1
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Bulle A, Liu P, Seehra K, Bansod S, Chen Y, Zahra K, Somani V, Khawar IA, Chen HP, Dodhiawala PB, Li L, Geng Y, Mo CK, Mahsl J, Ding L, Govindan R, Davies S, Mudd J, Hawkins WG, Fields RC, DeNardo DG, Knoerzer D, Held JM, Grierson PM, Wang-Gillam A, Ruzinova MB, Lim KH. Combined KRAS-MAPK pathway inhibitors and HER2-directed drug conjugate is efficacious in pancreatic cancer. Nat Commun 2024; 15:2503. [PMID: 38509064 PMCID: PMC10954758 DOI: 10.1038/s41467-024-46811-w] [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: 08/02/2023] [Accepted: 03/11/2024] [Indexed: 03/22/2024] Open
Abstract
Targeting the mitogen-activated protein kinase (MAPK) cascade in pancreatic ductal adenocarcinoma (PDAC) remains clinically unsuccessful. We aim to develop a MAPK inhibitor-based therapeutic combination with strong preclinical efficacy. Utilizing a reverse-phase protein array, we observe rapid phospho-activation of human epidermal growth factor receptor 2 (HER2) in PDAC cells upon pharmacological MAPK inhibition. Mechanistically, MAPK inhibitors lead to swift proteasomal degradation of dual-specificity phosphatase 6 (DUSP6). The carboxy terminus of HER2, containing a TEY motif also present in extracellular signal-regulated kinase 1/2 (ERK1/2), facilitates binding with DUSP6, enhancing its phosphatase activity to dephosphorylate HER2. In the presence of MAPK inhibitors, DUSP6 dissociates from the protective effect of the RING E3 ligase tripartite motif containing 21, resulting in its degradation. In PDAC patient-derived xenograft (PDX) models, combining ERK and HER inhibitors slows tumour growth and requires cytotoxic chemotherapy to achieve tumour regression. Alternatively, MAPK inhibitors with trastuzumab deruxtecan, an anti-HER2 antibody conjugated with cytotoxic chemotherapy, lead to sustained tumour regression in most tested PDXs without causing noticeable toxicity. Additionally, KRAS inhibitors also activate HER2, supporting testing the combination of KRAS inhibitors and trastuzumab deruxtecan in PDAC. This study identifies a rational and promising therapeutic combination for clinical testing in PDAC patients.
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Affiliation(s)
- Ashenafi Bulle
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Peng Liu
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Kuljeet Seehra
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Sapana Bansod
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Yali Chen
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kiran Zahra
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Vikas Somani
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Iftikhar Ali Khawar
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hung-Po Chen
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Paarth B Dodhiawala
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Lin Li
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Yutong Geng
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Chia-Kuei Mo
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jay Mahsl
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Li Ding
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ramaswamy Govindan
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Sherri Davies
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jacqueline Mudd
- Section of Hepatobiliary Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - William G Hawkins
- Section of Hepatobiliary Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ryan C Fields
- Section of Hepatobiliary Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David G DeNardo
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | | | - Jason M Held
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Patrick M Grierson
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Andrea Wang-Gillam
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Marianna B Ruzinova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kian-Huat Lim
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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2
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Pohl F, Germann AL, Mao J, Hou S, Bakare B, Kong Thoo Lin P, Yates K, Nonet ML, Akk G, Kornfeld K, Held JM. UNC-49 is a redox-sensitive GABA A receptor that regulates the mitochondrial unfolded protein response cell nonautonomously. Sci Adv 2023; 9:eadh2584. [PMID: 37910615 PMCID: PMC10619936 DOI: 10.1126/sciadv.adh2584] [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] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]
Abstract
The γ-aminobutyric acid-mediated (GABAergic) system participates in many aspects of organismal physiology and disease, including proteostasis, neuronal dysfunction, and life-span extension. Many of these phenotypes are also regulated by reactive oxygen species (ROS), but the redox mechanisms linking the GABAergic system to these phenotypes are not well defined. Here, we report that GABAergic redox signaling cell nonautonomously activates many stress response pathways in Caenorhabditis elegans and enhances vulnerability to proteostasis disease in the absence of oxidative stress. Cell nonautonomous redox activation of the mitochondrial unfolded protein response (mitoUPR) proteostasis network requires UNC-49, a GABAA receptor that we show is activated by hydrogen peroxide. MitoUPR induction by a spinocerebellar ataxia type 3 (SCA3) C. elegans neurodegenerative disease model was similarly dependent on UNC-49 in C. elegans. These results demonstrate a multi-tissue paradigm for redox signaling in the GABAergic system that is transduced via a GABAA receptor to function in cell nonautonomous regulation of health, proteostasis, and disease.
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Affiliation(s)
- Franziska Pohl
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Allison L. Germann
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jack Mao
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sydney Hou
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Bayode Bakare
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, UK
| | - Paul Kong Thoo Lin
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, UK
| | - Kyari Yates
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, UK
| | - Michael L. Nonet
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Gustav Akk
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, USA
- Taylor Family Institute for Innovative Psychiatric Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Kerry Kornfeld
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason M. Held
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
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3
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Iglesia MD, Jayasinghe RG, Chen S, Terekhanova NV, Herndon JM, Storrs E, Karpova A, Zhou DC, Al Deen NN, Shinkle AT, Lu RJH, Caravan W, Houston A, Zhao Y, Sato K, Lal P, Street C, Rodrigues FM, Southard-Smith AN, Targino da Costa ALN, Zhu H, Mo CK, Crowson L, Fulton RS, Wyczalkowski MA, Fronick CC, Fulton LA, Sun H, Davies SR, Appelbaum EL, Chasnoff SE, Carmody M, Brooks C, Liu R, Wendl MC, Oh C, Bender D, Cruchaga C, Harari O, Bredemeyer A, Lavine K, Bose R, Margenthaler J, Held JM, Achilefu S, Ademuyiwa F, Aft R, Ma C, Colditz GA, Ju T, Oh ST, Fitzpatrick J, Hwang ES, Shoghi KI, Chheda MG, Veis DJ, Chen F, Fields RC, Gillanders WE, Ding L. Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages. bioRxiv 2023:2023.10.31.565031. [PMID: 37961519 PMCID: PMC10634973 DOI: 10.1101/2023.10.31.565031] [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: 11/15/2023]
Abstract
Breast cancer is a heterogeneous disease, and treatment is guided by biomarker profiles representing distinct molecular subtypes. Breast cancer arises from the breast ductal epithelium, and experimental data suggests breast cancer subtypes have different cells of origin within that lineage. The precise cells of origin for each subtype and the transcriptional networks that characterize these tumor-normal lineages are not established. In this work, we applied bulk, single-cell (sc), and single-nucleus (sn) multi-omic techniques as well as spatial transcriptomics and multiplex imaging on 61 samples from 37 breast cancer patients to show characteristic links in gene expression and chromatin accessibility between breast cancer subtypes and their putative cells of origin. We applied the PAM50 subtyping algorithm in tandem with bulk RNA-seq and snRNA-seq to reliably subtype even low-purity tumor samples and confirm promoter accessibility using snATAC. Trajectory analysis of chromatin accessibility and differentially accessible motifs clearly connected progenitor populations with breast cancer subtypes supporting the cell of origin for basal-like and luminal A and B tumors. Regulatory network analysis of transcription factors underscored the importance of BHLHE40 in luminal breast cancer and luminal mature cells, and KLF5 in basal-like tumors and luminal progenitor cells. Furthermore, we identify key genes defining the basal-like ( PRKCA , SOX6 , RGS6 , KCNQ3 ) and luminal A/B ( FAM155A , LRP1B ) lineages, with expression in both precursor and cancer cells and further upregulation in tumors. Exhausted CTLA4-expressing CD8+ T cells were enriched in basal-like breast cancer, suggesting altered means of immune dysfunction among breast cancer subtypes. We used spatial transcriptomics and multiplex imaging to provide spatial detail for key markers of benign and malignant cell types and immune cell colocation. These findings demonstrate analysis of paired transcription and chromatin accessibility at the single cell level is a powerful tool for investigating breast cancer lineage development and highlight transcriptional networks that define basal and luminal breast cancer lineages.
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4
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Terekhanova NV, Karpova A, Liang WW, Strzalkowski A, Chen S, Li Y, Southard-Smith AN, Iglesia MD, Wendl MC, Jayasinghe RG, Liu J, Song Y, Cao S, Houston A, Liu X, Wyczalkowski MA, Lu RJH, Caravan W, Shinkle A, Naser Al Deen N, Herndon JM, Mudd J, Ma C, Sarkar H, Sato K, Ibrahim OM, Mo CK, Chasnoff SE, Porta-Pardo E, Held JM, Pachynski R, Schwarz JK, Gillanders WE, Kim AH, Vij R, DiPersio JF, Puram SV, Chheda MG, Fuh KC, DeNardo DG, Fields RC, Chen F, Raphael BJ, Ding L. Epigenetic regulation during cancer transitions across 11 tumour types. Nature 2023; 623:432-441. [PMID: 37914932 PMCID: PMC10632147 DOI: 10.1038/s41586-023-06682-5] [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: 10/15/2022] [Accepted: 09/27/2023] [Indexed: 11/03/2023]
Abstract
Chromatin accessibility is essential in regulating gene expression and cellular identity, and alterations in accessibility have been implicated in driving cancer initiation, progression and metastasis1-4. Although the genetic contributions to oncogenic transitions have been investigated, epigenetic drivers remain less understood. Here we constructed a pan-cancer epigenetic and transcriptomic atlas using single-nucleus chromatin accessibility data (using single-nucleus assay for transposase-accessible chromatin) from 225 samples and matched single-cell or single-nucleus RNA-sequencing expression data from 206 samples. With over 1 million cells from each platform analysed through the enrichment of accessible chromatin regions, transcription factor motifs and regulons, we identified epigenetic drivers associated with cancer transitions. Some epigenetic drivers appeared in multiple cancers (for example, regulatory regions of ABCC1 and VEGFA; GATA6 and FOX-family motifs), whereas others were cancer specific (for example, regulatory regions of FGF19, ASAP2 and EN1, and the PBX3 motif). Among epigenetically altered pathways, TP53, hypoxia and TNF signalling were linked to cancer initiation, whereas oestrogen response, epithelial-mesenchymal transition and apical junction were tied to metastatic transition. Furthermore, we revealed a marked correlation between enhancer accessibility and gene expression and uncovered cooperation between epigenetic and genetic drivers. This atlas provides a foundation for further investigation of epigenetic dynamics in cancer transitions.
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Affiliation(s)
- Nadezhda V Terekhanova
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Alla Karpova
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Wen-Wei Liang
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | | | - Siqi Chen
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Yize Li
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Austin N Southard-Smith
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Michael D Iglesia
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Michael C Wendl
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Reyka G Jayasinghe
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Jingxian Liu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Yizhe Song
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Song Cao
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Andrew Houston
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Xiuting Liu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Rita Jui-Hsien Lu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Wagma Caravan
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Andrew Shinkle
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Nataly Naser Al Deen
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - John M Herndon
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Jacqueline Mudd
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
| | - Cong Ma
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Hirak Sarkar
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Kazuhito Sato
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Omar M Ibrahim
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Chia-Kuei Mo
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Sara E Chasnoff
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Eduard Porta-Pardo
- Josep Carreras Leukaemia Research Institute, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Jason M Held
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Russell Pachynski
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Julie K Schwarz
- Department of Radiation Oncology, Washington University in St Louis, St Louis, MO, USA
| | - William E Gillanders
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Albert H Kim
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
- Department of Neurological Surgery, Washington University in St Louis, St Louis, MO, USA
| | - Ravi Vij
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - John F DiPersio
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Sidharth V Puram
- Department of Otolaryngology-Head & Neck Surgery, Washington University in St Louis, St Louis, MO, USA
| | - Milan G Chheda
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Katherine C Fuh
- Department of Obstetrics and Gynecology, University of California, San Francisco, San Francisco, CA, USA
- Department of Obstetrics and Gynecology, Washington University in St Louis, St Louis, MO, USA
| | - David G DeNardo
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Ryan C Fields
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
| | - Feng Chen
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
| | - Li Ding
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA.
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
- Department of Genetics, Washington University in St Louis, St Louis, MO, USA.
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5
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Barlin M, Erdmann-Gilmore P, Mudd JL, Zhang Q, Seymour RW, Guo Z, Miessner JR, Goedegebuure SP, Bi Y, Osorio OA, Alexander-Brett J, Li S, Ma CX, Fields RC, Townsend RR, Held JM. Proteins in Tumor-Derived Plasma Extracellular Vesicles Indicate Tumor Origin. Mol Cell Proteomics 2023; 22:100476. [PMID: 36470535 PMCID: PMC9801135 DOI: 10.1016/j.mcpro.2022.100476] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/12/2022] [Accepted: 11/28/2022] [Indexed: 12/09/2022] Open
Abstract
Cancer-derived extracellular vesicles (EVs) promote tumorigenesis, premetastatic niche formation, and metastasis via their protein cargo. However, the proteins packaged by patient tumors into EVs cannot be determined in vivo because of the presence of EVs derived from other tissues. We therefore developed a cross-species proteomic method to quantify the human tumor-derived proteome of plasma EVs produced by patient-derived xenografts of four cancer types. Proteomic profiling revealed individualized packaging of novel protein cargo, and machine learning accurately classified the type of the underlying tumor.
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Affiliation(s)
- Meltem Barlin
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Petra Erdmann-Gilmore
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Jacqueline L Mudd
- Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Department of Surgery, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Qiang Zhang
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Robert W Seymour
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Zhanfang Guo
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Julia R Miessner
- Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Department of Surgery, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - S Peter Goedegebuure
- Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Department of Surgery, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Ye Bi
- Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Department of Surgery, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Omar A Osorio
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Jennifer Alexander-Brett
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Shunqiang Li
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Cynthia X Ma
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Ryan C Fields
- Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Department of Surgery, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - R Reid Townsend
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | - Jason M Held
- Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA; Department of Anesthesiology, Washington University School of Medicine in St Louis, St Louis, Missouri, USA.
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6
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Brashears CB, Prudner BC, Rathore R, Caldwell KE, Dehner CA, Buchanan JL, Lange SE, Poulin N, Sehn JK, Roszik J, Spitzer D, Jones KB, O'Keefe R, Nielsen TO, Taylor EB, Held JM, Hawkins W, Van Tine BA. Malic Enzyme 1 Absence in Synovial Sarcoma Shifts Antioxidant System Dependence and Increases Sensitivity to Ferroptosis Induction with ACXT-3102. Clin Cancer Res 2022; 28:3573-3589. [PMID: 35421237 PMCID: PMC9378556 DOI: 10.1158/1078-0432.ccr-22-0470] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/29/2022] [Accepted: 04/12/2022] [Indexed: 01/09/2023]
Abstract
PURPOSE To investigate the metabolism of synovial sarcoma (SS) and elucidate the effect of malic enzyme 1 absence on SS redox homeostasis. EXPERIMENTAL DESIGN ME1 expression was measured in SS clinical samples, SS cell lines, and tumors from an SS mouse model. The effect of ME1 absence on glucose metabolism was evaluated utilizing Seahorse assays, metabolomics, and C13 tracings. The impact of ME1 absence on SS redox homeostasis was evaluated by metabolomics, cell death assays with inhibitors of antioxidant systems, and measurements of intracellular reactive oxygen species (ROS). The susceptibility of ME1-null SS to ferroptosis induction was interrogated in vitro and in vivo. RESULTS ME1 absence in SS was confirmed in clinical samples, SS cell lines, and an SS tumor model. Investigation of SS glucose metabolism revealed that ME1-null cells exhibit higher rates of glycolysis and higher flux of glucose into the pentose phosphate pathway (PPP), which is necessary to produce NADPH. Evaluation of cellular redox homeostasis demonstrated that ME1 absence shifts dependence from the glutathione system to the thioredoxin system. Concomitantly, ME1 absence drives the accumulation of ROS and labile iron. ROS and iron accumulation enhances the susceptibility of ME1-null cells to ferroptosis induction with inhibitors of xCT (erastin and ACXT-3102). In vivo xenograft models of ME1-null SS demonstrate significantly increased tumor response to ACXT-3102 compared with ME1-expressing controls. CONCLUSIONS These findings demonstrate the translational potential of targeting redox homeostasis in ME1-null cancers and establish the preclinical rationale for a phase I trial of ACXT-3102 in SS patients. See related commentary by Subbiah and Gan, p. 3408.
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Affiliation(s)
- Caitlyn B. Brashears
- Division of Medical Oncology, Washington University in St. Louis, St. Louis, Missouri
| | - Bethany C. Prudner
- Division of Medical Oncology, Washington University in St. Louis, St. Louis, Missouri
| | - Richa Rathore
- Division of Medical Oncology, Washington University in St. Louis, St. Louis, Missouri
| | - Katharine E. Caldwell
- Department of Surgery, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Carina A. Dehner
- Department of Pathology and Immunology, Division of Anatomic and Molecular Pathology, Washington University in St. Louis, St. Louis, Missouri
| | - Jane L. Buchanan
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Sara E.S. Lange
- Division of Medical Oncology, Washington University in St. Louis, St. Louis, Missouri
| | - Neal Poulin
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer K. Sehn
- Department of Pathology and Immunology, Division of Anatomic and Molecular Pathology, Washington University in St. Louis, St. Louis, Missouri
| | - Jason Roszik
- Departments of Melanoma Medical Oncology and Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dirk Spitzer
- Department of Surgery, Washington University in St. Louis School of Medicine, St. Louis, Missouri.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri
| | - Kevin B. Jones
- Department of Orthopedics, University of Utah, Salt Lake City, Utah.,Department of Oncological Sciences, University of Utah, Salt Lake City, Utah.,Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Regis O'Keefe
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri.,Department of Orthopedics, Washington University in St. Louis, St. Louis, Missouri
| | - Torsten O. Nielsen
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric B. Taylor
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa.,Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa
| | - Jason M. Held
- Division of Medical Oncology, Washington University in St. Louis, St. Louis, Missouri.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri.,Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri
| | - William Hawkins
- Department of Surgery, Washington University in St. Louis School of Medicine, St. Louis, Missouri.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri
| | - Brian A. Van Tine
- Division of Medical Oncology, Washington University in St. Louis, St. Louis, Missouri.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri.,Department of Pediatrics, Washington University in St. Louis, St. Louis, Missouri.,Corresponding Author: Brian A. Van Tine, Division of Medical Oncology, Washington University in St. Louis, 660 South Euclid, Campus Box 8007, St. Louis, MO 63110. Phone: 314-747-3096: E-mail:
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7
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van der Post S, Seymour RW, Mooradian AD, Held JM. Automating Assignment, Quantitation, and Biological Annotation of Redox Proteomics Datasets with ProteoSushi. Methods Mol Biol 2022; 2399:61-84. [PMID: 35604553 DOI: 10.1007/978-1-0716-1831-8_4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Redox proteomics plays an increasingly important role characterizing the cellular redox state and redox signaling networks. As these datasets grow larger and identify more redox regulated sites in proteins, they provide a systems-wide characterization of redox regulation across cellular organelles and regulatory networks. However, these large proteomic datasets require substantial data processing and analysis in order to fully interpret and comprehend the biological impact of oxidative posttranslational modifications. We therefore developed ProteoSushi, a software tool to biologically annotate and quantify redox proteomics and other modification-specific proteomics datasets. ProteoSushi can be applied to differentially alkylated samples to assay overall cysteine oxidation, chemically labeled samples such as those used to profile the cysteine sulfenome, or any oxidative posttranslational modification on any residue.Here we demonstrate how to use ProteoSushi to analyze a large, public cysteine redox proteomics dataset. ProteoSushi assigns each modified peptide to shared proteins and genes, sums or averages signal intensities for each modified site of interest, and annotates each modified site with the most up-to-date biological information available from UniProt. These biological annotations include known functional roles or modifications of the site, the protein domain(s) that the site resides in, the protein's subcellular location and function, and more.
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Affiliation(s)
- Sjoerd van der Post
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Robert W Seymour
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Arshag D Mooradian
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason M Held
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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8
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Seymour RW, van der Post S, Mooradian AD, Held JM. ProteoSushi: A Software Tool to Biologically Annotate and Quantify Modification-Specific, Peptide-Centric Proteomics Data Sets. J Proteome Res 2021; 20:3621-3628. [PMID: 34056901 DOI: 10.1021/acs.jproteome.1c00203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Large-scale proteomic profiling of protein post-translational modifications has provided important insights into the regulation of cell signaling and disease. These modification-specific proteomics workflows nearly universally enrich modified peptides prior to mass spectrometry analysis, but protein-centric proteomic software tools have many limitations evaluating and interpreting these peptide-centric data sets. We, therefore, developed ProteoSushi, a software tool tailored to analysis of each modified site in peptide-centric proteomic data sets that is compatible with any post-translational modification or chemical label. ProteoSushi uses a unique approach to assign identified peptides to shared proteins and genes, minimizing redundancy by prioritizing shared assignments based on UniProt annotation score and optional user-supplied protein/gene lists. ProteoSushi simplifies quantitation by summing or averaging intensities for each modified site, merging overlapping peptide charge states, missed cleavages, spectral matches, and variable modifications into a single value. ProteoSushi also annotates each PTM site with the most up-to-date biological information available from UniProt, such as functional roles or known modifications, the protein domain in which the site resides, the protein's subcellular location and function, and more. ProteoSushi has a graphical user interface for ease of use. ProteoSushi's flexibility and combination of analysis features streamlines peptide-centric data processing and knowledge mining of large modification-specific proteomics data sets.
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Affiliation(s)
- Robert W Seymour
- Department of Medicine, Washington University School of Medicine in St. Louis, Campus Box 8076, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Sjoerd van der Post
- Department of Medicine, Washington University School of Medicine in St. Louis, Campus Box 8076, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States.,Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Arshag D Mooradian
- Department of Medicine, Washington University School of Medicine in St. Louis, Campus Box 8076, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Jason M Held
- Department of Medicine, Washington University School of Medicine in St. Louis, Campus Box 8076, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States.,Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States.,Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
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9
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Zhu C, Rogers A, Asleh K, Won J, Gao D, Leung S, Li S, Vij KR, Zhu J, Held JM, You Z, Nielsen TO, Shao J. Phospho-Ser 784-VCP Is Required for DNA Damage Response and Is Associated with Poor Prognosis of Chemotherapy-Treated Breast Cancer. Cell Rep 2021; 31:107745. [PMID: 32521270 PMCID: PMC7282751 DOI: 10.1016/j.celrep.2020.107745] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 01/27/2020] [Revised: 05/01/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022] Open
Abstract
Spatiotemporal protein reorganization at DNA damage sites induced by genotoxic chemotherapies is crucial for DNA damage response (DDR), which influences treatment response by directing cancer cell fate. This process is orchestrated by valosin-containing protein (VCP), an AAA+ ATPase that extracts polyubiquinated chromatin proteins and facilitates their turnover. However, because of the essential and pleiotropic effects of VCP in global proteostasis, it remains challenging practically to understand and target its DDR-specific functions. We describe a DNA-damage-induced phosphorylation event (Ser784), which selectively enhances chromatin-associated protein degradation mediated by VCP and is required for DNA repair, signaling, and cell survival. These functional effects of Ser784 phosphorylation on DDR correlate with a decrease in VCP association with chromatin, cofactors NPL4/UFD1, and polyubiquitinated substrates. Clinically, high phospho-Ser784-VCP levels are significantly associated with poor outcome among chemotherapy-treated breast cancer patients. Thus, Ser784 phosphorylation is a DDR-specific enhancer of VCP function and a potential predictive biomarker for chemotherapy treatments.
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Affiliation(s)
- Cuige Zhu
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anna Rogers
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Karama Asleh
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Jennifer Won
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Dongxia Gao
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Samuel Leung
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Shan Li
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kiran R Vij
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jian Zhu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jason M Held
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zhongsheng You
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Torsten O Nielsen
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Jieya Shao
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA.
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10
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van der Post S, Birchenough GMH, Held JM. NOX1-dependent redox signaling potentiates colonic stem cell proliferation to adapt to the intestinal microbiota by linking EGFR and TLR activation. Cell Rep 2021; 35:108949. [PMID: 33826887 PMCID: PMC10327654 DOI: 10.1016/j.celrep.2021.108949] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 01/25/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
The colon epithelium is a primary point of interaction with the microbiome and is regenerated by a few rapidly cycling colonic stem cells (CSCs). CSC self-renewal and proliferation are regulated by growth factors and the presence of bacteria. However, the molecular link connecting the diverse inputs that maintain CSC homeostasis remains largely unknown. We report that CSC proliferation is mediated by redox-dependent activation of epidermal growth factor receptor (EGFR) signaling via NADPH oxidase 1 (NOX1). NOX1 expression is CSC specific and is restricted to proliferative CSCs. In the absence of NOX1, CSCs fail to generate ROS and have a reduced proliferation rate. NOX1 expression is regulated by Toll-like receptor activation in response to the microbiota and serves to link CSC proliferation with the presence of bacterial components in the crypt. The TLR-NOX1-EGFR axis is therefore a critical redox signaling node in CSCs facilitating the quiescent-proliferation transition and responds to the microbiome to maintain colon homeostasis.
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Affiliation(s)
- Sjoerd van der Post
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - George M H Birchenough
- Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Jason M Held
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
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11
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Zhu C, Kim SJ, Mooradian A, Wang F, Li Z, Holohan S, Collins PL, Wang K, Guo Z, Hoog J, Ma CX, Oltz EM, Held JM, Shao J. Cancer-associated exportin-6 upregulation inhibits the transcriptionally repressive and anticancer effects of nuclear profilin-1. Cell Rep 2021; 34:108749. [PMID: 33596420 PMCID: PMC8006859 DOI: 10.1016/j.celrep.2021.108749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 12/29/2020] [Accepted: 01/21/2021] [Indexed: 01/22/2023] Open
Abstract
Aberrant expression of nuclear transporters and deregulated subcellular localization of their cargo proteins are emerging as drivers and therapeutic targets of cancer. Here, we present evidence that the nuclear exporter exportin-6 and its cargo profilin-1 constitute a functionally important and frequently deregulated axis in cancer. Exportin-6 upregulation occurs in numerous cancer types and is associated with poor patient survival. Reducing exportin-6 level in breast cancer cells triggers antitumor effects by accumulating nuclear profilin-1. Mechanistically, nuclear profilin-1 interacts with eleven-nineteen-leukemia protein (ENL) within the super elongation complex (SEC) and inhibits the ability of the SEC to drive transcription of numerous pro-cancer genes including MYC. XPO6 and MYC are positively correlated across diverse cancer types including breast cancer. Therapeutically, exportin-6 loss sensitizes breast cancer cells to the bromodomain and extra-terminal (BET) inhibitor JQ1. Thus, exportin-6 upregulation is a previously unrecognized cancer driver event by spatially inhibiting nuclear profilin-1 as a tumor suppressor.
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Affiliation(s)
- Cuige Zhu
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sun-Joong Kim
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Arshag Mooradian
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Faliang Wang
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Surgical Oncology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Ziqian Li
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Sean Holohan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Patrick L Collins
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Keren Wang
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zhanfang Guo
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeremy Hoog
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Cynthia X Ma
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eugene M Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Jason M Held
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jieya Shao
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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12
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Clements JL, Pohl F, Muthupandi P, Rogers SC, Mao J, Doctor A, Birman VB, Held JM. A clickable probe for versatile characterization of S-nitrosothiols. Redox Biol 2020; 37:101707. [PMID: 32916549 PMCID: PMC7490559 DOI: 10.1016/j.redox.2020.101707] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 08/12/2020] [Accepted: 08/27/2020] [Indexed: 12/23/2022] Open
Abstract
S-nitrosation of cysteine thiols (SNOs), commonly referred to as S-nitrosylation, is a cysteine oxoform that plays an important role in cellular signaling and impacts protein function and stability. Direct labeling of SNOs in cells with the flexibility to perform a wide range of cellular and biochemical assays remains a bottleneck as all SNO-targeted probes to date employ a single analytical modality such as biotin or a specific fluorophore. We therefore developed a clickable, alkyne-containing SNO probe 'PBZyn' based on the o-phosphino-benzoyl group warhead that enables multi-modal analysis via click conjugation. We demonstrate the utility of PBZyn to assay SNOs using in situ cellular imaging, protein blotting and affinity purification, as well as mass spectrometry. The flexible PBZyn probe will greatly facilitate investigation into the regulation of SNOs.
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Affiliation(s)
- Jenna L Clements
- Department of Medicine, Washington University Medical School, St. Louis, MO, 63110, USA
| | - Franziska Pohl
- Department of Medicine, Washington University Medical School, St. Louis, MO, 63110, USA
| | - Pandi Muthupandi
- Department of Chemistry, Washington University in Saint Louis, St. Louis, MO, 63110, USA
| | - Stephen C Rogers
- Department of Pediatrics and Center for Blood Oxygen Transport and Hemostasis, University of Maryland, School of Medicine, Baltimore, MD, 21201, USA
| | - Jack Mao
- Department of Medicine, Washington University Medical School, St. Louis, MO, 63110, USA
| | - Allan Doctor
- Department of Pediatrics and Center for Blood Oxygen Transport and Hemostasis, University of Maryland, School of Medicine, Baltimore, MD, 21201, USA
| | - Vladimir B Birman
- Department of Chemistry, Washington University in Saint Louis, St. Louis, MO, 63110, USA
| | - Jason M Held
- Department of Medicine, Washington University Medical School, St. Louis, MO, 63110, USA; Siteman Cancer Center, Washington University Medical School, St. Louis, MO, 63110, USA; Department of Anesthesiology, Washington University Medical School, St. Louis, MO, 63110, USA.
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13
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Abstract
Significance: Cellular redox processes are highly interconnected, yet not in equilibrium, and governed by a wide range of biochemical parameters. Technological advances continue refining how specific redox processes are regulated, but broad understanding of the dynamic interconnectivity between cellular redox modules remains limited. Systems biology investigates multiple components in complex environments and can provide integrative insights into the multifaceted cellular redox state. This review describes the state of the art in redox systems biology as well as provides an updated perspective and practical guide for harnessing thousands of cysteine sensors in the redoxome for multiparameter characterization of cellular redox networks. Recent Advances: Redox systems biology has been applied to genome-scale models and large public datasets, challenged common conceptions, and provided new insights that complement reductionist approaches. Advances in public knowledge and user-friendly tools for proteome-wide annotation of cysteine sentinels can now leverage cysteine redox proteomics datasets to provide spatial, functional, and protein structural information. Critical Issues: Careful consideration of available analytical approaches is needed to broadly characterize the systems-level properties of redox signaling networks and be experimentally feasible. The cysteine redoxome is an informative focal point since it integrates many aspects of redox biology. The mechanisms and redox modules governing cysteine redox regulation, cysteine oxidation assays, proteome-wide annotation of the biophysical and biochemical properties of individual cysteines, and their clinical application are discussed. Future Directions: Investigating the cysteine redoxome at a systems level will uncover new insights into the mechanisms of selectivity and context dependence of redox signaling networks.
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Affiliation(s)
- Jason M. Held
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
- Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, Missouri
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14
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Mooradian AD, van der Post S, Naegle KM, Held JM. ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis. PLoS Comput Biol 2020; 16:e1007741. [PMID: 32150535 PMCID: PMC7082058 DOI: 10.1371/journal.pcbi.1007741] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/19/2020] [Accepted: 02/18/2020] [Indexed: 01/06/2023] Open
Abstract
We present ProteoClade, a Python toolkit that performs taxa-specific peptide assignment, protein inference, and quantitation for multi-species proteomics experiments. ProteoClade scales to hundreds of millions of protein sequences, requires minimal computational resources, and is open source, multi-platform, and accessible to non-programmers. We demonstrate its utility for processing quantitative proteomic data derived from patient-derived xenografts and its speed and scalability enable a novel de novo proteomic workflow for complex microbiota samples. The exponential growth of the number of available reference protein sequences has provided an opportunity to taxonomically annotate and quantify complex mixtures of organisms using bottom-up proteomics. However, the ability to annotate relevant taxa to proteomics data is computationally challenging when data sets generate millions of candidate sequences and the reference database contains billions of peptide sequences. Here, we provide a software tool that enables users to perform taxon-specific quantitation on large proteomic data sets without requiring high performance computing. This tool flexibly enables users to match the reference database settings to their experimental conditions, and can scale from two-organism studies to the entire UniProt repository. In addition, we provide a de novo analysis workflow that enables the identification of organisms in the sample without prior specification, analogous to 16S rRNA sequencing.
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Affiliation(s)
- Arshag D. Mooradian
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
| | - Sjoerd van der Post
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
| | - Kristen M. Naegle
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jason M. Held
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
- Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
- * E-mail:
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15
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Behring JB, van der Post S, Mooradian AD, Egan MJ, Zimmerman MI, Clements JL, Bowman GR, Held JM. Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation. Sci Signal 2020; 13:eaay7315. [PMID: 31964804 PMCID: PMC7263378 DOI: 10.1126/scisignal.aay7315] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Stimulation of plasma membrane receptor tyrosine kinases (RTKs), such as the epidermal growth factor receptor (EGFR), locally increases the abundance of reactive oxygen species (ROS). These ROS then oxidize cysteine residues in proteins to potentiate downstream signaling. Spatial confinement of ROS is an important regulatory mechanism of redox signaling that enables the stimulation of different RTKs to oxidize distinct sets of downstream proteins. To uncover additional mechanisms that specify cysteines that are redox regulated by EGF stimulation, we performed time-resolved quantification of the EGF-dependent oxidation of 4200 cysteine sites in A431 cells. Fifty-one percent of cysteines were statistically significantly oxidized by EGF stimulation. Furthermore, EGF induced three distinct spatiotemporal patterns of cysteine oxidation in functionally organized protein networks, consistent with the spatial confinement model. Unexpectedly, protein crystal structure analysis and molecular dynamics simulations indicated widespread redox regulation of cryptic cysteine residues that are solvent exposed only upon changes in protein conformation. Phosphorylation and increased flux of nucleotide substrates served as two distinct modes by which EGF specified the cryptic cysteine residues that became solvent exposed and redox regulated. Because proteins that are structurally regulated by different RTKs or cellular perturbations are largely unique, these findings suggest that solvent exposure and redox regulation of cryptic cysteine residues contextually delineate redox signaling networks.
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Affiliation(s)
- Jessica B Behring
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Sjoerd van der Post
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Arshag D Mooradian
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Matthew J Egan
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Maxwell I Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Jenna L Clements
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Jason M Held
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
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16
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Mundt F, Rajput S, Li S, Ruggles KV, Mooradian AD, Mertins P, Gillette MA, Krug K, Guo Z, Hoog J, Erdmann-Gilmore P, Primeau T, Huang S, Edwards DP, Wang X, Wang X, Kawaler E, Mani DR, Clauser KR, Gao F, Luo J, Davies SR, Johnson GL, Huang KL, Yoon CJ, Ding L, Fenyö D, Ellis MJ, Townsend RR, Held JM, Carr SA, Ma CX. Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers. Cancer Res 2018; 78:2732-2746. [PMID: 29472518 PMCID: PMC5955814 DOI: 10.1158/0008-5472.can-17-1990] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 01/09/2018] [Accepted: 02/19/2018] [Indexed: 12/20/2022]
Abstract
Activation of PI3K signaling is frequently observed in triple-negative breast cancer (TNBC), yet PI3K inhibitors have shown limited clinical activity. To investigate intrinsic and adaptive mechanisms of resistance, we analyzed a panel of patient-derived xenograft models of TNBC with varying responsiveness to buparlisib, a pan-PI3K inhibitor. In a subset of patient-derived xenografts, resistance was associated with incomplete inhibition of PI3K signaling and upregulated MAPK/MEK signaling in response to buparlisib. Outlier phosphoproteome and kinome analyses identified novel candidates functionally important to buparlisib resistance, including NEK9 and MAP2K4. Knockdown of NEK9 or MAP2K4 reduced both baseline and feedback MAPK/MEK signaling and showed synthetic lethality with buparlisib in vitro A complex in/del frameshift in PIK3CA decreased sensitivity to buparlisib via NEK9/MAP2K4-dependent mechanisms. In summary, our study supports a role for NEK9 and MAP2K4 in mediating buparlisib resistance and demonstrates the value of unbiased omic analyses in uncovering resistance mechanisms to targeted therapy.Significance: Integrative phosphoproteogenomic analysis is used to determine intrinsic resistance mechanisms of triple-negative breast tumors to PI3K inhibition. Cancer Res; 78(10); 2732-46. ©2018 AACR.
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Affiliation(s)
- Filip Mundt
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sandeep Rajput
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Shunqiang Li
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Kelly V Ruggles
- Department of Medicine, New York University Langone Health, New York, New York
| | - Arshag D Mooradian
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Philipp Mertins
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Proteomics Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany and Berlin Institute of Health, Berlin, Germany
| | - Michael A Gillette
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Karsten Krug
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Zhanfang Guo
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Jeremy Hoog
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Petra Erdmann-Gilmore
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Tina Primeau
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Shixia Huang
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Dean P Edwards
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Xiaowei Wang
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Xuya Wang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, New York
| | - Emily Kawaler
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, New York
| | - D R Mani
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Karl R Clauser
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Feng Gao
- Division of Public Health Science, Siteman Cancer Center Biostatistics Core, Washington University School of Medicine, St. Louis, Missouri
| | - Jingqin Luo
- Division of Public Health Science, Siteman Cancer Center Biostatistics Core, Washington University School of Medicine, St. Louis, Missouri
| | - Sherri R Davies
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Gary L Johnson
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Kuan-Lin Huang
- Department of Medicine, McDonnell Genome Institute, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Christopher J Yoon
- Department of Medicine, McDonnell Genome Institute, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Li Ding
- Department of Medicine, McDonnell Genome Institute, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, New York
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Dan L. Duncan Comprehensive Cancer Center and Departments of Medicine and Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - R Reid Townsend
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Jason M Held
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
| | - Cynthia X Ma
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri.
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17
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Mooradian AD, Held JM, Naegle KM. Using ProteomeScout: A Resource of Post‐Translational Modifications, Their Experiments, and the Proteins That They Annotate. ACTA ACUST UNITED AC 2018; 59:13.32.1-13.32.27. [DOI: 10.1002/cpbi.31] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Arshag D. Mooradian
- Department of Medicine, Division of Hematology and Oncology, Washington University School of Medicine in St. Louis St. Louis Missouri
| | - Jason M. Held
- Department of Medicine, Division of Hematology and Oncology, Washington University School of Medicine in St. Louis St. Louis Missouri
- Department of Anesthesiology, Washington University School of Medicine in St. Louis St. Louis Missouri
| | - Kristen M. Naegle
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis St. Louis Missouri
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18
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Collins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras AC, Held JM, Hirayama-Kurogi M, Hou G, Krisp C, Larsen B, Lin L, Liu S, Molloy MP, Moritz RL, Ohtsuki S, Schlapbach R, Selevsek N, Thomas SN, Tzeng SC, Zhang H, Aebersold R. Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. Nat Commun 2017; 8:291. [PMID: 28827567 PMCID: PMC5566333 DOI: 10.1038/s41467-017-00249-5] [Citation(s) in RCA: 338] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/12/2017] [Indexed: 01/15/2023] Open
Abstract
Quantitative proteomics employing mass spectrometry is an indispensable tool in life science research. Targeted proteomics has emerged as a powerful approach for reproducible quantification but is limited in the number of proteins quantified. SWATH-mass spectrometry consists of data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics (accuracy, sensitivity, and selectivity) of targeted proteomics at large scale. While previous SWATH-mass spectrometry studies have shown high intra-lab reproducibility, this has not been evaluated between labs. In this multi-laboratory evaluation study including 11 sites worldwide, we demonstrate that using SWATH-mass spectrometry data acquisition we can consistently detect and reproducibly quantify >4000 proteins from HEK293 cells. Using synthetic peptide dilution series, we show that the sensitivity, dynamic range and reproducibility established with SWATH-mass spectrometry are uniformly achieved. This study demonstrates that the acquisition of reproducible quantitative proteomics data by multiple labs is achievable, and broadly serves to increase confidence in SWATH-mass spectrometry data acquisition as a reproducible method for large-scale protein quantification.SWATH-mass spectrometry consists of a data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics on the scale of thousands of proteins. Here, using data generated by eleven groups worldwide, the authors show that SWATH-MS is capable of generating highly reproducible data across different laboratories.
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Affiliation(s)
- Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Birgit Schilling
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA
| | - George Rosenberger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland
- PhD. Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, 8057, Switzerland
| | - Samuel L Bader
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Daniel W Chan
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Bradford W Gibson
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94143, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, M5G 1X5, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Ontario, Canada
| | - Jason M Held
- Departments of Medicine and Anesthesiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - Mio Hirayama-Kurogi
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Guixue Hou
- Proteomics Division, BGI-Shenzhen, Shenzhen, 518083, China
| | - Christoph Krisp
- Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, 2109, Australia
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, M5G 1X5, Ontario, Canada
| | - Liang Lin
- Proteomics Division, BGI-Shenzhen, Shenzhen, 518083, China
| | - Siqi Liu
- Proteomics Division, BGI-Shenzhen, Shenzhen, 518083, China
| | - Mark P Molloy
- Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, 2109, Australia
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
| | - Nathalie Selevsek
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
| | - Stefani N Thomas
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Shin-Cheng Tzeng
- Departments of Medicine and Anesthesiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - Hui Zhang
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland.
- Faculty of Science, University of Zurich, Zurich, Switzerland.
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19
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Wang X, Mooradian AD, Erdmann-Gilmore P, Zhang Q, Viner R, Davies SR, Huang KL, Bomgarden R, Van Tine BA, Shao J, Ding L, Li S, Ellis MJ, Rogers JC, Townsend RR, Fenyö D, Held JM. Breast tumors educate the proteome of stromal tissue in an individualized but coordinated manner. Sci Signal 2017; 10:10/491/eaam8065. [PMID: 28790197 DOI: 10.1126/scisignal.aam8065] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cancer forms specialized microenvironmental niches that promote local invasion and colonization. Engrafted patient-derived xenografts (PDXs) locally invade and colonize naïve stroma in mice while enabling unambiguous molecular discrimination of human proteins in the tumor from mouse proteins in the microenvironment. To characterize how patient breast tumors form a niche and educate naïve stroma, subcutaneous breast cancer PDXs were globally profiled by species-specific quantitative proteomics. Regulation of PDX stromal proteins by breast tumors was extensive, with 35% of the stromal proteome altered by tumors consistently across different animals and passages. Differentially regulated proteins in the stroma clustered into six signatures, which included both known and previously unappreciated contributors to tumor invasion and colonization. Stromal proteomes were coordinately regulated; however, the sets of proteins altered by each tumor were highly distinct. Integrated analysis of tumor and stromal proteins, a comparison made possible in these xenograft models, indicated that the known hallmarks of cancer contribute pleiotropically to establishing and maintaining the microenvironmental niche of the tumor. Education of the stroma by the tumor is therefore an intrinsic property of breast tumors that is highly individualized, yet proceeds by consistent, nonrandom, and defined tumor-promoting molecular alterations.
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Affiliation(s)
- Xuya Wang
- Institute for Systems Genetics, New York University School of Medicine, New York, NY 10016, USA.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Arshag D Mooradian
- Department of Medicine, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA
| | - Petra Erdmann-Gilmore
- Department of Medicine, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA
| | - Qiang Zhang
- Department of Medicine, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | - Sherri R Davies
- Department of Medicine, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA
| | - Kuan-Lin Huang
- Department of Medicine, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA
| | | | - Brian A Van Tine
- Department of Medicine, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA.,Siteman Cancer Center, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA
| | - Jieya Shao
- Department of Medicine, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA.,Siteman Cancer Center, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA
| | - Li Ding
- Department of Medicine, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA.,Siteman Cancer Center, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA.,McDonnell Genome Institute, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA
| | - Shunqiang Li
- Department of Medicine, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA.,Siteman Cancer Center, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Department of Oncology, and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - R Reid Townsend
- Department of Medicine, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA.,Siteman Cancer Center, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA
| | - David Fenyö
- Institute for Systems Genetics, New York University School of Medicine, New York, NY 10016, USA. .,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Jason M Held
- Department of Medicine, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA. .,Siteman Cancer Center, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA.,Department of Anesthesiology, Washington University in Saint Louis Medical School, St. Louis, MO 63110, USA
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20
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Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Fenyö D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Townsend RR, Chen X, Carr SA, Ellis MJ, Ding L. Corrigendum: Proteogenomic integration reveals therapeutic targets in breast cancer xenografts. Nat Commun 2017; 8:15479. [PMID: 28440318 PMCID: PMC5414030 DOI: 10.1038/ncomms15479] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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21
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Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Fenyö D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Reid Townsend R, Chen X, Carr SA, Ellis MJ, Ding L. Proteogenomic integration reveals therapeutic targets in breast cancer xenografts. Nat Commun 2017; 8:14864. [PMID: 28348404 PMCID: PMC5379071 DOI: 10.1038/ncomms14864] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/06/2017] [Indexed: 01/08/2023] Open
Abstract
Recent advances in mass spectrometry (MS) have enabled extensive analysis of cancer proteomes. Here, we employed quantitative proteomics to profile protein expression across 24 breast cancer patient-derived xenograft (PDX) models. Integrated proteogenomic analysis shows positive correlation between expression measurements from transcriptomic and proteomic analyses; further, gene expression-based intrinsic subtypes are largely re-capitulated using non-stromal protein markers. Proteogenomic analysis also validates a number of predicted genomic targets in multiple receptor tyrosine kinases. However, several protein/phosphoprotein events such as overexpression of AKT proteins and ARAF, BRAF, HSP90AB1 phosphosites are not readily explainable by genomic analysis, suggesting that druggable translational and/or post-translational regulatory events may be uniquely diagnosed by MS. Drug treatment experiments targeting HER2 and components of the PI3K pathway supported proteogenomic response predictions in seven xenograft models. Our study demonstrates that MS-based proteomics can identify therapeutic targets and highlights the potential of PDX drug response evaluation to annotate MS-based pathway activities. Patient-derived xenografts recapitulate major genomic signatures and transcriptome profiles of their original tumours. Here, the authors, performing proteomic and phosphoproteomic analyses of 24 breast cancer PDX models, demonstrate that druggable candidates can be identified based on a comprehensive proteogenomic profiling.
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Affiliation(s)
- Kuan-Lin Huang
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Shunqiang Li
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Philipp Mertins
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Song Cao
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Harsha P Gunawardena
- Department of Biochemistry &Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Kelly V Ruggles
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York 10016, USA
| | - D R Mani
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Karl R Clauser
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Maki Tanioka
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Jerry Usary
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Shyam M Kavuri
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ling Xie
- Department of Biochemistry &Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Christopher Yoon
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Jana W Qiao
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - John Wrobel
- Department of Biochemistry &Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Matthew A Wyczalkowski
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Petra Erdmann-Gilmore
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Jacqueline E Snider
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Jeremy Hoog
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Purba Singh
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Beifung Niu
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Zhanfang Guo
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Sam Qiancheng Sun
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Souzan Sanati
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Emily Kawaler
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York 10016, USA
| | - Xuya Wang
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York 10016, USA
| | - Adam Scott
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Kai Ye
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Department of Genetics, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Michael D McLellan
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Michael C Wendl
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Department of Genetics, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Department of Mathematics, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Anna Malovannaya
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jason M Held
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Michael A Gillette
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - David Fenyö
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York 10016, USA
| | | | - Mehdi Mesri
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Henry Rodriguez
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sherri R Davies
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Cynthia Ma
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - R Reid Townsend
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri 63108, USA
| | - Xian Chen
- Department of Biochemistry &Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Department of Genetics, Washington University in St. Louis, St. Louis, Missouri 63108, USA.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri 63108, USA
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22
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Wang X, Erdmann-Gilmore P, Viner R, Meyer M, Stuhlmiller T, Davies S, Li S, Zhang Q, Mooradian A, Huang KL, Bomgarden R, Ding L, Ellis M, Rogers J, Johnson G, Townsend R, Fenyo D, Held JM. Abstract LB-267: The proteomic landscape of patient-derived breast cancer xenografts reveals tumor-specific differences in the breast tumor microenvironment. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-lb-267] [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
Crosstalk between the tumor and surrounding microenvironment has emerged as an important regulator of tumor growth, metastasis and drug response. Patient-derived breast xenografts (PDXs) closely mimic the tumor microenvironment including the tumor architecture and interactions among cancer cells and stromal cells. PDXs provide a unique opportunity to study tumor-stroma interactions and the regulation of protein expression in the tumor microenvironment since species-specific amino acid sequences of the tumor (human) can be distinguished from the stroma (mouse) by LC-MS. However, quantitative proteomics workflows usually do not report species-specific peptides. We therefore developed a proteomics workflow based on 10-plex isobaric tagging to quantitatively profile the protein expression of PDXs and their associated microenvironment. Three biological replicates of seven breast cancer PDXs, representing three breast cancer subtypes, were profiled. Selecting only gene- and species-specific peptides for quantification of protein expression, we identified 8,113 human proteins (4,867 genes) and 2,251 mouse proteins (1,763 genes). Surprisingly, hierarchical clustering by mouse protein expression tightly clustered 4 of the 7 PDXs, with each of the 3 biological replicates next to one another. Notably, the 4 tightly clustered PDXs were from tumors with claudin-low, Her2-E and luminal B subtypes, whereas the biological replicates of three basal subtypes in the dataset were not tightly clustered. Gene set enrichment analysis of the stromal protein expression revealed upregulation of MTORC1 signaling, EMT, and interferon gamma response signaling with false discovery rates below 5%. We further investigated expression of signaling proteins in the tumor microenvironment by enriching active kinases with multiplexed kinase inhibitor beads. 152 mouse kinases were identified in the tumor microenvironment many tumor-specific differences in kinase levels. Taken together, our results imply that individual patient-derived breast tumors can actively and consistently orchestrate unique alterations in the proteins expressed in their microenvironment. Furthermore, we demonstrate the utility of our proteomic analysis workflow to delineate tumor-stroma signaling networks in PDXs.
Citation Format: Xuya Wang, Petra Erdmann-Gilmore, Rosa Viner, Matthew Meyer, Tim Stuhlmiller, Sherri Davies, Shunqiang Li, Qiang Zhang, Arshag Mooradian, Kuan-lin Huang, Ryan Bomgarden, Li Ding, Matthew Ellis, John Rogers, Gary Johnson, Reid Townsend, David Fenyo, Jason M. Held. The proteomic landscape of patient-derived breast cancer xenografts reveals tumor-specific differences in the breast tumor microenvironment. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-267.
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Affiliation(s)
| | | | | | - Matthew Meyer
- 2Washington University in Saint Louis Medical School, Saint Louis, MO
| | | | - Sherri Davies
- 2Washington University in Saint Louis Medical School, Saint Louis, MO
| | - Shunqiang Li
- 2Washington University in Saint Louis Medical School, Saint Louis, MO
| | - Qiang Zhang
- 2Washington University in Saint Louis Medical School, Saint Louis, MO
| | - Arshag Mooradian
- 2Washington University in Saint Louis Medical School, Saint Louis, MO
| | - Kuan-lin Huang
- 2Washington University in Saint Louis Medical School, Saint Louis, MO
| | | | - Li Ding
- 2Washington University in Saint Louis Medical School, Saint Louis, MO
| | | | | | | | - Reid Townsend
- 2Washington University in Saint Louis Medical School, Saint Louis, MO
| | | | - Jason M. Held
- 2Washington University in Saint Louis Medical School, Saint Louis, MO
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Reis Rodrigues P, Kaul TK, Ho JH, Lucanic M, Burkewitz K, Mair WB, Held JM, Bohn LM, Gill MS. Synthetic Ligands of Cannabinoid Receptors Affect Dauer Formation in the Nematode Caenorhabditis elegans. G3 (Bethesda) 2016; 6:1695-705. [PMID: 27172180 PMCID: PMC4889665 DOI: 10.1534/g3.116.026997] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/04/2016] [Indexed: 01/20/2023]
Abstract
Under adverse environmental conditions the nematode Caenorhabditis elegans can enter an alternate developmental stage called the dauer larva. To identify lipophilic signaling molecules that influence this process, we screened a library of bioactive lipids and found that AM251, an antagonist of the human cannabinoid (CB) receptor, suppresses dauer entry in daf-2 insulin receptor mutants. AM251 acted synergistically with glucose supplementation indicating that the metabolic status of the animal influenced the activity of this compound. Similarly, loss of function mutations in the energy-sensing AMP-activated kinase subunit, aak-2, enhanced the dauer-suppressing effects of AM251, while constitutive activation of aak-2 in neurons was sufficient to inhibit AM251 activity. Chemical epistasis experiments indicated that AM251 acts via G-protein signaling and requires the TGF-β ligand DAF-7, the insulin peptides DAF-28 and INS-6, and a functional ASI neuron to promote reproductive growth. AM251 also required the presence of the SER-5 serotonin receptor, but in vitro experiments suggest that this may not be via a direct interaction. Interestingly, we found that other antagonists of mammalian CB receptors also suppress dauer entry, while the nonselective CB receptor agonist, O-2545, not only inhibited the activity of AM251, but also was able to promote dauer entry when administered alone. Since worms do not have obvious orthologs of CB receptors, the effects of synthetic CBs on neuroendocrine signaling in C. elegans are likely to be mediated via another, as yet unknown, receptor mechanism. However, we cannot exclude the existence of a noncanonical CB receptor in C. elegans.
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Affiliation(s)
- Pedro Reis Rodrigues
- Department of Metabolism and Aging, The Scripps Research Institute, Jupiter, Florida 33458
| | - Tiffany K Kaul
- Department of Metabolism and Aging, The Scripps Research Institute, Jupiter, Florida 33458
| | - Jo-Hao Ho
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458
| | - Mark Lucanic
- The Buck Institute for Research on Aging, Novato, California 94945
| | - Kristopher Burkewitz
- Department of Genetics and Complex Diseases, School of Public Health, Harvard University, Boston, Massachusetts 02115
| | - William B Mair
- Department of Genetics and Complex Diseases, School of Public Health, Harvard University, Boston, Massachusetts 02115
| | - Jason M Held
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri 63110 Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Laura M Bohn
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458
| | - Matthew S Gill
- Department of Metabolism and Aging, The Scripps Research Institute, Jupiter, Florida 33458
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Schilling B, MacLean B, Held JM, Sahu AK, Rardin MJ, Sorensen DJ, Peters T, Wolfe AJ, Hunter CL, MacCoss MJ, Gibson BW. Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflows. Anal Chem 2015; 87:10222-9. [PMID: 26398777 DOI: 10.1021/acs.analchem.5b02983] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent advances in commercial mass spectrometers with higher resolving power and faster scanning capabilities have expanded their functionality beyond traditional data-dependent acquisition (DDA) to targeted proteomics with higher precision and multiplexing. Using an orthogonal quadrupole time-of flight (QqTOF) LC-MS system, we investigated the feasibility of implementing large-scale targeted quantitative assays using scheduled, high resolution multiple reaction monitoring (sMRM-HR), also referred to as parallel reaction monitoring (sPRM). We assessed the selectivity and reproducibility of PRM, also referred to as parallel reaction monitoring, by measuring standard peptide concentration curves and system suitability assays. By evaluating up to 500 peptides in a single assay, the robustness and accuracy of PRM assays were compared to traditional SRM workflows on triple quadrupole instruments. The high resolution and high mass accuracy of the full scan MS/MS spectra resulted in sufficient selectivity to monitor 6-10 MS/MS fragment ions per target precursor, providing flexibility in postacquisition assay refinement and optimization. The general applicability of the sPRM workflow was assessed in complex biological samples by first targeting 532 peptide precursor ions in a yeast lysate, and then 466 peptide precursors from a previously generated candidate list of differentially expressed proteins in whole cell lysates from E. coli. Lastly, we found that sPRM assays could be rapidly and efficiently developed in Skyline from DDA libraries when acquired on the same QqTOF platform, greatly facilitating their successful implementation. These results establish a robust sPRM workflow on a QqTOF platform to rapidly transition from discovery analysis to highly multiplexed, targeted peptide quantitation.
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Affiliation(s)
- Birgit Schilling
- Buck Institute for Research on Aging , 8001 Redwood Boulevard, Novato, California 94945, United States
| | - Brendan MacLean
- Department of Genome Sciences, University of Washington School of Medicine , Foege Building S113, 3720 15th Avenue NE, Seattle, Washington 98195, United States
| | - Jason M Held
- Departments of Medicine and Anesthesiology, Washington University School of Medicine , 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Alexandria K Sahu
- Buck Institute for Research on Aging , 8001 Redwood Boulevard, Novato, California 94945, United States
| | - Matthew J Rardin
- Buck Institute for Research on Aging , 8001 Redwood Boulevard, Novato, California 94945, United States
| | - Dylan J Sorensen
- Buck Institute for Research on Aging , 8001 Redwood Boulevard, Novato, California 94945, United States
| | - Theodore Peters
- Buck Institute for Research on Aging , 8001 Redwood Boulevard, Novato, California 94945, United States
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago , 2160 South First Avenue, Maywood, Illinois 60153, United States
| | - Christie L Hunter
- SCIEX, 1201 Radio Road, Redwood City, California 94065, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington School of Medicine , Foege Building S113, 3720 15th Avenue NE, Seattle, Washington 98195, United States
| | - Bradford W Gibson
- Buck Institute for Research on Aging , 8001 Redwood Boulevard, Novato, California 94945, United States.,Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94143, United States
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Wilson-Edell KA, Kehasse A, Scott GK, Yau C, Rothschild DE, Schilling B, Gabriel BS, Yevtushenko MA, Hanson IM, Held JM, Gibson BW, Benz CC. RPL24: a potential therapeutic target whose depletion or acetylation inhibits polysome assembly and cancer cell growth. Oncotarget 2015; 5:5165-76. [PMID: 24970821 PMCID: PMC4148130 DOI: 10.18632/oncotarget.2099] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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: 12/12/2022] Open
Abstract
Partial loss of large ribosomal subunit protein 24 (RPL24) function is known to protect mice against Akt or Myc-driven cancers, in part via translational inhibition of a subset of cap(eIF4E)-dependently translated mRNAs. The role of RPL24 in human malignancies is unknown. By analyzing a public dataset of matched human breast cancers and normal mammary tissue, we found that breast cancers express significantly more RPL24 than matched normal breast samples. Depletion of RPL24 in breast cancer cells by >70% reduced cell viability by 80% and decreased protein expression of the eIF4E-dependently translated proteins cyclin D1 (75%), survivin (46%) and NBS1 (30%) without altering GAPDH or beta-tubulin levels. RPL24 knockdown also reduced 80S subunit levels relative to 40S and 60S levels. These effects on expression of eIF4E-dependent proteins and ribosome assembly were mimicked by 2-24 h treatment with the pan-HDACi, trichostatin A (TSA), which induced acetylation of 15 different polysome-associated proteins including RPL24. Furthermore, HDAC6-selective inhibition or HDAC6 knockdown induced ribosomal protein acetylation. Via mass spectrometry, we found that 60S-associated, but not, polysome-associated, RPL24 undergoes HDACi-induced acetylation on K27. Thus, RPL24 K27 acetylation may play a role in ribosome assembly. These findings point toward a novel acetylation-dependent polysome assembly mechanism regulating tumorigenesis.
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Affiliation(s)
| | | | - Gary K Scott
- Buck Institute for Research on Aging; Novato, CA, USA
| | - Christina Yau
- Buck Institute for Research on Aging; Novato, CA, USA
| | | | | | - Bianca S Gabriel
- Buck Institute for Research on Aging; Novato, CA, USA. Master of Science in Biology Program; Dominican University; San Rafael, CA, USA
| | - Mariya A Yevtushenko
- Buck Institute for Research on Aging; Novato, CA, USA. Master of Science in Biology Program; Dominican University; San Rafael, CA, USA
| | | | - Jason M Held
- Buck Institute for Research on Aging; Novato, CA, USA
| | - Bradford W Gibson
- Buck Institute for Research on Aging; Novato, CA, USA. Department of Pharmaceutical Chemistry, University of California, San Francisco, CA USA
| | - Christopher C Benz
- Buck Institute for Research on Aging; Novato, CA, USA. Oncology-Hematology Division, Department of Medicine, University of California, San Francisco, CA USA
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Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA. Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma. Mol Cell Proteomics 2015; 14:2357-74. [PMID: 25693799 DOI: 10.1074/mcp.m114.047050] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Indexed: 11/06/2022] Open
Abstract
There is an increasing need in biology and clinical medicine to robustly and reliably measure tens to hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility, and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here, we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and seven control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data, we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to subnanogram/ml sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intra- and interlaboratory reproducibility was <20%, sufficient for most biological studies and candidate protein biomarker verification. Digestion recovery of peptides was assessed and quantitative accuracy improved using heavy-isotope-labeled versions of the proteins as internal standards. Using the highly multiplexed assay, participating laboratories were able to precisely and reproducibly determine the levels of a series of analytes in blinded samples used to simulate an interlaboratory clinical study of patient samples. Our study further establishes that LC-MRM-MS using stable isotope dilution, with appropriate attention to analytical validation and appropriate quality control measures, enables sensitive, specific, reproducible, and quantitative measurements of proteins and peptides in complex biological matrices such as plasma.
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Affiliation(s)
- Susan E Abbatiello
- From the Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | | | - D R Mani
- From the Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Lisa J Zimmerman
- Department of Biochemistry, Vanderbilt University School of Medicine, and the Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232
| | - Steven C Hall
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California 94143
| | - Brendan MacLean
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Matthew Albertolle
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California 94143
| | - Simon Allen
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California 94143
| | - Michael Burgess
- From the Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | | | - Mousumi Gosh
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065
| | | | - Jason M Held
- Buck Institute for Research on Aging, Novato, California 94945
| | | | - Angela Jackson
- University of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia V8Z 7X8 CAN
| | - Hasmik Keshishian
- From the Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | | | - John Lyssand
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016
| | - Lee Makowski
- Argonne National Laboratory (currently at Northeastern University, Boston Massachusetts 02115
| | - Mehdi Mesri
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Henry Rodriguez
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Paul Rudnick
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| | - Pawel Sadowski
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016
| | - Nell Sedransk
- National Institute of Statistical Sciences, Research Triangle Park, North Carolina 27709
| | - Kent Shaddox
- Department of Biochemistry, Vanderbilt University School of Medicine, and the Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232
| | - Stephen J Skates
- Biostatistics Center, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Eric Kuhn
- From the Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Derek Smith
- University of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia V8Z 7X8 CAN
| | | | - Corbin Whitwell
- Department of Biochemistry, Vanderbilt University School of Medicine, and the Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232
| | - Shucha Zhang
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Christoph H Borchers
- University of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia V8Z 7X8 CAN
| | - Susan J Fisher
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California 94143
| | | | - Daniel C Liebler
- Department of Biochemistry, Vanderbilt University School of Medicine, and the Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016
| | | | | | - Paul Tempst
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065
| | - Steven A Carr
- From the Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
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Post DMB, Held JM, Ketterer MR, Phillips NJ, Sahu A, Apicella MA, Gibson BW. Comparative analyses of proteins from Haemophilus influenzae biofilm and planktonic populations using metabolic labeling and mass spectrometry. BMC Microbiol 2014; 14:329. [PMID: 25551439 PMCID: PMC4302520 DOI: 10.1186/s12866-014-0329-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [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: 09/15/2014] [Accepted: 12/16/2014] [Indexed: 11/25/2022] Open
Abstract
Background Non-typeable H. influenzae (NTHi) is a nasopharyngeal commensal that can become an opportunistic pathogen causing infections such as otitis media, pneumonia, and bronchitis. NTHi is known to form biofilms. Resistance of bacterial biofilms to clearance by host defense mechanisms and antibiotic treatments is well-established. In the current study, we used stable isotope labeling by amino acids in cell culture (SILAC) to compare the proteomic profiles of NTHi biofilm and planktonic organisms. Duplicate continuous-flow growth chambers containing defined media with either “light” (L) isoleucine or “heavy” (H) 13C6-labeled isoleucine were used to grow planktonic (L) and biofilm (H) samples, respectively. Bacteria were removed from the chambers, mixed based on weight, and protein extracts were generated. Liquid chromatography-mass spectrometry (LC-MS) was performed on the tryptic peptides and 814 unique proteins were identified with 99% confidence. Results Comparisons of the NTHi biofilm to planktonic samples demonstrated that 127 proteins showed differential expression with p-values ≤0.05. Pathway analysis demonstrated that proteins involved in energy metabolism, protein synthesis, and purine, pyrimidine, nucleoside, and nucleotide processes showed a general trend of downregulation in the biofilm compared to planktonic organisms. Conversely, proteins involved in transcription, DNA metabolism, and fatty acid and phospholipid metabolism showed a general trend of upregulation under biofilm conditions. Selected reaction monitoring (SRM)-MS was used to validate a subset of these proteins; among these were aerobic respiration control protein ArcA, NAD nucleotidase and heme-binding protein A. Conclusions The present proteomic study indicates that the NTHi biofilm exists in a semi-dormant state with decreased energy metabolism and protein synthesis yet is still capable of managing oxidative stress and in acquiring necessary cofactors important for biofilm survival. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0329-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deborah M B Post
- The Buck Institute for Research on Aging, Novato, CA, 94945, USA.
| | - Jason M Held
- Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | | | - Nancy J Phillips
- The University of California San Francisco, San Francisco, CA, 94143, USA.
| | - Alexandria Sahu
- The Buck Institute for Research on Aging, Novato, CA, 94945, USA.
| | | | - Bradford W Gibson
- The Buck Institute for Research on Aging, Novato, CA, 94945, USA. .,The University of California San Francisco, San Francisco, CA, 94143, USA.
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Zawadzka AM, Schilling B, Held JM, Sahu AK, Cusack MP, Drake PM, Fisher SJ, Gibson BW. Variation and quantification among a target set of phosphopeptides in human plasma by multiple reaction monitoring and SWATH-MS2 data-independent acquisition. Electrophoresis 2014; 35:3487-97. [PMID: 24853916 PMCID: PMC4565165 DOI: 10.1002/elps.201400167] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 04/26/2014] [Accepted: 05/13/2014] [Indexed: 11/07/2022]
Abstract
Human plasma contains proteins that reflect overall health and represents a rich source of proteins for identifying and understanding disease pathophysiology. However, few studies have investigated changes in plasma phosphoproteins. In addition, little is known about the normal variations in these phosphoproteins, especially with respect to specific sites of modification. To address these questions, we evaluated variability in plasma protein phosphorylation in healthy individuals using multiple reaction monitoring (MRM) and SWATH-MS2 data-independent acquisition. First, we developed a discovery workflow for phosphopeptide enrichment from plasma and identified targets for MRM assays. Next, we analyzed plasma from healthy donors using an analytical workflow consisting of MRM and SWATH-MS2 that targeted phosphopeptides from 58 and 68 phosphoproteins, respectively. These two methods produced similar results showing low variability in 13 phosphosites from 10 phosphoproteins (CVinter < 30%) and high interpersonal variation of 16 phosphosites from 14 phosphoproteins (CVinter > 30%). Moreover, these phosphopeptides originate from phosphoproteins involved in cellular processes governing homeostasis, immune response, cell-extracellular matrix interactions, lipid and sugar metabolism, and cell signaling. This limited assessment of technical and biological variability in phosphopeptides generated from plasma phosphoproteins among healthy volunteers constitutes a reference for future studies that target protein phosphorylation as biomarkers.
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Affiliation(s)
- Anna M. Zawadzka
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945
| | - Birgit Schilling
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945
| | - Jason M. Held
- Division of Oncology and Department of Anesthesiology, Washington University School of Medicine, Campus Box 8069, 660 S. Euclid Avenue, St. Louis, MO 63110
| | - Alexandria K. Sahu
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945
| | - Michael P. Cusack
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945
| | - Penelope M. Drake
- Department of Obstetrics, Gynecology and Reproductive Sciences, 513 Parnassus Ave., Box 0556, University of California San Francisco, San Francisco, CA 94143
| | - Susan J. Fisher
- Department of Obstetrics, Gynecology and Reproductive Sciences, 513 Parnassus Ave., Box 0556, University of California San Francisco, San Francisco, CA 94143
| | - Bradford W. Gibson
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945
- Department of Pharmaceutical Chemistry, 513 Parnassus Ave., Box 0556, University of California San Francisco, San Francisco, CA 94143
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Wilson-Edell KA, Kehasse A, Yau C, Scott GK, Held JM, Gabriel BS, Gibson BW, Benz CC. Abstract 4224: Histone deacetylase inhibitors induce ribosomal protein acetylation and modulate breast cancer cell viability. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-4224] [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
Dysregulation of protein synthesis is crucial for tumorigenesis. The PI3K/AKT/mTOR pathway regulates ribosomes and mRNA translation. Inhibition of this pathway is an important approach under clinical evaluation for the treatment of malignancies including breast cancer. However, many are resistant to PI3K/AKT/mTOR inhibitors, necessitating alternative inhibitors of oncoprotein synthesis. Our studies in breast cancer cells implicate histone deacetylase inhibition (HDACi) in the impairment of ribosome function and oncoprotein synthesis. In particular, pan-HDAC inhibitors like Trichostatin A (TSA) induce decay of specific oncogenic transcripts (e.g. HER2) within 6 h of treatment via a polyribosome-dependent mechanism. Furthermore, we found that TSA induces the acetylation of the large ribosomal subunit protein L24. TSA also decreased 80S ribosome formation and selectively reduced the expression of the cap-dependently translated oncoproteins NBS1, cyclin D1, and survivin without inhibition of β-tubulin and GAPDH.
To elucidate the link between ribosomes and HDACi, we used tandem mass spectrometry to interrogate global acetylation changes within ribosomal proteins following treatment of HER2-positive SKBR3 breast cancer cells by either TSA or the HDAC6-selective inhibitor tubacin. Control and treated SKBR3 ribosomal proteins were immunoprecipitated by an anti-acetyl-lysine antibody and subsequently digested by trypsin. The resulting acetyl-lysine peptides were analyzed by LC-MS/MS (AB SCIEX TripleTOF 5600) and identified from Mascot and ProteinPilot databases. Peptides were quantitated by Skyline MS1 Filtering. We identified three ribosomal proteins (RPL24, RPL37A, RPL7A) with acetylation induced at least two-fold by 2 h of TSA treatment and 12 others whose acetylation was induced two-fold or greater by 6 h of TSA treatment (RPL19, RPL22, RPL27, RPL28, RPL3, RPL35A, RPL3L, RPL6, RPS13, RPS17L, RPS23, RPS27A). The profile of ribosomal proteins acetylated by treatment with the HDAC6 selective inhibitor tubacin was significantly different.
To further evaluate the cancer-association of these ribosomal proteins with pan-HDACi-induced acetylation, we analyzed a publically available microarray dataset including mRNA from breast cancers and normal mammary tissue from the same patient. Of the ribosomal protein genes with HDACi-inducible acetylation, we found 6 whose mRNA expression levels were significantly higher in breast cancers relative to matched normal mammary tissue: RPL19 (p=0.001), RPL24 (p=0.001), RPL3 (p=0.001), RPL7a (p=0.002), RPS23 (p=0.004), and RPL22 (p=0.05). These findings point toward a novel role of HDACi in modulating the acetylation of ribosomal proteins, some of which are upregulated in breast cancer. This acetylation could result in altered ribosome function, decreased oncoprotein translation, and ultimately reduced breast cancer cell growth and survival.
Citation Format: Kathleen Ann Wilson-Edell, Amanuel Kehasse, Christina Yau, Gary K. Scott, Jason M. Held, Bianca S. Gabriel, Bradford W. Gibson, Christopher C. Benz. Histone deacetylase inhibitors induce ribosomal protein acetylation and modulate breast cancer cell viability. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4224. doi:10.1158/1538-7445.AM2014-4224
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Abbatiello SE, Mani DR, Schilling B, Maclean B, Zimmerman LJ, Feng X, Cusack MP, Sedransk N, Hall SC, Addona T, Allen S, Dodder NG, Ghosh M, Held JM, Hedrick V, Inerowicz HD, Jackson A, Keshishian H, Kim JW, Lyssand JS, Riley CP, Rudnick P, Sadowski P, Shaddox K, Smith D, Tomazela D, Wahlander A, Waldemarson S, Whitwell CA, You J, Zhang S, Kinsinger CR, Mesri M, Rodriguez H, Borchers CH, Buck C, Fisher SJ, Gibson BW, Liebler D, Maccoss M, Neubert TA, Paulovich A, Regnier F, Skates SJ, Tempst P, Wang M, Carr SA. Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS). Mol Cell Proteomics 2013; 12:2623-39. [PMID: 23689285 DOI: 10.1074/mcp.m112.027078] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Multiple reaction monitoring (MRM) mass spectrometry coupled with stable isotope dilution (SID) and liquid chromatography (LC) is increasingly used in biological and clinical studies for precise and reproducible quantification of peptides and proteins in complex sample matrices. Robust LC-SID-MRM-MS-based assays that can be replicated across laboratories and ultimately in clinical laboratory settings require standardized protocols to demonstrate that the analysis platforms are performing adequately. We developed a system suitability protocol (SSP), which employs a predigested mixture of six proteins, to facilitate performance evaluation of LC-SID-MRM-MS instrument platforms, configured with nanoflow-LC systems interfaced to triple quadrupole mass spectrometers. The SSP was designed for use with low multiplex analyses as well as high multiplex approaches when software-driven scheduling of data acquisition is required. Performance was assessed by monitoring of a range of chromatographic and mass spectrometric metrics including peak width, chromatographic resolution, peak capacity, and the variability in peak area and analyte retention time (RT) stability. The SSP, which was evaluated in 11 laboratories on a total of 15 different instruments, enabled early diagnoses of LC and MS anomalies that indicated suboptimal LC-MRM-MS performance. The observed range in variation of each of the metrics scrutinized serves to define the criteria for optimized LC-SID-MRM-MS platforms for routine use, with pass/fail criteria for system suitability performance measures defined as peak area coefficient of variation <0.15, peak width coefficient of variation <0.15, standard deviation of RT <0.15 min (9 s), and the RT drift <0.5min (30 s). The deleterious effect of a marginally performing LC-SID-MRM-MS system on the limit of quantification (LOQ) in targeted quantitative assays illustrates the use and need for a SSP to establish robust and reliable system performance. Use of a SSP helps to ensure that analyte quantification measurements can be replicated with good precision within and across multiple laboratories and should facilitate more widespread use of MRM-MS technology by the basic biomedical and clinical laboratory research communities.
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Affiliation(s)
- Susan E Abbatiello
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
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Wilson-Edell KA, Scott GK, Gabriel BS, Yevtushenko M, Held JM, Hanson IM, Benz CC. Abstract 5179: Manipulating the ribosomal protein RPL24 by depletion, truncation, or acetylation alters ribosome formation and inhibits cancer cell growth. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-5179] [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
Control of protein synthesis is critical for cell growth and oncogenic transformation. Inhibiting the PI3K/AKT/mTOR pathway upstream of ribosomes is one approach currently in clinical trials to treat various cancers, including breast cancer. However, many cancers are resistant to such therapies and may respond to translation inhibition via alternate mechanisms. Our previous studies identify a link between histone deacetylase inhibition (HDACi) and ribosomes, in that pan-HDAC inhibitors like Trichostatin A (TSA) induce the decay of HER2 and other oncogeneic transcripts via a polyribosome-dependent mechanism. In recent studies using HER2-overexpressing SKBR3 breast cancer cells, we also found that TSA inhibits phosphorylation of the ribosomal protein S6 and the translation initiation factor 4eBP1. Thus, we investigated the effect of TSA on polysome dynamics and post-translational modifications of ribosomal proteins to better understand how HDACi inhibits cancer cell proliferation and to identify novel cancer therapeutic targets.
We found that TSA reduces the amount of 80S ribosomes relative to free 40S and 60S subunits, implicating impaired ribosome assembly. Eukaryotic translation initiation factor 6 (eIF6) promotes the maturation of nucleolar 60S but must be released from cytoplasmic 60S in order for the 40S and 60S to join and form functional 80S ribosomes. Therefore, we asked if TSA impedes eIF6 release from the 60S and found that eIF6 remains 60S-associated in TSA relative to control treated SKBR3 cells. To determine how TSA affects ribosomal proteins, we performed immunoblotting and 2D-electrophoresis/mass spectrometry screening of ribosomal proteins and identified the large ribosomal subunit protein, RPL24, as acetylated after TSA treatment. Additional interest in this acetylation candidate was driven by two recent reports. One provides structural evidence that the lysine-containing C-terminus of RPL24 resides in proximity to eIF6 on the 60S and also contacts the 40S subunit. The other reports that mice haploinsufficient for RPL24 exhibit greater survival of AKT-driven tumorigenesis. Our analyses produced three additional observations: i) depletion of RPL24 in SKBR3 cells via shRNA, similar to TSA treatment, impairs 80S formation and increases the amount of eIF6 associated with ribosomal 60S; ii) a mutant form of RPL24 with truncated C terminus increases 60S retention of eIF6; and iii) depletion of RPL24, as well as TSA treatment, inhibits SKBR3 proliferation. In summary, altering polysome dynamics by impairing 80S formation and prolonging 60S retention of eIF6, by TSA and/or altered RPL24 function, inhibits cancer cell growth and proliferation. Furthermore, RPL24 acetylation may serve as a biomarker for therapeutic response to pan-HDAC inhibitors and as a drug target for the design of novel cancer therapeutics.
Citation Format: Kathleen A. Wilson-Edell, Gary K. Scott, Bianca S. Gabriel, Mariya Yevtushenko, Jason M. Held, Ingrid M. Hanson, Christopher C. Benz. Manipulating the ribosomal protein RPL24 by depletion, truncation, or acetylation alters ribosome formation and inhibits cancer cell growth. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5179. doi:10.1158/1538-7445.AM2013-5179
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Rardin MJ, Held JM, Gibson BW. Targeted quantitation of acetylated lysine peptides by selected reaction monitoring mass spectrometry. Methods Mol Biol 2013; 1077:121-31. [PMID: 24014403 PMCID: PMC4378680 DOI: 10.1007/978-1-62703-637-5_8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Mass spectrometry (MS) allows for the large-scale identification of multiple peptide analytes in complex mixtures. However, the low abundance of acetylated peptides in the overall mixture requires an enrichment step. After enrichment, the resulting acetylated peptides of interest can be quantitated using selected reaction monitoring (SRM)-MS with stable isotope dilution. Here, we describe the enrichment of lysine acetylated peptides from typsin digested mouse liver mitochondria, and the targeted quantitation of a known lysine acetylation site in succinate dehydrogenase A using SRM-MS on a triple quadrupole instrument.
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Held JM, Britton DJ, Scott GK, Lee EL, Schilling B, Baldwin MA, Gibson BW, Benz CC. Ligand binding promotes CDK-dependent phosphorylation of ER-alpha on hinge serine 294 but inhibits ligand-independent phosphorylation of serine 305. Mol Cancer Res 2012; 10:1120-32. [PMID: 22669764 DOI: 10.1158/1541-7786.mcr-12-0099] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Phosphorylation of estrogen receptor-α (ERα) is critical for its transcription factor activity and may determine its predictive and therapeutic value as a biomarker for ERα-positive breast cancers. Recent attention has turned to the poorly understood ERα hinge domain, as phosphorylation at serine 305 (Ser305) associates with poor clinical outcome and endocrine resistance. We show that phosphorylation of a neighboring hinge domain site, Ser294, analyzed by multiple reaction monitoring mass spectrometry of ERα immunoprecipitates from human breast cancer cells is robustly phosphorylated exclusively by ligand (estradiol and tamoxifen) activation of ERα and not by growth factor stimulation (EGF, insulin, heregulin-β). In a reciprocal fashion, Ser305 phosphorylation is induced by growth factors but not ligand activation of ERα. Phosphorylation at Ser294 and Ser305 is suppressed upon co-stimulation by EGF and ligand, respectively, unlike the N-terminal (AF-1) domain Ser118 and Ser167 sites of ERα where phosphorylation is enhanced by ligand and growth factor co-stimulation. Inhibition of cyclin-dependent kinases (CDK) by roscovitine or SNS-032 suppresses ligand-activated Ser294 phosphorylation without affecting Ser118 or Ser104/Ser106 phosphorylation. Likewise, cell-free studies using recombinant ERα and specific cyclin-CDK complexes suggest that Ser294 phosphorylation is primarily induced by the transcription-regulating and cell-cycle-independent kinase CDK7. Thus, CDK-dependent phosphorylation at Ser294 differentiates ligand-dependent from ligand-independent activation of Ser305 phosphorylation, showing that hinge domain phosphorylation patterns uniquely inform on the various ERα activation mechanisms thought to underlie the biologic and clinical diversity of hormone-dependent breast cancers.
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Affiliation(s)
- Jason M Held
- Buck Institute for Research on Aging, Novato, CA 94945, USA
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Zhang N, Li B, Al-Ramahi I, Cong X, Held JM, Kim E, Botas J, Gibson BW, Ellerby LM. Inhibition of lipid signaling enzyme diacylglycerol kinase epsilon attenuates mutant huntingtin toxicity. J Biol Chem 2012; 287:21204-13. [PMID: 22511757 DOI: 10.1074/jbc.m111.321661] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Huntington disease (HD) is a dominantly inherited neurodegenerative disease caused by a polyglutamine expansion in the protein huntingtin (Htt). Striatal and cortical neuronal loss are prominent features of this disease. No disease-modifying treatments have been discovered for HD. To identify new therapeutic targets in HD, we screened a kinase inhibitor library for molecules that block mutant Htt cellular toxicity in a mouse HD striatal cell model, Hdh(111Q/111Q) cells. We found that diacylglycerol kinase (DGK) inhibitor II (R59949) decreased caspase-3/7 activity after serum withdrawal in striatal Hdh(111Q/111Q) cells. In addition, R59949 decreased the accumulation of a 513-amino acid N-terminal Htt fragment processed by caspase-3 and blocked alterations in lipid metabolism during serum withdrawal. To identify the diacylglycerol kinase mediating this effect, we knocked down all four DGK isoforms expressed in the brain (β, γ, ε, and ζ) using siRNA. Only the knockdown of the family member, DGKε, blocked striatal Hdh(111Q/111Q)-mediated toxicity. We also investigated the significance of these findings in vivo. First, we found that reduced function of the Drosophila DGKε homolog significantly improves Htt-induced motor dysfunction in a fly model of HD. In addition, we find that the levels of DGKε are increased in the striatum of R6/2 HD transgenic mice when compared with littermate controls. Together, these findings indicate that increased levels of kinase DGKε contribute to HD pathogenesis and suggest that reducing its levels or activity is a potential therapy for HD.
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Affiliation(s)
- Ningzhe Zhang
- Buck Institute for Research on Aging, Novato, California 94945, USA
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Drake PM, Schilling B, Niles RK, Prakobphol A, Li B, Jung K, Cho W, Braten M, Inerowicz HD, Williams K, Albertolle M, Held JM, Iacovides D, Sorensen DJ, Griffith OL, Johansen E, Zawadzka AM, Cusack MP, Allen S, Gormley M, Hall SC, Witkowska HE, Gray JW, Regnier F, Gibson BW, Fisher SJ. Lectin chromatography/mass spectrometry discovery workflow identifies putative biomarkers of aggressive breast cancers. J Proteome Res 2012; 11:2508-20. [PMID: 22309216 DOI: 10.1021/pr201206w] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We used a lectin chromatography/MS-based approach to screen conditioned medium from a panel of luminal (less aggressive) and triple negative (more aggressive) breast cancer cell lines (n=5/subtype). The samples were fractionated using the lectins Aleuria aurantia (AAL) and Sambucus nigra agglutinin (SNA), which recognize fucose and sialic acid, respectively. The bound fractions were enzymatically N-deglycosylated and analyzed by LC-MS/MS. In total, we identified 533 glycoproteins, ∼90% of which were components of the cell surface or extracellular matrix. We observed 1011 glycosites, 100 of which were solely detected in ≥3 triple negative lines. Statistical analyses suggested that a number of these glycosites were triple negative-specific and thus potential biomarkers for this tumor subtype. An analysis of RNaseq data revealed that approximately half of the mRNAs encoding the protein scaffolds that carried potential biomarker glycosites were up-regulated in triple negative vs luminal cell lines, and that a number of genes encoding fucosyl- or sialyltransferases were differentially expressed between the two subtypes, suggesting that alterations in glycosylation may also drive candidate identification. Notably, the glycoproteins from which these putative biomarker candidates were derived are involved in cancer-related processes. Thus, they may represent novel therapeutic targets for this aggressive tumor subtype.
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Affiliation(s)
- Penelope M Drake
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, 513 Parnassus Avenue, Box 0665, San Francisco, California 94143, United States
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Held JM, Gibson BW. Regulatory control or oxidative damage? Proteomic approaches to interrogate the role of cysteine oxidation status in biological processes. Mol Cell Proteomics 2011; 11:R111.013037. [PMID: 22159599 DOI: 10.1074/mcp.r111.013037] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Oxidation is a double-edged sword for cellular processes and its role in normal physiology, cancer and aging remains only partially understood. Although oxidative stress may disrupt biological function, oxidation-reduction (redox) reactions in a cell are often tightly regulated and play essential physiological roles. Cysteines lie at the interface between these extremes since the chemical properties that make specific thiols exquisitely redox-sensitive also predispose them to oxidative damage by reactive oxygen or nitrogen species during stress. Thus, these modifications can be either under reversible redox regulatory control or, alternatively, a result of reversible or irreversible oxidative damage. In either case, it has become increasingly important to assess the redox status of protein thiols since these modifications often impact such processes as catalytic activity, conformational alterations, or metal binding. To better understand the redox changes that accompany protein cysteine residues in complex biological systems, new experimental approaches have been developed to identify and characterize specific thiol modifications and/or changes in their overall redox status. In this review, we describe the recent technologies in redox proteomics that have pushed the boundaries for detecting and quantifying redox cysteine modifications in a cellular context. While there is no one-size-fits-all analytical solution, we highlight the rationale, strengths, and limitations of each technology in order to effectively apply them to specific biological questions. Several technological limitations still remain unsolved, however these approaches and future developments play an important role toward understanding the interplay between oxidative stress and redox signaling in health and disease.
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Affiliation(s)
- Jason M Held
- Buck Institute for Research on Aging, Novato, CA 94945, USA
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Cong X, Held JM, DeGiacomo F, Bonner A, Chen JM, Schilling B, Czerwieniec GA, Gibson BW, Ellerby LM. Mass spectrometric identification of novel lysine acetylation sites in huntingtin. Mol Cell Proteomics 2011; 10:M111.009829. [PMID: 21685499 PMCID: PMC3205870 DOI: 10.1074/mcp.m111.009829] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [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] [Received: 03/22/2011] [Revised: 06/02/2011] [Indexed: 12/26/2022] Open
Abstract
Huntingtin (Htt) is a protein with a polyglutamine stretch in the N-terminus and expansion of the polyglutamine stretch causes Huntington's disease (HD). Htt is a multiple domain protein whose function has not been well characterized. Previous reports have shown, however, that post-translational modifications of Htt such as phosphorylation and acetylation modulate mutant Htt toxicity, localization, and vesicular trafficking. Lysine acetylation of Htt is of particular importance in HD as this modification regulates disease progression and toxicity. Treatment of mouse models with histone deacetylase inhibitors ameliorates HD-like symptoms and alterations in acetylation of Htt promotes clearance of the protein. Given the importance of acetylation in HD and other diseases, we focused on the systematic identification of lysine acetylation sites in Htt23Q (1-612) in a cell culture model using mass spectrometry. Myc-tagged Htt23Q (1-612) overexpressed in the HEK 293T cell line was immunoprecipitated, separated by SDS-PAGE, digested and subjected to high performance liquid chromatography tandem MS analysis. Five lysine acetylation sites were identified, including three novel sites Lys-178, Lys-236, Lys-345 and two previously described sites Lys-9 and Lys-444. Antibodies specific to three of the Htt acetylation sites were produced and confirmed the acetylation sites in Htt. A multiple reaction monitoring MS assay was developed to compare quantitatively the Lys-178 acetylation level between wild-type Htt23Q and mutant Htt148Q (1-612). This report represents the first comprehensive mapping of lysine acetylation sites in N-terminal region of Htt.
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Affiliation(s)
- Xin Cong
- From the ‡Buck Institute for Research on Aging, Novato, CA 94945
| | - Jason M. Held
- From the ‡Buck Institute for Research on Aging, Novato, CA 94945
| | | | - Akilah Bonner
- From the ‡Buck Institute for Research on Aging, Novato, CA 94945
| | - Jan Marie Chen
- From the ‡Buck Institute for Research on Aging, Novato, CA 94945
| | - Birgit Schilling
- From the ‡Buck Institute for Research on Aging, Novato, CA 94945
| | | | | | - Lisa M. Ellerby
- From the ‡Buck Institute for Research on Aging, Novato, CA 94945
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Lucanic M, Held JM, Vantipalli MC, Klang IM, Graham JB, Gibson BW, Lithgow GJ, Gill MS. N-acylethanolamine signalling mediates the effect of diet on lifespan in Caenorhabditis elegans. Nature 2011; 473:226-9. [PMID: 21562563 PMCID: PMC3093655 DOI: 10.1038/nature10007] [Citation(s) in RCA: 110] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 03/17/2011] [Indexed: 02/01/2023]
Abstract
Dietary restriction (DR) is a robust means of extending adult lifespan and postponing age-related disease in many species, including yeast, worms, flies and rodents1,2. Studies of the genetic requirements for lifespan extension by DR in the nematode Caenorhabditis elegans (C. elegans) have implicated a number of key players in this process3–5, including the nutrient-sensing target of rapamycin (TOR) pathway6 and the Foxa transcription factor PHA-47. However, little is known about the metabolic signals that coordinate the organismal response to DR and maintain homeostasis when nutrients are limited. The endocannabinoid (EC) system is an excellent candidate to play such a role given its involvement in regulating nutrient intake and energy balance8. Despite this, a direct role for EC signaling in DR or lifespan determination has yet to be demonstrated, in part due to the apparent absence of EC signaling pathways in model organisms that are amenable to lifespan analysis9. N-acylethanolamines (NAEs) are lipid-derived signaling molecules, which include the mammalian EC arachidonoyl ethanolamide (AEA). Here we identify NAEs in C. elegans, show that NAE abundance is reduced under DR and that NAE deficiency is sufficient to extend lifespan through a DR mechanism requiring PHA-4. Conversely, dietary supplementation with the nematode NAE eicosapentaenoyl ethanolamide (EPEA) not only inhibits DR-induced lifespan extension in wild type animals, but also suppresses lifespan extension in a TOR pathway mutant. This demonstrates a role for NAE signaling in aging and suggests that NAEs represent a signal that coordinates nutrient status with metabolic changes that ultimately determine lifespan.
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Affiliation(s)
- Mark Lucanic
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, California 94945, USA
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Danielson SR, Held JM, Oo M, Riley R, Gibson BW, Andersen JK. Quantitative mapping of reversible mitochondrial Complex I cysteine oxidation in a Parkinson disease mouse model. J Biol Chem 2011; 286:7601-8. [PMID: 21196577 DOI: 10.1074/jbc.m110.190108] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Differential cysteine oxidation within mitochondrial Complex I has been quantified in an in vivo oxidative stress model of Parkinson disease. We developed a strategy that incorporates rapid and efficient immunoaffinity purification of Complex I followed by differential alkylation and quantitative detection using sensitive mass spectrometry techniques. This method allowed us to quantify the reversible cysteine oxidation status of 34 distinct cysteine residues out of a total 130 present in murine Complex I. Six Complex I cysteine residues were found to display an increase in oxidation relative to controls in brains from mice undergoing in vivo glutathione depletion. Three of these residues were found to reside within iron-sulfur clusters of Complex I, suggesting that their redox state may affect electron transport function.
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Abstract
The overexpressed ErbB2/HER2 receptor is a clinically validated cancer target whose surface localization and internalization mechanisms remain poorly understood. Downregulation of the overexpressed 185-kDa ErbB2 receptor is rapidly (2-6 hours) induced by the HSP90 chaperone inhibitor geldanamycin (GA), whereas its downregulation and lysosomal degradation are more slowly (24 hours) induced by the proteasome inhibitor bortezomib/PS341. In PS341-treated SK-BR-3 cells, overexpressed ErbB2 coprecipitates with the E3 ubiquitin ligase c-Cbl and also with the deubiquitinating enzyme USP9x; moreover, siRNA downregulation of USP9x enhances PS341-induced ErbB2 downregulation. Because polyubiquitin linkages via lysine 48 (K48) or 63 (K63) can differentially address proteins for 26S proteasomal degradation or endosome trafficking to the lysosome, multiple reaction monitoring (MRM)/mass spectrometry (MS) and polyubiquitin linkage-specific antibodies were used to quantitatively track K48-linked and K63-linked ErbB2 polyubiquitination following either GA or PS341 treatment of SK-BR-3 cells. MRM/MS revealed that unlike the rapid, modest (4-fold to 8-fold), and synchronous GA induction of K48 and K63 polyubiquitinated ErbB2, PS341 produces a dramatic (20-fold to 40-fold) sequential increase in polyubiquitinated ErbB2 consistent with K48 polyubiquitination followed by K63 editing. Fluorescence microscopic imaging confirmed that PS341, but not GA, induces colocalization of K48-linked and K63-linked polyubiquitin with perinuclear lysosome-sequestered ErbB2. Thus, ErbB2 surface overexpression and recycling seem to depend on its polyubiquitination and deubiquitination; as well, the contrasting effects of PS341 and GA on ErbB2 receptor localization, polyubiquitination, and degradation point to alternate cytoplasmic trafficking likely regulated by different K48 and K63 polyubiquitin editing mechanisms.
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Affiliation(s)
- Corina Marx
- Buck Institute for Age Research, Novato, California 94945, USA
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Held JM, Danielson SR, Behring JB, Atsriku C, Britton DJ, Puckett RL, Schilling B, Campisi J, Benz CC, Gibson BW. Targeted quantitation of site-specific cysteine oxidation in endogenous proteins using a differential alkylation and multiple reaction monitoring mass spectrometry approach. Mol Cell Proteomics 2010; 9:1400-10. [PMID: 20233844 DOI: 10.1074/mcp.m900643-mcp200] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Reactive oxygen species (ROS) are both physiological intermediates in cellular signaling and mediators of oxidative stress. The cysteine-specific redox-sensitivity of proteins can shed light on how ROS are regulated and function, but low sensitivity has limited quantification of the redox state of many fundamental cellular regulators in a cellular context. Here we describe a highly sensitive and reproducible oxidation analysis approach (OxMRM) that combines protein purification, differential alkylation with stable isotopes, and multiple reaction monitoring mass spectrometry that can be applied in a targeted manner to virtually any cysteine or protein. Using this approach, we quantified the site-specific cysteine oxidation status of endogenous p53 for the first time and found that Cys182 at the dimerization interface of the DNA binding domain is particularly susceptible to diamide oxidation intracellularly. OxMRM enables analysis of sulfinic and sulfonic acid oxidation levels, which we validate by assessing the oxidation of the catalytic Cys215 of protein tyrosine phosphatase-1B under numerous oxidant conditions. OxMRM also complements unbiased redox proteomics discovery studies as a verification tool through its high sensitivity, accuracy, precision, and throughput.
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Affiliation(s)
- Jason M Held
- double daggerBuck Institute for Age Research, Novato, California 94945, USA
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Danielson SR, Held JM, Schilling B, Oo M, Gibson BW, Andersen JK. Preferentially increased nitration of alpha-synuclein at tyrosine-39 in a cellular oxidative model of Parkinson's disease. Anal Chem 2009; 81:7823-8. [PMID: 19697948 PMCID: PMC2748813 DOI: 10.1021/ac901176t] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [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: 02/07/2023]
Abstract
Alpha-synuclein is a major component of Lewy bodies, proteinacious inclusions which are a major hallmark of Parkinson's disease (PD). Lewy bodies contain high levels of nitrated tyrosine residues as determined by antibodies specific for 3-nitrotyrosine (3NT) and via mass spectrometry (MS). We have developed a multiple reaction monitoring (MRM) mass spectrometry method to sensitively quantitate the 3NT levels of specific alpha-synuclein tyrosine residues. We found a 9-fold increase (relative to controls) in levels of 3NT at Tyr-39 of alpha-synuclein in an inducible transgenic cellular model of Parkinson's disease in which monoamine oxidase B (MAO-B) is overexpressed and which emulates several features of PD. Increased nitration of Tyr-39 on endogenous alpha-synuclein via elevations in MAO-B levels could be abrogated by the addition of deprenyl, a specific MAO-B inhibitor. The increased levels of 3NT was selective for Tyr-39 as no significant increases in 3NT levels were detected at other tyrosine residues present in the protein (Tyr-125, Tyr-133, and Tyr-136). This is the first report of increased 3NT levels of a specific tyrosine in a PD model and the first use of MRM mass spectrometry to quantify changes in 3NT modifications at specific sites within a target protein.
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Affiliation(s)
- Steven R Danielson
- Buck Institute for Age Research, 8001 Redwood Boulevard, Novato, California 94945, USA
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Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJL, Keshishian H, Hall SC, Allen S, Blackman RK, Borchers CH, Buck C, Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, Hiltke T, Jackson A, Johansen EB, Kinsinger CR, Li J, Mesri M, Neubert TA, Niles RK, Pulsipher TC, Ransohoff D, Rodriguez H, Rudnick PA, Smith D, Tabb DL, Tegeler TJ, Variyath AM, Vega-Montoto LJ, Wahlander Å, Waldemarson S, Wang M, Whiteaker JR, Zhao L, Anderson NL, Fisher SJ, Liebler DC, Paulovich AG, Regnier FE, Tempst P, Carr SA. Erratum: Corrigendum: Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma. Nat Biotechnol 2009. [DOI: 10.1038/nbt0909-864b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJL, Keshishian H, Hall SC, Allen S, Blackman RK, Borchers CH, Buck C, Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, Hiltke T, Jackson A, Johansen EB, Kinsinger CR, Li J, Mesri M, Neubert TA, Niles RK, Pulsipher TC, Ransohoff D, Rodriguez H, Rudnick PA, Smith D, Tabb DL, Tegeler TJ, Variyath AM, Vega-Montoto LJ, Wahlander A, Waldemarson S, Wang M, Whiteaker JR, Zhao L, Anderson NL, Fisher SJ, Liebler DC, Paulovich AG, Regnier FE, Tempst P, Carr SA. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol 2009; 27:633-41. [PMID: 19561596 DOI: 10.1038/nbt.1546] [Citation(s) in RCA: 819] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 05/31/2009] [Indexed: 01/13/2023]
Abstract
Verification of candidate biomarkers relies upon specific, quantitative assays optimized for selective detection of target proteins, and is increasingly viewed as a critical step in the discovery pipeline that bridges unbiased biomarker discovery to preclinical validation. Although individual laboratories have demonstrated that multiple reaction monitoring (MRM) coupled with isotope dilution mass spectrometry can quantify candidate protein biomarkers in plasma, reproducibility and transferability of these assays between laboratories have not been demonstrated. We describe a multilaboratory study to assess reproducibility, recovery, linear dynamic range and limits of detection and quantification of multiplexed, MRM-based assays, conducted by NCI-CPTAC. Using common materials and standardized protocols, we demonstrate that these assays can be highly reproducible within and across laboratories and instrument platforms, and are sensitive to low mug/ml protein concentrations in unfractionated plasma. We provide data and benchmarks against which individual laboratories can compare their performance and evaluate new technologies for biomarker verification in plasma.
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Affiliation(s)
- Terri A Addona
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Atsriku C, Britton DJ, Held JM, Schilling B, Scott GK, Gibson BW, Benz CC, Baldwin MA. Systematic mapping of posttranslational modifications in human estrogen receptor-alpha with emphasis on novel phosphorylation sites. Mol Cell Proteomics 2008; 8:467-80. [PMID: 18984578 DOI: 10.1074/mcp.m800282-mcp200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A systematic study of posttranslational modifications of the estrogen receptor isolated from the MCF-7 human breast cancer cell line is reported. Proteolysis with multiple enzymes, mass spectrometry, and tandem mass spectrometry achieved very high sequence coverage for the full-length 66-kDa endogenous protein from estradiol-treated cell cultures. Nine phosphorylated serine residues were identified, three of which were previously unreported and none of which were previously observed by mass spectrometry by any other laboratory. Two additional modified serine residues were identified in recombinant protein, one previously reported but not observed here in endogenous protein and the other previously unknown. Although major emphasis was placed on identifying new phosphorylation sites, N-terminal loss of methionine accompanied by amino acetylation and a lysine side chain acetylation (or possibly trimethylation) were also detected. The use of both HPLC-ESI and MALDI interfaced to different mass analyzers gave higher sequence coverage and identified more sites than could be achieved by either method alone. The estrogen receptor is critical in the development and progression of breast cancer. One previously unreported phosphorylation site identified here was shown to be strongly dependent on estradiol, confirming its potential significance to breast cancer. Greater knowledge of this array of posttranslational modifications of estrogen receptor, particularly phosphorylation, will increase our understanding of the processes that lead to estradiol-induced activation of this protein and may aid the development of therapeutic strategies for management of hormone-dependent breast cancer.
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Britton DJ, Scott GK, Schilling B, Atsriku C, Held JM, Gibson BW, Benz CC, Baldwin MA. A novel serine phosphorylation site detected in the N-terminal domain of estrogen receptor isolated from human breast cancer cells. J Am Soc Mass Spectrom 2008; 19:729-740. [PMID: 18367407 PMCID: PMC7456516 DOI: 10.1016/j.jasms.2008.02.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 02/19/2008] [Accepted: 02/19/2008] [Indexed: 05/26/2023]
Abstract
Activated estrogen receptor (ERalpha) plays a critical role in breast cancer development and is a major target for drug treatment. Serine phosphorylation within the N-terminal domain (NTD) contributes to ERalpha activation and may also cause drug resistance. Previous biochemical identification of phosphorylated ERalpha residues was limited to protein artificially overexpressed in transfected cell lines. We report mass spectrometric methods that have allowed the identification of a new site within the NTD of ERalpha isolated from cultured human breast cancer cells. Immunoprecipitation, trypsin digestion, and analysis by nano-LC-ESI-MS/MS (Q-STAR, MDS Sciex) and vMALDI-MS(n) (Finnigan LTQ, Thermo-Electron) identified peptides containing 8 of 14 serine residues within the NTD, one being partially phosphorylated Ser-167, known but not previously reported by MS. Chymotrypsin digestion revealed other known sites at Ser-102/104/106 and 118. Tandem methods developed for the peptide containing Ser-118 and the use of hypothesis-driven experiments--i.e., the assumption that an intact phosphopeptide showing no molecular ion might yield fragment ions including loss of phosphoric acid in vMALDI-MS/MS--allowed the identification of a novel site at Ser-154. Quantitation by selected reaction monitoring demonstrated 6-fold and 2.5-fold increases in Ser-154 phosphorylation in estradiol- and EGF-treated cells, respectively, compared to controls, confirmed by immunoblotting with a novel rabbit polyclonal antibody. Thus, the protein isolation and MS strategies described here can facilitate discovery of novel phosphorylation sites within low abundance, clinically important cancer targets like ERalpha, and may thereby contribute to our understanding of the role of phosphorylation in the development of breast cancer.
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Affiliation(s)
- David J Britton
- Buck Institute for Age Research, Novato, California 94945, USA
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Held JM, White MP, Fisher AL, Gibson BW, Lithgow GJ, Gill MS. DAF-12-dependent rescue of dauer formation in Caenorhabditis elegans by (25S)-cholestenoic acid. Aging Cell 2006; 5:283-91. [PMID: 16913876 DOI: 10.1111/j.1474-9726.2006.00218.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [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: 12/01/2022] Open
Abstract
Population density, temperature and food availability all regulate the formation of the Caenorhabditis elegans dauer larva by modulating endocrine signaling pathways. The orphan nuclear receptor DAF-12 is pivotal for the decision to form a dauer or to undergo normal reproductive development. The DAF-12 ligand has been predicted to be a sterol that is metabolized by DAF-9, a cytochrome P450. Here we chemically characterize purified lipophilic nematode extracts and show that the ligand for DAF-12 contains a carboxyl moiety and is likely to be derived from a sterol. Using a candidate ligand approach we find that the C27 bile acid cholestenoic acid (5-cholesten-3beta-ol-(25S)-carboxylic acid) promotes reproductive growth in dauer-constitutive mutants in a daf-9- and daf-12-dependent manner. Furthermore, we find that cholestenoic acid can act as a DAF-12 ligand by activating DAF-12 in a cell-based transcription assay. Analysis of dauer-rescuing lipophilic extracts from nematodes by gas chromatography-mass spectrometry indicates the presence of several regioisomers of cholestenoic acid that are distinct from Delta(5)-cholestenoic acid and are not present in extracts from daf-9 mutants. These data suggest that carboxylated sterols may be key determinants of life history.
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Affiliation(s)
- Jason M Held
- Buck Institute for Age Research, 8001 Redwood Boulevard, Novato, CA 94945, USA
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48
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Abstract
Abstract In Caenorhabditis elegans, the decision to develop into a reproductive adult or arrest as a dauer larva is influenced by multiple pathways including insulin-like and transforming growth factor beta (TGFbeta)-like signalling pathways. It has been proposed that lipophilic hormones act downstream of these pathways to regulate dauer formation. One likely target for such a hormone is DAF-12, an orphan nuclear hormone receptor that mediates these developmental decisions and also influences adult lifespan. In order to find lipophilic hormones we have generated lipophilic extracts from mass cultures of C. elegans and shown that they rescue the dauer constitutive phenotype of class 1 daf-2 insulin signalling mutants and the TGFbeta signalling mutant daf-7. These extracts are also able to rescue the lethal dauer phenotype of daf-9 mutants, which lack a P450 steroid hydroxylase thought to be involved in the synthesis of the DAF-12 ligand; extracts, however, have no effect on a DAF-12 ligand binding domain mutant that is predicted to be ligand insensitive. The production of this hormone appears to be DAF-9 dependent as extracts from a daf-9;daf-12 double mutant do not exhibit this activity. Preliminary fractionation of the lipophilic extracts shows that the activity is hydrophobic with some polar properties, consistent with a small lipophilic hormone. We propose that the dauer rescuing activity is a hormone synthesized by DAF-9 that acts through DAF-12.
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Affiliation(s)
- Matthew S Gill
- Buck Institute, 8001 Redwood Boulevard, Novato, CA 94945, USA.
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Abstract
The purpose of this project was to study the role of somatosensory information in the performance of a constrained locomotor task by rats and to further examine the influence of structural recovery in the somatosensory thalamus, specifically the ventral posterolateral nucleus (VPL). Groups of rats were trained to traverse an elevated, one inch bar for a reward. The time taken to run across the bar (run time) was used as a measure of the success of the goal-directed behavior. The movement pattern of the hindlimb during the swing phase of the locomotor task was quantified from videotape on Preoperative (PRE) Day 15 and during the 46-day postoperative period. The movement pattern was characterized using six different parameters: the area, the X and Y values of the centroid under the normalized curve of the hindlimb trajectory, the vertical displacement of the hindlimb in the flexion and extension phases of the swing cycle, the maximum instantaneous hindlimb velocity, and the proportion of time spent in the acceleration versus deceleration phases of the swing cycle. In order to disrupt the central pathways for somatosensory information, lesions were made in (i) the right gracile nucleus (GN) (n = 18), (ii) bilateral GN (n = 7), (iii) the right GN and the left VPL (n = 6), and (iv) bilateral VPL (n = 8), and (v) sham-operated animals (n = 5). The run time and the pattern of the hindlimb swing cycle were used as measures of loss and recovery of function. Only the bilateral VPL group showed an impairment in run time and they recovered by Postoperative (POST) Week 4. All groups demonstrated an impairment in initial flexion of the hindlimb during the swing cycle that recovered in the right GN group only. On POST Day 49, the right GN, bilateral GN, and the sham groups received injections of 5% WGA-HRP into both CN to determine the location of these projections in VPL. The CN projections were not redistributed into the gracile area of VPL after GN lesions. Since our previous study (24) had shown the number of synapses in VPL returned to normal after dorsal column nuclei (DCN) lesions by POST Day 50, the recovery of the number of synapses alone was not sufficient to restore the normal gait pattern, while the recovery of the run time preceded the complete recovery of the number of synapses.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- S M Henry
- Department of Anatomy and Neurobiology, College of Medicine, University of Vermont, Burlington 05405, USA
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Reed BV, Held JM. Effects of sequential connective tissue massage on autonomic nervous system of middle-aged and elderly adults. Phys Ther 1988; 68:1231-4. [PMID: 3399521] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The purpose of this study was to describe autonomic nervous system responses to serial connective tissue massage (CTM) in healthy middle-aged and elderly subjects. Fourteen healthy middle-aged or elderly subjects (means age = 61.3 years) were randomly assigned to either a CTM or placebo group. Subjects received nine separate treatments (CTM or placebo) on alternate days over a three-week period. Each treatment was divided into 15-minute control, intervention, and recovery periods. Subjects in the CTM Group (n = 8) were given CTM on the basic section (low back), and subjects in the Placebo Group (n = 6) had sham ultrasound applied to the same area. Variables monitored were skin temperature (right great toe and popliteal fossa), galvanic skin response, mean arterial blood pressure, and heart rate. Variable measurements were made every five minutes. An analysis of variance and single-case analyses showed no changes in the variables measured in the CTM or Placebo Group. The results of this study suggest that CTM has no consistent immediate or long-term effects on the autonomic nervous system in healthy middle-aged and elderly subjects.
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Affiliation(s)
- B V Reed
- Department of Physical Therapy, School of Allied Health Sciences, University of Vermont, Burlington 05405
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