to improve adoptive cell therapies and to expand their utility to new disease indications.
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Affiliation(s)
- Khloe S. Gordon
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602, Singapore
| | - Taeyoon Kyung
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Caleb R. Perez
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Patrick V. Holec
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Azucena Ramos
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Angela Q. Zhang
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA,Department of Health, Science, and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yash Agarwal
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yunpeng Liu
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Catherine Koch
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alina Starchenko
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Brian A. Joughin
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Douglas A. Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Ragon Institute of MIT, MGH, and Harvard, Cambridge, MA, 02139, USA
| | - Darrell J. Irvine
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Ragon Institute of MIT, MGH, and Harvard, Cambridge, MA, 02139, USA
| | - Michael T. Hemann
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Michael E. Birnbaum
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602, Singapore,Ragon Institute of MIT, MGH, and Harvard, Cambridge, MA, 02139, USA,Correspondence and requests for materials should be addressed to M.E.B.
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7
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Moore HB, Neal MD, Bertolet M, Joughin BA, Yaffe MB, Barrett CD, Bird MA, Tracy RP, Moore EE, Sperry JL, Zuckerbraun BS, Park MS, Cohen MJ, Wisniewski SR, Morrissey JH. Proteomics of Coagulopathy Following Injury Reveals Limitations of Using Laboratory Assessment to Define Trauma-Induced Coagulopathy to Predict Massive Transfusion. Ann Surg Open 2022; 3:e167. [PMID: 36177090 PMCID: PMC9514137 DOI: 10.1097/as9.0000000000000167] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 04/18/2022] [Indexed: 10/18/2022] Open
Abstract
Objective Trauma-induced coagulopathy (TIC) is provoked by multiple mechanisms and is perceived to be one driver of massive transfusions (MT). Single laboratory values using prothrombin time (INR) or thrombelastography (TEG) are used to clinically define this complex process. We used a proteomics approach to test whether current definitions of TIC (INR, TEG, or clinical judgement) are sufficient to capture the majority of protein changes associated with MT. Methods Eight level-I trauma centers contributed blood samples from patients available early after injury. TIC was defined as INR >1.5 (INR-TIC), TEG maximum amplitude <50mm (TEG-TIC), or clinical judgement (Clin-TIC) by the trauma surgeon. MT was defined as > 10 units of red blood cells in 24 hours or > 4 units RBC/hour during the first 4 hr. SomaLogic proteomic analysis of 1,305 proteins was performed. Pathways associated with proteins dysregulated in patients with each TIC definition and MT were identified. Results Patients (n=211) had a mean injury severity score of 24, with a MT and mortality rate of 22% and 12%, respectively. We identified 578 SOMAscan analytes dysregulated among MT patients, of which INR-TIC, TEG-TIC, and Clin-TIC patients showed dysregulation only in 25%, 3%, and 4% of these, respectively. TIC definitions jointly failed to show changes in 73% of the protein levels associated with MT, and failed to identify 26% of patients that received a massive transfusion. INR-TIC and TEG-TIC patients showed dysregulation of proteins significantly associated with complement activity. Proteins dysregulated in Clin-TIC or massive transfusion patients were not significantly associated with any pathway. Conclusion These data indicate there are unexplored opportunities to identify patients at risk for massive bleeding. Only a small subset of proteins that are dysregulated in patients receiving MT are statistically significantly dysregulated among patients whose TIC is defined based solely on laboratory measurements or clinical assessment.
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Affiliation(s)
- Hunter B. Moore
- From the Department of Surgery, University of Colorado, Denver, CO
| | - Matthew D. Neal
- Department of Surgery, Pittsburgh Trauma Research Center, University of Pittsburgh, Pittsburgh, PA
| | - Marnie Bertolet
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA
| | - Brian A. Joughin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA
- Center for Precision Cancer Medicine
| | - Michael B. Yaffe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA
- Center for Precision Cancer Medicine
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Cambridge, MA
| | - Christopher D. Barrett
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Cambridge, MA
| | - Molly A. Bird
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA
- Center for Precision Cancer Medicine
| | - Russell P. Tracy
- University of Vermont, Department of Biochemistry, Burlington, VT
| | - Ernest E Moore
- From the Department of Surgery, University of Colorado, Denver, CO
- Department of Surgery, Ernest E Moore Shock Trauma Center at Denver Health, Denver, CO
| | - Jason L. Sperry
- Department of Surgery, Pittsburgh Trauma Research Center, University of Pittsburgh, Pittsburgh, PA
| | - Brian S. Zuckerbraun
- Department of Surgery, Pittsburgh Trauma Research Center, University of Pittsburgh, Pittsburgh, PA
| | - Myung S. Park
- Department of Surgery, Mayo Clinic Rochester, Rochester, MN
| | | | | | - James H. Morrissey
- Departments of Biological Chemistry and Internal Medicine, University of Michigan Medical School, Ann Arbor, MI
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8
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Vega PN, Nilsson A, Kumar MP, Niitsu H, Simmons AJ, Ro J, Wang J, Chen Z, Joughin BA, Li W, McKinley ET, Liu Q, Roland JT, Washington MK, Coffey RJ, Lauffenburger DA, Lau KS. Cancer-Associated Fibroblasts and Squamous Epithelial Cells Constitute a Unique Microenvironment in a Mouse Model of Inflammation-Induced Colon Cancer. Front Oncol 2022; 12:878920. [PMID: 35600339 PMCID: PMC9114773 DOI: 10.3389/fonc.2022.878920] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
The tumor microenvironment plays a key role in the pathogenesis of colorectal tumors and contains various cell types including epithelial, immune, and mesenchymal cells. Characterization of the interactions between these cell types is necessary for revealing the complex nature of tumors. In this study, we used single-cell RNA-seq (scRNA-seq) to compare the tumor microenvironments between a mouse model of sporadic colorectal adenoma (Lrig1CreERT2/+;Apc2lox14/+) and a mouse model of inflammation-driven colorectal cancer induced by azoxymethane and dextran sodium sulfate (AOM/DSS). While both models develop tumors in the distal colon, we found that the two tumor types have distinct microenvironments. AOM/DSS tumors have an increased abundance of two populations of cancer-associated fibroblasts (CAFs) compared with APC tumors, and we revealed their divergent spatial association with tumor cells using multiplex immunofluorescence (MxIF) imaging. We also identified a unique squamous cell population in AOM/DSS tumors, whose origins were distinct from anal squamous epithelial cells. These cells were in higher proportions upon administration of a chemotherapy regimen of 5-Fluorouracil/Irinotecan. We used computational inference algorithms to predict cell-cell communication mediated by ligand-receptor interactions and downstream pathway activation, and identified potential mechanistic connections between CAFs and tumor cells, as well as CAFs and squamous epithelial cells. This study provides important preclinical insight into the microenvironment of two distinct models of colorectal tumors and reveals unique roles for CAFs and squamous epithelial cells in the AOM/DSS model of inflammation-driven cancer.
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Affiliation(s)
- Paige N Vega
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Avlant Nilsson
- Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Manu P Kumar
- Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Hiroaki Niitsu
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States.,Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Alan J Simmons
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - James Ro
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jiawei Wang
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Zhengyi Chen
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Brian A Joughin
- Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Wei Li
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States.,Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Eliot T McKinley
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Qi Liu
- Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Joseph T Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States.,Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - M Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Robert J Coffey
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States.,Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Douglas A Lauffenburger
- Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ken S Lau
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States.,Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
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9
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Lock JY, Caboni M, Strandwitz P, Morrissette M, DiBona K, Joughin BA, Lewis K, Carrier RL. An in vitro intestinal model captures immunomodulatory properties of the microbiota in inflammation. Gut Microbes 2022; 14:2039002. [PMID: 35316142 PMCID: PMC8942420 DOI: 10.1080/19490976.2022.2039002] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Considerable effort has been put forth to understand mechanisms by which the microbiota modulates and responds to inflammation. Here, we explored whether oxidation metabolites produced by the host during inflammation, sodium nitrate and trimethylamine oxide, impact the composition of a human stool bacterial population in a gut simulator. We then assessed whether an immune-competent in vitro intestinal model responded differently to spent medium from bacteria exposed to these cues compared to spent medium from a control bacterial population. The host-derived oxidation products were found to decrease levels of Bacteroidaceae and overall microbiota metabolic potential, while increasing levels of proinflammatory Enterobacteriaceae and lipopolysaccharide in bacterial cultures, reflecting shifts that occur in vivo in inflammation. Spent microbiota media induced elevated intracellular mucin levels and reduced intestinal monolayer integrity as reflected in transepithelial electrical resistance relative to fresh medium controls. However, multiplexed cytokine analysis revealed markedly different cytokine signatures from intestinal cultures exposed to spent medium with added oxidation products relative to spent control medium, while cytokine signatures of cultures exposed to fresh media were similar regardless of addition of host-derived cues. Further, the presence of immune cells in the intestinal model was required for this differentiation of cytokine signatures. This study indicates that simple in vitro immune-competent intestinal models can capture bacterial-mammalian cross-talk in response to host-derived oxidation products and supports utility of these systems for mechanistic studies of interactions between the gut microbiome and host in inflammation.
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Affiliation(s)
- Jaclyn Y. Lock
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
| | - Mariaelena Caboni
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Philip Strandwitz
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Madeleine Morrissette
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Kevin DiBona
- Department of Biochemistry, Northeastern University, Boston, Massachusetts, USA
| | - Brian A. Joughin
- The Koch Institute for Integrative Cancer Research at Mit and the Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massacusetts, USA
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Rebecca L. Carrier
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts, USA
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
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10
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Sriram G, Milling LE, Chen JK, Kong YW, Joughin BA, Abraham W, Swartwout S, Handly ED, Irvine DJ, Yaffe MB. The injury response to DNA damage in live tumor cells promotes antitumor immunity. Sci Signal 2021; 14:eabc4764. [PMID: 34665642 PMCID: PMC8791539 DOI: 10.1126/scisignal.abc4764] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although immune checkpoint blockade (ICB) has strong clinical benefit for treating some tumor types, it fails in others, indicating a need for additional modalities to enhance the ICB effect. Here, we identified one such modality by using DNA damage to create a live, injured tumor cell adjuvant. Using an optimized ex vivo coculture system, we found that treating tumor cells with specific concentrations of etoposide, mitoxantrone, or doxorubicin markedly enhanced dendritic cell–mediated T cell activation. These immune-enhancing effects of DNA damage did not correlate with immunogenic cell death markers or with the extent of apoptosis or necroptosis; instead, these effects were mediated by live injured cells with activation of the DNA-PK, ATR, NF-κB, p38 MAPK, and RIPK1 signaling pathways. In mice, intratumoral injection of ex vivo etoposide–treated tumor cells in combination with systemic ICB (by anti-PD-1 and anti-CTLA4 antibodies) increased the number of intratumoral CD103+ dendritic cells and circulating tumor-antigen–specific CD8+ T cells, decreased tumor growth, and improved survival. These effects were absent in Batf3−/− mice and in mice in which the DNA-damaging drug was injected directly into the tumor, due to DNA damage in the immune cells. The combination treatment induced complete tumor regression in a subset of mice that were then able to reject tumor rechallenge, indicating that the injured cell adjuvant treatment induced durable antitumor immunological memory. These results provide a strategy for enhancing the efficacy of immune checkpoint inhibition in tumor types that do not respond to this treatment modality by itself.
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Affiliation(s)
- Ganapathy Sriram
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139
- David. H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Lauren E. Milling
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
- David. H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jung-Kuei Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139
- David. H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Yi Wen Kong
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139
- David. H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Brian A. Joughin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139
- David. H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Wuhbet Abraham
- David. H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Susanne Swartwout
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139
- David. H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Erika D. Handly
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139
- David. H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Darrell J. Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
- David. H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Michael B. Yaffe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139
- David. H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Divisions of Acute Care Surgery, Trauma, and Surgical Critical Care and Surgical Oncology, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215
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11
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Krismer K, Bird MA, Varmeh S, Handly ED, Gattinger A, Bernwinkler T, Anderson DA, Heinzel A, Joughin BA, Kong YW, Cannell IG, Yaffe MB. Transite: A Computational Motif-Based Analysis Platform That Identifies RNA-Binding Proteins Modulating Changes in Gene Expression. Cell Rep 2021; 32:108064. [PMID: 32846122 PMCID: PMC8204639 DOI: 10.1016/j.celrep.2020.108064] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 06/28/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) play critical roles in regulating gene expression by modulating splicing, RNA stability, and protein translation. Stimulus-induced alterations in RBP function contribute to global changes in gene expression, but identifying which RBPs are responsible for the observed changes remains an unmet need. Here, we present Transite, a computational approach that systematically infers RBPs influencing gene expression through changes in RNA stability and degradation. As a proof of principle, we apply Transite to RNA expression data from human patients with non-small-cell lung cancer whose tumors were sampled at diagnosis or after recurrence following treatment with platinum-based chemotherapy. Transite implicates known RBP regulators of the DNA damage response and identifies hnRNPC as a new modulator of chemotherapeutic resistance, which we subsequently validated experimentally. Transite serves as a framework for the identification of RBPs that drive cell-state transitions and adds additional value to the vast collection of publicly available gene expression datasets. Krismer et al. present a computational approach to identify RNA-binding proteins (RBPs) that modulate post-transcriptional control of gene expression using RNA expression data as inputs. By applying this approach to publicly available patient datasets, they identify and experimentally confirm that the RBP hnRNPC contributes to chemotherapy resistance in lung cancer.
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Affiliation(s)
- Konstantin Krismer
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Molly A Bird
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Shohreh Varmeh
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA
| | - Erika D Handly
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Anna Gattinger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Thomas Bernwinkler
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Daniel A Anderson
- Synthetic Biology Center, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Andreas Heinzel
- Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Brian A Joughin
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Yi Wen Kong
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA.
| | - Ian G Cannell
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
| | - Michael B Yaffe
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Divisions of Acute Care Surgery, Trauma and Surgical Critical Care, and Surgical Oncology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.
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12
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Morshed N, Ralvenius WT, Nott A, Watson LA, Rodriguez FH, Akay LA, Joughin BA, Pao P, Penney J, LaRocque L, Mastroeni D, Tsai L, White FM. Phosphoproteomics identifies microglial Siglec-F inflammatory response during neurodegeneration. Mol Syst Biol 2020; 16:e9819. [PMID: 33289969 PMCID: PMC7722784 DOI: 10.15252/msb.20209819] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 06/27/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 12/20/2022] Open
Abstract
Alzheimer's disease (AD) is characterized by the appearance of amyloid-β plaques, neurofibrillary tangles, and inflammation in brain regions involved in memory. Using mass spectrometry, we have quantified the phosphoproteome of the CK-p25, 5XFAD, and Tau P301S mouse models of neurodegeneration. We identified a shared response involving Siglec-F which was upregulated on a subset of reactive microglia. The human paralog Siglec-8 was also upregulated on microglia in AD. Siglec-F and Siglec-8 were upregulated following microglial activation with interferon gamma (IFNγ) in BV-2 cell line and human stem cell-derived microglia models. Siglec-F overexpression activates an endocytic and pyroptotic inflammatory response in BV-2 cells, dependent on its sialic acid substrates and immunoreceptor tyrosine-based inhibition motif (ITIM) phosphorylation sites. Related human Siglecs induced a similar response in BV-2 cells. Collectively, our results point to an important role for mouse Siglec-F and human Siglec-8 in regulating microglial activation during neurodegeneration.
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Affiliation(s)
- Nader Morshed
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
| | - William T Ralvenius
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Alexi Nott
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain SciencesImperial College LondonUK
- UK Dementia Research Institute at Imperial College LondonLondonUK
| | - L Ashley Watson
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Felicia H Rodriguez
- Department of Chemical and Materials EngineeringNew Mexico State UniversityLas CrucesNMUSA
| | - Leyla A Akay
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Brian A Joughin
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Ping‐Chieh Pao
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Jay Penney
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Lauren LaRocque
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Diego Mastroeni
- ASU‐Banner Neurodegenerative Disease Research CenterTempeAZUSA
| | - Li‐Huei Tsai
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
- Broad Institute of MIT and HarvardCambridgeMAUSA
| | - Forest M White
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
- Center for Precision Cancer MedicineMassachusetts Institute of TechnologyCambridgeMAUSA
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13
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Cahill LA, Joughin BA, Kwon WY, Itagaki K, Kirk CH, Shapiro NI, Otterbein LE, Yaffe MB, Lederer JA, Hauser CJ. Multiplexed Plasma Immune Mediator Signatures Can Differentiate Sepsis From NonInfective SIRS: American Surgical Association 2020 Annual Meeting Paper. Ann Surg 2020; 272:604-610. [PMID: 32932316 DOI: 10.1097/sla.0000000000004379] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
OBJECTIVES Sepsis and sterile both release "danger signals' that induce the systemic inflammatory response syndrome (SIRS). So differentiating infection from SIRS can be challenging. Precision diagnostic assays could limit unnecessary antibiotic use, improving outcomes. METHODS After surveying human leukocyte cytokine production responses to sterile damage-associated molecular patterns (DAMPs), bacterial pathogen-associated molecular patterns, and bacteria we created a multiplex assay for 31 cytokines. We then studied plasma from patients with bacteremia, septic shock, "severe sepsis," or trauma (ISS ≥15 with circulating DAMPs) as well as controls. Infections were adjudicated based on post-hospitalization review. Plasma was studied in infection and injury using univariate and multivariate means to determine how such multiplex assays could best distinguish infective from noninfective SIRS. RESULTS Infected patients had high plasma interleukin (IL)-6, IL-1α, and triggering receptor expressed on myeloid cells-1 (TREM-1) compared to controls [false discovery rates (FDR) <0.01, <0.01, <0.0001]. Conversely, injury suppressed many mediators including MDC (FDR <0.0001), TREM-1 (FDR <0.001), IP-10 (FDR <0.01), MCP-3 (FDR <0.05), FLT3L (FDR <0.05), Tweak, (FDR <0.05), GRO-α (FDR <0.05), and ENA-78 (FDR <0.05). In univariate studies, analyte overlap between clinical groups prevented clinical relevance. Multivariate models discriminated injury and infection much better, with the 2-group random-forest model classifying 11/11 injury and 28/29 infection patients correctly in out-of-bag validation. CONCLUSIONS Circulating cytokines in traumatic SIRS differ markedly from those in health or sepsis. Variability limits the accuracy of single-mediator assays but machine learning based on multiplexed plasma assays revealed distinct patterns in sepsis- and injury-related SIRS. Defining biomarker release patterns that distinguish specific SIRS populations might allow decreased antibiotic use in those clinical situations. Large prospective studies are needed to validate and operationalize this approach.
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Affiliation(s)
- Laura A Cahill
- Department of Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Brian A Joughin
- Department of Biological Engineering, David H. Koch Institute for Integrative Cancer Research and Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA
| | - Woon Yong Kwon
- Department of Emergency Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Kiyoshi Itagaki
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Charlotte H Kirk
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Nathan I Shapiro
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Leo E Otterbein
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA
| | - Michael B Yaffe
- Departments of Biology and Biological Engineering; David H. Koch Institute for Integrative Cancer Research and the Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA.,Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - James A Lederer
- Department of Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Carl J Hauser
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
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14
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Amal H, Barak B, Bhat V, Gong G, Joughin BA, Wang X, Wishnok JS, Feng G, Tannenbaum SR. Shank3 mutation in a mouse model of autism leads to changes in the S-nitroso-proteome and affects key proteins involved in vesicle release and synaptic function. Mol Psychiatry 2020; 25:1835-1848. [PMID: 29988084 PMCID: PMC6614015 DOI: 10.1038/s41380-018-0113-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 05/14/2018] [Accepted: 06/05/2018] [Indexed: 12/25/2022]
Abstract
Mutation in the SHANK3 human gene leads to different neuropsychiatric diseases including Autism Spectrum Disorder (ASD), intellectual disabilities and Phelan-McDermid syndrome. Shank3 disruption in mice leads to dysfunction of synaptic transmission, behavior, and development. Protein S-nitrosylation, the nitric oxide (NO•)-mediated posttranslational modification (PTM) of cysteine thiols (SNO), modulates the activity of proteins that regulate key signaling pathways. We tested the hypothesis that Shank3 mutation would generate downstream effects on PTM of critical proteins that lead to modification of synaptic functions. SNO-proteins in two ASD-related brain regions, cortex and striatum of young and adult InsG3680(+/+) mice (a human mutation-based Shank3 mouse model), were identified by an innovative mass spectrometric method, SNOTRAP. We found changes of the SNO-proteome in the mutant compared to WT in both ages. Pathway analysis showed enrichment of processes affected in ASD. SNO-Calcineurin in mutant led to a significant increase of phosphorylated Synapsin1 and CREB, which affect synaptic vesicle mobilization and gene transcription, respectively. A significant increase of 3-nitrotyrosine was found in the cortical regions of the adult mutant, signaling both oxidative and nitrosative stress. Neuronal NO• Synthase (nNOS) was examined for levels and localization in neurons and no significant difference was found in WT vs. mutant. S-nitrosoglutathione concentrations were higher in mutant mice compared to WT. This is the first study on NO•-related molecular changes and SNO-signaling in the brain of an ASD mouse model that allows the characterization and identification of key proteins, cellular pathways, and neurobiological mechanisms that might be affected in ASD.
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Affiliation(s)
- Haitham Amal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Boaz Barak
- McGovern Institute for Brain Research, Massachusetts
Institute of Technology, Cambridge, MA 02139, USA
| | | | - Guanyu Gong
- Department of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, MA 02139, USA
| | - Brian A. Joughin
- Department of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xin Wang
- Department of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, MA 02139, USA
| | - John S. Wishnok
- Department of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, MA 02139, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Massachusetts
Institute of Technology, Cambridge, MA 02139, USA
| | - Steven R. Tannenbaum
- Department of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, MA 02139, USA,Department of Chemistry, Massachusetts Institute of
Technology, Cambridge, MA 02139, USA
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15
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Stopfer LE, Mesfin JM, Joughin BA, Lauffenburger DA, White FM. Multiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition. Nat Commun 2020; 11:2760. [PMID: 32488085 PMCID: PMC7265461 DOI: 10.1038/s41467-020-16588-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [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: 02/18/2020] [Accepted: 05/13/2020] [Indexed: 12/19/2022] Open
Abstract
Peptides bound to class I major histocompatibility complexes (MHC) play a critical role in immune cell recognition and can trigger an antitumor immune response in cancer. Surface MHC levels can be modulated by anticancer agents, altering immunity. However, understanding the peptide repertoire's response to treatment remains challenging and is limited by quantitative mass spectrometry-based strategies lacking normalization controls. We describe an experimental platform that leverages recombinant heavy isotope-coded peptide MHCs (hipMHCs) and multiplex isotope tagging to quantify peptide repertoire alterations using low sample input. HipMHCs improve quantitative accuracy of peptide repertoire changes by normalizing for variation across analyses and enable absolute quantification using internal calibrants to determine copies per cell of MHC antigens, which can inform immunotherapy design. Applying this platform in melanoma cell lines to profile the immunopeptidome response to CDK4/6 inhibition and interferon-γ - known modulators of antigen presentation - uncovers treatment-specific alterations, connecting the intracellular response to extracellular immune presentation.
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Affiliation(s)
- Lauren E Stopfer
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Joshua M Mesfin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Brian A Joughin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Douglas A Lauffenburger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Forest M White
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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16
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Strasser SD, Ghazi PC, Starchenko A, Boukhali M, Edwards A, Suarez-Lopez L, Lyons J, Changelian PS, Monahan JB, Jacobsen J, Brubaker DK, Joughin BA, Yaffe MB, Haas W, Lauffenburger DA, Haigis KM. Substrate-based kinase activity inference identifies MK2 as driver of colitis. Integr Biol (Camb) 2020; 11:301-314. [PMID: 31617572 DOI: 10.1093/intbio/zyz025] [Citation(s) in RCA: 12] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 07/19/2019] [Accepted: 07/28/2019] [Indexed: 12/30/2022]
Abstract
Inflammatory bowel disease (IBD) is a chronic and debilitating disorder that has few treatment options due to a lack of comprehensive understanding of its molecular pathogenesis. We used multiplexed mass spectrometry to collect high-content information on protein phosphorylation in two different mouse models of IBD. Because the biological function of the vast majority of phosphorylation sites remains unknown, we developed Substrate-based Kinase Activity Inference (SKAI), a methodology to infer kinase activity from phosphoproteomic data. This approach draws upon prior knowledge of kinase-substrate interactions to construct custom lists of kinases and their respective substrate sites, termed kinase-substrate sets that employ prior knowledge across organisms. This expansion as much as triples the amount of prior knowledge available. We then used these sets within the Gene Set Enrichment Analysis framework to infer kinase activity based on increased or decreased phosphorylation of its substrates in a dataset. When applied to the phosphoproteomic datasets from the two mouse models, SKAI predicted largely non-overlapping kinase activation profiles. These results suggest that chronic inflammation may arise through activation of largely divergent signaling networks. However, the one kinase inferred to be activated in both mouse models was mitogen-activated protein kinase-activated protein kinase 2 (MAPKAPK2 or MK2), a serine/threonine kinase that functions downstream of p38 stress-activated mitogen-activated protein kinase. Treatment of mice with active colitis with ATI450, an orally bioavailable small molecule inhibitor of the MK2 pathway, reduced inflammatory signaling in the colon and alleviated the clinical and histological features of inflammation. These studies establish MK2 as a therapeutic target in IBD and identify ATI450 as a potential therapy for the disease.
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Affiliation(s)
- Samantha Dale Strasser
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Cancer Research Institute and Division of Genetics, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Phaedra C Ghazi
- Cancer Research Institute and Division of Genetics, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Alina Starchenko
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Cancer Research Institute and Division of Genetics, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Myriam Boukhali
- Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.,Center for Cancer Research, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Amanda Edwards
- Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.,Center for Cancer Research, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Lucia Suarez-Lopez
- Cancer Research Institute and Division of Genetics, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jesse Lyons
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Cancer Research Institute and Division of Genetics, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Paul S Changelian
- Aclaris Therapeutics, Inc., 4320 Forest Park Avenue, St. Louis, MO 63108, USA
| | - Joseph B Monahan
- Aclaris Therapeutics, Inc., 4320 Forest Park Avenue, St. Louis, MO 63108, USA
| | - Jon Jacobsen
- Aclaris Therapeutics, Inc., 4320 Forest Park Avenue, St. Louis, MO 63108, USA
| | - Douglas K Brubaker
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Cancer Research Institute and Division of Genetics, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Brian A Joughin
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Michael B Yaffe
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Wilhelm Haas
- Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.,Center for Cancer Research, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Kevin M Haigis
- Cancer Research Institute and Division of Genetics, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.,Harvard Digestive Disease Center, Harvard Medical School, 320 Longwood Avenue, Boston, MA 02115, USA
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17
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Holland CH, Tanevski J, Perales-Patón J, Gleixner J, Kumar MP, Mereu E, Joughin BA, Stegle O, Lauffenburger DA, Heyn H, Szalai B, Saez-Rodriguez J. Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data. Genome Biol 2020; 21:36. [PMID: 32051003 PMCID: PMC7017576 DOI: 10.1186/s13059-020-1949-z] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [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: 09/03/2019] [Accepted: 01/29/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible to do such an analysis for single cells. However, scRNA-seq data has characteristics such as drop-out events and low library sizes. It is thus not clear if functional TF and pathway analysis tools established for bulk sequencing can be applied to scRNA-seq in a meaningful way. RESULTS To address this question, we perform benchmark studies on simulated and real scRNA-seq data. We include the bulk-RNA tools PROGENy, GO enrichment, and DoRothEA that estimate pathway and transcription factor (TF) activities, respectively, and compare them against the tools SCENIC/AUCell and metaVIPER, designed for scRNA-seq. For the in silico study, we simulate single cells from TF/pathway perturbation bulk RNA-seq experiments. We complement the simulated data with real scRNA-seq data upon CRISPR-mediated knock-out. Our benchmarks on simulated and real data reveal comparable performance to the original bulk data. Additionally, we show that the TF and pathway activities preserve cell type-specific variability by analyzing a mixture sample sequenced with 13 scRNA-seq protocols. We also provide the benchmark data for further use by the community. CONCLUSIONS Our analyses suggest that bulk-based functional analysis tools that use manually curated footprint gene sets can be applied to scRNA-seq data, partially outperforming dedicated single-cell tools. Furthermore, we find that the performance of functional analysis tools is more sensitive to the gene sets than to the statistic used.
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Affiliation(s)
- Christian H Holland
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, Aachen, Germany
| | - Jovan Tanevski
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany
- Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Javier Perales-Patón
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany
| | - Jan Gleixner
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Manu P Kumar
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Elisabetta Mereu
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Brian A Joughin
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Biology, MIT, Cambridge, MA, USA
| | - Oliver Stegle
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Bence Szalai
- Faculty of Medicine, Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany.
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, Aachen, Germany.
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18
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Brubaker DK, Paulo JA, Sheth S, Poulin EJ, Popow O, Joughin BA, Strasser SD, Starchenko A, Gygi SP, Lauffenburger DA, Haigis KM. Proteogenomic Network Analysis of Context-Specific KRAS Signaling in Mouse-to-Human Cross-Species Translation. Cell Syst 2019; 9:258-270.e6. [PMID: 31521603 PMCID: PMC6816257 DOI: 10.1016/j.cels.2019.07.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 12/30/2018] [Revised: 06/01/2019] [Accepted: 07/15/2019] [Indexed: 12/21/2022]
Abstract
The highest frequencies of KRAS mutations occur in colorectal carcinoma (CRC) and pancreatic ductal adenocarcinoma (PDAC). The ability to target downstream pathways mediating KRAS oncogenicity is limited by an incomplete understanding of the contextual cues modulating the signaling output of activated K-RAS. We performed mass spectrometry on mouse tissues expressing wild-type or mutant Kras to determine how tissue context and genetic background modulate oncogenic signaling. Mutant Kras dramatically altered the proteomes and phosphoproteomes of preneoplastic and neoplastic colons and pancreases in a context-specific manner. We developed an approach to statistically humanize the mouse networks with data from human cancer and identified genes within the humanized CRC and PDAC networks synthetically lethal with mutant KRAS. Our studies demonstrate the context-dependent plasticity of oncogenic signaling, identify non-canonical mediators of KRAS oncogenicity within the KRAS-regulated signaling network, and demonstrate how statistical integration of mouse and human datasets can reveal cross-species therapeutic insights.
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Affiliation(s)
- Douglas K Brubaker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Shikha Sheth
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Emily J Poulin
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Olesja Popow
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Brian A Joughin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Samantha Dale Strasser
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alina Starchenko
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Kevin M Haigis
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Harvard Digestive Disease Center, Harvard Medical School, Boston, MA 02115, USA.
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19
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Patterson JC, Joughin BA, Prota AE, Mühlethaler T, Jonas OH, Whitman MA, Varmeh S, Chen S, Balk SP, Steinmetz MO, Lauffenburger DA, Yaffe MB. VISAGE Reveals a Targetable Mitotic Spindle Vulnerability in Cancer Cells. Cell Syst 2019; 9:74-92.e8. [PMID: 31302152 PMCID: PMC6688637 DOI: 10.1016/j.cels.2019.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 08/28/2017] [Revised: 08/30/2018] [Accepted: 05/22/2019] [Indexed: 12/21/2022]
Abstract
There is an unmet need for new antimitotic drug combinations that target cancer-specific vulnerabilities. Based on our finding of elevated biomolecule oxidation in mitotically arrested cancer cells, we combined Plk1 inhibitors with TH588, an MTH1 inhibitor that prevents detoxification of oxidized nucleotide triphosphates. This combination showed robust synergistic killing of cancer, but not normal, cells that, surprisingly, was MTH1-independent. To dissect the underlying synergistic mechanism, we developed VISAGE, a strategy integrating experimental synergy quantification with computational-pathway-based gene expression analysis. VISAGE predicted, and we experimentally confirmed, that this synergistic combination treatment targeted the mitotic spindle. Specifically, TH588 binding to β-tubulin impaired microtubule assembly, which when combined with Plk1 blockade, synergistically disrupted mitotic chromosome positioning to the spindle midzone. These findings identify a cancer-specific mitotic vulnerability that is targetable using Plk1 inhibitors with microtubule-destabilizing agents and highlight the general utility of the VISAGE approach to elucidate molecular mechanisms of drug synergy.
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Affiliation(s)
- Jesse C Patterson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian A Joughin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andrea E Prota
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Tobias Mühlethaler
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Oliver H Jonas
- Department of Radiology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Matthew A Whitman
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shohreh Varmeh
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sen Chen
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Steven P Balk
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland; Biozentrum, University of Basel 4056 Basel, Switzerland
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael B Yaffe
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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20
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Poulin EJ, Bera AK, Lu J, Lin YJ, Strasser SD, Paulo JA, Huang TQ, Morales C, Yan W, Cook J, Nowak JA, Brubaker DK, Joughin BA, Johnson CW, DeStefanis RA, Ghazi PC, Gondi S, Wales TE, Iacob RE, Bogdanova L, Gierut JJ, Li Y, Engen JR, Perez-Mancera PA, Braun BS, Gygi SP, Lauffenburger DA, Westover KD, Haigis KM. Tissue-Specific Oncogenic Activity of KRAS A146T. Cancer Discov 2019; 9:738-755. [PMID: 30952657 PMCID: PMC6548671 DOI: 10.1158/2159-8290.cd-18-1220] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/06/2019] [Accepted: 04/02/2019] [Indexed: 12/16/2022]
Abstract
KRAS is the most frequently mutated oncogene. The incidence of specific KRAS alleles varies between cancers from different sites, but it is unclear whether allelic selection results from biological selection for specific mutant KRAS proteins. We used a cross-disciplinary approach to compare KRASG12D, a common mutant form, and KRASA146T, a mutant that occurs only in selected cancers. Biochemical and structural studies demonstrated that KRASA146T exhibits a marked extension of switch 1 away from the protein body and nucleotide binding site, which activates KRAS by promoting a high rate of intrinsic and guanine nucleotide exchange factor-induced nucleotide exchange. Using mice genetically engineered to express either allele, we found that KRASG12D and KRASA146T exhibit distinct tissue-specific effects on homeostasis that mirror mutational frequencies in human cancers. These tissue-specific phenotypes result from allele-specific signaling properties, demonstrating that context-dependent variations in signaling downstream of different KRAS mutants drive the KRAS mutational pattern seen in cancer. SIGNIFICANCE: Although epidemiologic and clinical studies have suggested allele-specific behaviors for KRAS, experimental evidence for allele-specific biological properties is limited. We combined structural biology, mass spectrometry, and mouse modeling to demonstrate that the selection for specific KRAS mutants in human cancers from different tissues is due to their distinct signaling properties.See related commentary by Hobbs and Der, p. 696.This article is highlighted in the In This Issue feature, p. 681.
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Affiliation(s)
- Emily J Poulin
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Asim K Bera
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Jia Lu
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Yi-Jang Lin
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Samantha Dale Strasser
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Tannie Q Huang
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Carolina Morales
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Wei Yan
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Joshua Cook
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jonathan A Nowak
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Douglas K Brubaker
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Brian A Joughin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christian W Johnson
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Rebecca A DeStefanis
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Phaedra C Ghazi
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Sudershan Gondi
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Lana Bogdanova
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Jessica J Gierut
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Yina Li
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Pedro A Perez-Mancera
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Benjamin S Braun
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.
| | - Kevin M Haigis
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts.
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Harvard Digestive Disease Center, Harvard Medical School, Boston, Massachusetts
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21
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van de Kooij B, Creixell P, van Vlimmeren A, Joughin BA, Miller CJ, Haider N, Simpson CD, Linding R, Stambolic V, Turk BE, Yaffe MB. Comprehensive substrate specificity profiling of the human Nek kinome reveals unexpected signaling outputs. eLife 2019; 8:44635. [PMID: 31124786 PMCID: PMC6570481 DOI: 10.7554/elife.44635] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/13/2019] [Indexed: 12/25/2022] Open
Abstract
Human NimA-related kinases (Neks) have multiple mitotic and non-mitotic functions, but few substrates are known. We systematically determined the phosphorylation-site motifs for the entire Nek kinase family, except for Nek11. While all Nek kinases strongly select for hydrophobic residues in the −3 position, the family separates into four distinct groups based on specificity for a serine versus threonine phospho-acceptor, and preference for basic or acidic residues in other positions. Unlike Nek1-Nek9, Nek10 is a dual-specificity kinase that efficiently phosphorylates itself and peptide substrates on serine and tyrosine, and its activity is enhanced by tyrosine auto-phosphorylation. Nek10 dual-specificity depends on residues in the HRD+2 and APE-4 positions that are uncommon in either serine/threonine or tyrosine kinases. Finally, we show that the phosphorylation-site motifs for the mitotic kinases Nek6, Nek7 and Nek9 are essentially identical to that of their upstream activator Plk1, suggesting that Nek6/7/9 function as phospho-motif amplifiers of Plk1 signaling.
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Affiliation(s)
- Bert van de Kooij
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States
| | - Pau Creixell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States
| | - Anne van Vlimmeren
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States
| | - Brian A Joughin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States
| | - Chad J Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, United States
| | - Nasir Haider
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Craig D Simpson
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rune Linding
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vuk Stambolic
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, United States
| | - Michael B Yaffe
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States.,Department of Surgery, Beth Israel Deaconess Medical Center, Divisions of Acute Care Surgery, Trauma, and Critical Care and Surgical Oncology, Harvard Medical School, Boston, United States
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22
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Rohani N, Hao L, Alexis MS, Joughin BA, Krismer K, Moufarrej MN, Soltis AR, Lauffenburger DA, Yaffe MB, Burge CB, Bhatia SN, Gertler FB. Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes. Cancer Res 2019; 79:1952-1966. [PMID: 30755444 PMCID: PMC6467770 DOI: 10.1158/0008-5472.can-18-1604] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [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: 05/25/2018] [Revised: 09/19/2018] [Accepted: 02/06/2019] [Indexed: 01/07/2023]
Abstract
Acidosis is a fundamental feature of the tumor microenvironment, which directly regulates tumor cell invasion by affecting immune cell function, clonal cell evolution, and drug resistance. Despite the important association of tumor microenvironment acidosis with tumor cell invasion, relatively little is known regarding which areas within a tumor are acidic and how acidosis influences gene expression to promote invasion. Here, we injected a labeled pH-responsive peptide to mark acidic regions within tumors. Surprisingly, acidic regions were not restricted to hypoxic areas and overlapped with highly proliferative, invasive regions at the tumor-stroma interface, which were marked by increased expression of matrix metalloproteinases and degradation of the basement membrane. RNA-seq analysis of cells exposed to low pH conditions revealed a general rewiring of the transcriptome that involved RNA splicing and enriched for targets of RNA binding proteins with specificity for AU-rich motifs. Alternative splicing of Mena and CD44, which play important isoform-specific roles in metastasis and drug resistance, respectively, was sensitive to histone acetylation status. Strikingly, this program of alternative splicing was reversed in vitro and in vivo through neutralization experiments that mitigated acidic conditions. These findings highlight a previously underappreciated role for localized acidification of tumor microenvironment in the expression of an alternative splicing-dependent tumor invasion program. SIGNIFICANCE: This study expands our understanding of acidosis within the tumor microenvironment and indicates that acidosis induces potentially therapeutically actionable changes to alternative splicing.
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Affiliation(s)
- Nazanin Rohani
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts.
| | - Liangliang Hao
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Maria S Alexis
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
| | - Brian A Joughin
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
- Center for Precision Cancer Medicine, MIT, Cambridge, Massachusetts
| | - Konstantin Krismer
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
- Center for Precision Cancer Medicine, MIT, Cambridge, Massachusetts
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts
| | - Mira N Moufarrej
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
| | - Anthony R Soltis
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
| | | | - Michael B Yaffe
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
- Center for Precision Cancer Medicine, MIT, Cambridge, Massachusetts
- Department of Biology, MIT, Cambridge, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | | | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Howard Hughes Medical Institute, Cambridge, Massachusetts
| | - Frank B Gertler
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts.
- Department of Biology, MIT, Cambridge, Massachusetts
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23
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Patterson JC, Joughin BA, van de Kooij B, Lim DC, Lauffenburger DA, Yaffe MB. ROS and Oxidative Stress Are Elevated in Mitosis during Asynchronous Cell Cycle Progression and Are Exacerbated by Mitotic Arrest. Cell Syst 2019; 8:163-167.e2. [PMID: 30797774 DOI: 10.1016/j.cels.2019.01.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/11/2019] [Accepted: 01/22/2019] [Indexed: 01/30/2023]
Abstract
Although elevated levels of reactive oxygen species (ROS) have been observed in cancer cells and cancer cells aberrantly proliferate, it is not known whether the level of reactive oxygen species and the accumulation of oxidative damage to macromolecules vary across the cell cycle. Here, we measure the prevalence of reactive oxygen species and of biomolecule oxidation across the cell cycle in freely cycling cancer cells. We report that reactive oxygen species vary during the cell cycle and peak in mitosis, resulting in mitotic accumulation of oxidized protein cysteine residues. Prolonged mitotic arrest further increased the levels of ROS and the abundance of oxidatively damaged biomolecules, including cysteine-sulfenic-acid-containing proteins and 8-oxoguanine. These finding suggest that mitotic arrest agents may enhance the effects of ROS-dependent anticancer therapies.
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Affiliation(s)
- Jesse C Patterson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian A Joughin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bert van de Kooij
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel C Lim
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael B Yaffe
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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24
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Randall EC, Emdal KB, Laramy JK, Kim M, Roos A, Calligaris D, Regan MS, Gupta SK, Mladek AC, Carlson BL, Johnson AJ, Lu FK, Xie XS, Joughin BA, Reddy RJ, Peng S, Abdelmoula WM, Jackson PR, Kolluri A, Kellersberger KA, Agar JN, Lauffenburger DA, Swanson KR, Tran NL, Elmquist WF, White FM, Sarkaria JN, Agar NYR. Integrated mapping of pharmacokinetics and pharmacodynamics in a patient-derived xenograft model of glioblastoma. Nat Commun 2018; 9:4904. [PMID: 30464169 PMCID: PMC6249307 DOI: 10.1038/s41467-018-07334-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 10/23/2018] [Indexed: 12/13/2022] Open
Abstract
Therapeutic options for the treatment of glioblastoma remain inadequate despite concerted research efforts in drug development. Therapeutic failure can result from poor permeability of the blood-brain barrier, heterogeneous drug distribution, and development of resistance. Elucidation of relationships among such parameters could enable the development of predictive models of drug response in patients and inform drug development. Complementary analyses were applied to a glioblastoma patient-derived xenograft model in order to quantitatively map distribution and resulting cellular response to the EGFR inhibitor erlotinib. Mass spectrometry images of erlotinib were registered to histology and magnetic resonance images in order to correlate drug distribution with tumor characteristics. Phosphoproteomics and immunohistochemistry were used to assess protein signaling in response to drug, and integrated with transcriptional response using mRNA sequencing. This comprehensive dataset provides simultaneous insight into pharmacokinetics and pharmacodynamics and indicates that erlotinib delivery to intracranial tumors is insufficient to inhibit EGFR tyrosine kinase signaling.
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Affiliation(s)
- Elizabeth C Randall
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kristina B Emdal
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St, Cambridge, MA, 02142, USA
| | - Janice K Laramy
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Minjee Kim
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Alison Roos
- Department of Cancer Biology, Mayo Clinic, 13400 E. Shea Blvd.MCCRB 03-055, Scottsdale, AZ, 85259, USA
| | - David Calligaris
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Michael S Regan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Shiv K Gupta
- Department of Radiation Oncology, Mayo Clinic, 200 First St SW, Rochester, MN, 55902, USA
| | - Ann C Mladek
- Department of Radiation Oncology, Mayo Clinic, 200 First St SW, Rochester, MN, 55902, USA
| | - Brett L Carlson
- Department of Radiation Oncology, Mayo Clinic, 200 First St SW, Rochester, MN, 55902, USA
| | - Aaron J Johnson
- Department of Immunology, Mayo Clinic, 200 First St SW, Rochester, MN, 55902, USA
| | - Fa-Ke Lu
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Biomedical Engineering, Binghamton University, State University of New York, Binghamton, NY, 13902, USA
| | - X Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Brian A Joughin
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St, Cambridge, MA, 02142, USA
| | - Raven J Reddy
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St, Cambridge, MA, 02142, USA
| | - Sen Peng
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Walid M Abdelmoula
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Pamela R Jackson
- Mathematical NeuroOncology Lab, Department of Neurosurgery, Mayo Clinic, 5777 E. Mayo Blvd, Phoenix, AZ, 85054, USA
| | - Aarti Kolluri
- Mathematical NeuroOncology Lab, Department of Neurosurgery, Mayo Clinic, 5777 E. Mayo Blvd, Phoenix, AZ, 85054, USA
| | | | - Jeffrey N Agar
- Department of Chemistry and Chemical Biology, Northeastern University, 412 TF (140 The Fenway), Boston, MA, 02111, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St, Cambridge, MA, 02142, USA
| | - Kristin R Swanson
- Mathematical NeuroOncology Lab, Department of Neurosurgery, Mayo Clinic, 5777 E. Mayo Blvd, Phoenix, AZ, 85054, USA
| | - Nhan L Tran
- Department of Cancer Biology, Mayo Clinic, 13400 E. Shea Blvd.MCCRB 03-055, Scottsdale, AZ, 85259, USA
| | - William F Elmquist
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Forest M White
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St, Cambridge, MA, 02142, USA
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, 200 First St SW, Rochester, MN, 55902, USA
| | - Nathalie Y R Agar
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.
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25
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Jones DS, Jenney AP, Joughin BA, Sorger PK, Lauffenburger DA. Inflammatory but not mitogenic contexts prime synovial fibroblasts for compensatory signaling responses to p38 inhibition. Sci Signal 2018; 11:11/520/eaal1601. [PMID: 29511118 DOI: 10.1126/scisignal.aal1601] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory disorder that causes joint pain, swelling, and loss of function. Development of effective new drugs has proven challenging in part because of the complexities and interconnected nature of intracellular signaling networks that complicate the effects of pharmacological interventions. We characterized the kinase signaling pathways that are activated in RA and evaluated the multivariate effects of targeted inhibitors. Synovial fluids from RA patients activated the kinase signaling pathways JAK, JNK, p38, and MEK in synovial fibroblasts (SFs), a stromal cell type that promotes RA progression. Kinase inhibitors enhanced signaling of "off-target" pathways in a manner dependent on stimulatory context. Inhibitors of p38, which have been widely explored in clinical trials for RA, resulted in undesirable increases in nuclear factor κB (NF-κB), JNK, and MEK signaling in SFs in inflammatory, but not mitogenic, contexts. This was mediated by the transcription factor CREB, which functions in part within a negative feedback loop in MAPK signaling. CREB activation was induced predominately by p38 in response to inflammatory stimuli, but by MEK in response to mitogenic stimuli; hence, the effects of drugs targeting p38 or MEK were markedly different in SFs cultured under mitogenic or inflammatory conditions. Together, these findings illustrate how stimulatory context can alter dominance in pathway cross-talk even for a fixed network topology, thereby providing a rationale for why p38 inhibitors deliver limited benefits in RA and demonstrating the need for careful consideration of p38-targeted drugs in inflammation-related disorders.
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Affiliation(s)
- Douglas S Jones
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Laboratory of Systems Pharmacology, Library of Integrated Network-based Cellular Signatures Center, Harvard Medical School, Boston, MA 02115, USA
| | - Anne P Jenney
- Laboratory of Systems Pharmacology, Library of Integrated Network-based Cellular Signatures Center, Harvard Medical School, Boston, MA 02115, USA
| | - Brian A Joughin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Library of Integrated Network-based Cellular Signatures Center, Harvard Medical School, Boston, MA 02115, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. .,Koch Institute for Integrative Cancer Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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26
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Archer TC, Fertig EJ, Gosline SJC, Hafner M, Hughes SK, Joughin BA, Meyer AS, Piccolo SR, Shajahan-Haq AN. Systems Approaches to Cancer Biology. Cancer Res 2016; 76:6774-6777. [PMID: 27864348 PMCID: PMC5135591 DOI: 10.1158/0008-5472.can-16-1580] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/27/2016] [Accepted: 09/12/2016] [Indexed: 01/30/2023]
Abstract
Cancer systems biology aims to understand cancer as an integrated system of genes, proteins, networks, and interactions rather than an entity of isolated molecular and cellular components. The inaugural Systems Approaches to Cancer Biology Conference, cosponsored by the Association of Early Career Cancer Systems Biologists and the National Cancer Institute of the NIH, focused on the interdisciplinary field of cancer systems biology and the challenging cancer questions that are best addressed through the combination of experimental and computational analyses. Attendees found that elucidating the many molecular features of cancer inevitably reveals new forms of complexity and concluded that ensuring the reproducibility and impact of cancer systems biology studies will require widespread method and data sharing and, ultimately, the translation of important findings to the clinic. Cancer Res; 76(23); 6774-7. ©2016 AACR.
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Affiliation(s)
- Tenley C Archer
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts
| | - Elana J Fertig
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | | | - Marc Hafner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| | - Shannon K Hughes
- Division of Cancer Biology, National Cancer Institute of the NIH, Rockville, Maryland
| | - Brian A Joughin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Aaron S Meyer
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.
| | | | - Ayesha N Shajahan-Haq
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
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27
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Nagel ZD, Kitange GJ, Gupta SK, Joughin BA, Chaim IA, Mazzucato P, Lauffenburger DA, Sarkaria JN, Samson LD. DNA Repair Capacity in Multiple Pathways Predicts Chemoresistance in Glioblastoma Multiforme. Cancer Res 2016; 77:198-206. [PMID: 27793847 DOI: 10.1158/0008-5472.can-16-1151] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 09/28/2016] [Accepted: 10/20/2016] [Indexed: 12/21/2022]
Abstract
Cancer cells can resist the effects of DNA-damaging therapeutic agents via utilization of DNA repair pathways, suggesting that DNA repair capacity (DRC) measurements in cancer cells could be used to identify patients most likely to respond to treatment. However, the limitations of available technologies have so far precluded adoption of this approach in the clinic. We recently developed fluorescence-based multiplexed host cell reactivation (FM-HCR) assays to measure DRC in multiple pathways. Here we apply a mathematical model that uses DRC in multiple pathways to predict cellular resistance to killing by DNA-damaging agents. This model, developed using FM-HCR and drug sensitivity measurements in 24 human lymphoblastoid cell lines, was applied to a panel of 12 patient-derived xenograft (PDX) models of glioblastoma to predict glioblastoma response to treatment with the chemotherapeutic DNA-damaging agent temozolomide. This work showed that, in addition to changes in O6-methylguanine DNA methyltransferase (MGMT) activity, small changes in mismatch repair (MMR), nucleotide excision repair (NER), and homologous recombination (HR) capacity contributed to acquired temozolomide resistance in PDX models and led to reduced relative survival prolongation following temozolomide treatment of orthotopic mouse models in vivo Our data indicate that measuring the combined status of MMR, HR, NER, and MGMT provided a more robust prediction of temozolomide resistance than assessments of MGMT activity alone. Cancer Res; 77(1); 198-206. ©2016 AACR.
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Affiliation(s)
- Zachary D Nagel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Gaspar J Kitange
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Shiv K Gupta
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Brian A Joughin
- David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts
| | - Isaac A Chaim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Patrizia Mazzucato
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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28
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Hughes SK, Oudin MJ, Tadros J, Neil J, Del Rosario A, Joughin BA, Ritsma L, Wyckoff J, Vasile E, Eddy R, Philippar U, Lussiez A, Condeelis JS, van Rheenen J, White F, Lauffenburger DA, Gertler FB. PTP1B-dependent regulation of receptor tyrosine kinase signaling by the actin-binding protein Mena. Mol Biol Cell 2015; 26:3867-78. [PMID: 26337385 PMCID: PMC4626070 DOI: 10.1091/mbc.e15-06-0442] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 06/29/2015] [Accepted: 08/25/2015] [Indexed: 12/17/2022] Open
Abstract
The actin-binding protein Mena regulates RTK signaling after growth factor stimulation in tumor cells by a novel mechanism. The alternatively spliced MenaINV isoform disrupts this attenuation to drive sensitivity to growth factors, resistance to targeted inhibitors, and ultimately tumor invasion and metastasis. During breast cancer progression, alternative mRNA splicing produces functionally distinct isoforms of Mena, an actin regulator with roles in cell migration and metastasis. Aggressive tumor cell subpopulations express MenaINV, which promotes tumor cell invasion by potentiating EGF responses. However, the mechanism by which this occurs is unknown. Here we report that Mena associates constitutively with the tyrosine phosphatase PTP1B and mediates a novel negative feedback mechanism that attenuates receptor tyrosine kinase signaling. On EGF stimulation, complexes containing Mena and PTP1B are recruited to the EGFR, causing receptor dephosphorylation and leading to decreased motility responses. Mena also interacts with the 5′ inositol phosphatase SHIP2, which is important for the recruitment of the Mena-PTP1B complex to the EGFR. When MenaINV is expressed, PTP1B recruitment to the EGFR is impaired, providing a mechanism for growth factor sensitization to EGF, as well as HGF and IGF, and increased resistance to EGFR and Met inhibitors in signaling and motility assays. In sum, we demonstrate that Mena plays an important role in regulating growth factor–induced signaling. Disruption of this attenuation by MenaINV sensitizes tumor cells to low–growth factor concentrations, thereby increasing the migration and invasion responses that contribute to aggressive, malignant cell phenotypes.
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Affiliation(s)
- Shannon K Hughes
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Madeleine J Oudin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jenny Tadros
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jason Neil
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Amanda Del Rosario
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Brian A Joughin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Laila Ritsma
- Cancer Genomics Netherlands-Hubrecht Institute-KNAW and University Medical Centre Utrecht, 3584 CX Utrecht, Netherlands
| | - Jeff Wyckoff
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461
| | - Eliza Vasile
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Robert Eddy
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461
| | - Ulrike Philippar
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Alisha Lussiez
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - John S Condeelis
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461
| | - Jacco van Rheenen
- Cancer Genomics Netherlands-Hubrecht Institute-KNAW and University Medical Centre Utrecht, 3584 CX Utrecht, Netherlands
| | - Forest White
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Douglas A Lauffenburger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Frank B Gertler
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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Travers T, Shao H, Joughin BA, Lauffenburger DA, Wells A, Camacho CJ. Tandem phosphorylation within an intrinsically disordered region regulates ACTN4 function. Sci Signal 2015; 8:ra51. [PMID: 26012634 PMCID: PMC4522051 DOI: 10.1126/scisignal.aaa1977] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Phosphorylated residues occur preferentially in the intrinsically disordered regions of eukaryotic proteins. In the disordered amino-terminal region of human α-actinin-4 (ACTN4), Tyr(4) and Tyr(31) are phosphorylated in cells stimulated with epidermal growth factor (EGF), and a mutant with phosphorylation-mimicking mutations of both tyrosines exhibits reduced interaction with actin in vitro. Cleavage of ACTN4 by m-calpain, a protease that in motile cells is predominantly activated at the rear, removes the Tyr(4) site. We found that introducing a phosphomimetic mutation at only Tyr(31) was sufficient to inhibit the interaction with actin in vitro. However, molecular dynamics simulations predicted that Tyr(31) is mostly buried and that phosphorylation of Tyr(4) would increase the solvent exposure and thus kinase accessibility of Tyr(31). In fibroblast cells, EGF stimulation increased tyrosine phosphorylation of a mutant form of ACTN4 with a phosphorylation-mimicking residue at Tyr(4), whereas a truncated mutant representing the product of m-calpain cleavage exhibited EGF-stimulated tyrosine phosphorylation at a background amount similar to that observed for a double phosphomimetic mutant of Tyr(4) and Tyr(31). We also found that inhibition of the receptor tyrosine kinases of the TAM family, such as AXL, blocked EGF-stimulated tyrosine phosphorylation of ACTN4. Mathematical modeling predicted that the kinetics of phosphorylation at Tyr(31) can be dictated by the kinase affinity for Tyr(4). This study suggests that tandem-site phosphorylation within intrinsically disordered regions provides a mechanism for a site to function as a switch to reveal a nearby function-regulating site.
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Affiliation(s)
- Timothy Travers
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Hanshuang Shao
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Brian A Joughin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alan Wells
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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Meacham CE, Lawton LN, Soto-Feliciano YM, Pritchard JR, Joughin BA, Ehrenberger T, Fenouille N, Zuber J, Williams RT, Young RA, Hemann MT. A genome-scale in vivo loss-of-function screen identifies Phf6 as a lineage-specific regulator of leukemia cell growth. Genes Dev 2015; 29:483-8. [PMID: 25737277 PMCID: PMC4358400 DOI: 10.1101/gad.254151.114] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [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] [Indexed: 11/24/2022]
Abstract
Meacham et al. performed a genome-scale shRNA screen for modulators of B-cell leukemia progression in vivo and revealed dramatic distinctions between the relative effects of shRNAs on the growth of tumor cells in culture versus in their native microenvironment. They identified “context-specific” regulators of leukemia development, including the gene encoding the zinc finger protein Phf6. While inactivating mutations in Phf6 are commonly observed in human myeloid and T-cell malignancies, they found that Phf6 suppression in B-cell malignancies impairs tumor progression. We performed a genome-scale shRNA screen for modulators of B-cell leukemia progression in vivo. Results from this work revealed dramatic distinctions between the relative effects of shRNAs on the growth of tumor cells in culture versus in their native microenvironment. Specifically, we identified many “context-specific” regulators of leukemia development. These included the gene encoding the zinc finger protein Phf6. While inactivating mutations in PHF6 are commonly observed in human myeloid and T-cell malignancies, we found that Phf6 suppression in B-cell malignancies impairs tumor progression. Thus, Phf6 is a “lineage-specific” cancer gene that plays opposing roles in developmentally distinct hematopoietic malignancies.
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Affiliation(s)
- Corbin E Meacham
- The Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Lee N Lawton
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Yadira M Soto-Feliciano
- The Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Justin R Pritchard
- The Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Brian A Joughin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tobias Ehrenberger
- The Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Nina Fenouille
- The Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Johannes Zuber
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Richard T Williams
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Michael T Hemann
- The Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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Joughin BA, Liu C, Lauffenburger DA, Hogue CWV, Yaffe MB. Protein kinases display minimal interpositional dependence on substrate sequence: potential implications for the evolution of signalling networks. Philos Trans R Soc Lond B Biol Sci 2012; 367:2574-83. [PMID: 22889908 DOI: 10.1098/rstb.2012.0010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Characterization of in vitro substrates of protein kinases by peptide library screening provides a wealth of information on the substrate specificity of kinases for amino acids at particular positions relative to the site of phosphorylation, but provides no information concerning interdependence among positions. High-throughput techniques have recently made it feasible to identify large numbers of in vivo kinase substrates. We used data from experiments on the kinases ATM/ATR and CDK1, and curated CK2 substrates to evaluate the prevalence of interactions between substrate positions within a motif and the utility of these interactions in predicting kinase substrates. Among these data, evidence of interpositional sequence dependencies is strikingly rare, and what dependency exists does little to aid in the prediction of novel kinase substrates. Significant increases in the ability of models to predict kinase-substrate specificity beyond position-independent models must come largely from inclusion of elements of biological and cellular context, rather than further analysis of substrate sequences alone. Our results suggest that, evolutionarily, kinase substrate fitness exists in a smooth energetic landscape. Taken with results from others indicating that phosphopeptide-binding domains do exhibit interpositional dependence, our data suggest that incorporation of new substrate molecules into phospho-signalling networks may be rate-limited by the evolution of suitability for binding by phosphopeptide-binding domains.
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Affiliation(s)
- Brian A Joughin
- The David H. Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Grosstessner-Hain K, Hegemann B, Novatchkova M, Rameseder J, Joughin BA, Hudecz O, Roitinger E, Pichler P, Kraut N, Yaffe MB, Peters JM, Mechtler K. Quantitative phospho-proteomics to investigate the polo-like kinase 1-dependent phospho-proteome. Mol Cell Proteomics 2011; 10:M111.008540. [PMID: 21857030 PMCID: PMC3226402 DOI: 10.1074/mcp.m111.008540] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 07/12/2011] [Indexed: 11/06/2022] Open
Abstract
Polo-like kinase 1 (PLK1) is a key regulator of mitotic progression and cell division, and small molecule inhibitors of PLK1 are undergoing clinical trials to evaluate their utility in cancer therapy. Despite this importance, current knowledge about the identity of PLK1 substrates is limited. Here we present the results of a proteome-wide analysis of PLK1-regulated phosphorylation sites in mitotic human cells. We compared phosphorylation sites in HeLa cells that were or were not treated with the PLK1-inhibitor BI 4834, by labeling peptides via methyl esterification, fractionation of peptides by strong cation exchange chromatography, and phosphopeptide enrichment via immobilized metal affinity chromatography. Analysis by quantitative mass spectrometry identified 4070 unique mitotic phosphorylation sites on 2069 proteins. Of these, 401 proteins contained one or multiple phosphorylation sites whose abundance was decreased by PLK1 inhibition. These include proteins implicated in PLK1-regulated processes such as DNA damage, mitotic spindle formation, spindle assembly checkpoint signaling, and chromosome segregation, but also numerous proteins that were not suspected to be regulated by PLK1. Analysis of amino acid sequence motifs among phosphorylation sites down-regulated under PLK1 inhibition in this data set identified two potential novel variants of the PLK1 consensus motif.
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Affiliation(s)
| | - Björn Hegemann
- From the ‡Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
- ¶¶Present address: Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zürich, Switzerland
| | - Maria Novatchkova
- From the ‡Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
| | - Jonathan Rameseder
- ¶Computational Systems Biology Initiative
- ‖Koch Institute for Integrated Cancer Research
| | | | - Otto Hudecz
- §Institute of Molecular Biotechnology (IMBA), 1030 Vienna, Austria
| | - Elisabeth Roitinger
- From the ‡Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
| | - Peter Pichler
- ‡‡Christian Doppler Laboratory for Proteome Analysis, 1030 Vienna, Austria; and
| | | | - Michael B. Yaffe
- ‖Koch Institute for Integrated Cancer Research
- **Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave Cambridge, MA 02139
| | - Jan-Michael Peters
- From the ‡Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
| | - Karl Mechtler
- From the ‡Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
- §Institute of Molecular Biotechnology (IMBA), 1030 Vienna, Austria
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Alexander J, Lim D, Joughin BA, Hegemann B, Hutchins JRA, Ehrenberger T, Ivins F, Sessa F, Hudecz O, Nigg EA, Fry AM, Musacchio A, Stukenberg PT, Mechtler K, Peters JM, Smerdon SJ, Yaffe MB. Spatial exclusivity combined with positive and negative selection of phosphorylation motifs is the basis for context-dependent mitotic signaling. Sci Signal 2011; 4:ra42. [PMID: 21712545 DOI: 10.1126/scisignal.2001796] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The timing and localization of events during mitosis are controlled by the regulated phosphorylation of proteins by the mitotic kinases, which include Aurora A, Aurora B, Nek2 (never in mitosis kinase 2), Plk1 (Polo-like kinase 1), and the cyclin-dependent kinase complex Cdk1/cyclin B. Although mitotic kinases can have overlapping subcellular localizations, each kinase appears to phosphorylate its substrates on distinct sites. To gain insight into the relative importance of local sequence context in kinase selectivity, identify previously unknown substrates of these five mitotic kinases, and explore potential mechanisms for substrate discrimination, we determined the optimal substrate motifs of these major mitotic kinases by positional scanning oriented peptide library screening (PS-OPLS). We verified individual motifs with in vitro peptide kinetic studies and used structural modeling to rationalize the kinase-specific selection of key motif-determining residues at the molecular level. Cross comparisons among the phosphorylation site selectivity motifs of these kinases revealed an evolutionarily conserved mutual exclusion mechanism in which the positively and negatively selected portions of the phosphorylation motifs of mitotic kinases, together with their subcellular localizations, result in proper substrate targeting in a coordinated manner during mitosis.
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Affiliation(s)
- Jes Alexander
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB, Lauffenburger DA, White FM. PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies. Mol Cell Proteomics 2010; 9:2558-70. [PMID: 20631208 DOI: 10.1074/mcp.m110.001206] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The rate of discovery of post-translational modification (PTM) sites is increasing rapidly and is significantly outpacing our biological understanding of the function and regulation of those modifications. To help meet this challenge, we have created PTMScout, a web-based interface for viewing, manipulating, and analyzing high throughput experimental measurements of PTMs in an effort to facilitate biological understanding of protein modifications in signaling networks. PTMScout is constructed around a custom database of PTM experiments and contains information from external protein and post-translational resources, including gene ontology annotations, Pfam domains, and Scansite predictions of kinase and phosphopeptide binding domain interactions. PTMScout functionality comprises data set comparison tools, data set summary views, and tools for protein assignments of peptides identified by mass spectrometry. Analysis tools in PTMScout focus on informed subset selection via common criteria and on automated hypothesis generation through subset labeling derived from identification of statistically significant enrichment of other annotations in the experiment. Subset selection can be applied through the PTMScout flexible query interface available for quantitative data measurements and data annotations as well as an interface for importing data set groupings by external means, such as unsupervised learning. We exemplify the various functions of PTMScout in application to data sets that contain relative quantitative measurements as well as data sets lacking quantitative measurements, producing a set of interesting biological hypotheses. PTMScout is designed to be a widely accessible tool, enabling generation of multiple types of biological hypotheses from high throughput PTM experiments and advancing functional assignment of novel PTM sites. PTMScout is available at http://ptmscout.mit.edu.
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Affiliation(s)
- Kristen M Naegle
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Joughin BA, Naegle KM, Huang PH, Yaffe MB, Lauffenburger DA, White FM. An integrated comparative phosphoproteomic and bioinformatic approach reveals a novel class of MPM-2 motifs upregulated in EGFRvIII-expressing glioblastoma cells. Mol Biosyst 2008; 5:59-67. [PMID: 19081932 DOI: 10.1039/b815075c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Glioblastoma (GBM, WHO grade IV) is an aggressively proliferative and invasive brain tumor that carries a poor clinical prognosis with a median survival of 9 to 12 months. In a prior phosphoproteomic study performed in the U87MG glioblastoma cell line, we identified tyrosine phosphorylation events that are regulated as a result of titrating EGFRvIII, a constitutively active mutant of the epidermal growth factor receptor (EGFR) associated with poor prognosis in GBM patients. In the present study, we have used the phosphoserine/phosphothreonine-specific antibody MPM-2 (mitotic protein monoclonal #2) to quantify serine/threonine phosphorylation events in the same cell lines. By employing a bioinformatic tool to identify amino acid sequence motifs regulated in response to increasing oncogene levels, a set of previously undescribed MPM-2 epitope sequence motifs orthogonal to the canonical "pS/pT-P" motif was identified. These motifs contain acidic amino acids in combinations of the -5, -2, +1, +3, and +5 positions relative to the phosphorylated amino acid. Phosphopeptides containing these motifs are upregulated in cells expressing EGFRvIII, raising the possibility of a general role for a previously unrecognized acidophilic kinase (e.g. casein kinase II (CK2)) in cell proliferation downstream of EGFR signaling.
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Affiliation(s)
- Brian A Joughin
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
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Abstract
The identification of protein mutations that enhance binding affinity may be achieved by computational or experimental means, or by a combination of the two. Sources of affinity enhancement may include improvements to the net balance of binding interactions of residues forming intermolecular contacts at the binding interface, such as packing and hydrogen-bonding interactions. Here we identify noncontacting residues that make substantial contributions to binding affinity and that also provide opportunities for mutations that increase binding affinity of the TEM1 beta-lactamase (TEM1) to the beta-lactamase inhibitor protein (BLIP). A region of BLIP not on the direct TEM1-binding surface was identified for which changes in net charge result in particularly large increases in computed binding affinity. Some mutations to the region have previously been characterized, and our results are in good correspondence with this results of that study. In addition, we propose novel mutations to BLIP that were computed to improve binding significantly without contacting TEM1 directly. This class of noncontacting electrostatic interactions could have general utility in the design and tuning of binding interactions.
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Affiliation(s)
- Brian A Joughin
- Computer Science and Artificial Intelligence Laboratory, Department of Biology, Center for Cancer Research, Massachusetts Institute of Technology, Room 32-212, Cambridge, MA 02139-4307, USA
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Abstract
Phosphopeptide-binding domains, including the FHA, SH2, WW, WD40, MH2, and Polo-box domains, as well as the 14-3-3 proteins, exert control functions in important processes such as cell growth, division, differentiation, and apoptosis. Structures and mechanisms of phosphopeptide binding are generally diverse, revealing few general principles. A computational method for analysis of phosphopeptide-binding domains was therefore developed to elucidate the physical and chemical nature of phosphopeptide binding, given this lack of structural similarity. The surfaces of nine phosphopeptide-binding proteins, representing seven distinct classes of phosphopeptide-binding modules, were discretized, and encoded with information about amino acid identity, surface curvature, and electrostatic potential at every point on the surface in order to identify local surface properties enriched in phosphoresidue contact sites. Cross-validation indicated that propensities corresponding to this enrichment calculated from a subset of the training data could be used to predict the phosphoresidue contact site on proteins not used in training with no false negative results, and with few unconfirmed positive predictions. The locations of phosphoresidue contact sites were then predicted on the surfaces of the checkpoint kinase Chk1 and the BRCA1 BRCT repeat domain, and these predictions are consistent with recent experimental evidence.
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Affiliation(s)
- Brian A Joughin
- Department of Biology, Center for Cancer Research, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Powell DW, Rane MJ, Joughin BA, Kalmukova R, Hong JH, Tidor B, Dean WL, Pierce WM, Klein JB, Yaffe MB, McLeish KR. Proteomic identification of 14-3-3zeta as a mitogen-activated protein kinase-activated protein kinase 2 substrate: role in dimer formation and ligand binding. Mol Cell Biol 2003; 23:5376-87. [PMID: 12861023 PMCID: PMC165733 DOI: 10.1128/mcb.23.15.5376-5387.2003] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mitogen-activated protein kinase (MAPK)-activated protein kinase 2 (MAPKAPK2) mediates multiple p38 MAPK-dependent inflammatory responses. To define the signal transduction pathways activated by MAPKAPK2, we identified potential MAPKAPK2 substrates by using a functional proteomic approach consisting of in vitro phosphorylation of neutrophil lysate by active recombinant MAPKAPK2, protein separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and phosphoprotein identification by peptide mass fingerprinting with matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) and protein database analysis. One of the eight candidate MAPKAPK2 substrates identified was the adaptor protein, 14-3-3zeta. We confirmed that MAPKAPK2 interacted with and phosphorylated 14-3-3zeta in vitro and in HEK293 cells. The chemoattractant formyl-methionyl-leucyl-phenylalanine (fMLP) stimulated p38-MAPK-dependent phosphorylation of 14-3-3 proteins in human neutrophils. Mutation analysis showed that MAPKAPK2 phosphorylated 14-3-3zeta at Ser-58. Computational modeling and calculation of theoretical binding energies predicted that both phosphorylation at Ser-58 and mutation of Ser-58 to Asp (S58D) compromised the ability of 14-3-3zeta to dimerize. Experimentally, S58D mutation significantly impaired both 14-3-3zeta dimerization and binding to Raf-1. These data suggest that MAPKAPK2-mediated phosphorylation regulates 14-3-3zeta functions, and this MAPKAPK2 activity may represent a novel pathway mediating p38 MAPK-dependent inflammation.
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Affiliation(s)
- David W Powell
- Departments of Biochemistry and Molecular Biology, University of Louisville, Louisville, KY 40202, USA
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