1
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Chowdhury S, Kennedy JJ, Ivey RG, Murillo OD, Hosseini N, Song X, Petralia F, Calinawan A, Savage SR, Berry AB, Reva B, Ozbek U, Krek A, Ma W, da Veiga Leprevost F, Ji J, Yoo S, Lin C, Voytovich UJ, Huang Y, Lee SH, Bergan L, Lorentzen TD, Mesri M, Rodriguez H, Hoofnagle AN, Herbert ZT, Nesvizhskii AI, Zhang B, Whiteaker JR, Fenyo D, McKerrow W, Wang J, Schürer SC, Stathias V, Chen XS, Barcellos-Hoff MH, Starr TK, Winterhoff BJ, Nelson AC, Mok SC, Kaufmann SH, Drescher C, Cieslik M, Wang P, Birrer MJ, Paulovich AG. Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer. Cell 2024; 187:1016. [PMID: 38364782 DOI: 10.1016/j.cell.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
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2
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Lundeen RA, Kennedy JJ, Murillo OD, Ivey RG, Zhao L, Schoenherr RM, Hoofnagle AN, Wang P, Whiteaker JR, Paulovich AG. Monitoring Both Extended and Tryptic Forms of Stable Isotope-Labeled Standard Peptides Provides an Internal Quality Control of Proteolytic Digestion in Targeted Mass Spectrometry-Based Assays. Mol Cell Proteomics 2023; 22:100621. [PMID: 37478973 PMCID: PMC10458721 DOI: 10.1016/j.mcpro.2023.100621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023] Open
Abstract
Targeted mass spectrometry (MS)-based proteomic assays, such as multiplexed multiple reaction monitoring (MRM)-MS assays, enable sensitive and specific quantification of proteotypic peptides as stoichiometric surrogates for proteins. Efforts are underway to expand the use of MRM-MS assays in clinical environments, which requires a reliable strategy to monitor proteolytic digestion efficiency within individual samples. Towards this goal, extended stable isotope-labeled standard (SIS) peptides (hE), which incorporate native proteolytic cleavage sites, can be spiked into protein lysates prior to proteolytic (trypsin) digestion, and release of the tryptic SIS peptide (hT) can be monitored. However, hT measurements alone cannot monitor the extent of digestion and may be confounded by matrix effects specific to individual patient samples; therefore, they are not sufficient to monitor sample-to-sample digestion variability. We hypothesized that measuring undigested hE, along with its paired hT, would improve detection of digestion issues compared to only measuring hT. We tested the ratio of the SIS pair measurements, or hE/hT, as a quality control (QC) metric of trypsin digestion for two MRM assays: a direct-MRM (398 targets) and an immuno-MRM (126 targets requiring immunoaffinity peptide enrichment) assay, with extended SIS peptides observable for 54% (216) and 62% (78) of the targets, respectively. We evaluated the quantitative bias for each target in a series of experiments that adversely affected proteolytic digestion (e.g., variable digestion times, pH, and temperature). We identified a subset of SIS pairs (36 for the direct-MRM, 7 for the immuno-MRM assay) for which the hE/hT ratio reliably detected inefficient digestion that resulted in decreased assay sensitivity and unreliable endogenous quantification. The hE/hT ratio was more responsive to a decrease in digestion efficiency than a metric based on hT measurements alone. For clinical-grade MRM-MS assays, this study describes a ready-to-use QC panel and also provides a road map for designing custom QC panels.
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Affiliation(s)
- Rachel A Lundeen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Oscar D Murillo
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Richard G Ivey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lei Zhao
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Regine M Schoenherr
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Mount Sinai Hospital, New York, New York, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
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3
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Chowdhury S, Kennedy JJ, Ivey RG, Murillo OD, Hosseini N, Song X, Petralia F, Calinawan A, Savage SR, Berry AB, Reva B, Ozbek U, Krek A, Ma W, da Veiga Leprevost F, Ji J, Yoo S, Lin C, Voytovich UJ, Huang Y, Lee SH, Bergan L, Lorentzen TD, Mesri M, Rodriguez H, Hoofnagle AN, Herbert ZT, Nesvizhskii AI, Zhang B, Whiteaker JR, Fenyo D, McKerrow W, Wang J, Schürer SC, Stathias V, Chen XS, Barcellos-Hoff MH, Starr TK, Winterhoff BJ, Nelson AC, Mok SC, Kaufmann SH, Drescher C, Cieslik M, Wang P, Birrer MJ, Paulovich AG. Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer. Cell 2023; 186:3476-3498.e35. [PMID: 37541199 PMCID: PMC10414761 DOI: 10.1016/j.cell.2023.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 09/30/2022] [Revised: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
To improve the understanding of chemo-refractory high-grade serous ovarian cancers (HGSOCs), we characterized the proteogenomic landscape of 242 (refractory and sensitive) HGSOCs, representing one discovery and two validation cohorts across two biospecimen types (formalin-fixed paraffin-embedded and frozen). We identified a 64-protein signature that predicts with high specificity a subset of HGSOCs refractory to initial platinum-based therapy and is validated in two independent patient cohorts. We detected significant association between lack of Ch17 loss of heterozygosity (LOH) and chemo-refractoriness. Based on pathway protein expression, we identified 5 clusters of HGSOC, which validated across two independent patient cohorts and patient-derived xenograft (PDX) models. These clusters may represent different mechanisms of refractoriness and implicate putative therapeutic vulnerabilities.
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Affiliation(s)
- Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Richard G Ivey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Oscar D Murillo
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Noshad Hosseini
- Department of Computational Medicine and Bioinformatics, Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Xiaoyu Song
- Tisch Cancer Institute, Department of Population Health Science and Policy, Institute for Health Care Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Umut Ozbek
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Jiayi Ji
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Chenwei Lin
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Uliana J Voytovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Yajue Huang
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Sun-Hee Lee
- Departments of Oncology and Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Lindsay Bergan
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Travis D Lorentzen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, Department of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - David Fenyo
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Joshua Wang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Stephan C Schürer
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, and Institute for Data Science & Computing, University of Miami, Miami, FL 33136, USA
| | - Vasileios Stathias
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, and Institute for Data Science & Computing, University of Miami, Miami, FL 33136, USA
| | - X Steven Chen
- Department of Public Health Sciences, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Mary Helen Barcellos-Hoff
- Helen Diller Family Comprehensive Cancer Center, Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Timothy K Starr
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Boris J Winterhoff
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samuel C Mok
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott H Kaufmann
- Departments of Oncology and Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Charles Drescher
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Marcin Cieslik
- Department of Pathology, Department of Computational Medicine and Bioinformatics, Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Michael J Birrer
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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4
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Murillo OD, Petrosyan V, LaPlante EL, Dobrolecki LE, Lewis MT, Milosavljevic A. Deconvolution of cancer cell states by the XDec-SM method. PLoS Comput Biol 2023; 19:e1011365. [PMID: 37578979 PMCID: PMC10449115 DOI: 10.1371/journal.pcbi.1011365] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 01/06/2023] [Revised: 08/24/2023] [Accepted: 07/17/2023] [Indexed: 08/16/2023] Open
Abstract
Proper characterization of cancer cell states within the tumor microenvironment is a key to accurately identifying matching experimental models and the development of precision therapies. To reconstruct this information from bulk RNA-seq profiles, we developed the XDec Simplex Mapping (XDec-SM) reference-optional deconvolution method that maps tumors and the states of constituent cells onto a biologically interpretable low-dimensional space. The method identifies gene sets informative for deconvolution from relevant single-cell profiling data when such profiles are available. When applied to breast tumors in The Cancer Genome Atlas (TCGA), XDec-SM infers the identity of constituent cell types and their proportions. XDec-SM also infers cancer cells states within individual tumors that associate with DNA methylation patterns, driver somatic mutations, pathway activation and metabolic coupling between stromal and breast cancer cells. By projecting tumors, cancer cell lines, and PDX models onto the same map, we identify in vitro and in vivo models with matching cancer cell states. Map position is also predictive of therapy response, thus opening the prospects for precision therapy informed by experiments in model systems matched to tumors in vivo by cancer cell state.
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Affiliation(s)
- Oscar D. Murillo
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Varduhi Petrosyan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Emily L. LaPlante
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lacey E. Dobrolecki
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael T. Lewis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- Departments of Molecular and Cellular Biology and Radiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Aleksandar Milosavljevic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
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5
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Whiteaker JR, Zhao L, Schoenherr RM, Huang D, Lundeen RA, Voytovich U, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Perry CD, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Chowdhury S, Vandermeer J, Smith SD, Gopal AK, Ramchurren N, Fling SP, Wang P, Paulovich AG. A multiplexed assay for quantifying immunomodulatory proteins supports correlative studies in immunotherapy clinical trials. Front Oncol 2023; 13:1168710. [PMID: 37205196 PMCID: PMC10185886 DOI: 10.3389/fonc.2023.1168710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/10/2023] [Indexed: 05/21/2023] Open
Abstract
Introduction Immunotherapy is an effective treatment for a subset of cancer patients, and expanding the benefits of immunotherapy to all cancer patients will require predictive biomarkers of response and immune-related adverse events (irAEs). To support correlative studies in immunotherapy clinical trials, we are developing highly validated assays for quantifying immunomodulatory proteins in human biospecimens. Methods Here, we developed a panel of novel monoclonal antibodies and incorporated them into a novel, multiplexed, immuno-multiple reaction monitoring mass spectrometry (MRM-MS)-based proteomic assay targeting 49 proteotypic peptides representing 43 immunomodulatory proteins. Results and discussion The multiplex assay was validated in human tissue and plasma matrices, where the linearity of quantification was >3 orders of magnitude with median interday CVs of 8.7% (tissue) and 10.1% (plasma). Proof-of-principle demonstration of the assay was conducted in plasma samples collected in clinical trials from lymphoma patients receiving an immune checkpoint inhibitor. We provide the assays and novel monoclonal antibodies as a publicly available resource for the biomedical community.
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Affiliation(s)
- Jeffrey R. Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Regine M. Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Dongqing Huang
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Rachel A. Lundeen
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Ulianna Voytovich
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Jacob J. Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Richard G. Ivey
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Oscar D. Murillo
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Travis D. Lorentzen
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Simona Colantonio
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Tessa W. Caceres
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Rhonda R. Roberts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Joseph G. Knotts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Joshua J. Reading
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Candice D. Perry
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Christopher W. Richardson
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Sandra S. Garcia-Buntley
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - William Bocik
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Stephen M. Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, United States
| | - Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jackie Vandermeer
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Division of Medical Oncology, Department of Internal Medicine, University of Washington, Seattle, WA, United States
| | - Stephen D. Smith
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Division of Medical Oncology, Department of Internal Medicine, University of Washington, Seattle, WA, United States
| | - Ajay K. Gopal
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Division of Medical Oncology, Department of Internal Medicine, University of Washington, Seattle, WA, United States
| | - Nirasha Ramchurren
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Steven P. Fling
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- *Correspondence: Amanda G. Paulovich,
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6
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Kennedy J, Whiteaker JR, Ivey RG, Burian A, Chowdhury S, Tsai CF, Liu T, Lin C, Murillo OD, Lundeen RA, Jones LA, Gafken PR, Longton G, Rodland KD, Skates SJ, Landua J, Wang P, Lewis MT, Paulovich AG. Internal Standard Triggered-Parallel Reaction Monitoring Mass Spectrometry Enables Multiplexed Quantification of Candidate Biomarkers in Plasma. Anal Chem 2022; 94:9540-9547. [PMID: 35767427 PMCID: PMC9280723 DOI: 10.1021/acs.analchem.1c04382] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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] [Indexed: 11/28/2022]
Abstract
Despite advances in proteomic technologies, clinical translation of plasma biomarkers remains low, partly due to a major bottleneck between the discovery of candidate biomarkers and costly clinical validation studies. Due to a dearth of multiplexable assays, generally only a few candidate biomarkers are tested, and the validation success rate is accordingly low. Previously, mass spectrometry-based approaches have been used to fill this gap but feature poor quantitative performance and were generally limited to hundreds of proteins. Here, we demonstrate the capability of an internal standard triggered-parallel reaction monitoring (IS-PRM) assay to greatly expand the numbers of candidates that can be tested with improved quantitative performance. The assay couples immunodepletion and fractionation with IS-PRM and was developed and implemented in human plasma to quantify 5176 peptides representing 1314 breast cancer biomarker candidates. Characterization of the IS-PRM assay demonstrated the precision (median % CV of 7.7%), linearity (median R2 > 0.999 over 4 orders of magnitude), and sensitivity (median LLOQ < 1 fmol, approximately) to enable rank-ordering of candidate biomarkers for validation studies. Using three plasma pools from breast cancer patients and three control pools, 893 proteins were quantified, of which 162 candidate biomarkers were verified in at least one of the cancer pools and 22 were verified in all three cancer pools. The assay greatly expands capabilities for quantification of large numbers of proteins and is well suited for prioritization of viable candidate biomarkers.
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Affiliation(s)
- Jacob
J. Kennedy
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Jeffrey R. Whiteaker
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Richard G. Ivey
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Aura Burian
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Shrabanti Chowdhury
- Department
of Genetics and Genomic Sciences and Icahn Institute for Data Science
and Genomic Technology, Icahn School of
Medicine at Mount Sinai, New York, New York 10029, United States
| | - Chia-Feng Tsai
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Tao Liu
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - ChenWei Lin
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Oscar D. Murillo
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Rachel A. Lundeen
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Lisa A. Jones
- Proteomics
and Metabolomics Shared Resources, Fred
Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Philip R. Gafken
- Proteomics
and Metabolomics Shared Resources, Fred
Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Gary Longton
- Public
Health Sciences Division, Fred Hutchinson
Cancer Research Center, Seattle, Washington 98109, United States
| | - Karin D. Rodland
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Steven J. Skates
- MGH
Biostatistics Center, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - John Landua
- Lester
and Sue Smith Breast Center, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Pei Wang
- Department
of Genetics and Genomic Sciences, Mount
Sinai Hospital, New York, New York 10065, United States
| | - Michael T. Lewis
- Lester
and Sue Smith Breast Center, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Amanda G. Paulovich
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States,Phone: 206-667-1912. . Fax: 206-667-2277
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7
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Whiteaker JR, Lundeen RA, Zhao L, Schoenherr RM, Burian A, Huang D, Voytovich U, Wang T, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Thiagarajan M, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Kaczmarczyk JA, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Murray KE, Do N, Brophy M, Wilz SW, Yu H, Ajjarapu S, Boja E, Hiltke T, Rodriguez H, Paulovich AG. Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens. Front Immunol 2021; 12:765898. [PMID: 34858420 PMCID: PMC8632241 DOI: 10.3389/fimmu.2021.765898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/22/2021] [Indexed: 12/11/2022] Open
Abstract
Immunotherapies are revolutionizing cancer care, producing durable responses and potentially cures in a subset of patients. However, response rates are low for most tumors, grade 3/4 toxicities are not uncommon, and our current understanding of tumor immunobiology is incomplete. While hundreds of immunomodulatory proteins in the tumor microenvironment shape the anti-tumor response, few of them can be reliably quantified. To address this need, we developed a multiplex panel of targeted proteomic assays targeting 52 peptides representing 46 proteins using peptide immunoaffinity enrichment coupled to multiple reaction monitoring-mass spectrometry. We validated the assays in tissue and plasma matrices, where performance figures of merit showed over 3 orders of dynamic range and median inter-day CVs of 5.2% (tissue) and 21% (plasma). A feasibility study in clinical biospecimens showed detection of 48/52 peptides in frozen tissue and 38/52 peptides in plasma. The assays are publicly available as a resource for the research community.
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Affiliation(s)
- Jeffrey R. Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Rachel A. Lundeen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Regine M. Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Aura Burian
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Dongqing Huang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Ulianna Voytovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Tao Wang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Jacob J. Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Richard G. Ivey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Oscar D. Murillo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Travis D. Lorentzen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | | | - Simona Colantonio
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Tessa W. Caceres
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Rhonda R. Roberts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Joseph G. Knotts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Joshua J. Reading
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Jan A. Kaczmarczyk
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Christopher W. Richardson
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Sandra S. Garcia-Buntley
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - William Bocik
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Stephen M. Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, United States
| | - Karen E. Murray
- Veteran’s Administration (VA) Cooperative Studies Program, Veteran’s Administration (VA) Boston Healthcare System (151MAV), Jamaica Plain, MA, United States
| | - Nhan Do
- Veteran’s Administration (VA) Cooperative Studies Program, Veteran’s Administration (VA) Boston Healthcare System (151MAV), Jamaica Plain, MA, United States
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Mary Brophy
- Veteran’s Administration (VA) Cooperative Studies Program, Veteran’s Administration (VA) Boston Healthcare System (151MAV), Jamaica Plain, MA, United States
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Stephen W. Wilz
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
- Pathology and Laboratory Medicine Service, Program, Veteran’s Administration (VA) Boston Healthcare System, Jamaica Plain, MA, United States
| | - Hongbo Yu
- Pathology and Laboratory Medicine Service, Program, Veteran’s Administration (VA) Boston Healthcare System, Jamaica Plain, MA, United States
- Department of Pathology, Harvard Medical School, Boston, MA, United States
| | - Samuel Ajjarapu
- Veteran’s Administration (VA) Cooperative Studies Program, Veteran’s Administration (VA) Boston Healthcare System (151MAV), Jamaica Plain, MA, United States
- Department of Medicine, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, United States
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, United States
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, United States
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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8
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Webster NJ, Maywald RL, Benton SM, Dawson EP, Murillo OD, LaPlante EL, Milosavljevic A, Lanza DG, Heaney JD. Testicular germ cell tumors arise in the absence of sex-specific differentiation. Development 2021; 148:260592. [PMID: 33912935 DOI: 10.1242/dev.197111] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/22/2021] [Indexed: 01/09/2023]
Abstract
In response to signals from the embryonic testis, the germ cell intrinsic factor NANOS2 coordinates a transcriptional program necessary for the differentiation of pluripotent-like primordial germ cells toward a unipotent spermatogonial stem cell fate. Emerging evidence indicates that genetic risk factors contribute to testicular germ cell tumor initiation by disrupting sex-specific differentiation. Here, using the 129.MOLF-Chr19 mouse model of testicular teratomas and a NANOS2 reporter allele, we report that the developmental phenotypes required for tumorigenesis, including failure to enter mitotic arrest, retention of pluripotency and delayed sex-specific differentiation, were exclusive to a subpopulation of germ cells failing to express NANOS2. Single-cell RNA sequencing revealed that embryonic day 15.5 NANOS2-deficient germ cells and embryonal carcinoma cells developed a transcriptional profile enriched for MYC signaling, NODAL signaling and primed pluripotency. Moreover, lineage-tracing experiments demonstrated that embryonal carcinoma cells arose exclusively from germ cells failing to express NANOS2. Our results indicate that NANOS2 is the nexus through which several genetic risk factors influence tumor susceptibility. We propose that, in the absence of sex specification, signals native to the developing testis drive germ cell transformation.
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Affiliation(s)
- Nicholas J Webster
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rebecca L Maywald
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Susan M Benton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily P Dawson
- Department of Cell Biology, New York University, New York, NY 10003, USA
| | - Oscar D Murillo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily L LaPlante
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Denise G Lanza
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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9
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Buffington SA, Dooling SW, Sgritta M, Noecker C, Murillo OD, Felice DF, Turnbaugh PJ, Costa-Mattioli M. Dissecting the contribution of host genetics and the microbiome in complex behaviors. Cell 2021; 184:1740-1756.e16. [PMID: 33705688 PMCID: PMC8996745 DOI: 10.1016/j.cell.2021.02.009] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/07/2020] [Accepted: 02/02/2021] [Indexed: 12/14/2022]
Abstract
The core symptoms of many neurological disorders have traditionally been thought to be caused by genetic variants affecting brain development and function. However, the gut microbiome, another important source of variation, can also influence specific behaviors. Thus, it is critical to unravel the contributions of host genetic variation, the microbiome, and their interactions to complex behaviors. Unexpectedly, we discovered that different maladaptive behaviors are interdependently regulated by the microbiome and host genes in the Cntnap2-/- model for neurodevelopmental disorders. The hyperactivity phenotype of Cntnap2-/- mice is caused by host genetics, whereas the social-behavior phenotype is mediated by the gut microbiome. Interestingly, specific microbial intervention selectively rescued the social deficits in Cntnap2-/- mice through upregulation of metabolites in the tetrahydrobiopterin synthesis pathway. Our findings that behavioral abnormalities could have distinct origins (host genetic versus microbial) may change the way we think about neurological disorders and how to treat them.
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Affiliation(s)
- Shelly A Buffington
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Memory and Brain Research Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sean W Dooling
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Memory and Brain Research Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Martina Sgritta
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Memory and Brain Research Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cecilia Noecker
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Oscar D Murillo
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniela F Felice
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Memory and Brain Research Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Mauro Costa-Mattioli
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Memory and Brain Research Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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10
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Lucero R, Zappulli V, Sammarco A, Murillo OD, Cheah PS, Srinivasan S, Tai E, Ting DT, Wei Z, Roth ME, Laurent LC, Krichevsky AM, Breakefield XO, Milosavljevic A. Glioma-Derived miRNA-Containing Extracellular Vesicles Induce Angiogenesis by Reprogramming Brain Endothelial Cells. Cell Rep 2021; 30:2065-2074.e4. [PMID: 32075753 DOI: 10.1016/j.celrep.2020.01.073] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 09/29/2019] [Accepted: 01/22/2020] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma (GBM) is characterized by aberrant vascularization and a complex tumor microenvironment. The failure of anti-angiogenic therapies suggests pathways of GBM neovascularization, possibly attributable to glioblastoma stem cells (GSCs) and their interplay with the tumor microenvironment. It has been established that GSC-derived extracellular vesicles (GSC-EVs) and their cargoes are proangiogenic in vitro. To further elucidate EV-mediated mechanisms of neovascularization in vitro, we perform RNA-seq and DNA methylation profiling of human brain endothelial cells exposed to GSC-EVs. To correlate these results to tumors in vivo, we perform histoepigenetic analysis of GBM molecular profiles in the TCGA collection. Remarkably, GSC-EVs and normal vascular growth factors stimulate highly distinct gene regulatory responses that converge on angiogenesis. The response to GSC-EVs shows a footprint of post-transcriptional gene silencing by EV-derived miRNAs. Our results provide insights into targetable angiogenesis pathways in GBM and miRNA candidates for liquid biopsy biomarkers.
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Affiliation(s)
- Rocco Lucero
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Valentina Zappulli
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua, Italy; Departments of Neurology and Radiology, Massachusetts General Hospital, Boston, MA 02114, USA; Neuroscience Program, Harvard Medical School, Boston, MA 02115, USA.
| | - Alessandro Sammarco
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua, Italy; Departments of Neurology and Radiology, Massachusetts General Hospital, Boston, MA 02114, USA; Neuroscience Program, Harvard Medical School, Boston, MA 02115, USA
| | - Oscar D Murillo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pike See Cheah
- Departments of Neurology and Radiology, Massachusetts General Hospital, Boston, MA 02114, USA; Neuroscience Program, Harvard Medical School, Boston, MA 02115, USA; Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Seri Kembangan, Selangor, Malaysia
| | - Srimeenakshi Srinivasan
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Eric Tai
- Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Zhiyun Wei
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew E Roth
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Anna M Krichevsky
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Xandra O Breakefield
- Departments of Neurology and Radiology, Massachusetts General Hospital, Boston, MA 02114, USA; Neuroscience Program, Harvard Medical School, Boston, MA 02115, USA
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11
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Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah RV, Yeri A, Jenkins LM, Ahsen ME, Cordon-Cardo C, Dogra N, Gifford SM, Smith JT, Stolovitzky G, Tewari AK, Wunsch BH, Yadav KK, Danielson KM, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong DK, Zhang X, Balaj L, Gandhi R, Sood AK, Alexander RP, Wang L, Wu C, Wong DTW, Galas DJ, Van Keuren-Jensen K, Patel T, Jones JC, Das S, Cheung KH, Pico AR, Su AI, Raffai RL, Laurent LC, Roth ME, Gerstein MB, Milosavljevic A. exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids. Cell 2019; 177:463-477.e15. [PMID: 30951672 PMCID: PMC6616370 DOI: 10.1016/j.cell.2019.02.018] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [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: 04/28/2018] [Revised: 11/06/2018] [Accepted: 02/11/2019] [Indexed: 12/11/2022]
Abstract
To develop a map of cell-cell communication mediated by extracellular RNA (exRNA), the NIH Extracellular RNA Communication Consortium created the exRNA Atlas resource (https://exrna-atlas.org). The Atlas version 4P1 hosts 5,309 exRNA-seq and exRNA qPCR profiles from 19 studies and a suite of analysis and visualization tools. To analyze variation between profiles, we apply computational deconvolution. The analysis leads to a model with six exRNA cargo types (CT1, CT2, CT3A, CT3B, CT3C, CT4), each detectable in multiple biofluids (serum, plasma, CSF, saliva, urine). Five of the cargo types associate with known vesicular and non-vesicular (lipoprotein and ribonucleoprotein) exRNA carriers. To validate utility of this model, we re-analyze an exercise response study by deconvolution to identify physiologically relevant response pathways that were not detected previously. To enable wide application of this model, as part of the exRNA Atlas resource, we provide tools for deconvolution and analysis of user-provided case-control studies.
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Affiliation(s)
- Oscar D Murillo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - William Thistlethwaite
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joel Rozowsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Sai Lakshmi Subramanian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rocco Lucero
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neethu Shah
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew R Jackson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Srimeenakshi Srinivasan
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Allen Chung
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Surgical Service, San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - Clara D Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | | | - Timur Galeev
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jonathan Warrell
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - James A Diao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua A Welsh
- Translational Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | | | - Ravi V Shah
- Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ashish Yeri
- Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, NIH, Bethesda, MD 20892, USA
| | - Mehmet E Ahsen
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Navneet Dogra
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; IBM T.J. Watson Research Center, IBM Research, Yorktown Heights, NY 10598, USA
| | - Stacey M Gifford
- IBM T.J. Watson Research Center, IBM Research, Yorktown Heights, NY 10598, USA
| | - Joshua T Smith
- IBM T.J. Watson Research Center, IBM Research, Yorktown Heights, NY 10598, USA
| | - Gustavo Stolovitzky
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; IBM T.J. Watson Research Center, IBM Research, Yorktown Heights, NY 10598, USA
| | - Ashutosh K Tewari
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benjamin H Wunsch
- IBM T.J. Watson Research Center, IBM Research, Yorktown Heights, NY 10598, USA
| | - Kamlesh K Yadav
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Sema4, Stamford, CT 06902, USA
| | - Kirsty M Danielson
- Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Justyna Filant
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Courtney Moeller
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Parham Nejad
- Department of Neurology, Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anu Paul
- Department of Neurology, Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bridget Simonson
- Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - David K Wong
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Surgical Service, San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - Xuan Zhang
- Exosome Diagnostics, Inc., Waltham, MA 02451, USA
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Roopali Gandhi
- Department of Neurology, Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Liang Wang
- Department of Pathology and MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chunlei Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David T W Wong
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David J Galas
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | | | - Tushar Patel
- Department of Transplantation, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Jennifer C Jones
- Translational Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Saumya Das
- Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kei-Hoi Cheung
- Department of Emergency Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | | | - Andrew I Su
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert L Raffai
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Surgical Service, San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Matthew E Roth
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mark B Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA
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