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Lin HY, M Hosseini M, McClatchy J, Villamor-Payà M, Jeng S, Bottomly D, Tsai CF, Posso C, Jacobson J, Adey AC, Gosline SJC, Liu T, McWeeney SK, Stracker TH, Agarwal A. The TLK-ASF1 histone chaperone pathway plays a critical role in IL-1b-mediated AML progression. Blood 2024:blood.2023022079. [PMID: 38498025 DOI: 10.1182/blood.2023022079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/19/2024] Open
Abstract
Identifying and targeting microenvironment-driven pathways that are active across acute myeloid leukemia (AML) genetic subtypes should allow the development of more broadly effective therapies. The pro-inflammatory cytokine IL-1 is abundant in the AML microenvironment and promotes leukemic growth. Through RNA-sequencing analysis, we identify that IL-1 upregulated ASF1B (anti-silencing function-1B), a histone chaperone, in AML progenitors compared to healthy progenitors. ASF1B, along with its paralogous protein ASF1A recruits H3-H4 histones onto the replication fork during S-phase, a process regulated by tousled-like kinase 1 and 2 (TLKs). While ASF1s and TLKs are known to be overexpressed in multiple solid tumors and associated with poor prognosis, their functional roles in hematopoiesis and inflammation-driven leukemia remain unexplored. In this study, we identify that ASF1s and TLKs are over-expressed in multiple genetic subtypes of AML. We demonstrate that depletion of ASF1s significantly reduces leukemic cell growth in both in vitro and in vivo models using human cells. Using a murine model we show that overexpression of ASF1B accelerates leukemia progression. Moreover, Asf1b or Tlk2 deletion delayed leukemia progression while these proteins are dispensable for normal hematopoiesis. Through proteomics and phosphoproteomics analyses, we uncover that the TLK-ASF1 pathway promotes leukemogenesis by impacting the cell cycle and DNA damage pathways. Collectively, our findings identify the TLK1-ASF1 pathway as a novel mediator of inflammatory signaling and a promising therapeutic target for AML treatment across diverse genetic subtypes. Selective inhibition of this pathway offers potential opportunities to intervene effectively, address intratumoral heterogeneity, and ultimately improve clinical outcomes in AML.
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Affiliation(s)
- Hsin-Yun Lin
- Oregon Health & Science University, Portland, Oregon, United States
| | - Mona M Hosseini
- Oregon Health & Science University, Portland, Oregon, United States
| | - John McClatchy
- Oregon Health & Science University, Portland, Oregon, United States
| | | | - Sophia Jeng
- Oregon Health and Science University, Portland, United States
| | - Daniel Bottomly
- Oregon Health & Science University,Knight Cancer Institute, Portland, Oregon, United States
| | - Chia-Feng Tsai
- Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Camilo Posso
- Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Jeremy Jacobson
- Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Andrew C Adey
- Oregon Health & Science University, Portland, Oregon, United States
| | - Sara J C Gosline
- Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Tao Liu
- Pacific Northwest National Laboratory
| | | | | | - Anupriya Agarwal
- Oregon Health & Science University, Portland, Oregon, United States
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2
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Kim YK, Kim YR, Wells KL, Sarbaugh D, Guney M, Tsai CF, Zee T, Karsenty G, Nakayasu ES, Sussel L. PTPN2 Regulates Metabolic Flux to Affect β-Cell Susceptibility to Inflammatory Stress. Diabetes 2024; 73:434-447. [PMID: 38015772 PMCID: PMC10882156 DOI: 10.2337/db23-0355] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 11/08/2023] [Indexed: 11/30/2023]
Abstract
Protein tyrosine phosphatase N2 (PTPN2) is a type 1 diabetes (T1D) candidate gene identified from human genome-wide association studies. PTPN2 is highly expressed in human and murine islets and becomes elevated upon inflammation and models of T1D, suggesting that PTPN2 may be important for β-cell survival in the context of T1D. To test whether PTPN2 contributed to β-cell dysfunction in an inflammatory environment, we generated a β-cell-specific deletion of Ptpn2 in mice (PTPN2-β knockout [βKO]). Whereas unstressed animals exhibited normal metabolic profiles, low- and high-dose streptozotocin-treated PTPN2-βKO mice displayed hyperglycemia and accelerated death, respectively. Furthermore, cytokine-treated Ptpn2-KO islets resulted in impaired glucose-stimulated insulin secretion, mitochondrial defects, and reduced glucose-induced metabolic flux, suggesting β-cells lacking Ptpn2 are more susceptible to inflammatory stress associated with T1D due to maladaptive metabolic fitness. Consistent with the phenotype, proteomic analysis identified an important metabolic enzyme, ATP-citrate lyase, as a novel PTPN2 substrate. ARTICLE HIGHLIGHTS
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Affiliation(s)
- Yong Kyung Kim
- Barbara Davis Center for Diabetes, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
| | - Youngjung Rachel Kim
- Department of Genetics and Development, Columbia University Irving Medical Campus, New York, NY
| | - Kristen L. Wells
- Barbara Davis Center for Diabetes, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
| | - Dylan Sarbaugh
- Barbara Davis Center for Diabetes, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
| | - Michelle Guney
- Barbara Davis Center for Diabetes, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Tiffany Zee
- Department of Genetics and Development, Columbia University Irving Medical Campus, New York, NY
| | - Gerard Karsenty
- Department of Genetics and Development, Columbia University Irving Medical Campus, New York, NY
| | - Ernesto S. Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Lori Sussel
- Barbara Davis Center for Diabetes, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
- Department of Genetics and Development, Columbia University Irving Medical Campus, New York, NY
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3
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Humphrey J, Brophy E, Kosoy R, Zeng B, Coccia E, Mattei D, Ravi A, Efthymiou AG, Navarro E, Muller BZ, Snijders GJLJ, Allan A, Münch A, Kitata RB, Kleopoulos SP, Argyriou S, Shao Z, Francoeur N, Tsai CF, Gritsenko MA, Monroe ME, Paurus VL, Weitz KK, Shi T, Sebra R, Liu T, de Witte LD, Goate AM, Bennett DA, Haroutunian V, Hoffman GE, Fullard JF, Roussos P, Raj T. Long-read RNA-seq atlas of novel microglia isoforms elucidates disease-associated genetic regulation of splicing. medRxiv 2023:2023.12.01.23299073. [PMID: 38076956 PMCID: PMC10705658 DOI: 10.1101/2023.12.01.23299073] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Microglia, the innate immune cells of the central nervous system, have been genetically implicated in multiple neurodegenerative diseases. We previously mapped the genetic regulation of gene expression and mRNA splicing in human microglia, identifying several loci where common genetic variants in microglia-specific regulatory elements explain disease risk loci identified by GWAS. However, identifying genetic effects on splicing has been challenging due to the use of short sequencing reads to identify causal isoforms. Here we present the isoform-centric microglia genomic atlas (isoMiGA) which leverages the power of long-read RNA-seq to identify 35,879 novel microglia isoforms. We show that the novel microglia isoforms are involved in stimulation response and brain region specificity. We then quantified the expression of both known and novel isoforms in a multi-ethnic meta-analysis of 555 human microglia short-read RNA-seq samples from 391 donors, the largest to date, and found associations with genetic risk loci in Alzheimer's disease and Parkinson's disease. We nominate several loci that may act through complex changes in isoform and splice site usage.
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Affiliation(s)
- Jack Humphrey
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erica Brophy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Biao Zeng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Elena Coccia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniele Mattei
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ashvin Ravi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anastasia G. Efthymiou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elisa Navarro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Biochemistry and Molecular Biology, Faculty of Medicine (Universidad Complutense de Madrid), Madrid, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto Ramon y Cajal de Investigacion Sanitaria (IRYCIS), Madrid, Spain
| | - Benjamin Z. Muller
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gijsje JLJ Snijders
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Amanda Allan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra Münch
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Reta Birhanu Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Steven P Kleopoulos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Stathis Argyriou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Zhiping Shao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Nancy Francoeur
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Vanessa L Paurus
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lot D. de Witte
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Alison M. Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Vahram Haroutunian
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Gabriel E. Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - John F. Fullard
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
- Mental Illness Research Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Towfique Raj
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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4
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Schutzer SE, Liu T, Tsai CF, Petyuk VA, Schepmoes AA, Wang YT, Weitz KK, Bergquist J, Smith RD, Natelson BH. Myalgic encephalomyelitis/chronic fatigue syndrome and fibromyalgia are indistinguishable by their cerebrospinal fluid proteomes. Ann Med 2023; 55:2208372. [PMID: 37722890 PMCID: PMC10512920 DOI: 10.1080/07853890.2023.2208372] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 04/24/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and fibromyalgia have overlapping neurologic symptoms particularly disabling fatigue. This has given rise to the question whether they are distinct central nervous system (CNS) entities or is one an extension of the other. MATERIAL AND METHODS To investigate this, we used unbiased quantitative mass spectrometry-based proteomics to examine the most proximal fluid to the brain, cerebrospinal fluid (CSF). This was to ascertain if the proteome profile of one was the same or different from the other. We examined two separate groups of ME/CFS, one with (n = 15) and one without (n = 15) fibromyalgia. RESULTS We quantified a total of 2083 proteins using immunoaffinity depletion, tandem mass tag isobaric labelling and offline two-dimensional liquid chromatography coupled to tandem mass spectrometry, including 1789 that were quantified in all the CSF samples. ANOVA analysis did not yield any proteins with an adjusted p value <.05. CONCLUSION This supports the notion that ME/CFS and fibromyalgia as currently defined are not distinct entities.Key messageME/CFS and fibromyalgia as currently defined are not distinct entities.Unbiased quantitative mass spectrometry-based proteomics can be used to discover cerebrospinal fluid proteins that are biomarkers for a condition such as we are studying.
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Affiliation(s)
| | - Tao Liu
- Integrative Omics, Biological Sciences, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chia-Feng Tsai
- Integrative Omics, Biological Sciences, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Vladislav A. Petyuk
- Integrative Omics, Biological Sciences, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Athena A. Schepmoes
- Integrative Omics, Biological Sciences, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yi-Ting Wang
- Analytical Chemistry and Neurochemistry in Department of Chemistry, Uppsala University, Uppsala, Sweden
| | - Karl K. Weitz
- Integrative Omics, Biological Sciences, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jonas Bergquist
- Analytical Chemistry and Neurochemistry in Department of Chemistry, Uppsala University, Uppsala, Sweden
| | - Richard D. Smith
- Integrative Omics, Biological Sciences, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Benjamin H. Natelson
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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5
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Sarkar S, Syed F, Webb-Robertson BJ, Melchior JT, Chang G, Gritsenko M, Wang YT, Tsai CF, Liu J, Yi X, Cui Y, Eizirik DL, Metz TO, Rewers M, Evans-Molina C, Mirmira RG, Nakayasu ES. Protection of β cells against pro-inflammatory cytokine stress by the GDF15-ERBB2 signaling. medRxiv 2023:2023.11.27.23298904. [PMID: 38076918 PMCID: PMC10705646 DOI: 10.1101/2023.11.27.23298904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Aim/hypothesis Growth/differentiation factor 15 (GDF15) is a therapeutic target for a variety of metabolic diseases, including type 1 diabetes (T1D). However, the nausea caused by GDF15 is a challenging point for therapeutic development. In addition, it is unknown why the endogenous GDF15 fails to protect from T1D development. Here, we investigate the GDF15 signaling in pancreatic islets towards opening possibilities for therapeutic targeting in β cells and to understand why this protection fails to occur naturally. Methods GDF15 signaling in islets was determined by proximity-ligation assay, untargeted proteomics, pathway analysis, and treatment of cells with specific inhibitors. To determine if GDF15 levels would increase prior to disease onset, plasma levels of GDF15 were measured in a longitudinal prospective study of children during T1D development (n=132 cases vs. n=40 controls) and in children with islet autoimmunity but normoglycemia (n=47 cases vs. n=40 controls) using targeted mass spectrometry. We also investigated the regulation of GDF15 production in islets by fluorescence microscopy and western blot analysis. Results The proximity-ligation assay identified ERBB2 as the GDF15 receptor in islets, which was confirmed using its specific antagonist, tucatinib. The untargeted proteomics analysis and caspase assay showed that ERBB2 activation by GDF15 reduces β cell apoptosis by downregulating caspase 8. In plasma, GDF15 levels were higher (p=0.0024) during T1D development compared to controls, but not in islet autoimmunity with normoglycemia. However, in the pancreatic islets GDF15 was depleted via sequestration of its mRNA into stress granules, resulting in translation halting. Conclusions/interpretation GDF15 protects against T1D via ERBB2-mediated decrease of caspase 8 expression in pancreatic islets. Circulating levels of GDF15 increases pre-T1D onset, which is insufficient to promote protection due to its localized depletion in the islets. These findings open opportunities for targeting GDF15 downstream signaling for pancreatic β cell protection in T1D and help to explain the lack of natural protection by the endogenous protein.
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6
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You Y, Tsai CF, Patel R, Sarkar S, Clair G, Zhou M, Liu T, Metz TO, Das C, Nakayasu ES. Analysis of a macrophage carbamylated proteome reveals a function in post-translational modification crosstalk. Cell Commun Signal 2023; 21:241. [PMID: 37723562 PMCID: PMC10506243 DOI: 10.1186/s12964-023-01257-3] [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: 06/09/2023] [Accepted: 08/05/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Lysine carbamylation is a biomarker of rheumatoid arthritis and kidney diseases. However, its cellular function is understudied due to the lack of tools for systematic analysis of this post-translational modification (PTM). METHODS We adapted a method to analyze carbamylated peptides by co-affinity purification with acetylated peptides based on the cross-reactivity of anti-acetyllysine antibodies. We also performed immobilized-metal affinity chromatography to enrich for phosphopeptides, which allowed us to obtain multi-PTM information from the same samples. RESULTS By testing the pipeline with RAW 264.7 macrophages treated with bacterial lipopolysaccharide, 7,299, 8,923 and 47,637 acetylated, carbamylated, and phosphorylated peptides were identified, respectively. Our analysis showed that carbamylation occurs on proteins from a variety of functions on sites with similar as well as distinct motifs compared to acetylation. To investigate possible PTM crosstalk, we integrated the carbamylation data with acetylation and phosphorylation data, leading to the identification 1,183 proteins that were modified by all 3 PTMs. Among these proteins, 54 had all 3 PTMs regulated by lipopolysaccharide and were enriched in immune signaling pathways, and in particular, the ubiquitin-proteasome pathway. We found that carbamylation of linear diubiquitin blocks the activity of the anti-inflammatory deubiquitinase OTULIN. CONCLUSIONS Overall, our data show that anti-acetyllysine antibodies can be used for effective enrichment of carbamylated peptides. Moreover, carbamylation may play a role in PTM crosstalk with acetylation and phosphorylation, and that it is involved in regulating ubiquitination in vitro. Video Abstract.
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Affiliation(s)
- Youngki You
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Rishi Patel
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Soumyadeep Sarkar
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Geremy Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Mowei Zhou
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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7
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Dou Y, Katsnelson L, Gritsenko MA, Hu Y, Reva B, Hong R, Wang YT, Kolodziejczak I, Lu RJH, Tsai CF, Bu W, Liu W, Guo X, An E, Arend RC, Bavarva J, Chen L, Chu RK, Czekański A, Davoli T, Demicco EG, DeLair D, Devereaux K, Dhanasekaran SM, Dottino P, Dover B, Fillmore TL, Foxall M, Hermann CE, Hiltke T, Hostetter G, Jędryka M, Jewell SD, Johnson I, Kahn AG, Ku AT, Kumar-Sinha C, Kurzawa P, Lazar AJ, Lazcano R, Lei JT, Li Y, Liao Y, Lih TSM, Lin TT, Martignetti JA, Masand RP, Matkowski R, McKerrow W, Mesri M, Monroe ME, Moon J, Moore RJ, Nestor MD, Newton C, Omelchenko T, Omenn GS, Payne SH, Petyuk VA, Robles AI, Rodriguez H, Ruggles KV, Rykunov D, Savage SR, Schepmoes AA, Shi T, Shi Z, Tan J, Taylor M, Thiagarajan M, Wang JM, Weitz KK, Wen B, Williams CM, Wu Y, Wyczalkowski MA, Yi X, Zhang X, Zhao R, Mutch D, Chinnaiyan AM, Smith RD, Nesvizhskii AI, Wang P, Wiznerowicz M, Ding L, Mani DR, Zhang H, Anderson ML, Rodland KD, Zhang B, Liu T, Fenyö D. Proteogenomic insights suggest druggable pathways in endometrial carcinoma. Cancer Cell 2023; 41:1586-1605.e15. [PMID: 37567170 PMCID: PMC10631452 DOI: 10.1016/j.ccell.2023.07.007] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 03/25/2023] [Accepted: 07/18/2023] [Indexed: 08/13/2023]
Abstract
We characterized a prospective endometrial carcinoma (EC) cohort containing 138 tumors and 20 enriched normal tissues using 10 different omics platforms. Targeted quantitation of two peptides can predict antigen processing and presentation machinery activity, and may inform patient selection for immunotherapy. Association analysis between MYC activity and metformin treatment in both patients and cell lines suggests a potential role for metformin treatment in non-diabetic patients with elevated MYC activity. PIK3R1 in-frame indels are associated with elevated AKT phosphorylation and increased sensitivity to AKT inhibitors. CTNNB1 hotspot mutations are concentrated near phosphorylation sites mediating pS45-induced degradation of β-catenin, which may render Wnt-FZD antagonists ineffective. Deep learning accurately predicts EC subtypes and mutations from histopathology images, which may be useful for rapid diagnosis. Overall, this study identified molecular and imaging markers that can be further investigated to guide patient stratification for more precise treatment of EC.
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Affiliation(s)
- Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lizabeth Katsnelson
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Yingwei Hu
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Runyu Hong
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Iga Kolodziejczak
- International Institute for Molecular Oncology, 20-203 Poznań, Poland; Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Rita Jui-Hsien Lu
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Wen Bu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Xiaofang Guo
- Division of Gynecologic Oncology, University of South Florida Morsani College of Medicine and Tampa General Hospital Cancer Institute, Tampa, FL 33606, USA
| | - Eunkyung An
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Rebecca C Arend
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - Jasmin Bavarva
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Lijun Chen
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Rosalie K Chu
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Andrzej Czekański
- Wroclaw Medical University and Lower Silesian Oncology, Pulmonology and Hematology Center (DCOPIH), Wrocław, Poland
| | - Teresa Davoli
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Elizabeth G Demicco
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1X5, Canada
| | - Deborah DeLair
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kelly Devereaux
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Saravana M Dhanasekaran
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter Dottino
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bailee Dover
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - Thomas L Fillmore
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - McKenzie Foxall
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - Catherine E Hermann
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | | | - Marcin Jędryka
- Wroclaw Medical University and Lower Silesian Oncology, Pulmonology and Hematology Center (DCOPIH), Wrocław, Poland
| | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Isabelle Johnson
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Andrea G Kahn
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - Amy T Ku
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paweł Kurzawa
- Heliodor Swiecicki Clinical Hospital in Poznan ul. Przybyszewskiego 49, 60-355 Poznań, Poland; Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | - Alexander J Lazar
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rossana Lazcano
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yi Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tung-Shing M Lih
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - John A Martignetti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ramya P Masand
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rafał Matkowski
- Wroclaw Medical University and Lower Silesian Oncology, Pulmonology and Hematology Center (DCOPIH), Wrocław, Poland
| | - Wilson McKerrow
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Michael D Nestor
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Chelsea Newton
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | | | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA; School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ana I Robles
- 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
| | - Kelly V Ruggles
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Division of Precision Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Dmitry Rykunov
- 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, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jimin Tan
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Mason Taylor
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Joshua M Wang
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - C M Williams
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Yige Wu
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Matthew A Wyczalkowski
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Xinpei Yi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xu Zhang
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Rui Zhao
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - David Mutch
- Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, 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
| | - Maciej Wiznerowicz
- International Institute for Molecular Oncology, 60-203 Poznań, Poland; Heliodor Swiecicki Clinical Hospital in Poznan ul. Przybyszewskiego 49, 60-355 Poznań, Poland; Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | - Li Ding
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Hui Zhang
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Matthew L Anderson
- Division of Gynecologic Oncology, University of South Florida Morsani College of Medicine and Tampa General Hospital Cancer Institute, Tampa, FL 33606, USA.
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA.
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8
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Abstract
Plant phosphoproteomics provides a global view of phosphorylation-mediated signaling in plants; however, it demands high-throughput methods with sensitive detection and accurate quantification. Despite the widespread use of protein precipitation for removing contaminants and improving sample purity, it limits the sensitivity and throughput of plant phosphoproteomic analysis. The multiple handling steps involved in protein precipitation lead to sample loss and process variability. Herein, we developed an approach based on suspension trapping (S-Trap), termed tandem S-Trap-IMAC (immobilized metal ion affinity chromatography), by integrating an S-Trap micro-column with a Fe-IMAC tip. Compared with a precipitation-based workflow, the tandem S-Trap-IMAC method deepened the coverage of the Arabidopsis (Arabidopsis thaliana) phosphoproteome by more than 30%, with improved number of multiply phosphorylated peptides, quantification accuracy, and short sample processing time. We applied the tandem S-Trap-IMAC method for studying abscisic acid (ABA) signaling in Arabidopsis seedlings. We thus discovered that a significant proportion of the phosphopeptides induced by ABA are multiply phosphorylated peptides, indicating their importance in early ABA signaling and quantified several key phosphorylation sites on core ABA signaling components across four time points. Our results show that the optimized workflow aids high-throughput phosphoproteome profiling of low-input plant samples.
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Affiliation(s)
- Chin-Wen Chen
- Institution of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Miao-Hsia Lin
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei 100233, Taiwan
| | - Shu-Yu Lin
- Academia Sinica Common Mass Spectrometry Facilities for Proteomics and Protein Modification Analysis, Academia Sinica, Taipei 115201, Taiwan
| | - Chuan-Chih Hsu
- Institution of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
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9
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Kitata RB, Velickovic M, Xu Z, Zhao R, Scholten D, Chu RK, Orton DJ, Chrisler WB, Mathews JV, Piehowski PD, Liu T, Smith RD, Liu H, Wasserfall CH, Tsai CF, Shi T. Robust collection and processing for label-free single voxel proteomics. bioRxiv 2023:2023.08.14.553333. [PMID: 37645907 PMCID: PMC10462033 DOI: 10.1101/2023.08.14.553333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk tissues. However, such bulk measurement lacks spatial resolution and obscures important tissue heterogeneity, which make it impossible for proteome mapping of tissue microenvironment. Here we report an integrated wet collection of single tissue voxel and Surfactant-assisted One-Pot voxel processing method termed wcSOP for robust label-free single voxel proteomics. wcSOP capitalizes on buffer droplet-assisted wet collection of single tissue voxel dissected by LCM into the PCR tube cap and MS-compatible surfactant-assisted one-pot voxel processing in the collection cap. This convenient method allows reproducible label-free quantification of ∼900 and ∼4,600 proteins for single voxel from fresh frozen human spleen tissue at 20 μm × 20 μm × 10 μm (close to single cells) and 200 μm × 200 μm × 10 μm (∼100 cells), respectively. 100s-1000s of protein signatures with differential expression levels were identified to be spatially resolved between spleen red and white pulp regions depending on the voxel size. Region-specific signaling pathways were enriched from single voxel proteomics data. Antibody-based CODEX imaging was used to validate label-free MS quantitation for single voxel analysis. The wcSOP-MS method paves the way for routine robust single voxel proteomics and spatial proteomics.
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10
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You Y, Tsai CF, Patel R, Sarkar S, Clair G, Zhou M, Liu T, Metz TO, Das C, Nakayasu ES. Analysis of a macrophage carbamylated proteome reveals a function in post-translational modification crosstalk. Res Sq 2023:rs.3.rs-3044777. [PMID: 37398265 PMCID: PMC10312928 DOI: 10.21203/rs.3.rs-3044777/v1] [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: 07/04/2023]
Abstract
Background. Lysine carbamylation is a biomarker of rheumatoid arthritis and kidney diseases. However, its cellular function is understudied due to the lack of tools for systematic analysis of this post-translational modification (PTM). Methods. We adapted a method to analyze carbamylated peptides by co-affinity purification with acetylated peptides based on the cross-reactivity of anti-acetyllysine antibodies. We integrated this method into a mass spectrometry-based multi-PTM pipeline to simultaneously analyze carbamylated and acetylated peptides in addition to phosphopeptides were enriched by sequential immobilized-metal affinity chromatography. Results. By testing the pipeline with RAW 264.7 macrophages treated with bacterial lipopolysaccharide, 7,299, 8,923 and 47,637 acetylated, carbamylated, and phosphorylated peptides were identified, respectively. Our analysis showed that carbamylation occurs on proteins from a variety of functions on sites with similar as well as distinct motifs compared to acetylation. To investigate possible PTM crosstalk, we integrated the carbamylation data with acetylation and phosphorylation data, leading to the identification 1,183 proteins that were modified by all 3 PTMs. Among these proteins, 54 had all 3 PTMs regulated by lipopolysaccharide and were enriched in immune signaling pathways, and in particular, the ubiquitin-proteasome pathway. We found that carbamylation of linear diubiquitin blocks the activity of the anti-inflammatory deubiquitinase OTULIN. Conclusions Overall, our data show that anti-acetyllysine antibodies can be used for effective enrichment of carbamylated peptides. Moreover, carbamylation may play a role in PTM crosstalk with acetylation and phosphorylation, and that it is involved in regulating ubiquitination in vitro .
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Affiliation(s)
| | | | | | | | | | | | - Tao Liu
- Pacific Northwest National Laboratory
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11
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LaPlante EL, Stürchler A, Fullem R, Chen D, Starner AC, Esquivel E, Alsop E, Jackson AR, Ghiran I, Pereira G, Rozowsky J, Chang J, Gerstein MB, Alexander RP, Roth ME, Franklin JL, Coffey RJ, Raffai RL, Mansuy IM, Stavrakis S, deMello AJ, Laurent LC, Wang YT, Tsai CF, Liu T, Jones J, Van Keuren-Jensen K, Van Nostrand E, Mateescu B, Milosavljevic A. exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers. Cell Genom 2023; 3:100303. [PMID: 37228754 PMCID: PMC10203258 DOI: 10.1016/j.xgen.2023.100303] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 01/01/2023] [Accepted: 03/24/2023] [Indexed: 05/27/2023]
Abstract
Although the role of RNA binding proteins (RBPs) in extracellular RNA (exRNA) biology is well established, their exRNA cargo and distribution across biofluids are largely unknown. To address this gap, we extend the exRNA Atlas resource by mapping exRNAs carried by extracellular RBPs (exRBPs). This map was developed through an integrative analysis of ENCODE enhanced crosslinking and immunoprecipitation (eCLIP) data (150 RBPs) and human exRNA profiles (6,930 samples). Computational analysis and experimental validation identified exRBPs in plasma, serum, saliva, urine, cerebrospinal fluid, and cell-culture-conditioned medium. exRBPs carry exRNA transcripts from small non-coding RNA biotypes, including microRNA (miRNA), piRNA, tRNA, small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), Y RNA, and lncRNA, as well as protein-coding mRNA fragments. Computational deconvolution of exRBP RNA cargo reveals associations of exRBPs with extracellular vesicles, lipoproteins, and ribonucleoproteins across human biofluids. Overall, we mapped the distribution of exRBPs across human biofluids, presenting a resource for the community.
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Affiliation(s)
- Emily L. LaPlante
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alessandra Stürchler
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
- Brain Research Institute, University of Zürich, 8057 Zürich, Switzerland
| | - Robert Fullem
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anne C. Starner
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 76706, USA
| | - Emmanuel Esquivel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Alsop
- Neurogenomics Division, TGen, Phoenix, AZ 85004, USA
| | - Andrew R. Jackson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ionita Ghiran
- Department of Anesthesia, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Getulio Pereira
- Department of Anesthesia, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Joel Rozowsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Justin Chang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Mark B. Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Matthew E. Roth
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey L. Franklin
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Robert J. Coffey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Robert L. Raffai
- Department of Veterans Affairs, Surgical Service (112G), San Francisco VA Medical Center, San Francisco, CA 94121, USA
- Division of Endovascular and Vascular Surgery, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Isabelle M. Mansuy
- Brain Research Institute, University of Zürich, 8057 Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Andrew J. deMello
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jennifer Jones
- Laboratory of Pathology Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Eric Van Nostrand
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 76706, USA
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bogdan Mateescu
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
- Brain Research Institute, University of Zürich, 8057 Zürich, Switzerland
| | - Aleksandar Milosavljevic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
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12
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Eiger DS, Smith JS, Shi T, Stepniewski TM, Tsai CF, Honeycutt C, Boldizsar N, Gardner J, Nicora CD, Moghieb AM, Kawakami K, Choi I, Hicks C, Zheng K, Warman A, Alagesan P, Knape NM, Huang O, Silverman JD, Smith RD, Inoue A, Selent J, Jacobs JM, Rajagopal S. Phosphorylation barcodes direct biased chemokine signaling at CXCR3. Cell Chem Biol 2023; 30:362-382.e8. [PMID: 37030291 PMCID: PMC10147449 DOI: 10.1016/j.chembiol.2023.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 07/15/2022] [Revised: 02/10/2023] [Accepted: 03/13/2023] [Indexed: 04/10/2023]
Abstract
G protein-coupled receptor (GPCR)-biased agonism, selective activation of certain signaling pathways relative to others, is thought to be directed by differential GPCR phosphorylation "barcodes." At chemokine receptors, endogenous chemokines can act as "biased agonists", which may contribute to the limited success when pharmacologically targeting these receptors. Here, mass spectrometry-based global phosphoproteomics revealed that CXCR3 chemokines generate different phosphorylation barcodes associated with differential transducer activation. Chemokine stimulation resulted in distinct changes throughout the kinome in global phosphoproteomics studies. Mutation of CXCR3 phosphosites altered β-arrestin 2 conformation in cellular assays and was consistent with conformational changes observed in molecular dynamics simulations. T cells expressing phosphorylation-deficient CXCR3 mutants resulted in agonist- and receptor-specific chemotactic profiles. Our results demonstrate that CXCR3 chemokines are non-redundant and act as biased agonists through differential encoding of phosphorylation barcodes, leading to distinct physiological processes.
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Affiliation(s)
- Dylan S Eiger
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Jeffrey S Smith
- Department of Dermatology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Dermatology, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Dermatology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Dermatology Program, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Tomasz Maciej Stepniewski
- Research Program on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF), 08003 Barcelona, Spain
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | | | | | - Julia Gardner
- Trinity College, Duke University, Durham, NC 27710, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | | | - Kouki Kawakami
- Department of Pharmaceutical Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Issac Choi
- Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Chloe Hicks
- Trinity College, Duke University, Durham, NC 27710, USA
| | - Kevin Zheng
- Harvard Medical School, Boston, MA 02115, USA
| | - Anmol Warman
- Trinity College, Duke University, Durham, NC 27710, USA
| | - Priya Alagesan
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Nicole M Knape
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Ouwen Huang
- Department of Biomedical Engineering, Duke University, Durham, NC 27710, USA
| | - Justin D Silverman
- College of Information Sciences and Technology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Asuka Inoue
- Department of Pharmaceutical Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Jana Selent
- Research Program on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF), 08003 Barcelona, Spain
| | - Jon M Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Sudarshan Rajagopal
- Department of Biochemistry, Duke University, Durham, NC 27710, USA; Department of Pharmaceutical Sciences, Tohoku University, Sendai 980-8577, Japan.
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13
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Yao L, Wang JT, Jayasinghe RG, O'Neal J, Tsai CF, Rettig MP, Song Y, Liu R, Zhao Y, Ibrahim OM, Fiala MA, Fortier JM, Chen S, Gehrs L, Rodrigues FM, Wendl MC, Kohnen D, Shinkle A, Cao S, Foltz SM, Zhou DC, Storrs E, Wyczalkowski MA, Mani S, Goldsmith SR, Zhu Y, Hamilton M, Liu T, Chen F, Vij R, Ding L, DiPersio JF. Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma. Cancer Res 2023; 83:1214-1233. [PMID: 36779841 PMCID: PMC10102848 DOI: 10.1158/0008-5472.can-22-1769] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 05/28/2022] [Revised: 12/10/2022] [Accepted: 02/07/2023] [Indexed: 02/14/2023]
Abstract
Multiple myeloma (MM) is a highly refractory hematologic cancer. Targeted immunotherapy has shown promise in MM but remains hindered by the challenge of identifying specific yet broadly representative tumor markers. We analyzed 53 bone marrow (BM) aspirates from 41 MM patients using an unbiased, high-throughput pipeline for therapeutic target discovery via single-cell transcriptomic profiling, yielding 38 MM marker genes encoding cell-surface proteins and 15 encoding intracellular proteins. Of these, 20 candidate genes were highlighted that are not yet under clinical study, 11 of which were previously uncharacterized as therapeutic targets. The findings were cross-validated using bulk RNA sequencing, flow cytometry, and proteomic mass spectrometry of MM cell lines and patient BM, demonstrating high overall concordance across data types. Independent discovery using bulk RNA sequencing reiterated top candidates, further affirming the ability of single-cell transcriptomics to accurately capture marker expression despite limitations in sample size or sequencing depth. Target dynamics and heterogeneity were further examined using both transcriptomic and immuno-imaging methods. In summary, this study presents a robust and broadly applicable strategy for identifying tumor markers to better inform the development of targeted cancer therapy. SIGNIFICANCE Single-cell transcriptomic profiling and multiomic cross-validation to uncover therapeutic targets identifies 38 myeloma marker genes, including 11 transcribing surface proteins with previously uncharacterized potential for targeted antitumor therapy.
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Affiliation(s)
- Lijun Yao
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Julia T. Wang
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Reyka G. Jayasinghe
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Julie O'Neal
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Michael P. Rettig
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Yizhe Song
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Ruiyang Liu
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Yanyan Zhao
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Omar M. Ibrahim
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Mark A. Fiala
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Julie M. Fortier
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Siqi Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Leah Gehrs
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Fernanda Martins Rodrigues
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Michael C. Wendl
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Daniel Kohnen
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Andrew Shinkle
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Song Cao
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Steven M. Foltz
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Daniel Cui Zhou
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Erik Storrs
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Matthew A. Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Smrithi Mani
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Scott R. Goldsmith
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Ying Zhu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Mark Hamilton
- Multiple Myeloma Research Foundation, Norwalk, Connecticut
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Ravi Vij
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - John F. DiPersio
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
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14
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Schuster E, Dashzeveg N, Jia Y, Golam K, Zhang T, Hoffman A, Zhang Y, Zheng C, Ramos E, Taftaf R, Shennawy LE, Scholten D, Kitata RB, Adorno-Cruz V, Reduzzi C, Spahija S, Xu R, Siziopikou KP, Platanias LC, Shah A, Gradishar WJ, Cristofanilli M, Tsai CF, Shi T, Liu H. Computational ranking-assisted identification of Plexin-B2 in homotypic and heterotypic clustering of circulating tumor cells in breast cancer metastasis. bioRxiv 2023:2023.04.10.536233. [PMID: 37090580 PMCID: PMC10120645 DOI: 10.1101/2023.04.10.536233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Metastasis is the cause of over 90% of all deaths associated with breast cancer, yet the strategies to predict cancer spreading based on primary tumor profiles and therefore prevent metastasis are egregiously limited. As rare precursor cells to metastasis, circulating tumor cells (CTCs) in multicellular clusters in the blood are 20-50 times more likely to produce viable metastasis than single CTCs. However, the molecular mechanisms underlying various CTC clusters, such as homotypic tumor cell clusters and heterotypic tumor-immune cell clusters, are yet to be fully elucidated. Combining machine learning-assisted computational ranking with experimental demonstration to assess cell adhesion candidates, we identified a transmembrane protein Plexin- B2 (PB2) as a new therapeutic target that drives the formation of both homotypic and heterotypic CTC clusters. High PB2 expression in human primary tumors predicts an unfavorable distant metastasis-free survival and is enriched in CTC clusters compared to single CTCs in advanced breast cancers. Loss of PB2 reduces formation of homotypic tumor cell clusters as well as heterotypic tumor-myeloid cell clusters in triple-negative breast cancer. Interactions between PB2 and its ligand Sema4C on tumor cells promote homotypic cluster formation, and PB2 binding with Sema4A on myeloid cells (monocytes) drives heterotypic CTC cluster formation, suggesting that metastasizing tumor cells hijack the PB2/Sema family axis to promote lung metastasis in breast cancer. Additionally, using a global proteomic analysis, we identified novel downstream effectors of the PB2 pathway associated with cancer stemness, cell cycling, and tumor cell clustering in breast cancer. Thus, PB2 is a novel therapeutic target for preventing new metastasis.
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15
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Eiger DS, Smith JS, Shi T, Stepniewski TM, Tsai CF, Honeycutt C, Boldizsar N, Gardner J, Nicora CD, Moghieb AM, Kawakami K, Choi I, Zheng K, Warman A, Alagesan P, Knape NM, Huang O, Silverman JD, Smith RD, Inoue A, Selent J, Jacobs JM, Rajagopal S. Phosphorylation barcodes direct biased chemokine signaling at CXCR3. bioRxiv 2023:2023.03.14.532634. [PMID: 36993369 PMCID: PMC10055163 DOI: 10.1101/2023.03.14.532634] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
G protein-coupled receptor (GPCR) biased agonism, the activation of some signaling pathways over others, is thought to largely be due to differential receptor phosphorylation, or "phosphorylation barcodes." At chemokine receptors, ligands act as "biased agonists" with complex signaling profiles, which contributes to the limited success in pharmacologically targeting these receptors. Here, mass spectrometry-based global phosphoproteomics revealed that CXCR3 chemokines generate different phosphorylation barcodes associated with differential transducer activation. Chemokine stimulation resulted in distinct changes throughout the kinome in global phosphoproteomic studies. Mutation of CXCR3 phosphosites altered β-arrestin conformation in cellular assays and was confirmed by molecular dynamics simulations. T cells expressing phosphorylation-deficient CXCR3 mutants resulted in agonist- and receptor-specific chemotactic profiles. Our results demonstrate that CXCR3 chemokines are non-redundant and act as biased agonists through differential encoding of phosphorylation barcodes and lead to distinct physiological processes.
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Affiliation(s)
- Dylan S. Eiger
- Department of Biochemistry, Duke University, Durham, NC, 27710, USA
| | - Jeffrey S. Smith
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Dermatology, Brigham and Women’s Hospital, Boston, MA, 02115, USA
- Department of Dermatology, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
- Dermatology Program, Boston Children’s Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Tomasz Maciej Stepniewski
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF)-Hospital del Mar Medical Research Institute (IMIM), Barcelona, 08003, Spain
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | | | | | - Julia Gardner
- Trinity College, Duke University, Durham, NC, 27710, USA
| | - Carrie D. Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | | | - Kouki Kawakami
- Department of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Issac Choi
- Department of Medicine, Duke University, Durham, NC 27710 USA
| | - Kevin Zheng
- Trinity College, Duke University, Durham, NC, 27710, USA
| | - Anmol Warman
- Trinity College, Duke University, Durham, NC, 27710, USA
| | - Priya Alagesan
- Department of Biochemistry, Duke University, Durham, NC, 27710, USA
| | - Nicole M. Knape
- Department of Biochemistry, Duke University, Durham, NC, 27710, USA
| | - Ouwen Huang
- Department of Biomedical Engineering, Duke University, Durham, NC, 27710, USA
| | - Justin D. Silverman
- College of Information Sciences and Technology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Asuka Inoue
- Department of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF)-Hospital del Mar Medical Research Institute (IMIM), Barcelona, 08003, Spain
| | - Jon M. Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Sudarshan Rajagopal
- Department of Biochemistry, Duke University, Durham, NC, 27710, USA
- Department of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8577, Japan
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16
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Tsai CF, Wang YT, Hsu CC, Kitata RB, Chu RK, Velickovic M, Zhao R, Williams SM, Chrisler WB, Jorgensen ML, Moore RJ, Zhu Y, Rodland KD, Smith RD, Wasserfall CH, Shi T, Liu T. A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics. Commun Biol 2023; 6:70. [PMID: 36653408 PMCID: PMC9849344 DOI: 10.1038/s42003-022-04400-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 12/23/2022] [Indexed: 01/19/2023] Open
Abstract
Effective phosphoproteome of nanoscale sample analysis remains a daunting task, primarily due to significant sample loss associated with non-specific surface adsorption during enrichment of low stoichiometric phosphopeptide. We develop a tandem tip phosphoproteomics sample preparation method that is capable of sample cleanup and enrichment without additional sample transfer, and its integration with our recently developed SOP (Surfactant-assisted One-Pot sample preparation) and iBASIL (improved Boosting to Amplify Signal with Isobaric Labeling) approaches provides a streamlined workflow enabling sensitive, high-throughput nanoscale phosphoproteome measurements. This approach significantly reduces both sample loss and processing time, allowing the identification of >3000 (>9500) phosphopeptides from 1 (10) µg of cell lysate using the label-free method without a spectral library. It also enables precise quantification of ~600 phosphopeptides from 100 sorted cells (single-cell level input for the enriched phosphopeptides) and ~700 phosphopeptides from human spleen tissue voxels with a spatial resolution of 200 µm (equivalent to ~100 cells) in a high-throughput manner. The new workflow opens avenues for phosphoproteome profiling of mass-limited samples at the low nanogram level.
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Affiliation(s)
- Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Chuan-Chih Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Reta Birhanu Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Rosalie K Chu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Marija Velickovic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - William B Chrisler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Marda L Jorgensen
- Department of Pathology, Immunology, and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Clive H Wasserfall
- Department of Pathology, Immunology, and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
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17
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Wei X, Zhang L, Zhang Y, Cooper C, Brewer C, Tsai CF, Wang YT, Glaz M, Wessells HB, Que J, Titus MA, Cirulli V, Glaser A, Liu T, Reder NP, Creighton CJ, Xin L. Ablating Lgr5-expressing prostatic stromal cells activates the ERK-mediated mechanosensory signaling and disrupts prostate tissue homeostasis. Cell Rep 2022; 40:111313. [PMID: 36070687 PMCID: PMC9491244 DOI: 10.1016/j.celrep.2022.111313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/12/2022] [Accepted: 08/12/2022] [Indexed: 01/19/2023] Open
Abstract
Functional implication of stromal heterogeneity in the prostate remains incompletely understood. Using lineage tracing and light-sheet imaging, we show that some fibroblast cells at the mouse proximal prostatic ducts and prostatic urethra highly express Lgr5. Genetic ablation of these anatomically restricted stromal cells, but not nonselective ablation of prostatic stromal cells, rapidly induces prostate epithelial turnover and dedifferentiation that are reversed following spontaneous restoration of the Lgr5+ stromal cells. RNA sequencing (RNA-seq) analysis indicates that ablating the Lgr5+ stromal cells activates a mechanosensory response. Ablating the Lgr5+ stromal cells impairs the control of prostatic ductal outlet, increases prostate tissue stiffness, and activates the mitogen-activated protein kinase (MAPK). Suppressing MAPK overrides the elevated epithelial proliferation. In summary, the Lgr5+ stromal cells regulate prostate tissue homeostasis and maintain its functional integrity in a long-distance manner. Our study implies that the cells at organ junctions most likely control organ homeostasis by sustaining a balanced mechanoforce.
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Affiliation(s)
- Xing Wei
- Department of Urology, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Li Zhang
- Department of Urology, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cody Cooper
- Alpenglow Biosciences, Inc., Seattle, WA 98103, USA
| | - Chris Brewer
- Alpenglow Biosciences, Inc., Seattle, WA 98103, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Micah Glaz
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98109, USA
| | - Hunter B Wessells
- Department of Urology, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Jianwen Que
- Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Mark A Titus
- Department of Genitourinary Medical Oncology, MD Anderson Cancer Center, University of Texas, Houston TX 77030, USA
| | - Vincenzino Cirulli
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Adam Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98109, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | | | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Li Xin
- Department of Urology, University of Washington, 850 Republican Street, Seattle, WA 98109, USA; Department of Genitourinary Medical Oncology, MD Anderson Cancer Center, University of Texas, Houston TX 77030, USA.
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18
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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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19
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Tsai CF, Wen IJ. Assessment of the Thermal Hazard Characteristics of Three Low-Temperature Active Azo Initiators for Polymer Resin in Construction Industries under Adiabatic Conditions. ACS Omega 2022; 7:21378-21384. [PMID: 35785297 PMCID: PMC9245147 DOI: 10.1021/acsomega.1c06269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Resins continue to occupy a place in the waterproof building market. Unlike traditional concrete building materials, the polymerization of resins requires initiators to support the required energy to drive the reaction or reduce the polymerization threshold, which shows a high reaction rate and low energy consumption in the polymerization process. Azo compounds (azos) are energetic substances commonly used in polymerization, but they can cause process hazards due to the amount of heat release and accumulation of the resulting heat. To ensure that similar hazards do not occur, the emerging azo initiators 2,2'-azobis(2-methylpropionamide)dihydrochloride (AIBA), 2-cyanopropan-2-yliminourea (CABN), and 2,2'-azodi(2-methylbutyronitrile) (AMBN) are explored. Depending on the process conditions, it is critical to examine how chemical reactions from a laboratory behave at a large scale. Kinetic models can be used to estimate fundamental safety parameters suitable for assessing the reaction hazards and as control measures, such as time to the maximum reaction rate under adiabatic conditions, time to the conversion limit, and runaway determination for process operation. The structure of this study is a combination of adiabatic calorimeter data and a nonlinear adiabatic dynamics model with the goal of helping to fill the void in research on thermal hazard analysis of emerging azo initiators. The adiabatic data is used to analyze the reaction mode characteristics of the azo compounds, and combined with the external environment, the reaction and temperature parameter changes of the azo compounds due to the reaction are discussed in the actual situation.
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Affiliation(s)
- Chia-Feng Tsai
- Graduate
School of Engineering Science and Technology, National Yunlin University of Science and Technology (YunTech), 123 University Road, Section 3, Douliou, Yunlin 64002, Taiwan
| | - I-Jyh Wen
- Department
of Civil and Construction Engineering, National
Yunlin University of Science and Technology (YunTech), 123 University Road, Section 3, Douliou, Yunlin 64002, Taiwan
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20
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Tailor D, Tsai CF, Honkala A, Li W, Liu T, Pejovic T, Malhotra SV. Abstract 2645: Targeting mRNA processing pathways in ovarian cancer with a small molecule inhibitor. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
mRNA processing related pathways, including spliceosome and ribosome are over-expressed and unregulated in cancer cells. To investigate the mRNA processing pathways in patient samples, we performed a comprehensive, tandem mass tag (TMT) labeling-based proteome and phosphoproteome profiling of the normal and ovarian cancerous tissues from patients treated with different chemotherapy revealed that malignant cells have overexpression of mRNA processing pathways compared to normal cells. For this analysis, equal amount of tissues were homogenized, and tissue lysates were collected and processed for the quantitative proteomics and phosphoproteomics analysis. KEGG pathway enrichment analysis revealed that spliceosome, basal transcription factors, mRNA surveillance, ribosome and ribosome biogenesis in eukaryotes pathways are upregulated in cancer cells compared to control. On other hand, pathways associated with metabolism and fatty acid biosynthesis were downregulated in malignant cells. Moreover, kinase Enrichment Analysis shows that CDK2, ATM, ATR, and MAPK associated kinases are upregulated in cancer cells compared to normal. Based on proteome analysis of patient samples, we investigated the pharmacological inhibition of Y-box binding protein 1 (YB-1). This is an RNA binding protein and key regulator of pre-mRNA alternative splicing and processing. We recently showed that a natural product-derived small molecule (SU056) inhibits YB-1 activity. We found that SU056 binds to the YB-1 and blocks the RNA binding pocket. Proteomics results suggest that treatment with this drug strongly inhibits the spliceosome pathway. SU056 treatment arrests the ovarian cancer cells in G1 phase and inhibits the CDK2 and Cyclin E. SU056 inhibits the tumor progression and metastasis in the ID8 mice model and sensitizes the OVCAR8 NSG mice model for paclitaxel treatment. Our study provides a compelling case for YB-1 inhibition using SU056 as a potential therapy for ovarian cancer.
Citation Format: Dhanir Tailor, Chia-Feng Tsai, Alexander Honkala, Wenqi Li, Tao Liu, Tanja Pejovic, Sanjay V. Malhotra. Targeting mRNA processing pathways in ovarian cancer with a small molecule inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2645.
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Affiliation(s)
| | | | | | - Wenqi Li
- 1Oregon Health & Science University, Portland, OR
| | - Tao Liu
- 2Pacific Northwest National Laboratory, Richland, WA
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21
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Lin A, Piehowski PD, Tsai CF, Makushok T, Yi L, Diaz U, Yan C, Summers D, Sood P, Smith RD, Liu T, Marshall WF. Determining protein polarization proteome-wide using physical dissection of individual Stentor coeruleus cells. Curr Biol 2022; 32:2300-2308.e4. [PMID: 35447087 PMCID: PMC9133221 DOI: 10.1016/j.cub.2022.03.078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/08/2022] [Accepted: 03/30/2022] [Indexed: 12/18/2022]
Abstract
Cellular components are non-randomly arranged with respect to the shape and polarity of the whole cell.1-4 Patterning within cells can extend down to the level of individual proteins and mRNA.5,6 But how much of the proteome is actually localized with respect to cell polarity axes? Proteomics combined with cellular fractionation7-11 has shown that most proteins localize to one or more organelles but does not tell us how many proteins have a polarized localization with respect to the large-scale polarity axes of the intact cell. Genome-wide localization studies in yeast12-15 found that only a few percent of proteins have a localized position relative to the cell polarity axis defined by sites of polarized cell growth. Here, we describe an approach for analyzing protein distribution within a cell with a visibly obvious global patterning-the giant ciliate Stentor coeruleus.16,17 Ciliates, including Stentor, have highly polarized cell shapes with visible surface patterning.1,18 A Stentor cell is roughly 2 mm long, allowing a "proteomic dissection" in which microsurgery is used to separate cellular fragments along the anterior-posterior axis, followed by comparative proteomic analysis. In our analysis, 25% of the proteome, including signaling proteins, centrin/SFI proteins, and GAS2 orthologs, shows a polarized location along the cell's anterior-posterior axis. We conclude that a large proportion of all proteins are polarized with respect to global cell polarity axes and that proteomic dissection provides a simple and effective approach for spatial proteomics.
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Affiliation(s)
- Athena Lin
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Paul D Piehowski
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Chia-Feng Tsai
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Tatyana Makushok
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lian Yi
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ulises Diaz
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Connie Yan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Diana Summers
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Pranidhi Sood
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Richard D Smith
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Tao Liu
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, United States of America.
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22
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Woo J, Clair GC, Williams SM, Feng S, Tsai CF, Moore RJ, Chrisler WB, Smith RD, Kelly RT, Paša-Tolić L, Ansong C, Zhu Y. Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering. Cell Syst 2022; 13:426-434.e4. [PMID: 35298923 PMCID: PMC9119937 DOI: 10.1016/j.cels.2022.02.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [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: 10/22/2020] [Revised: 12/04/2021] [Accepted: 02/17/2022] [Indexed: 12/13/2022]
Abstract
Single-cell proteomics (scProteomics) promises to advance our understanding of cell functions within complex biological systems. However, a major challenge of current methods is their inability to identify and provide accurate quantitative information for low-abundance proteins. Herein, we describe an ion-mobility-enhanced mass spectrometry acquisition and peptide identification method, transferring identification based on FAIMS filtering (TIFF), to improve the sensitivity and accuracy of label-free scProteomics. TIFF extends the ion accumulation times for peptide ions by filtering out singly charged ions. The peptide identities are assigned by a three-dimensional MS1 feature matching approach (retention time, accurate mass, and FAIMS compensation voltage). The TIFF method enabled unbiased proteome analysis to a depth of >1,700 proteins in single HeLa cells, with >1,100 proteins consistently identified. As a demonstration, we applied the TIFF method to obtain temporal proteome profiles of >150 single murine macrophage cells during lipopolysaccharide stimulation and identified time-dependent proteome changes. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Jongmin Woo
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Geremy C Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Song Feng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - William B Chrisler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
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23
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Tsai CF, Ogata K, Sugiyama N, Ishihama Y. Motif-centric phosphoproteomics to target kinase-mediated signaling pathways. Cell Rep Methods 2022; 2:100138. [PMID: 35474870 PMCID: PMC9017188 DOI: 10.1016/j.crmeth.2021.100138] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/08/2021] [Accepted: 12/13/2021] [Indexed: 12/27/2022]
Abstract
Identifying cellular phosphorylation pathways based on kinase-substrate relationships is a critical step to understanding the regulation of physiological functions in cells. Mass spectrometry-based phosphoproteomics workflows have made it possible to comprehensively collect information on individual phosphorylation sites in a variety of samples. However, there is still no generic approach to uncover phosphorylation networks based on kinase-substrate relationships in rare cell populations. Here, we describe a motif-centric phosphoproteomics approach combined with multiplexed isobaric labeling, in which in vitro kinase reactions are used to generate targeted phosphopeptides, which are spiked into one of the isobaric channels to increase detectability. Proof-of-concept experiments demonstrate selective and comprehensive quantification of targeted phosphopeptides by using multiple kinases for motif-centric channels. More than 7,000 tyrosine phosphorylation sites were quantified from several tens of micrograms of starting materials. This approach enables the quantification of multiple phosphorylation pathways under physiological or pathological regulation in a motif-centric manner.
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Affiliation(s)
- Chia-Feng Tsai
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kosuke Ogata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Naoyuki Sugiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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24
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El-Shennawy L, Hoffmann AD, Dashzeveg NK, McAndrews KM, Mehl PJ, Cornish D, Yu Z, Tokars VL, Nicolaescu V, Tomatsidou A, Mao C, Felicelli CJ, Tsai CF, Ostiguin C, Jia Y, Li L, Furlong K, Wysocki J, Luo X, Ruivo CF, Batlle D, Hope TJ, Shen Y, Chae YK, Zhang H, LeBleu VS, Shi T, Swaminathan S, Luo Y, Missiakas D, Randall GC, Demonbreun AR, Ison MG, Kalluri R, Fang D, Liu H. Circulating ACE2-expressing extracellular vesicles block broad strains of SARS-CoV-2. Nat Commun 2022; 13:405. [PMID: 35058437 PMCID: PMC8776790 DOI: 10.1038/s41467-021-27893-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [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: 09/19/2021] [Accepted: 12/23/2021] [Indexed: 12/20/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the pandemic of the coronavirus induced disease 2019 (COVID-19) with evolving variants of concern. It remains urgent to identify novel approaches against broad strains of SARS-CoV-2, which infect host cells via the entry receptor angiotensin-converting enzyme 2 (ACE2). Herein, we report an increase in circulating extracellular vesicles (EVs) that express ACE2 (evACE2) in plasma of COVID-19 patients, which levels are associated with severe pathogenesis. Importantly, evACE2 isolated from human plasma or cells neutralizes SARS-CoV-2 infection by competing with cellular ACE2. Compared to vesicle-free recombinant human ACE2 (rhACE2), evACE2 shows a 135-fold higher potency in blocking the binding of the viral spike protein RBD, and a 60- to 80-fold higher efficacy in preventing infections by both pseudotyped and authentic SARS-CoV-2. Consistently, evACE2 protects the hACE2 transgenic mice from SARS-CoV-2-induced lung injury and mortality. Furthermore, evACE2 inhibits the infection of SARS-CoV-2 variants (α, β, and δ) with equal or higher potency than for the wildtype strain, supporting a broad-spectrum antiviral mechanism of evACE2 for therapeutic development to block the infection of existing and future coronaviruses that use the ACE2 receptor.
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Affiliation(s)
- Lamiaa El-Shennawy
- grid.16753.360000 0001 2299 3507Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Andrew D. Hoffmann
- grid.16753.360000 0001 2299 3507Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Nurmaa Khund Dashzeveg
- grid.16753.360000 0001 2299 3507Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Kathleen M. McAndrews
- grid.240145.60000 0001 2291 4776Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Paul J. Mehl
- grid.16753.360000 0001 2299 3507Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Daphne Cornish
- grid.16753.360000 0001 2299 3507Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Zihao Yu
- grid.16753.360000 0001 2299 3507Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Valerie L. Tokars
- grid.16753.360000 0001 2299 3507Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Vlad Nicolaescu
- The University of Chicago Howard T. Ricketts Laboratory and Department of Microbiology, Chicago, IL 60637 USA
| | - Anastasia Tomatsidou
- The University of Chicago Howard T. Ricketts Laboratory and Department of Microbiology, Chicago, IL 60637 USA
| | - Chengsheng Mao
- grid.16753.360000 0001 2299 3507Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Christopher J. Felicelli
- grid.16753.360000 0001 2299 3507Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Chia-Feng Tsai
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Carolina Ostiguin
- grid.16753.360000 0001 2299 3507Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Yuzhi Jia
- grid.16753.360000 0001 2299 3507Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Lin Li
- grid.16753.360000 0001 2299 3507Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Kevin Furlong
- The University of Chicago Howard T. Ricketts Laboratory and Department of Microbiology, Chicago, IL 60637 USA
| | - Jan Wysocki
- grid.16753.360000 0001 2299 3507Division of Nephrology and Hypertension, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Xin Luo
- grid.240145.60000 0001 2291 4776Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Carolina F. Ruivo
- grid.240145.60000 0001 2291 4776Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Daniel Batlle
- grid.16753.360000 0001 2299 3507Division of Nephrology and Hypertension, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Thomas J. Hope
- grid.16753.360000 0001 2299 3507Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Yang Shen
- grid.264756.40000 0004 4687 2082Department of Electrical and Computer Engineering, TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843 USA
| | - Young Kwang Chae
- grid.16753.360000 0001 2299 3507Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Hui Zhang
- grid.16753.360000 0001 2299 3507Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Valerie S. LeBleu
- grid.16753.360000 0001 2299 3507Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA ,grid.240145.60000 0001 2291 4776Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA ,grid.16753.360000 0001 2299 3507Kellogg School of Management, Northwestern University, Evanston, IL 60208 USA
| | - Tujin Shi
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Suchitra Swaminathan
- grid.16753.360000 0001 2299 3507Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA ,grid.16753.360000 0001 2299 3507Division of Rheumatology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Yuan Luo
- grid.16753.360000 0001 2299 3507Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Dominique Missiakas
- The University of Chicago Howard T. Ricketts Laboratory and Department of Microbiology, Chicago, IL 60637 USA
| | - Glenn C. Randall
- The University of Chicago Howard T. Ricketts Laboratory and Department of Microbiology, Chicago, IL 60637 USA
| | - Alexis R. Demonbreun
- grid.16753.360000 0001 2299 3507Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Michael G. Ison
- grid.16753.360000 0001 2299 3507Division of Infectious Disease, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA ,grid.16753.360000 0001 2299 3507Division of Organ Transplantation, Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Raghu Kalluri
- grid.240145.60000 0001 2291 4776Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA ,grid.21940.3e0000 0004 1936 8278Department of Bioengineering, Rice University, Houston, TX 77005 USA ,grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Deyu Fang
- grid.16753.360000 0001 2299 3507Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA ,grid.16753.360000 0001 2299 3507Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Huiping Liu
- grid.16753.360000 0001 2299 3507Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA ,grid.16753.360000 0001 2299 3507Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA ,grid.16753.360000 0001 2299 3507Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
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25
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Ramos EK, Tsai CF, Jia Y, Cao Y, Manu M, Taftaf R, Hoffmann AD, El-Shennawy L, Gritsenko MA, Adorno-Cruz V, Schuster EJ, Scholten D, Patel D, Liu X, Patel P, Wray B, Zhang Y, Zhang S, Moore RJ, Mathews JV, Schipma MJ, Liu T, Tokars VL, Cristofanilli M, Shi T, Shen Y, Dashzeveg NK, Liu H. Machine learning-assisted elucidation of CD81-CD44 interactions in promoting cancer stemness and extracellular vesicle integrity. eLife 2022; 11:82669. [PMID: 36193887 PMCID: PMC9581534 DOI: 10.7554/elife.82669] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 08/26/2022] [Indexed: 11/30/2022] Open
Abstract
Tumor-initiating cells with reprogramming plasticity or stem-progenitor cell properties (stemness) are thought to be essential for cancer development and metastatic regeneration in many cancers; however, elucidation of the underlying molecular network and pathways remains demanding. Combining machine learning and experimental investigation, here we report CD81, a tetraspanin transmembrane protein known to be enriched in extracellular vesicles (EVs), as a newly identified driver of breast cancer stemness and metastasis. Using protein structure modeling and interface prediction-guided mutagenesis, we demonstrate that membrane CD81 interacts with CD44 through their extracellular regions in promoting tumor cell cluster formation and lung metastasis of triple negative breast cancer (TNBC) in human and mouse models. In-depth global and phosphoproteomic analyses of tumor cells deficient with CD81 or CD44 unveils endocytosis-related pathway alterations, leading to further identification of a quality-keeping role of CD44 and CD81 in EV secretion as well as in EV-associated stemness-promoting function. CD81 is coexpressed along with CD44 in human circulating tumor cells (CTCs) and enriched in clustered CTCs that promote cancer stemness and metastasis, supporting the clinical significance of CD81 in association with patient outcomes. Our study highlights machine learning as a powerful tool in facilitating the molecular understanding of new molecular targets in regulating stemness and metastasis of TNBC.
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Affiliation(s)
- Erika K Ramos
- Department of Pharmacology, Northwestern UniversityChicagoUnited States,Driskill Graduate Program in Life Science, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National LaboratoryWashingtonUnited States
| | - Yuzhi Jia
- Department of Pharmacology, Northwestern UniversityChicagoUnited States
| | - Yue Cao
- Department of Electrical and Computer Engineering, TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M UniversityCollege StationUnited States
| | - Megan Manu
- Department of Pharmacology, Northwestern UniversityChicagoUnited States
| | - Rokana Taftaf
- Department of Pharmacology, Northwestern UniversityChicagoUnited States,Driskill Graduate Program in Life Science, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Andrew D Hoffmann
- Department of Pharmacology, Northwestern UniversityChicagoUnited States
| | | | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National LaboratoryWashingtonUnited States
| | | | - Emma J Schuster
- Department of Pharmacology, Northwestern UniversityChicagoUnited States,Driskill Graduate Program in Life Science, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - David Scholten
- Department of Pharmacology, Northwestern UniversityChicagoUnited States,Driskill Graduate Program in Life Science, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Dhwani Patel
- Department of Pharmacology, Northwestern UniversityChicagoUnited States
| | - Xia Liu
- Department of Pharmacology, Northwestern UniversityChicagoUnited States,Department of Toxicology and Cancer Biology, University of KentuckyLexingtonUnited States
| | - Priyam Patel
- Quantitative Data Science Core, Center for Genetic Medicine, Northwestern University Feinberg School of MedicineChicagoUnited States
| | - Brian Wray
- Quantitative Data Science Core, Center for Genetic Medicine, Northwestern University Feinberg School of MedicineChicagoUnited States
| | - Youbin Zhang
- Department of Medicine, Hematology/Oncology Division, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Shanshan Zhang
- Pathology Core Facility, Northwestern UniversityChicagoUnited States
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National LaboratoryWashingtonUnited States
| | - Jeremy V Mathews
- Pathology Core Facility, Northwestern UniversityChicagoUnited States
| | - Matthew J Schipma
- Quantitative Data Science Core, Center for Genetic Medicine, Northwestern University Feinberg School of MedicineChicagoUnited States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National LaboratoryWashingtonUnited States
| | - Valerie L Tokars
- Department of Pharmacology, Northwestern UniversityChicagoUnited States
| | - Massimo Cristofanilli
- Department of Medicine, Hematology/Oncology Division, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National LaboratoryWashingtonUnited States
| | - Yang Shen
- Department of Electrical and Computer Engineering, TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M UniversityCollege StationUnited States
| | | | - Huiping Liu
- Department of Pharmacology, Northwestern UniversityChicagoUnited States,Department of Medicine, Hematology/Oncology Division, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
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26
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Woo J, Williams SM, Markillie LM, Feng S, Tsai CF, Aguilera-Vazquez V, Sontag RL, Moore RJ, Hu D, Mehta HS, Cantlon-Bruce J, Liu T, Adkins JN, Smith RD, Clair GC, Pasa-Tolic L, Zhu Y. Author Correction: High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip. Nat Commun 2021; 12:7075. [PMID: 34848696 PMCID: PMC8632992 DOI: 10.1038/s41467-021-27110-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Jongmin Woo
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Lye Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Song Feng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Victor Aguilera-Vazquez
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ryan L Sontag
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Dehong Hu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Hardeep S Mehta
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Joshua Cantlon-Bruce
- Scienion AG, Volmerstraße 7, 12489, Berlin, Germany
- Cellenion SASU, 60 Avenue Rockefeller, Bâtiment BioSerra2, 69008, Lyon, France
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Geremy C Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
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27
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Woo J, Williams SM, Markillie LM, Feng S, Tsai CF, Aguilera-Vazquez V, Sontag RL, Moore RJ, Hu D, Mehta HS, Cantlon-Bruce J, Liu T, Adkins JN, Smith RD, Clair GC, Pasa-Tolic L, Zhu Y. High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip. Nat Commun 2021; 12:6246. [PMID: 34716329 PMCID: PMC8556371 DOI: 10.1038/s41467-021-26514-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [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] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/12/2021] [Indexed: 12/22/2022] Open
Abstract
Global quantification of protein abundances in single cells could provide direct information on cellular phenotypes and complement transcriptomics measurements. However, single-cell proteomics is still immature and confronts many technical challenges. Herein we describe a nested nanoPOTS (N2) chip to improve protein recovery, operation robustness, and processing throughput for isobaric-labeling-based scProteomics workflow. The N2 chip reduces reaction volume to <30 nL and increases capacity to >240 single cells on a single microchip. The tandem mass tag (TMT) pooling step is simplified by adding a microliter droplet on the nested nanowells to combine labeled single-cell samples. In the analysis of ~100 individual cells from three different cell lines, we demonstrate that the N2 chip-based scProteomics platform can robustly quantify ~1500 proteins and reveal membrane protein markers. Our analyses also reveal low protein abundance variations, suggesting the single-cell proteome profiles are highly stable for the cells cultured under identical conditions.
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Affiliation(s)
- Jongmin Woo
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Lye Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Song Feng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Victor Aguilera-Vazquez
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ryan L Sontag
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Dehong Hu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Hardeep S Mehta
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Joshua Cantlon-Bruce
- Scienion AG, Volmerstraße 7, 12489, Berlin, Germany
- Cellenion SASU, 60 Avenue Rockefeller, Bâtiment BioSerra2, 69008, Lyon, France
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Geremy C Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
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Su CH, Lo CH, Tsai CF. CHA2DS2-VASc score as independent outcome predictor in patients with acute ischemic stroke with and without atrial fibrillation. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.2740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Introduction
Atrial fibrillation (AF) was a significant independent risk factor for 1-year mortality of first acute ischemic stroke. The CHA2DS2-VASc scores were initially developed to assess the risk of stroke or systemic embolism in patients with AF. Recently, this scoring system have been demonstrated to have clinical value for predicting the severity of infarction and long-term clinical outcomes in acute ischemic stroke but the evidence is not strong enough due to limited numbers and single center data.
Purpose
This large-scale prospective cohort study aimed to investigate the independent predictive value of CHA2DS2-VASc scores and AF in such patients.
Materials and methods
We included patients from Taiwan Stroke Registry (TSR) with ischemic stroke within 2006 to 2016 as the present study population. Patients were mainly divided in atrial fibrillation (AF) group and non-AF group. We future classified patient by CHA2DS2-VASc (congestive heart failure, hypertension, age≥75 years, diabetes, previous stroke, vascular disease, age 65–74 years, sex category) score 0–1 and ≥2. The primary outcome was major adverse cardiovascular events (MACE), which include re-stroke, myocardial infarction and cardiovascular death, occurred within 1 year after the onset of stroke. The secondary outcome was the all-cause mortality.
Results
We defined 2972 patients with MACE and 61,937 patients without MACE. With adjusting with the confounding of CHA2DS2-VASc scores, The AF group was associated with increased MACE (OR=1.15; 95% CI=1.00, 1.33), myocardial infarction (adjusted OR=3.89; 95% CI=1.81, 8.34), CV death (OR=5.73; 95% CI=3.77, 8.69) and all-cause mortality (OR=1.50; 95% CI=1.37, 1.65) but not in re-stroke (adjusted OR=1.02; 95% CI=0.88, 1.18). After controlling for AF, patients with CHA2DS2-VASc scores ≥2 had significantly higher odds of MACE (OR=1.28; 95% CI=1.16, 1.41), re-stroke (OR=1.27; 95% CI=1.16, 1.40) and all-cause mortality (OR=2.26; 95% CI=2.06, 2.48) than that of patients with CHA2DS2-VASc scores 0–1. The survival curve revealed both AF and CHA2DS2-VASc scores are independent risk factors of 1 year MACE and mortality. By investigating the individual risk factor of CHA2DS2-VASc score, diabetes, hypertension and age over 65 years old increase the risk of MACE significantly.
Conclusions
CHA2DS2-VASc scores appear to have potent independent value as AF for predicting 1 year MACE and all-cause mortality in patients of acute ischemic stroke.
Funding Acknowledgement
Type of funding sources: None. Figure 1Figure 2
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Affiliation(s)
- C H Su
- Chung Shan Medical University Hospital, Division of Cardiology, Department of Internal Medicine, Taichung, Taiwan
| | - C H Lo
- Chung Shan Medical University Hospital, Division of Cardiology, Department of Internal Medicine, Taichung, Taiwan
| | - C F Tsai
- Chung Shan Medical University Hospital, Division of Cardiology, Department of Internal Medicine, Taichung, Taiwan
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29
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Martin K, Zhang T, Lin TT, Habowski AN, Zhao R, Tsai CF, Chrisler WB, Sontag RL, Orton DJ, Lu YJ, Rodland KD, Yang B, Liu T, Smith RD, Qian WJ, Waterman ML, Wiley HS, Shi T. Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50-1000 Mammalian Cells. J Proteome Res 2021; 20:4452-4461. [PMID: 34351778 PMCID: PMC8945255 DOI: 10.1021/acs.jproteome.1c00403] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recent advances in sample preparation enable label-free mass spectrometry (MS)-based proteome profiling of small numbers of mammalian cells. However, specific devices are often required to downscale sample processing volume from the standard 50-200 μL to sub-μL for effective nanoproteomics, which greatly impedes the implementation of current nanoproteomics methods by the proteomics research community. Herein, we report a facile one-pot nanoproteomics method termed SOPs-MS (surfactant-assisted one-pot sample processing at the standard volume coupled with MS) for convenient robust proteome profiling of 50-1000 mammalian cells. Building upon our recent development of SOPs-MS for label-free single-cell proteomics at a low μL volume, we have systematically evaluated its processing volume at 10-200 μL using 100 human cells. The processing volume of 50 μL that is in the range of volume for standard proteomics sample preparation has been selected for easy sample handling with a benchtop micropipette. SOPs-MS allows for reliable label-free quantification of ∼1200-2700 protein groups from 50 to 1000 MCF10A cells. When applied to small subpopulations of mouse colon crypt cells, SOPs-MS has revealed protein signatures between distinct subpopulation cells with identification of ∼1500-2500 protein groups for each subpopulation. SOPs-MS may pave the way for routine deep proteome profiling of small numbers of cells and low-input samples.
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Affiliation(s)
| | | | - Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Amber N. Habowski
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California 92697, United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - William B. Chrisler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ryan L. Sontag
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Daniel J. Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Yong-Jie Lu
- Centre for Cancer Biomarker and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Karin D. Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Bin Yang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States; Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, Washington 99354, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Marian L. Waterman
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California 92697, United States
| | - H. Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Tujin Shi
- Corresponding Author Tujin Shi – Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States; Phone: (509) 371-6579;
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Abstract
We established a workflow for highly sensitive multiplexed quantitative phosphoproteomics using a nanoscale solid-phase tandem mass tag (TMT) labeling reactor. Phosphopeptides were first enriched by titanium oxide chromatography and then labeled with isobaric TMT reagents in a StageTip packed with hydrophobic polymer-based sorbents. We found that TMT-labeled singly phosphorylated peptides tend to flow through the titanium oxide column. Therefore, TMT labeling should be performed after the enrichment step from tryptic peptides, resulting in the need for microscale reactions with small amounts of phosphopeptides. Using an optimized protocol for tens to hundreds of nanograms of phosphopeptides, we obtained a nearly 10-fold increase in sensitivity compared to the conventional solution-based TMT protocol. We demonstrate that this nanoscale phosphoproteomics protocol works for 50 μg of HeLa proteins treated with selumetinib, and we successfully quantified the selumetinib-regulated phosphorylated sites on a proteome scale. The MS raw data files have been deposited with the ProteomeXchange Consortium via the jPOST partner repository (https://jpostdb.org) with the data set identifier PXD025536.
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Affiliation(s)
- Kosuke Ogata
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Chia-Feng Tsai
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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31
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Joshi SK, Nechiporuk T, Bottomly D, Piehowski PD, Reisz JA, Pittsenbarger J, Kaempf A, Gosline SJC, Wang YT, Hansen JR, Gritsenko MA, Hutchinson C, Weitz KK, Moon J, Cendali F, Fillmore TL, Tsai CF, Schepmoes AA, Shi T, Arshad OA, McDermott JE, Babur O, Watanabe-Smith K, Demir E, D'Alessandro A, Liu T, Tognon CE, Tyner JW, McWeeney SK, Rodland KD, Druker BJ, Traer E. The AML microenvironment catalyzes a stepwise evolution to gilteritinib resistance. Cancer Cell 2021; 39:999-1014.e8. [PMID: 34171263 PMCID: PMC8686208 DOI: 10.1016/j.ccell.2021.06.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/22/2021] [Accepted: 06/03/2021] [Indexed: 12/18/2022]
Abstract
Our study details the stepwise evolution of gilteritinib resistance in FLT3-mutated acute myeloid leukemia (AML). Early resistance is mediated by the bone marrow microenvironment, which protects residual leukemia cells. Over time, leukemia cells evolve intrinsic mechanisms of resistance, or late resistance. We mechanistically define both early and late resistance by integrating whole-exome sequencing, CRISPR-Cas9, metabolomics, proteomics, and pharmacologic approaches. Early resistant cells undergo metabolic reprogramming, grow more slowly, and are dependent upon Aurora kinase B (AURKB). Late resistant cells are characterized by expansion of pre-existing NRAS mutant subclones and continued metabolic reprogramming. Our model closely mirrors the timing and mutations of AML patients treated with gilteritinib. Pharmacological inhibition of AURKB resensitizes both early resistant cell cultures and primary leukemia cells from gilteritinib-treated AML patients. These findings support a combinatorial strategy to target early resistant AML cells with AURKB inhibitors and gilteritinib before the expansion of pre-existing resistance mutations occurs.
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MESH Headings
- Aniline Compounds/pharmacology
- Aurora Kinase B/genetics
- Aurora Kinase B/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Drug Resistance, Neoplasm
- Exome
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Metabolome
- Protein Kinase Inhibitors/pharmacology
- Proteome
- Pyrazines/pharmacology
- Tumor Cells, Cultured
- Tumor Microenvironment
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Affiliation(s)
- Sunil K Joshi
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Department of Physiology & Pharmacology, School of Medicine, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Tamilla Nechiporuk
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Daniel Bottomly
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Paul D Piehowski
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Janét Pittsenbarger
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Andy Kaempf
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Biostatistics Shared Resource, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Sara J C Gosline
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Joshua R Hansen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chelsea Hutchinson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Francesca Cendali
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Thomas L Fillmore
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Osama A Arshad
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ozgun Babur
- Department of Computer Science, University of Massachusetts, Boston, MA, USA
| | - Kevin Watanabe-Smith
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Computational Biology Program, Oregon Health & Science University, Portland, OR, USA
| | - Emek Demir
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA; Computational Biology Program, Oregon Health & Science University, Portland, OR, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Department of Cell, Development, & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Shannon K McWeeney
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA; Department of Cell, Development, & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Department of Cell, Development, & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Department of Cell, Development, & Cancer Biology, Oregon Health & Science University, Portland, OR, USA.
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32
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Tsai CF, Wen IJ, Liu SH, Cao CR, Zhang H. Evaluation of thermal hazard characteristics of four low temperature reactive azo compounds under isothermal conditions. J Loss Prev Process Ind 2021. [DOI: 10.1016/j.jlp.2021.104453] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Kitata RB, Choong WK, Tsai CF, Lin PY, Chen BS, Chang YC, Nesvizhskii AI, Sung TY, Chen YJ. A data-independent acquisition-based global phosphoproteomics system enables deep profiling. Nat Commun 2021; 12:2539. [PMID: 33953186 PMCID: PMC8099862 DOI: 10.1038/s41467-021-22759-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [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: 08/05/2020] [Accepted: 03/29/2021] [Indexed: 01/07/2023] Open
Abstract
Phosphoproteomics can provide insights into cellular signaling dynamics. To achieve deep and robust quantitative phosphoproteomics profiling for minute amounts of sample, we here develop a global phosphoproteomics strategy based on data-independent acquisition (DIA) mass spectrometry and hybrid spectral libraries derived from data-dependent acquisition (DDA) and DIA data. Benchmarking the method using 166 synthetic phosphopeptides shows high sensitivity (<0.1 ng), accurate site localization and reproducible quantification (~5% median coefficient of variation). As a proof-of-concept, we use lung cancer cell lines and patient-derived tissue to construct a hybrid phosphoproteome spectral library covering 159,524 phosphopeptides (88,107 phosphosites). Based on this library, our single-shot streamlined DIA workflow quantifies 36,350 phosphosites (19,755 class 1) in cell line samples within two hours. Application to drug-resistant cells and patient-derived lung cancer tissues delineates site-specific phosphorylation events associated with resistance and tumor progression, showing that our workflow enables the characterization of phosphorylation signaling with deep coverage, high sensitivity and low between-run missing values. Phosphoproteomics can provide systematic insights into disease-associated cell signaling changes. Here, the authors present a sensitive workflow integrating library-based and direct data-independent acquisition approaches, and a hybrid spectral library resource for in-depth phosphoproteomic profiling.
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Affiliation(s)
| | - Wai-Kok Choong
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | - Pei-Yi Lin
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Bo-Shiun Chen
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Yun-Chien Chang
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, and Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA
| | - Ting-Yi Sung
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan. .,Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan.
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34
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Wang LB, Karpova A, Gritsenko MA, Kyle JE, Cao S, Li Y, Rykunov D, Colaprico A, Rothstein JH, Hong R, Stathias V, Cornwell M, Petralia F, Wu Y, Reva B, Krug K, Pugliese P, Kawaler E, Olsen LK, Liang WW, Song X, Dou Y, Wendl MC, Caravan W, Liu W, Cui Zhou D, Ji J, Tsai CF, Petyuk VA, Moon J, Ma W, Chu RK, Weitz KK, Moore RJ, Monroe ME, Zhao R, Yang X, Yoo S, Krek A, Demopoulos A, Zhu H, Wyczalkowski MA, McMichael JF, Henderson BL, Lindgren CM, Boekweg H, Lu S, Baral J, Yao L, Stratton KG, Bramer LM, Zink E, Couvillion SP, Bloodsworth KJ, Satpathy S, Sieh W, Boca SM, Schürer S, Chen F, Wiznerowicz M, Ketchum KA, Boja ES, Kinsinger CR, Robles AI, Hiltke T, Thiagarajan M, Nesvizhskii AI, Zhang B, Mani DR, Ceccarelli M, Chen XS, Cottingham SL, Li QK, Kim AH, Fenyö D, Ruggles KV, Rodriguez H, Mesri M, Payne SH, Resnick AC, Wang P, Smith RD, Iavarone A, Chheda MG, Barnholtz-Sloan JS, Rodland KD, Liu T, Ding L. Proteogenomic and metabolomic characterization of human glioblastoma. Cancer Cell 2021; 39:509-528.e20. [PMID: 33577785 PMCID: PMC8044053 DOI: 10.1016/j.ccell.2021.01.006] [Citation(s) in RCA: 275] [Impact Index Per Article: 91.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/02/2020] [Accepted: 01/11/2021] [Indexed: 02/07/2023]
Abstract
Glioblastoma (GBM) is the most aggressive nervous system cancer. Understanding its molecular pathogenesis is crucial to improving diagnosis and treatment. Integrated analysis of genomic, proteomic, post-translational modification and metabolomic data on 99 treatment-naive GBMs provides insights to GBM biology. We identify key phosphorylation events (e.g., phosphorylated PTPN11 and PLCG1) as potential switches mediating oncogenic pathway activation, as well as potential targets for EGFR-, TP53-, and RB1-altered tumors. Immune subtypes with distinct immune cell types are discovered using bulk omics methodologies, validated by snRNA-seq, and correlated with specific expression and histone acetylation patterns. Histone H2B acetylation in classical-like and immune-low GBM is driven largely by BRDs, CREBBP, and EP300. Integrated metabolomic and proteomic data identify specific lipid distributions across subtypes and distinct global metabolic changes in IDH-mutated tumors. This work highlights biological relationships that could contribute to stratification of GBM patients for more effective treatment.
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Affiliation(s)
- Liang-Bo Wang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alla Karpova
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Song Cao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Antonio Colaprico
- Sylvester Comprehensive Cancer Center, University of Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami, FL 33136, USA
| | - Joseph H Rothstein
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Runyu Hong
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Vasileios Stathias
- Sylvester Comprehensive Cancer Center, University of Miami, FL 33136, USA; Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; BD2K-LINCS Data Coordination and Integration Center, Miami, FL 33136, USA
| | - MacIntosh Cornwell
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yige Wu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Pietro Pugliese
- Department of Science and Technology, University of Sannio, 82100, Benevento, Italy
| | - Emily Kawaler
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Lindsey K Olsen
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Wen-Wei Liang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Xiaoyu Song
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael C Wendl
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Mathematics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Wagma Caravan
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Daniel Cui Zhou
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jiayi Ji
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rosalie K Chu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Xiaolu Yang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | - Seungyeul Yoo
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexis Demopoulos
- Department of Neurology, Northwell Health System, Lake Success, NY 11042 USA
| | - Houxiang Zhu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Joshua F McMichael
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | - Caleb M Lindgren
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Hannah Boekweg
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Shuangjia Lu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jessika Baral
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lijun Yao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Kelly G Stratton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Lisa M Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Erika Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Sneha P Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kent J Bloodsworth
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Weiva Sieh
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Simina M Boca
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Stephan Schürer
- Sylvester Comprehensive Cancer Center, University of Miami, FL 33136, USA; Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; BD2K-LINCS Data Coordination and Integration Center, Miami, FL 33136, USA; Institute for Data Science & Computing, University of Miami, FL 33136, USA
| | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Maciej Wiznerowicz
- International Institute for Molecular Oncology, 60-203 Poznań, Poland; Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | | | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Michele Ceccarelli
- Department of Electrical Engineering and Information Technology, University of Naples "Federico II", 80128, Naples, Italy; BIOGEM, 83031 Ariano Irpino, Italy
| | - Xi S Chen
- Sylvester Comprehensive Cancer Center, University of Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami, FL 33136, USA
| | - Sandra L Cottingham
- Department of Pathology, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, MI 49503, USA
| | - Qing Kay Li
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Albert H Kim
- Department of Neurological Surgery, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kelly V Ruggles
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Adam C Resnick
- Center for Data Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032, USA; Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Milan G Chheda
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Neurology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center and Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Research and Education, University Hospitals Health System, Cleveland, OH 44106, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA.
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA.
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35
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Tsai CF, Zhang P, Scholten D, Martin K, Wang YT, Zhao R, Chrisler WB, Patel DB, Dou M, Jia Y, Reduzzi C, Liu X, Moore RJ, Burnum-Johnson KE, Lin MH, Hsu CC, Jacobs JM, Kagan J, Srivastava S, Rodland KD, Steven Wiley H, Qian WJ, Smith RD, Zhu Y, Cristofanilli M, Liu T, Liu H, Shi T. Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics. Commun Biol 2021; 4:265. [PMID: 33649493 PMCID: PMC7921383 DOI: 10.1038/s42003-021-01797-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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: 07/20/2020] [Accepted: 12/24/2020] [Indexed: 12/12/2022] Open
Abstract
Large numbers of cells are generally required for quantitative global proteome profiling due to surface adsorption losses associated with sample processing. Such bulk measurement obscures important cell-to-cell variability (cell heterogeneity) and makes proteomic profiling impossible for rare cell populations (e.g., circulating tumor cells (CTCs)). Here we report a surfactant-assisted one-pot sample preparation coupled with mass spectrometry (MS) method termed SOP-MS for label-free global single-cell proteomics. SOP-MS capitalizes on the combination of a MS-compatible nonionic surfactant, n-Dodecyl-β-D-maltoside, and hydrophobic surface-based low-bind tubes or multi-well plates for ‘all-in-one’ one-pot sample preparation. This ‘all-in-one’ method including elimination of all sample transfer steps maximally reduces surface adsorption losses for effective processing of single cells, thus improving detection sensitivity for single-cell proteomics. This method allows convenient label-free quantification of hundreds of proteins from single human cells and ~1200 proteins from small tissue sections (close to ~20 cells). When applied to a patient CTC-derived xenograft (PCDX) model at the single-cell resolution, SOP-MS can reveal distinct protein signatures between primary tumor cells and early metastatic lung cells, which are related to the selection pressure of anti-tumor immunity during breast cancer metastasis. The approach paves the way for routine, precise, quantitative single-cell proteomics. Tsai, Zhang, Scholten et al. develop a surfactant- assisted one-pot sample preparation coupled with mass spectrometry method (SOP-MS) for label-free global single-cell proteomics. This method allows researchers to measure hundreds of proteins from single human cells, suggesting its utility for quantitative single-cell proteomics.
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Affiliation(s)
- Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Pengfei Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.,NHC Key Laboratory of Cancer Proteomics, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - David Scholten
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Kendall Martin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - William B Chrisler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Dhwani B Patel
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Maowei Dou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuzhi Jia
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Carolina Reduzzi
- Division of Hematology and Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Xia Liu
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Miao-Hsia Lin
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chuan-Chih Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Jon M Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jacob Kagan
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - H Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Massimo Cristofanilli
- Division of Hematology and Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Huiping Liu
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA. .,Division of Hematology and Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA. .,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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36
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Habowski AN, Flesher JL, Bates JM, Tsai CF, Martin K, Zhao R, Ganesan AK, Edwards RA, Shi T, Wiley HS, Shi Y, Hertel KJ, Waterman ML. Publisher Correction: Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt. Commun Biol 2020; 3:495. [PMID: 32884070 PMCID: PMC7471919 DOI: 10.1038/s42003-020-01237-0] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Amber N Habowski
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA
| | - Jessica L Flesher
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - Jennifer M Bates
- Institute for Immunology, University of California Irvine, Irvine, CA, 92697, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Kendall Martin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Anand K Ganesan
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department of Dermatology, University of California Irvine, Irvine, CA, 92697, USA
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - H Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Yongsheng Shi
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA
| | - Klemens J Hertel
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA
| | - Marian L Waterman
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA.
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37
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McDermott JE, Arshad OA, Petyuk VA, Fu Y, Gritsenko MA, Clauss TR, Moore RJ, Schepmoes AA, Zhao R, Monroe ME, Schnaubelt M, Tsai CF, Payne SH, Huang C, Wang LB, Foltz S, Wyczalkowski M, Wu Y, Song E, Brewer MA, Thiagarajan M, Kinsinger CR, Robles AI, Boja ES, Rodriguez H, Chan DW, Zhang B, Zhang Z, Ding L, Smith RD, Liu T, Rodland KD. Correction: Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. Cell Rep Med 2020; 1. [PMID: 32954372 PMCID: PMC7500561 DOI: 10.1016/j.xcrm.2020.100075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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Habowski AN, Flesher JL, Bates JM, Tsai CF, Martin K, Zhao R, Ganesan AK, Edwards RA, Shi T, Wiley HS, Shi Y, Hertel KJ, Waterman ML. Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt. Commun Biol 2020; 3:453. [PMID: 32814826 PMCID: PMC7438495 DOI: 10.1038/s42003-020-01181-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/16/2020] [Indexed: 02/07/2023] Open
Abstract
Intestinal stem cells are non-quiescent, dividing epithelial cells that rapidly differentiate into progenitor cells of the absorptive and secretory cell lineages. The kinetics of this process is rapid such that the epithelium is replaced weekly. To determine how the transcriptome and proteome keep pace with rapid differentiation, we developed a new cell sorting method to purify mouse colon epithelial cells. Here we show that alternative mRNA splicing and polyadenylation dominate changes in the transcriptome as stem cells differentiate into progenitors. In contrast, as progenitors differentiate into mature cell types, changes in mRNA levels dominate the transcriptome. RNA processing targets regulators of cell cycle, RNA, cell adhesion, SUMOylation, and Wnt and Notch signaling. Additionally, global proteome profiling detected >2,800 proteins and revealed RNA:protein patterns of abundance and correlation. Paired together, these data highlight new potentials for autocrine and feedback regulation and provide new insights into cell state transitions in the crypt.
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Affiliation(s)
- Amber N Habowski
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA
| | - Jessica L Flesher
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - Jennifer M Bates
- Institute for Immunology, University of California Irvine, Irvine, CA, 92697, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Kendall Martin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Anand K Ganesan
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department of Dermatology, University of California Irvine, Irvine, CA, 92697, USA
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - H Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Yongsheng Shi
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA
| | - Klemens J Hertel
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA
| | - Marian L Waterman
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA.
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McDermott J, Arshad O, Petyuk V, Fu Y, Gritsenko M, Tsai CF, Payne S, Thiagarajan M, Kinsinger C, Robles A, Boja E, Rodriguez H, Chan D, Zhang B, Zhang Z, Ding L, Smith R, Liu T, Rodland K. Abstract 5123: Proteogenomic characterization reveals mitotic kinase and replication stress implicated in ovarian high-grade serous cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
High-grade serous cancer (HGSC), the most prevalent histotype of ovarian cancer, has the lowest survival rates and is the leading cause of gynecological cancer-related deaths in the developed world. HGSC is characterized by the presence of nearly universal TP53 mutations, diverse and widespread chromosomal instability, and a general shortage of targetable driving mutations. The major clinical needs in HGSC include the identification of alternative therapeutic targets and an improved understanding of the mechanisms driving chromosomal heterogeneity. We prospectively collected 83 new ovarian HGSC samples and 20 normal precursor tissue samples (Fallopian tube, FT) for deep characterization at the genomic, transcriptomic, proteomic, and phosphoproteomic levels. We were also able to obtain cytobrush samples of Fallopian tube epithelium and provide the first extensive comparison of HGSC and FT proteomes and phosphoproteomes that used surgical specimens rather than cell lines. The ability to compare tumor and normal precursor tissues provided new biological insights regarding the role of increased proliferation in promoting replication stress in a DNA repair-deficient background, potentially explaining the high degree of chromosomal instability associated with HGSC. Our collection protocols were specifically designed to minimize the effect of ischemia on protein phosphorylation, which has been identified as a significant confounding variable. Thus, we were able to identify novel signaling interactions that would have been lost in the background of ischemic stress, most notably the activation of CDK4 and CDK7. Widespread increases in protein phosphorylation and pathway activation in tumors compared to normal tissues, particularly in the proliferation-associated CDK/RB and AURKA pathways that are targetable by FDA-approved inhibitors, provide a rational basis for the use of these therapeutics in ovarian cancer. Phosphosite-specific analysis of CDKs and FANCD was consistent with an elevated response to replication stress, potentially induced by proliferative signals. Additionally, pathway-level observations from the retrospective TCGA cohort were conserved in the prospective cohort, including histone acetylation marks associated with homologous repair deficiency. In addition to confirming key features of HGSC from previous proteogenomic study, analysis of prospectively collected HGSC samples provided significant new insights stemming from direct comparisons to normal precursor tissues; deep phosphoproteomics revealed new insights regarding the potential role of proliferation-induced replication stress in promoting the characteristic chromosomal instability of HGSC and suggested novel therapeutic targets for use in precision medicine trials.
Citation Format: Jason McDermott, Osama Arshad, Vladislav Petyuk, Yi Fu, Marina Gritsenko, Chia-Feng Tsai, Samuel Payne, Mathangi Thiagarajan, Christopher Kinsinger, Ana Robles, Emily Boja, Henry Rodriguez, Daniel Chan, Bing Zhang, Zhen Zhang, Li Ding, Richard Smith, Tao Liu, Karin Rodland. Proteogenomic characterization reveals mitotic kinase and replication stress implicated in ovarian high-grade serous cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5123.
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Affiliation(s)
| | - Osama Arshad
- 1Pacific Northwest National Laboratory, Richland, WA
| | | | - Yi Fu
- 2Johns Hopkins Medical Institutions, Baltimore, MD
| | | | | | | | | | | | - Ana Robles
- 5National Cancer Institute, Bethesda, MD
| | - Emily Boja
- 5National Cancer Institute, Bethesda, MD
| | | | - Daniel Chan
- 2Johns Hopkins Medical Institutions, Baltimore, MD
| | - Bing Zhang
- 6Baylor College of Medicine, Houston, TX
| | - Zhen Zhang
- 2Johns Hopkins Medical Institutions, Baltimore, MD
| | - Li Ding
- 7Washington University in St. Louis, St. Louis, MO
| | - Richard Smith
- 1Pacific Northwest National Laboratory, Richland, WA
| | - Tao Liu
- 1Pacific Northwest National Laboratory, Richland, WA
| | - Karin Rodland
- 1Pacific Northwest National Laboratory, Richland, WA
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40
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Tsai CF, Zhao R, Moore R, Williams S, Schultz K, Piehowski P, Pasa-Tolic L, Rodland K, Smith R, Shi T, Zhu Y, Zhu Y, Liu T. Abstract 2856: An intelligent boosting to amplify signal with isobaric labeling (iBASIL) strategy for precise quantitative single-cell proteomics analysis. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-2856] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Mass spectrometry (MS)-based proteomics has great potential for overcoming the limitations of antibody-based immunoassays for antibody-independent, comprehensive, and quantitative proteomic analysis of single cells. Indeed, recent advances in nanoscale sample preparation have enabled effective processing of single cells. In particular, the concept of using boosting/carrier channels in isobaric labeling to increase the sensitivity in MS detection (e.g., our recent boosting to amplify signal with isobaric labeling (BASIL) approach) has also been increasingly used for quantitative proteomic analysis of small-sized samples including single cells. However, the full potential of such boosting/carrier approaches has not been significantly explored, nor has the resulting quantitation quality been carefully evaluated. Herein, we have systematically evaluated and optimized the BASIL approach, originally developed for quantifying phosphorylation in small number of cells, for highly effective analysis of single cells. This improved, intelligent BASIL (iBASIL) approach enables comprehensive and quantitative single-cell proteomics analysis by carefully controlling the boosting-to-sample ratio and optimizing MS automatic gain control and ion injection time settings. Using standard LC-MS platforms, iBASIL enabled precise quantification of 800-1,200 proteins from single FACS-isolated cells (depending on the cell type). Moreover, coupling iBASIL to nanoscale fractionation enabled identification of >3,000 proteins and reliable quantification of >2,000 proteins while readily separating single cells from 3 different acute myeloid leukemia cell lines. We believe iBASIL has broad utility for comprehensive and precise quantitative single-cell proteomics for systems biology and biomedical research, as well as for comprehensive proteomic analysis of size-limited clinical specimens that cannot be readily accessed by regular proteomics platforms. It also has the potential to be adapted for phosphoproteome analysis of as few as 100 cells.
Citation Format: Chia-Feng Tsai, Rui Zhao, Ronald Moore, Sarah Williams, Kendall Schultz, Paul Piehowski, Ljiljana Pasa-Tolic, Karin Rodland, Richard Smith, Tujin Shi, Ying Zhu, Ying Zhu, Tao Liu. An intelligent boosting to amplify signal with isobaric labeling (iBASIL) strategy for precise quantitative single-cell proteomics analysis [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2856.
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Affiliation(s)
| | - Rui Zhao
- Pacific Northwest National Laboratory, Richland, WA
| | - Ronald Moore
- Pacific Northwest National Laboratory, Richland, WA
| | | | | | | | | | | | | | - Tujin Shi
- Pacific Northwest National Laboratory, Richland, WA
| | - Ying Zhu
- Pacific Northwest National Laboratory, Richland, WA
| | - Ying Zhu
- Pacific Northwest National Laboratory, Richland, WA
| | - Tao Liu
- Pacific Northwest National Laboratory, Richland, WA
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41
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Williams SM, Liyu AV, Tsai CF, Moore RJ, Orton DJ, Chrisler WB, Gaffrey MJ, Liu T, Smith RD, Kelly RT, Pasa-Tolic L, Zhu Y. Automated Coupling of Nanodroplet Sample Preparation with Liquid Chromatography-Mass Spectrometry for High-Throughput Single-Cell Proteomics. Anal Chem 2020; 92:10588-10596. [PMID: 32639140 DOI: 10.1021/acs.analchem.0c01551] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Single-cell proteomics can provide critical biological insight into the cellular heterogeneity that is masked by bulk-scale analysis. We have developed a nanoPOTS (nanodroplet processing in one pot for trace samples) platform and demonstrated its broad applicability for single-cell proteomics. However, because of nanoliter-scale sample volumes, the nanoPOTS platform is not compatible with automated LC-MS systems, which significantly limits sample throughput and robustness. To address this challenge, we have developed a nanoPOTS autosampler allowing fully automated sample injection from nanowells to LC-MS systems. We also developed a sample drying, extraction, and loading workflow to enable reproducible and reliable sample injection. The sequential analysis of 20 samples containing 10 ng tryptic peptides demonstrated high reproducibility with correlation coefficients of >0.995 between any two samples. The nanoPOTS autosampler can provide analysis throughput of 9.6, 16, and 24 single cells per day using 120, 60, and 30 min LC gradients, respectively. As a demonstration for single-cell proteomics, the autosampler was first applied to profiling protein expression in single MCF10A cells using a label-free approach. At a throughput of 24 single cells per day, an average of 256 proteins was identified from each cell and the number was increased to 731 when the Match Between Runs algorithm of MaxQuant was used. Using a multiplexed isobaric labeling approach (TMT-11plex), ∼77 single cells could be analyzed per day. We analyzed 152 cells from three acute myeloid leukemia cell lines, resulting in a total of 2558 identified proteins with 1465 proteins quantifiable (70% valid values) across the 152 cells. These data showed quantitative single-cell proteomics can cluster cells to distinct groups and reveal functionally distinct differences.
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Affiliation(s)
- Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354 United States
| | - Andrey V Liyu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354 United States
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354 United States
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354 United States
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354 United States
| | - William B Chrisler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354 United States
| | - Matthew J Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354 United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354 United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354 United States
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354 United States.,Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354 United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354 United States
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42
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Abstract
Protein phosphorylation is crucial for the regulation of enzyme activity and gene expression under osmotic condition. Mass spectrometry (MS)-based phosphoproteomics has transformed the way of studying plant signal transduction. However, requirement of lots of starting materials and prolonged MS measurement time to achieve the depth of coverage has been the limiting factor for the high throughput study of global phosphoproteomic changes in plants. To improve the sensitivity and throughput of plant phosphoproteomics, we have developed a stop and go extraction (stage) tip based phosphoproteomics approach coupled with Tandem Mass Tag (TMT) labeling for the rapid and comprehensive analysis of plant phosphorylation perturbation in response to osmotic stress. Leveraging the simplicity and high throughput of stage tip technique, the whole procedure takes approximately one hour using two tips to finish phosphopeptide enrichment, fractionation, and sample cleaning steps, suggesting an easy-to-use and high efficiency of the approach. This approach not only provides an in-depth plant phosphoproteomics analysis (> 11,000 phosphopeptide identification) but also demonstrates the superior separation efficiency (< 5% overlap) between adjacent fractions. Further, multiplexing has been achieved using TMT labeling to quantify the phosphoproteomic changes of wild-type and snrk2 decuple mutant plants. This approach has successfully been used to reveal the phosphorylation events of Raf-like kinases in response to osmotic stress, which sheds light on the understanding of early osmotic signaling in land plants.
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Affiliation(s)
- Chuan-Chih Hsu
- Department of Plant Biology, Carnegie Institute for Science; Department of Biochemistry, Purdue University
| | - Chia-Feng Tsai
- Graduate School of Pharmaceutical Sciences, Kyoto University
| | - W Andy Tao
- Department of Biochemistry, Purdue University; Department of Chemistry, Purdue University
| | - Pengcheng Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences;
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43
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Tsai CF, Zhao R, Williams SM, Moore RJ, Schultz K, Chrisler WB, Pasa-Tolic L, Rodland KD, Smith RD, Shi T, Zhu Y, Liu T. An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics. Mol Cell Proteomics 2020; 19:828-838. [PMID: 32127492 PMCID: PMC7196584 DOI: 10.1074/mcp.ra119.001857] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [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: 10/30/2019] [Revised: 02/24/2020] [Indexed: 12/31/2022] Open
Abstract
Mass spectrometry (MS)-based proteomics has great potential for overcoming the limitations of antibody-based immunoassays for antibody-independent, comprehensive, and quantitative proteomic analysis of single cells. Indeed, recent advances in nanoscale sample preparation have enabled effective processing of single cells. In particular, the concept of using boosting/carrier channels in isobaric labeling to increase the sensitivity in MS detection has also been increasingly used for quantitative proteomic analysis of small-sized samples including single cells. However, the full potential of such boosting/carrier approaches has not been significantly explored, nor has the resulting quantitation quality been carefully evaluated. Herein, we have further evaluated and optimized our recent boosting to amplify signal with isobaric labeling (BASIL) approach, originally developed for quantifying phosphorylation in small number of cells, for highly effective analysis of proteins in single cells. This improved BASIL (iBASIL) approach enables reliable quantitative single-cell proteomics analysis with greater proteome coverage by carefully controlling the boosting-to-sample ratio (e.g. in general <100×) and optimizing MS automatic gain control (AGC) and ion injection time settings in MS/MS analysis (e.g. 5E5 and 300 ms, respectively, which is significantly higher than that used in typical bulk analysis). By coupling with a nanodroplet-based single cell preparation (nanoPOTS) platform, iBASIL enabled identification of ∼2500 proteins and precise quantification of ∼1500 proteins in the analysis of 104 FACS-isolated single cells, with the resulting protein profiles robustly clustering the cells from three different acute myeloid leukemia cell lines. This study highlights the importance of carefully evaluating and optimizing the boosting ratios and MS data acquisition conditions for achieving robust, comprehensive proteomic analysis of single cells.
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Affiliation(s)
- Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Kendall Schultz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - William B Chrisler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354.
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354.
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McDermott JE, Arshad OA, Petyuk VA, Fu Y, Gritsenko MA, Clauss TR, Moore RJ, Schepmoes AA, Zhao R, Monroe ME, Schnaubelt M, Tsai CF, Payne SH, Huang C, Wang LB, Foltz S, Wyczalkowski M, Wu Y, Song E, Brewer MA, Thiagarajan M, Kinsinger CR, Robles AI, Boja ES, Rodriguez H, Chan DW, Zhang B, Zhang Z, Ding L, Smith RD, Liu T, Rodland KD. Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. Cell Rep Med 2020; 1. [PMID: 32529193 PMCID: PMC7289043 DOI: 10.1016/j.xcrm.2020.100004] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the absence of a dominant driving mutation other than uniformly present TP53 mutations, deeper understanding of the biology driving ovarian high-grade serous cancer (HGSC) requires analysis at a functional level, including post-translational modifications. Comprehensive proteogenomic and phosphoproteomic characterization of 83 prospectively collected ovarian HGSC and appropriate normal precursor tissue samples (fallopian tube) under strict control of ischemia time reveals pathways that significantly differentiate between HGSC and relevant normal tissues in the context of homologous repair deficiency (HRD) status. In addition to confirming key features of HGSC from previous studies, including a potential survival-associated signature and histone acetylation as a marker of HRD, deep phosphoproteomics provides insights regarding the potential role of proliferation-induced replication stress in promoting the characteristic chromosomal instability of HGSC and suggests potential therapeutic targets for use in precision medicine trials. Comparison of ovarian cancer and normal precursors identifies key signaling pathways Mitotic and cyclin-dependent kinases emerge as potential therapeutic targets Previously identified hallmarks of homologous repair status and survival are confirmed Replication stress appears to drive increased chromosomal instability
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Affiliation(s)
- Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.,Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97201, USA.,These authors contributed equally
| | - Osama A Arshad
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.,These authors contributed equally
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Yi Fu
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Therese R Clauss
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Chen Huang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liang-Bo Wang
- The McDonnell Genome Institute, Washington University in St. Louis, St Louis, MO 63108, USA
| | - Steven Foltz
- The McDonnell Genome Institute, Washington University in St. Louis, St Louis, MO 63108, USA
| | - Matthew Wyczalkowski
- The McDonnell Genome Institute, Washington University in St. Louis, St Louis, MO 63108, USA
| | - Yige Wu
- The McDonnell Genome Institute, Washington University in St. Louis, St Louis, MO 63108, USA
| | - Ehwang Song
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Molly A Brewer
- Department of Obstetrics and Gynecology, University of Connecticut, Farmington, CT 06030, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhen Zhang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
| | - Li Ding
- The McDonnell Genome Institute, Washington University in St. Louis, St Louis, MO 63108, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.,Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97201, USA.,Lead Contact
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Eiger DS, Smith J, Tsai CF, Jacobs J, Shi T, Rajagopal S. Biased Agonism at CXCR3 Drives Differential Phosphoproteomic and Transcriptomic Profiles and Cellular Outputs. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.00292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | - Tujin Shi
- Pacific Northwest National Laboratory
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46
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Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekański A, Jędryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Fenyö D. Proteogenomic Characterization of Endometrial Carcinoma. Cell 2020; 180:729-748.e26. [PMID: 32059776 PMCID: PMC7233456 DOI: 10.1016/j.cell.2020.01.026] [Citation(s) in RCA: 247] [Impact Index Per Article: 61.8] [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: 05/29/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
Abstract
We undertook a comprehensive proteogenomic characterization of 95 prospectively collected endometrial carcinomas, comprising 83 endometrioid and 12 serous tumors. This analysis revealed possible new consequences of perturbations to the p53 and Wnt/β-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and provided new information about proteomic markers of clinical and genomic tumor subgroups, including relationships to known druggable pathways. An extensive genome-wide acetylation survey yielded insights into regulatory mechanisms linking Wnt signaling and histone acetylation. We also characterized aspects of the tumor immune landscape, including immunogenic alterations, neoantigens, common cancer/testis antigens, and the immune microenvironment, all of which can inform immunotherapy decisions. Collectively, our multi-omic analyses provide a valuable resource for researchers and clinicians, identify new molecular associations of potential mechanistic significance in the development of endometrial cancers, and suggest novel approaches for identifying potential therapeutic targets.
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Affiliation(s)
- Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily A Kawaler
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Daniel Cui Zhou
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Chen Huang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lili Blumenberg
- Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Alla Karpova
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shankha Satpathy
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Yige Wu
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhi Li
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Song Cao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - MacIntosh Cornwell
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Matthew A Wyczalkowski
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Rosalie K Chu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Suhas Vasaikar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hua Zhou
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Qingsong Gao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kai Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sunantha Sethuraman
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - David Heiman
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karsten Krug
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karl Clauser
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramani Kothadia
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yosef Maruvka
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Amanda E Oliphant
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Emily L Hoskins
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Samuel L Pugh
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Sean J I Beecroft
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - David W Adams
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Jonathan C Jarman
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Andy Kong
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hui-Yin Chang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Antonio Colaprico
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xi Steven Chen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Andrzej Czekański
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Marcin Jędryka
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Rafał Matkowski
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Maciej Wiznerowicz
- Poznan University of Medical Sciences, 61-701 Poznań, Poland; University Hospital of Lord's Transfiguration, 60-569 Poznań, Poland; International Institute for Molecular Oncology, 60-203 Poznań, Poland
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - David Mutch
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine Fuh
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Deborah DeLair
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - D R Mani
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael Noble
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew L Anderson
- College of Medicine Obstetrics & Gynecology, University of South Florida Health, Tampa, FL 33620, USA
| | - Douglas A Levine
- Gynecologic Oncology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Kelly V Ruggles
- Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA.
| | - Li Ding
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - David Fenyö
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA.
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47
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Dou M, Clair G, Tsai CF, Xu K, Chrisler WB, Sontag RL, Zhao R, Moore RJ, Liu T, Pasa-Tolic L, Smith RD, Shi T, Adkins JN, Qian WJ, Kelly RT, Ansong C, Zhu Y. High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labeling in a Nanodroplet Sample Preparation Platform. Anal Chem 2019; 91:13119-13127. [PMID: 31509397 DOI: 10.1021/acs.analchem.9b03349] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Effective extension of mass spectrometry-based proteomics to single cells remains challenging. Herein we combined microfluidic nanodroplet technology with tandem mass tag (TMT) isobaric labeling to significantly improve analysis throughput and proteome coverage for single mammalian cells. Isobaric labeling facilitated multiplex analysis of single cell-sized protein quantities to a depth of ∼1 600 proteins with a median CV of 10.9% and correlation coefficient of 0.98. To demonstrate in-depth high throughput single cell analysis, the platform was applied to measure protein expression in 72 single cells from three murine cell populations (epithelial, immune, and endothelial cells) in <2 days instrument time with over 2 300 proteins identified. Principal component analysis grouped the single cells into three distinct populations based on protein expression with each population characterized by well-known cell-type specific markers. Our platform enables high throughput and unbiased characterization of single cell heterogeneity at the proteome level.
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Affiliation(s)
- Maowei Dou
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Geremy Clair
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Chia-Feng Tsai
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Kerui Xu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - William B Chrisler
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ryan L Sontag
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ronald J Moore
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Tao Liu
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Richard D Smith
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Tujin Shi
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Joshua N Adkins
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Wei-Jun Qian
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States.,Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84604 , United States
| | - Charles Ansong
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
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48
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Tsai CF, Smith JS, Krajewski K, Zhao R, Moghieb AM, Nicora CD, Xiong X, Moore RJ, Liu T, Smith RD, Jacobs JM, Rajagopal S, Shi T. Tandem Mass Tag Labeling Facilitates Reversed-Phase Liquid Chromatography-Mass Spectrometry Analysis of Hydrophilic Phosphopeptides. Anal Chem 2019; 91:11606-11613. [PMID: 31418558 PMCID: PMC7197904 DOI: 10.1021/acs.analchem.9b01814] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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
Protein phosphorylation is a critical post-translational modification (PTM). Despite recent technological advances in reversed-phase liquid chromatography (RPLC)-mass spectrometry (MS)-based proteomics, comprehensive phosphoproteomic coverage in complex biological systems remains challenging, especially for hydrophilic phosphopeptides with enriched regions of serines, threonines, and tyrosines that often orchestrate critical biological functions. To address this issue, we developed a simple, easily implemented method to introduce a commonly used tandem mass tag (TMT) to increase peptide hydrophobicity, effectively enhancing RPLC-MS analysis of hydrophilic peptides. Different from conventional TMT labeling, this method capitalizes on using a nonprimary amine buffer and TMT labeling occurring before C18-based solid phase extraction. Through phosphoproteomic analyses of MCF7 cells, we have demonstrated that this method can greatly increase the number of identified hydrophilic phosphopeptides and improve MS detection signals. We applied this method to study the peptide QPSSSR, a very hydrophilic tryptic peptide located on the C-terminus of the G protein-coupled receptor (GPCR) CXCR3. Identification of QPSSSR has never been reported, and we were unable to detect it by traditional methods. We validated our TMT labeling strategy by comparative RPLC-MS analyses of both a hydrophilic QPSSSR peptide library as well as common phosphopeptides. We further confirmed the utility of this method by quantifying QPSSSR phosphorylation abundances in HEK 293 cells under different treatment conditions predicted to alter QPSSSR phosphorylation. We anticipate that this simple TMT labeling method can be broadly used not only for decoding GPCR phosphoproteome but also for effective RPLC-MS analysis of other highly hydrophilic analytes.
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Affiliation(s)
- Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jeffrey S. Smith
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
- Department of Medicine, Duke University, Durham, North Carolina 27710, United States
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599,United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ahmed M. Moghieb
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Carrie D. Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Xinyu Xiong
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
| | - Ronald J. Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jon M. Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Sudarshan Rajagopal
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
- Department of Medicine, Duke University, Durham, North Carolina 27710, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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49
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Cuesta R, Gritsenko MA, Petyuk VA, Shukla AK, Tsai CF, Liu T, McDermott JE, Holz MK. Phosphoproteome Analysis Reveals Estrogen-ER Pathway as a Modulator of mTOR Activity Via DEPTOR. Mol Cell Proteomics 2019; 18:1607-1618. [PMID: 31189691 PMCID: PMC6683011 DOI: 10.1074/mcp.ra119.001506] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 04/17/2019] [Revised: 05/22/2019] [Indexed: 12/14/2022] Open
Abstract
ER-positive breast tumors represent ∼70% of all breast cancer cases. Although their treatment with endocrine therapies is effective in the adjuvant or recurrent settings, the development of resistance compromises their effectiveness. The binding of estrogen to ERα, a transcription factor, triggers the regulation of the target genes (genomic pathway). Additionally, a cytoplasmic fraction of estrogen-bound ERα activates oncogenic signaling pathways such as PI3K/AKT/mTOR (nongenomic pathway). The upregulation of the estrogenic and the PI3K/AKT/mTOR signaling pathways are frequently associated with a poor outcome. To better characterize the connection between these two pathways, we performed a phosphoproteome analysis of ER-positive MCF7 breast cancer cells treated with estrogen or estrogen and the mTORC1 inhibitor rapamycin. Many proteins were identified as estrogen-regulated mTORC1 targets and among them, DEPTOR was selected for further characterization. DEPTOR binds to mTOR and inhibits the kinase activity of both mTOR complexes mTORC1 and mTORC2, but mitogen-activated mTOR promotes phosphorylation-mediated DEPTOR degradation. Although estrogen enhances the phosphorylation of DEPTOR by mTORC1, DEPTOR levels increase in estrogen-stimulated cells. We demonstrated that DEPTOR accumulation is the result of estrogen-ERα-mediated transcriptional upregulation of DEPTOR expression. Consequently, the elevated levels of DEPTOR partially counterbalance the estrogen-induced activation of mTORC1 and mTORC2. These results underscore the critical role of estrogen-ERα as a modulator of the PI3K/AKT/mTOR signaling pathway in ER-positive breast cancer cells. Additionally, these studies provide evidence supporting the use of dual PI3K/mTOR or dual mTORC1/2 inhibitors in combination with endocrine therapies as a first-line treatment option for the patients with ER-positive advanced breast cancer.
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Affiliation(s)
- Rafael Cuesta
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla NY 10595
| | - Marina A Gritsenko
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Vladislav A Petyuk
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Anil K Shukla
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Chia-Feng Tsai
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Tao Liu
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Jason E McDermott
- ¶Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland WA 99352
| | - Marina K Holz
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla NY 10595; ‖Albert Einstein Cancer Center, Bronx NY 10461.
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50
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Dou M, Tsai CF, Piehowski PD, Wang Y, Fillmore TL, Zhao R, Moore RJ, Zhang P, Qian WJ, Smith RD, Liu T, Kelly RT, Shi T, Zhu Y. Automated Nanoflow Two-Dimensional Reversed-Phase Liquid Chromatography System Enables In-Depth Proteome and Phosphoproteome Profiling of Nanoscale Samples. Anal Chem 2019; 91:9707-9715. [PMID: 31241912 DOI: 10.1021/acs.analchem.9b01248] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Two-dimensional reversed-phase capillary liquid chromatography (2D RPLC) separations have enabled comprehensive proteome profiling of biological systems. However, milligram sample quantities of proteins are typically required due to significant losses during offline fractionation. Such a large sample requirement generally precludes the application samples in the nanogram to low-microgram range. To achieve in-depth proteomic analysis of such small-sized samples, we have developed the nanoFAC (nanoflow Fractionation and Automated Concatenation) 2D RPLC platform, in which the first dimension high-pH fractionation was performed on a 75-μm i.d. capillary column at a 300 nL/min flow rate with automated fraction concatenation, instead of on a typically used 2.1 mm column at a 200 μL/min flow rate with manual concatenation. Each fraction was then fully transferred to the second-dimension low-pH nanoLC separation using an autosampler equipped with a custom-machined syringe. We have found that using a polypropylene 96-well plate as collection device as well as the addition of n-Dodecyl β-d-maltoside (0.01%) in the collection buffer can significantly improve sample recovery. We have demonstrated the nanoFAC 2D RPLC platform can achieve confident identifications of ∼49,000-94,000 unique peptides, corresponding to ∼6,700-8,300 protein groups using only 100-1000 ng of HeLa tryptic digest (equivalent to ∼500-5,000 cells). Furthermore, by integrating with phosphopeptide enrichment, the nanoFAC 2D RPLC platform can identify ∼20,000 phosphopeptides from 100 μg of MCF-7 cell lysate.
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Affiliation(s)
- Maowei Dou
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Chia-Feng Tsai
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Paul D Piehowski
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Yang Wang
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Thomas L Fillmore
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ronald J Moore
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Pengfei Zhang
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Wei-Jun Qian
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Richard D Smith
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Tao Liu
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States.,Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84604 , United States
| | - Tujin Shi
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
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