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Li Y, Pillar N, Li J, Liu T, Wu D, Sun S, Ma G, de Haan K, Huang L, Zhang Y, Hamidi S, Urisman A, Keidar Haran T, Wallace WD, Zuckerman JE, Ozcan A. Virtual histological staining of unlabeled autopsy tissue. Nat Commun 2024; 15:1684. [PMID: 38396004 PMCID: PMC10891155 DOI: 10.1038/s41467-024-46077-2] [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: 08/05/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Traditional histochemical staining of post-mortem samples often confronts inferior staining quality due to autolysis caused by delayed fixation of cadaver tissue, and such chemical staining procedures covering large tissue areas demand substantial labor, cost and time. Here, we demonstrate virtual staining of autopsy tissue using a trained neural network to rapidly transform autofluorescence images of label-free autopsy tissue sections into brightfield equivalent images, matching hematoxylin and eosin (H&E) stained versions of the same samples. The trained model can effectively accentuate nuclear, cytoplasmic and extracellular features in new autopsy tissue samples that experienced severe autolysis, such as COVID-19 samples never seen before, where the traditional histochemical staining fails to provide consistent staining quality. This virtual autopsy staining technique provides a rapid and resource-efficient solution to generate artifact-free H&E stains despite severe autolysis and cell death, also reducing labor, cost and infrastructure requirements associated with the standard histochemical staining.
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Affiliation(s)
- Yuzhu Li
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA
- Bioengineering Department, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, 90095, USA
| | - Nir Pillar
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA
- Bioengineering Department, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, 90095, USA
| | - Jingxi Li
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA
- Bioengineering Department, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, 90095, USA
| | - Tairan Liu
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA
- Bioengineering Department, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, 90095, USA
| | - Di Wu
- Computer Science Department, University of California, Los Angeles, CA, 90095, USA
| | - Songyu Sun
- Computer Science Department, University of California, Los Angeles, CA, 90095, USA
| | - Guangdong Ma
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA
- School of Physics, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Kevin de Haan
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA
- Bioengineering Department, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, 90095, USA
| | - Luzhe Huang
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA
- Bioengineering Department, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, 90095, USA
| | - Yijie Zhang
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA
- Bioengineering Department, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, 90095, USA
| | - Sepehr Hamidi
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Anatoly Urisman
- Department of Pathology, University of California, San Francisco, CA, 94143, USA
| | - Tal Keidar Haran
- Department of Pathology, Hadassah Hebrew University Medical Center, Jerusalem, 91120, Israel
| | - William Dean Wallace
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Jonathan E Zuckerman
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Aydogan Ozcan
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA.
- Bioengineering Department, University of California, Los Angeles, CA, 90095, USA.
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, 90095, USA.
- Department of Surgery, University of California, Los Angeles, CA, 90095, USA.
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Riley AK, Grant M, Snell A, Vichas A, Moorthi S, Urisman A, Castel P, Wan L, Berger AH. The deubiquitinase USP9X regulates RIT1 protein abundance and oncogenic phenotypes. bioRxiv 2023:2023.11.30.569313. [PMID: 38077017 PMCID: PMC10705424 DOI: 10.1101/2023.11.30.569313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
RIT1 is a rare and understudied oncogene in lung cancer. Despite structural similarity to other RAS GTPase proteins such as KRAS, oncogenic RIT1 activity does not appear to be tightly regulated by nucleotide exchange or hydrolysis. Instead, there is a growing understanding that the protein abundance of RIT1 is important for its regulation and function. We previously identified the deubiquitinase USP9X as a RIT1 dependency in RIT1-mutant cells. Here, we demonstrate that both wild-type and mutant forms of RIT1 are substrates of USP9X. Depletion of USP9X leads to decreased RIT1 protein stability and abundance and resensitizes cells to EGFR tyrosine kinase inhibitors. Our work expands upon the current understanding of RIT1 protein regulation and presents USP9X as a key regulator of RIT1-driven oncogenic phenotypes.
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Affiliation(s)
- Amanda K. Riley
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Michael Grant
- Department of Molecular Oncology, Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Aidan Snell
- Department of Molecular Oncology, Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Athea Vichas
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sitapriya Moorthi
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Anatoly Urisman
- Department of Pathology, University of California San Francisco, CA, USA
| | - Pau Castel
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Lixin Wan
- Department of Molecular Oncology, Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Alice H. Berger
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Herbold Computational Biology Program, Public Health Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Lead contact:
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3
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Ye J, Croom N, Troxell ML, Kambham N, Zuckerman JE, Andeen N, Dall’Era M, Hsu R, Walavalkar V, Laszik ZG, Urisman A. Non-Full House Membranous Lupus Nephritis Represents a Clinically Distinct Subset. Kidney360 2023; 4:935-942. [PMID: 37257088 PMCID: PMC10371271 DOI: 10.34067/kid.0000000000000161] [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] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/21/2023] [Indexed: 06/02/2023]
Abstract
Key Points Non-full house (NFH) membranous lupus nephritis (MLN) is a minor subset of all MLN cases. Patients with NFH MLN tend to be older when diagnosed with systemic lupus erythematosus, undergo first renal biopsy at an older age, and have fewer extrarenal systemic manifestations. Lower load of C3 glomerular deposits seen in NFH MLN biopsies suggests attenuation of complement-mediated injury, which may have wider systemic implications. Background Renal involvement in systemic lupus erythematosus (SLE) is a key predictor of morbidity and mortality. Immunofluorescence (IF) staining of glomeruli is typically positive for IgG, IgA, IgM, C3, and C1q—the full house (FH) pattern. However, a subset of patients with membranous lupus nephritis (MLN) have a Non-FH (NFH) IF pattern more typical of idiopathic membranous nephropathy. Methods From a multi-institutional cohort of 113 MLN cases, we identified 29 NFH MLN biopsies. NFH MLN was defined by IF criteria: ≥1+ glomerular capillary loop IgG staining and<1+ IgA, IgM, and C1q. FH MLN was defined as ≥1+ staining for all five antibodies. Intermediate (Int) cases did not meet criteria for FH or NFH. We compared the pathological and clinical characteristics and outcomes among patients with FH, NFH, and Int IF patterns on kidney biopsy. Results NFH MLN represents a subset of MLN biopsies (13.4%). Compared with patients with FH MLN, patients with NFH MLN were older at SLE diagnosis (29 versus 22.5 years), had a longer time to initial kidney biopsy (8 versus 3.16 years), and had fewer SLE manifestations (2.5 versus 3.36 involved systems). NFH MLN biopsies showed lower C3 IF intensity (1.16+ versus 2.38+). Int biopsies had findings intermediate between those of NFH and FH groups. Conclusions NFH IF pattern defines a small subset of MLN biopsies and appears to be associated with milder clinical manifestations and slower disease progression. Less robust C3 deposition in NFH MLN may suggest a pathophysiology distinct from that of FH MLN.
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Affiliation(s)
- Julia Ye
- Department of Pathology, University of California, San Francisco, San Francisco, California
| | - Nicole Croom
- Department of Pathology, University of California, San Francisco, San Francisco, California
| | - Megan L. Troxell
- Department of Pathology, Stanford University, Palo Alto, California
| | - Neeraja Kambham
- Department of Pathology, Stanford University, Palo Alto, California
| | - Jonathan E. Zuckerman
- Department of Pathology, University of California, Los Angeles, Los Angeles, California
| | - Nicole Andeen
- Department of Pathology, Oregon Health and Science University, Portland, Oregon
| | - Maria Dall’Era
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Raymond Hsu
- Division of Nephrology, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Vighnesh Walavalkar
- Department of Pathology, University of California, San Francisco, San Francisco, California
| | - Zoltan G. Laszik
- Department of Pathology, University of California, San Francisco, San Francisco, California
| | - Anatoly Urisman
- Department of Pathology, University of California, San Francisco, San Francisco, California
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Lopez J, Bonsor DA, Sale MJ, Urisman A, Mehalko JL, Cabanski-Dunning M, Castel P, Simanshu DK, McCormick F. The Ribosomal S6 Kinase 2 (RSK2)-SPRED2 complex regulates phosphorylation of RSK substrates and MAPK signaling. J Biol Chem 2023:104789. [PMID: 37149146 DOI: 10.1016/j.jbc.2023.104789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/08/2023] Open
Abstract
Sprouty-related EVH-1 domain-containing (SPRED) proteins are a family of proteins that negatively regulate the RAS-MAPK pathway, which is involved in the regulation of the mitogenic response and cell proliferation. However, the mechanism by which these proteins affect RAS-MAPK signaling has not been fully elucidated. Patients with mutations in SPRED give rise to unique disease phenotypes, thus we hypothesized that distinct interactions across SPRED proteins may account for alternative nodes of regulation. To characterize the SPRED interactome and evaluate how members of the SPRED family function through unique binding partners, here we performed affinity purification mass spectrometry. We identified 90-kDa ribosomal S6 kinase 2 (RSK2) as a specific interactor of SPRED2, but not SPRED1 or SPRED3. We identified that the N-terminal kinase domain of RSK2 mediates interaction between amino acids 123-201 of SPRED2. Using X-ray crystallography, we determined the structure of the SPRED2-RSK2 complex and identified the SPRED2 motif, F145A, as critical for interaction. Additionally, we found that formation of this interaction is regulated by MAPK signaling events. We also find that that this interaction between SPRED2 and RSK2 has functional consequences, whereby knockdown of SPRED2 resulted in increased phosphorylation of RSK substrates, YB1 and CREB. Furthermore, SPRED2 knockdown hindered phospho-RSK membrane and nuclear subcellular localization. Lastly, we report that disruption of the SPRED2-RSK complex has effects on RAS-MAPK signaling dynamics. Overall, our analysis reveals that members of the SPRED family have unique protein binding partners and describes the molecular and functional determinants of SPRED2-RSK2 complex dynamics.
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Affiliation(s)
- Jocelyne Lopez
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd Street, San Francisco, CA 94158, USA
| | - Daniel A Bonsor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Matthew J Sale
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd Street, San Francisco, CA 94158, USA
| | - Anatoly Urisman
- Department of Pathology, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Jennifer L Mehalko
- Protein Expression Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702, United States
| | - Miranda Cabanski-Dunning
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd Street, San Francisco, CA 94158, USA
| | - Pau Castel
- Department of Biochemistry and Molecular Pharmacology, New York University, 450 E 29(th) Street, New York, NY 10016, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd Street, San Francisco, CA 94158, USA.
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Sadiq S, Urisman A, Cil O. Case report: Short-term eculizumab use in atypical HUS associated with Lemierre's syndrome and post-infectious glomerulonephritis. Front Med (Lausanne) 2023; 10:1167806. [PMID: 37206472 PMCID: PMC10189804 DOI: 10.3389/fmed.2023.1167806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/30/2023] [Indexed: 05/21/2023] Open
Abstract
Atypical hemolytic uremic syndrome (aHUS) is a rare disease caused by genetic abnormalities, infections, autoimmune diseases, drugs, and malignancies. Anti-C5 monoclonal antibody eculizumab is the mainstay of treatment of aHUS caused by the genetic defects of the alternative complement pathway. However, the utility of eculizumab in non-genetic forms of aHUS and the timing of treatment discontinuation remain controversial. Here, we report successful short-term eculizumab use in two young adult patients with aHUS due to rare infectious and autoimmune etiologies: Lemierre's syndrome and post-infectious glomerulonephritis, respectively. Eculizumab was rapidly discontinued in both patients with no aHUS recurrence during long-term follow-up. Considering its favorable safety profile with appropriate meningococcal prophylaxis, eculizumab can be considered as a treatment option for non-genetic aHUS.
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Affiliation(s)
- Sanober Sadiq
- Division of Nephrology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
| | - Anatoly Urisman
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Onur Cil
- Division of Nephrology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
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6
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Bromberger B, McLafferty F, Smith J, Elicker B, Jones K, Mulvey C, Urisman A, Venado A, Hays S, Kukreja J, Trinh B. Bilateral Lung Transplant with Recognition of Diffuse Idiopathic Pulmonary Neuroendocrine Cell Hyperplasia (DIPNECH) of rhe Donor Lungs in the Immediate Postoperative Period. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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7
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Bons J, Pan D, Shah S, Bai R, Chen‐Tanyolac C, Wang X, Elliott DRF, Urisman A, O'Broin A, Basisty N, Rose J, Sangwan V, Camilleri‐Broët S, Tankel J, Gascard P, Ferri L, Tlsty TD, Schilling B. Data-independent acquisition and quantification of extracellular matrix from human lung in chronic inflammation-associated carcinomas. Proteomics 2023; 23:e2200021. [PMID: 36228107 PMCID: PMC10391693 DOI: 10.1002/pmic.202200021] [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: 07/29/2022] [Revised: 09/17/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022]
Abstract
Early events associated with chronic inflammation and cancer involve significant remodeling of the extracellular matrix (ECM), which greatly affects its composition and functional properties. Using lung squamous cell carcinoma (LSCC), a chronic inflammation-associated cancer (CIAC), we optimized a robust proteomic pipeline to discover potential biomarker signatures and protein changes specifically in the stroma. We combined ECM enrichment from fresh human tissues, data-independent acquisition (DIA) strategies, and stringent statistical processing to analyze "Tumor" and matched adjacent histologically normal ("Matched Normal") tissues from patients with LSCC. Overall, 1802 protein groups were quantified with at least two unique peptides, and 56% of those proteins were annotated as "extracellular." Confirming dramatic ECM remodeling during CIAC progression, 529 proteins were significantly altered in the "Tumor" compared to "Matched Normal" tissues. The signature was typified by a coordinated loss of basement membrane proteins and small leucine-rich proteins. The dramatic increase in the stromal levels of SERPINH1/heat shock protein 47, that was discovered using our ECM proteomic pipeline, was validated by immunohistochemistry (IHC) of "Tumor" and "Matched Normal" tissues, obtained from an independent cohort of LSCC patients. This integrated workflow provided novel insights into ECM remodeling during CIAC progression, and identified potential biomarker signatures and future therapeutic targets.
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Affiliation(s)
- Joanna Bons
- Buck Institute for Research on AgingNovatoCaliforniaUSA
| | - Deng Pan
- Department of PathologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Samah Shah
- Buck Institute for Research on AgingNovatoCaliforniaUSA
| | - Rosemary Bai
- Department of PathologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | | | - Xianhong Wang
- Department of PathologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Daffolyn R. Fels Elliott
- Department of PathologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Present address:
Pathology and Laboratory MedicineKansas University Medical Center, the University of KansasKansas CityKansasUSA
| | - Anatoly Urisman
- Department of PathologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Amy O'Broin
- Buck Institute for Research on AgingNovatoCaliforniaUSA
| | | | - Jacob Rose
- Buck Institute for Research on AgingNovatoCaliforniaUSA
| | - Veena Sangwan
- Division of Thoracic and Upper Gastrointestinal SurgeryMontreal General HospitalMcGill University Health CentreMontrealQuebecCanada
| | | | - James Tankel
- Division of Thoracic and Upper Gastrointestinal SurgeryMontreal General HospitalMcGill University Health CentreMontrealQuebecCanada
| | - Philippe Gascard
- Department of PathologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Lorenzo Ferri
- Division of Thoracic and Upper Gastrointestinal SurgeryMontreal General HospitalMcGill University Health CentreMontrealQuebecCanada
| | - Thea D. Tlsty
- Department of PathologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
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8
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Waldman M, Sinaii N, Lerma EV, Kurien AA, Jhaveri KD, Uppal NN, Wanchoo R, Avasare R, Zuckerman JE, Liew A, Gallan AJ, El-Meanawy A, Yagil Y, Lebedev L, Baskaran K, Vilayur E, Cohen A, Weerasinghe N, Petrakis I, Stylianou K, Gakiopoulou H, Hamilton AJ, Edney N, Millner R, Marinaki S, Rein JL, Killen JP, Rodríguez Chagolla JM, Bassil C, Lopez del Valle R, Evans J, Urisman A, Zawaideh M, Baxi PV, Rodby R, Vankalakunti M, Mejia Vilet JM, Ramirez Andrade SE, Homan MP, Vásquez Jiménez E, Perinpanayagam N, Velez JCQ, Mohamed MM, Mohammed KM, Sekar A, Ollila L, Aron AW, Arellano Arteaga KJ, Islam M, Berrio EM, Maoujoud O, Morales RR, Seipp R, Schulze CE, Yenchek RH, Vancea I, Muneeb M, Howard L, Caza TN. COVID-19 Vaccination and New Onset Glomerular Disease: Results from the IRocGN2 International Registry. Kidney360 2023; 4:349-362. [PMID: 36996301 PMCID: PMC10103269 DOI: 10.34067/kid.0006832022] [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] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Key Points IgAN and MCD are the most common de novo glomerular diseases reported after COVID-19 vaccination, particularly after mRNA vaccination. Membranous nephropathy, pauci-immune GN, and collapsing GN have also been attributed to COVID-19 vaccination, some with dual histologies. Recovery of kidney function and proteinuria remission is more likely in IgAN and MCD by 4–6 months compared with the other glomerular diseases. Background Patients with de novo glomerular disease (GD) with various renal histologies have been reported after vaccination against SARS-CoV-2. Causality has not been established, and the long-term outcomes are not known. To better characterize the GDs and clinical courses/outcomes, we created the International Registry of COVID-19 vaccination and Glomerulonephritis to study in aggregate patients with de novo GN suspected after COVID-19 vaccine exposure. Methods A REDCap survey was used for anonymized data collection. Detailed information on vaccination type and timing and GD histology were recorded in the registry. We collected serial information on laboratory values (before and after vaccination and during follow-up), treatments, and kidney-related outcomes. Results Ninety-eight patients with GD were entered into the registry over 11 months from 44 centers throughout the world. Median follow-up was 89 days after diagnosis. IgA nephropathy (IgAN) and minimal change disease (MCD) were the most common kidney diseases reported. Recovery of kidney function and remission of proteinuria were more likely in IgAN and MCD at 4–6 months than with pauci-immune GN/vasculitis and membranous nephropathy. Conclusions The development of GD after vaccination against SARS-CoV-2 may be a very rare adverse event. Temporal association is present for IgAN and MCD, but causality is not firmly established. Kidney outcomes for IgAN and MCD are favorable. No changes in vaccination risk-benefit assessment are recommended based on these findings.
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Affiliation(s)
- Meryl Waldman
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Ninet Sinaii
- Biostatistics and Clinical Epidemiology Service, National Institutes of Health Clinical Center, Bethesda, Maryland
| | - Edgar V. Lerma
- University of Illinois at Chicago/Advocate Christ Medical Center, Oak Lawn, Illinois
| | | | - Kenar D. Jhaveri
- Division of Kidney Diseases and Hypertension, Glomerular Center at Northwell Health, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Great Neck, New York
| | - Nupur N. Uppal
- Division of Kidney Diseases and Hypertension, Glomerular Center at Northwell Health, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Great Neck, New York
| | - Rimda Wanchoo
- Division of Kidney Diseases and Hypertension, Glomerular Center at Northwell Health, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Great Neck, New York
| | - Rupali Avasare
- Division of Nephrology and Hypertension, Department of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Jonathan E. Zuckerman
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Adrian Liew
- The Kidney and Transplant Practice, Mount Elizabeth Novena Hospital, Singapore
| | | | - Ashraf El-Meanawy
- Division of Nephrology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Yoram Yagil
- Department of Nephrology and Hypertension, Barzilai University Medical Center, Ashkelon, Israel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheba, Israel
| | - Larissa Lebedev
- Department of Nephrology and Hypertension, Barzilai University Medical Center, Ashkelon, Israel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheba, Israel
| | - Krishoban Baskaran
- Department of Nephrology, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
- School of Medicine and Public Health, The University of Newcastle, Callaghan,New South Wales, Australia
| | - Eswari Vilayur
- Department of Nephrology, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Adrienne Cohen
- Department of Nephrology, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Nethmi Weerasinghe
- Department of Nephrology, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Ioannis Petrakis
- Department of Nephrology, General University Hospital of Heraklion, Crete, Greece
| | | | | | - Alexander J. Hamilton
- Exeter Kidney Unit, Royal Devon University Healthcare NHS Foundation Trust, United Kingdom
| | - Naomi Edney
- Exeter Kidney Unit, Royal Devon University Healthcare NHS Foundation Trust, United Kingdom
| | - Rachel Millner
- Department of Pediatrics, Pediatric Nephrology, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Smaragdi Marinaki
- Clinic of Nephrology and Renal Transplantation, NKUA, Medical School, Laiko General Hospital, Athens, Greece
| | - Joshua L. Rein
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - John Paul Killen
- Department of Nephrology, Northern Beaches Hospital, Frenchs Forest, New South Wales, Australia
- Faculty of Medicine, Health and Human Sciences, Macquarie University, New South Wales, Australia
| | | | - Claude Bassil
- Division of Nephrology and Hypertension, University of South Florida, Tampa, Florida
- Renal Service, H. Lee Moffitt Cancer Center, Tampa, Florida
| | | | - Jordan Evans
- Department of Nephrology, David Grant Medical Center, Travis Air Force Base, California
| | - Anatoly Urisman
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Mona Zawaideh
- Division of Pediatric Nephrology, Peyton Manning Children's Hospital, Indianapolis, Indiana
| | - Pravir V. Baxi
- Division of Nephrology, Rush University Medical Center, Chicago, Illinois
| | - Roger Rodby
- Division of Nephrology, Rush University Medical Center, Chicago, Illinois
| | | | - Juan M. Mejia Vilet
- Department of Nephrology, Instituto Nacional de Ciencas Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico
| | - Silvia E. Ramirez Andrade
- Department of Nephrology and Mineral Metabolism, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico
| | - Mal P. Homan
- Division of Nephrology, Department of Medicine, Lehigh Valley Health Network, Allentown, Pennsylvania
| | | | | | - Juan Carlos Q. Velez
- Department of Nephrology, Ochsner Health, New Orleans, Louisiana
- Ochsner Clinical School, The University of Queensland, Brisbane, Queensland, Australia
| | - Muner M.B. Mohamed
- Department of Nephrology, Ochsner Health, New Orleans, Louisiana
- Ochsner Clinical School, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Arjun Sekar
- Rochester General Hospital, Rochester, New York
| | - Laura Ollila
- Helsinki University Central Hospital, Helsinki, Finland
| | - Abraham W. Aron
- Department of Internal Medicine, Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut
| | - Kevin Javier Arellano Arteaga
- Internal Medicine Department, Nuevo Hospital Civil De Guadalajara Dr. Juan I Menchaca, Guadalajara, Mexico; Department of Clinical Medicine, University Center for Health Science, University of Guadalajara
| | - Mahmud Islam
- Division of Nephrology, Zonguldak Ataturk State Hospital, Zonguldak, Turkey
| | - Esperanza Moral Berrio
- Department of Nephrology, Hospital General Universitario de Ciudad Real, Ciudad Real, Spain
| | - Omar Maoujoud
- Faculty of Medicine, Cadi Ayyad University, Marrakech, Morocco
| | | | | | - Carl E. Schulze
- Division of Nephrology, Department of Medicine, University of California, Los Angeles, California
| | - Robert H. Yenchek
- Division of Nephrology, Department of Medicine, University of Utah, Salt Lake City, Utah
| | - Irina Vancea
- Southern Colorado Nephrology Associates, Pueblo, Colorado
| | | | - Lilian Howard
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
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9
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Basso P, Dang EV, Urisman A, Cowen LE, Madhani HD, Noble SM. Deep tissue infection by an invasive human fungal pathogen requires lipid-based suppression of the IL-17 response. Cell Host Microbe 2022; 30:1589-1601.e5. [PMID: 36323314 PMCID: PMC9744107 DOI: 10.1016/j.chom.2022.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 08/17/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022]
Abstract
Candida albicans is the most common cause of fungal infection in humans. IL-17 is critical for defense against superficial fungal infections, but the role of this response in invasive disease is less understood. We show that C. albicans secretes a lipase, Lip2, that facilitates invasive disease via lipid-based suppression of the IL-17 response. Lip2 was identified as an essential virulence factor in a forward genetic screen in a mouse model of bloodstream infection. Murine infection with C. albicans strains lacking Lip2 display exaggerated IL-17 responses that lead to fungal clearance from solid organs and host survival. Both IL-17 signaling and lipase activity are required for Lip2-mediated suppression. Lip2 inhibits IL-17 production indirectly by suppressing IL-23 production by tissue-resident dendritic cells. The lipase hydrolysis product, palmitic acid, similarly suppresses dendritic cell activation in vitro. Thus, C. albicans suppresses antifungal IL-17 defense in solid organs by altering the tissue lipid milieu.
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Affiliation(s)
- Pauline Basso
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Eric V Dang
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Anatoly Urisman
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Suzanne M Noble
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA; Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
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10
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Kerr DL, Wu W, Tamaki W, Urisman A, Chou YT, Gui P, Jablons DM, Bivona TG, Blakely CM. Abstract 3808: Spatially resolved transcriptomics of cellular architecture in EGFR-mutated lung cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3808] [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
Introduction: Single-cell RNA sequencing of dissociated tumors enables the profiling of cellular states in fine detail, but erases the cellular organization of the analyzed tissue. Spatially resolved transcriptomics (SRT) using 10X Genomics’ Visium platform combines histological staining and RNA sequencing by capturing each transcript across spatially barcoded microarrays. SRT yields gene-expression matrices resolved within 55-micron array spots, and creates opportunities to explore how lung biology is affected by lung adenocarcinoma and how tumor cells and the proximal microenvironment are modulated by targeted therapy.
Methods: SRT reactions (n=8) were performed on surgical specimens from human lung adenocarcinomas driven by kinase domain mutations of EGFR (exon 19 deletion, L858R point mutation, exon 20 insertion). SRT reactions analyzed primary lung cancer (n=5) or paired tumor-adjacent lung tissues (n=3).
Results: 28458 array spots were recorded across all samples, and array spots captured a median of 5800 total transcripts and a median of 2416 unique transcripts. Single marker gene expression and unsupervised clustering across array spots corresponded with histological annotations of lung structures and adenocarcinoma. Integration of single-cell RNA sequencing data from lung adenocarcinoma specimens permitted mapping and quantification of 15 major cell types, including cancer cells, T- and B- lymphocytes, macrophages, dendritic cells, fibroblasts, and endothelial cells. Compared with paired tumor-adjacent lung tissues, adenocarcinoma tissues contained fibroblast-enriched desmoplasia and B-cell enriched tertiary lymphoid structures. In a clinical case with resistance to Osimertinib, the standard tyrosine kinase inhibitor, gene signature analysis of cancer-containing array spots revealed enrichment of gap-junction, fatty acid metabolism, and kynurenine pathway signatures compared to treatment naïve array spots.
Conclusion: This pilot study demonstrates the feasibility of using SRT in lung adenocarcinoma. Paired with a single-cell atlas of lung adenocarcinoma during targeted therapy, this approach enables hypothesis-generation to investigate the alterations of tumor and tumor microenvironmental architecture in relation to targeted therapy.
Citation Format: Daniel L. Kerr, Wei Wu, Whitney Tamaki, Anatoly Urisman, Yu-Ting Chou, Philippe Gui, David M. Jablons, Trever G. Bivona, Collin M. Blakely. Spatially resolved transcriptomics of cellular architecture in EGFR-mutated lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3808.
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Affiliation(s)
- Daniel L. Kerr
- 1University of California, San Francisco, San Francisco, CA
| | - Wei Wu
- 1University of California, San Francisco, San Francisco, CA
| | - Whitney Tamaki
- 1University of California, San Francisco, San Francisco, CA
| | | | - Yu-Ting Chou
- 1University of California, San Francisco, San Francisco, CA
| | - Philippe Gui
- 1University of California, San Francisco, San Francisco, CA
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11
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Nanjo S, Wu W, Karachaliou N, Blakely CM, Suzuki J, Chou YT, Ali SM, Kerr DL, Olivas VR, Shue J, Rotow J, Mayekar MK, Haderk F, Chatterjee N, Urisman A, Yeo JC, Skanderup AJ, Tan AC, Tam WL, Arrieta O, Hosomichi K, Nishiyama A, Yano S, Kirichok Y, Tan DS, Rosell R, Okimoto RA, Bivona TG. Deficiency of the splicing factor RBM10 limits EGFR inhibitor response in EGFR mutant lung cancer. J Clin Invest 2022; 132:145099. [PMID: 35579943 PMCID: PMC9246391 DOI: 10.1172/jci145099] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 05/13/2022] [Indexed: 11/18/2022] Open
Abstract
Molecularly targeted cancer therapy has improved outcomes for patients with cancer with targetable oncoproteins, such as mutant EGFR in lung cancer. Yet, the long-term survival of these patients remains limited, because treatment responses are typically incomplete. One potential explanation for the lack of complete and durable responses is that oncogene-driven cancers with activating mutations of EGFR often harbor additional co-occurring genetic alterations. This hypothesis remains untested for most genetic alterations that co-occur with mutant EGFR. Here, we report the functional impact of inactivating genetic alterations of the mRNA splicing factor RNA-binding motif 10 (RBM10) that co-occur with mutant EGFR. RBM10 deficiency decreased EGFR inhibitor efficacy in patient-derived EGFR-mutant tumor models. RBM10 modulated mRNA alternative splicing of the mitochondrial apoptotic regulator Bcl-x to regulate tumor cell apoptosis during treatment. Genetic inactivation of RBM10 diminished EGFR inhibitor–mediated apoptosis by decreasing the ratio of (proapoptotic) Bcl-xS to (antiapoptotic) Bcl-xL isoforms of Bcl-x. RBM10 deficiency was a biomarker of poor response to EGFR inhibitor treatment in clinical samples. Coinhibition of Bcl-xL and mutant EGFR overcame the resistance induced by RBM10 deficiency. This study sheds light on the role of co-occurring genetic alterations and on the effect of splicing factor deficiency on the modulation of sensitivity to targeted kinase inhibitor cancer therapy.
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Affiliation(s)
- Shigeki Nanjo
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Niki Karachaliou
- Cancer Biology and Precision Medicine Program, Germans Trias i Pujol Research Institute and Hospital, Badalona, Spain
| | - Collin M Blakely
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Junji Suzuki
- Department of Physiology, University of California, San Francisco, San Francisco, United States of America
| | - Yu-Ting Chou
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Siraj M Ali
- Foundation Medicine, Inc., Foundation Medicine, Inc., Cambridge, United States of America
| | - D Lucas Kerr
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Victor R Olivas
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Jonathan Shue
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Julia Rotow
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Manasi K Mayekar
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Franziska Haderk
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Nilanjana Chatterjee
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Anatoly Urisman
- Department of Pathology, University of California, San Francisco, San Francisco, United States of America
| | - Jia Chi Yeo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Anders J Skanderup
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Aaron C Tan
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Oscar Arrieta
- Thoracic Oncology Unit, National Cancer Center Institute (INCan), México City, Mexico
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomic, Kanazawa Universuty, Kanazawa, Japan
| | - Akihiro Nishiyama
- Division of Medical Oncology, Kanazawa University Cancer Research Institute, Kanazawa, Japan
| | - Seiji Yano
- Kanazawa University Cancer Research Institute, Kanazawa, Japan
| | - Yuriy Kirichok
- Department of Physiology, University of California, San Francisco, San Francisco, United States of America
| | - Daniel Sw Tan
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Rafael Rosell
- Cancer Biology and Precision Medicine Program, Germans Trias i Pujol Research Institute and Hospital, Badalona, Spain
| | - Ross A Okimoto
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Trever G Bivona
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, United States of America
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12
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Patel P, Buchanan CN, Zdradzinski MD, Sahoo PK, Kar AN, Lee SJ, Vaughn LS, Urisman A, Oses-Prieto J, Dell'Orco M, Cassidy DE, Costa ID, Miller S, Thames E, Smith TP, Burlingame AL, Perrone-Bizzozero N, Twiss JL. Intra-axonal translation of Khsrp mRNA slows axon regeneration by destabilizing localized mRNAs. Nucleic Acids Res 2022; 50:5772-5792. [PMID: 35556128 PMCID: PMC9177972 DOI: 10.1093/nar/gkac337] [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: 11/17/2020] [Revised: 04/21/2022] [Accepted: 05/09/2022] [Indexed: 11/28/2022] Open
Abstract
Axonally synthesized proteins support nerve regeneration through retrograde signaling and local growth mechanisms. RNA binding proteins (RBP) are needed for this and other aspects of post-transcriptional regulation of neuronal mRNAs, but only a limited number of axonal RBPs are known. We used targeted proteomics to profile RBPs in peripheral nerve axons. We detected 76 proteins with reported RNA binding activity in axoplasm, and levels of several change with axon injury and regeneration. RBPs with altered levels include KHSRP that decreases neurite outgrowth in developing CNS neurons. Axonal KHSRP levels rapidly increase after injury remaining elevated up to 28 days post axotomy. Khsrp mRNA localizes into axons and the rapid increase in axonal KHSRP is through local translation of Khsrp mRNA in axons. KHSRP can bind to mRNAs with 3’UTR AU-rich elements and targets those transcripts to the cytoplasmic exosome for degradation. KHSRP knockout mice show increased axonal levels of KHSRP target mRNAs, Gap43, Snap25, and Fubp1, following sciatic nerve injury and these mice show accelerated nerve regeneration in vivo. Together, our data indicate that axonal translation of the RNA binding protein Khsrp mRNA following nerve injury serves to promote decay of other axonal mRNAs and slow axon regeneration.
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Affiliation(s)
- Priyanka Patel
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Courtney N Buchanan
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Matthew D Zdradzinski
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Pabitra K Sahoo
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Amar N Kar
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Seung Joon Lee
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Lauren S Vaughn
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Anatoly Urisman
- Department of Pharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
| | - Juan Oses-Prieto
- Department of Pharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
| | - Michela Dell'Orco
- Department of Neurosciences, University of New Mexico School of Health Sciences, Albuquerque, NM 87131, USA
| | - Devon E Cassidy
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Irene Dalla Costa
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Sharmina Miller
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Elizabeth Thames
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Terika P Smith
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
| | - Nora Perrone-Bizzozero
- Department of Neurosciences, University of New Mexico School of Health Sciences, Albuquerque, NM 87131, USA
| | - Jeffery L Twiss
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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13
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Cuevas-Navarro A, Rodriguez-Muñoz L, Grego-Bessa J, Cheng A, Rauen KA, Urisman A, McCormick F, Jimenez G, Castel P. Cross-species analysis of LZTR1 loss-of-function mutants demonstrates dependency to RIT1 orthologs. eLife 2022; 11:76495. [PMID: 35467524 PMCID: PMC9068208 DOI: 10.7554/elife.76495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/22/2022] [Indexed: 11/25/2022] Open
Abstract
RAS GTPases are highly conserved proteins involved in the regulation of mitogenic signaling. We have previously described a novel Cullin 3 RING E3 ubiquitin ligase complex formed by the substrate adaptor protein LZTR1 that binds, ubiquitinates, and promotes proteasomal degradation of the RAS GTPase RIT1. In addition, others have described that this complex is also responsible for the ubiquitination of classical RAS GTPases. Here, we have analyzed the phenotypes of Lztr1 loss-of-function mutants in both fruit flies and mice and have demonstrated a biochemical preference for their RIT1 orthologs. Moreover, we show that Lztr1 is haplosufficient in mice and that embryonic lethality of the homozygous null allele can be rescued by deletion of Rit1. Overall, our results indicate that, in model organisms, RIT1 orthologs are the preferred substrates of LZTR1.
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Affiliation(s)
- Antonio Cuevas-Navarro
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
| | - Laura Rodriguez-Muñoz
- Institute for Molecular Biology of Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Joaquim Grego-Bessa
- Intercellular Signalling in Cardiovascular Development and Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Alice Cheng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
| | - Katherine A Rauen
- MIND Institute, University of California, Davis, Sacramento, United States
| | - Anatoly Urisman
- Department of Anatomic Pathology, University of California, San Francisco, San Francisco, United States
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
| | - Gerardo Jimenez
- Institute for Molecular Biology of Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Pau Castel
- Department of Biochemistry and Molecular Pharmacology, New York University, New York, United States
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14
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Maheshwari J, Perez A, Kolaitis N, Calabrese D, Estrada AV, Golden J, Shah R, Leard L, Kleinhenz M, Jones K, Urisman A, Kukreja J, Trinh B, Gesthalter Y, Singer J, Hays S. Immunosuppression-Induced Pulmonary Alveolar Proteinosis Following Bilateral Lung Transplantation. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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15
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Essien F, Evans J, Kyle A, Urisman A, Adams N. 'Granulomatosis with polyangiitis after Pfizer vaccination': a case report. Ther Adv Rare Dis 2022; 3:26330040221130084. [PMID: 37180416 PMCID: PMC10032451 DOI: 10.1177/26330040221130084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/14/2022] [Indexed: 05/16/2023]
Abstract
The advent of COVID-19, caused by the SARS-CoV-2 virus, has resulted in over 541 million cases with 6.32 million deaths worldwide as of June 2022. The devastating consequences of this global pandemic resulted in the expedited generation of mRNA-based vaccines such as the Pfizer-BioNTech and Moderna vaccines. Although the vaccines have been effective, with recent data indicating greater than 95% effectiveness, rare complications have been reported, including manifestations of autoimmune phenomena. Herein, we report a rare case of Granulomatosis with polyangiitis (GPA) in an active duty military male soon after receiving the first dose of the Pfizer-BioNTech COVID-19 vaccine.
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Affiliation(s)
- Francis Essien
- Department of Internal Medicine, David Grant
USAF Medical Center, Travis Air Force Base, 101 Bodin Circle, Fairfield, CA
94535, USA
| | - Jordan Evans
- Division of Nephrology, Department of Internal
Medicine, David Grant USAF Medical Center, Travis Air Force Base, Fairfield,
CA, USA
| | - Andrew Kyle
- Department of Internal Medicine, David Grant
USAF Medical Center, Travis Air Force Base, Fairfield, CA, USA
| | - Anatoly Urisman
- Department of Pathology, University of
California San Francisco, San Francisco, CA, USA
| | - Nicholas Adams
- Department of Radiology, David Grant USAF
Medical Center, Travis Air Force Base, Fairfield, CA, USA
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16
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Bean GR, Najjar S, Shin SJ, Hosfield EM, Caswell-Jin JL, Urisman A, Jones KD, Chen YY, Krings G. Correction to: Genetic and immunohistochemical profiling of small cell and large cell neuroendocrine carcinomas of the breast. Mod Pathol 2022; 35:1494-1495. [PMID: 35697932 PMCID: PMC9514987 DOI: 10.1038/s41379-022-01099-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gregory R. Bean
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, Stanford, CA USA
| | - Saleh Najjar
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, Stanford, CA USA
| | - Sandra J. Shin
- grid.413558.e0000 0001 0427 8745Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY USA
| | - Elizabeth M. Hosfield
- grid.414890.00000 0004 0461 9476Department of Pathology, Kaiser Permanente San Francisco Medical Center, San Francisco, CA USA
| | - Jennifer L. Caswell-Jin
- grid.168010.e0000000419368956Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA USA
| | - Anatoly Urisman
- grid.266102.10000 0001 2297 6811Department of Pathology, University of California San Francisco, San Francisco, CA USA
| | - Kirk D. Jones
- grid.266102.10000 0001 2297 6811Department of Pathology, University of California San Francisco, San Francisco, CA USA
| | - Yunn-Yi Chen
- grid.266102.10000 0001 2297 6811Department of Pathology, University of California San Francisco, San Francisco, CA USA
| | - Gregor Krings
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
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17
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Bean GR, Najjar S, Shin SJ, Hosfield EM, Caswell-Jin JL, Urisman A, Jones KD, Chen YY, Krings G. Genetic and immunohistochemical profiling of small cell and large cell neuroendocrine carcinomas of the breast. Mod Pathol 2022; 35:1349-1361. [PMID: 35590107 PMCID: PMC9514991 DOI: 10.1038/s41379-022-01090-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 11/09/2022]
Abstract
Neuroendocrine carcinomas (NEC) of the breast are exceedingly rare tumors, which are classified in the WHO system as small cell (SCNEC) and large cell (LCNEC) carcinoma based on indistinguishable features from their lung counterparts. In contrast to lung and enteropancreatic NEC, the genomics of breast NEC have not been well-characterized. In this study, we examined the clinicopathologic, immunohistochemical, and genetic features of 13 breast NEC (7 SCNEC, 4 LCNEC, 2 NEC with ambiguous small versus large cell morphology [ANEC]). Co-alterations of TP53 and RB1 were identified in 86% (6/7) SCNEC, 100% (2/2) ANEC, and 50% (2/4) LCNEC. The one SCNEC without TP53/RB1 alteration had other p53 pathway aberrations (MDM2 and MDM4 amplification) and was immunohistochemically RB negative. PIK3CA/PTEN pathway alterations and ZNF703 amplifications were each identified in 46% (6/13) NEC. Two tumors (1 SCNEC, 1 LCNEC) were CDH1 mutated. By immunohistochemistry, 100% SCNEC (6/6) and ANEC (2/2) and 50% (2/4) LCNEC (83% NEC) showed RB loss, compared to 0% (0/8) grade 3 neuroendocrine tumors (NET) (p < 0.001) and 38% (36/95) grade 3 invasive ductal carcinomas of no special type (IDC-NST) (p = 0.004). NEC were also more often p53 aberrant (60% vs 0%, p = 0.013), ER negative (69% vs 0%, p = 0.005), and GATA3 negative (67% vs 0%, p = 0.013) than grade 3 NET. Two mixed NEC had IDC-NST components, and 69% (9/13) of tumors were associated with carcinoma in situ (6 neuroendocrine DCIS, 2 non-neuroendocrine DCIS, 1 non-neuroendocrine LCIS). NEC and IDC-NST components of mixed tumors were clonally related and immunophenotypically distinct, lacking ER and GATA3 expression in NEC relative to IDC-NST, with RB loss only in NEC of one ANEC. The findings provide insight into the pathogenesis of breast NEC, underscore their classification as a distinct tumor type, and highlight genetic similarities to extramammary NEC, including highly prevalent p53/RB pathway aberrations in SCNEC.
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Affiliation(s)
- Gregory R. Bean
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, Stanford, CA USA
| | - Saleh Najjar
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, Stanford, CA USA
| | - Sandra J. Shin
- grid.413558.e0000 0001 0427 8745Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY USA
| | - Elizabeth M. Hosfield
- grid.414890.00000 0004 0461 9476Department of Pathology, Kaiser Permanente San Francisco Medical Center, San Francisco, CA USA
| | - Jennifer L. Caswell-Jin
- grid.168010.e0000000419368956Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA USA
| | - Anatoly Urisman
- grid.266102.10000 0001 2297 6811Department of Pathology, University of California San Francisco, San Francisco, CA USA
| | - Kirk D. Jones
- grid.266102.10000 0001 2297 6811Department of Pathology, University of California San Francisco, San Francisco, CA USA
| | - Yunn-Yi Chen
- grid.266102.10000 0001 2297 6811Department of Pathology, University of California San Francisco, San Francisco, CA USA
| | - Gregor Krings
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
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18
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Blakely C, Urisman A, Kerr D, Wu W, Bacaltos B, Rotow J, Gubens M, Jones K, Bivona T, Joo S, Riess J, Aisner D, Doebele R, Patil T, Schenk E, Kratz J, Jablons D. P26.02 A Phase II Trial of Neoadjuvant Osimertinib for Surgically Resectable EGFR-Mutant Non-Small Cell Lung Cancer: Updated Results. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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19
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Castel P, Dharmaiah S, Sale MJ, Messing S, Rizzuto G, Cuevas-Navarro A, Cheng A, Trnka MJ, Urisman A, Esposito D, Simanshu DK, McCormick F. RAS interaction with Sin1 is dispensable for mTORC2 assembly and activity. Proc Natl Acad Sci U S A 2021; 118:e2103261118. [PMID: 34380736 PMCID: PMC8379911 DOI: 10.1073/pnas.2103261118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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] [Indexed: 12/14/2022] Open
Abstract
RAS proteins are molecular switches that interact with effector proteins when bound to guanosine triphosphate, stimulating downstream signaling in response to multiple stimuli. Although several canonical downstream effectors have been extensively studied and tested as potential targets for RAS-driven cancers, many of these remain poorly characterized. In this study, we undertook a biochemical and structural approach to further study the role of Sin1 as a RAS effector. Sin1 interacted predominantly with KRAS isoform 4A in cells through an atypical RAS-binding domain that we have characterized by X-ray crystallography. Despite the essential role of Sin1 in the assembly and activity of mTORC2, we find that the interaction with RAS is not required for these functions. Cells and mice expressing a mutant of Sin1 that is unable to bind RAS are proficient for activation and assembly of mTORC2. Our results suggest that Sin1 is a bona fide RAS effector that regulates downstream signaling in an mTORC2-independent manner.
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Affiliation(s)
- Pau Castel
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158
| | - Srisathiyanarayanan Dharmaiah
- National Cancer Institute (NCI) RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Matthew J Sale
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158
| | - Simon Messing
- National Cancer Institute (NCI) RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Gabrielle Rizzuto
- Department of Anatomic Pathology, University of California, San Francisco, CA 94158
| | - Antonio Cuevas-Navarro
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158
| | - Alice Cheng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Anatoly Urisman
- Department of Anatomic Pathology, University of California, San Francisco, CA 94158
| | - Dominic Esposito
- National Cancer Institute (NCI) RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Dhirendra K Simanshu
- National Cancer Institute (NCI) RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702;
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158;
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20
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May RM, Cassol C, Hannoudi A, Larsen CP, Lerma E, Haun RS, Braga JR, Hassen SI, Wilson J, VanBeek C, Vankalakunti M, Barnum L, Walker PD, Bourne TD, Messias NC, Ambruzs JM, Boils CL, Sharma SS, Cossey LN, Baxi PV, Palmer M, Zuckerman J, Walavalkar V, Urisman A, Gallan A, Al-Rabadi LF, Rodby R, Luyckx V, Espino G, Santhana-Krishnan S, Alper B, Lam SG, Hannoudi GN, Matthew D, Belz M, Singer G, Kunaparaju S, Price D, Sauabh C, Rondla C, Abdalla MA, Britton ML, Paul S, Ranjit U, Bichu P, Williamson SR, Sharma Y, Gaspert A, Grosse P, Meyer I, Vasudev B, El Kassem M, Velez JCQ, Caza TN. A multi-center retrospective cohort study defines the spectrum of kidney pathology in Coronavirus 2019 Disease (COVID-19). Kidney Int 2021; 100:1303-1315. [PMID: 34352311 PMCID: PMC8328528 DOI: 10.1016/j.kint.2021.07.015] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/14/2021] [Accepted: 07/23/2021] [Indexed: 12/12/2022]
Abstract
Kidney failure is common in patients with Coronavirus Disease-19 (COVID-19) resulting in increased morbidity and mortality. In an international collaboration, 284 kidney biopsies were evaluated to improve understanding of kidney disease in COVID-19. Diagnoses were compared to five years of 63,575 native biopsies prior to the pandemic and 13,955 allograft biopsies to identify diseases increased in patients with COVID-19. Genotyping for APOL1 G1 and G2 alleles was performed in 107 African American and Hispanic patients. Immunohistochemistry for SARS-CoV-2 was utilized to assess direct viral infection in 273 cases along with clinical information at the time of biopsy. The leading indication for native biopsy was acute kidney injury (45.4%), followed by proteinuria with or without concurrent acute kidney injury (42.6%). There were more African American patients (44.6%) than patients of other ethnicities. The most common diagnosis in native biopsies was collapsing glomerulopathy (25.8%) which associated with high-risk APOL1 genotypes in 91.7% of cases. Compared to the five-year biopsy database, the frequency of myoglobin cast nephropathy and proliferative glomerulonephritis with monoclonal IgG deposits was also increased in patients with COVID-19 (3.3% and 1.7%, respectively), while there was a reduced frequency of chronic conditions (including diabetes mellitus, IgA nephropathy, and arterionephrosclerosis) as the primary diagnosis. In transplants, the leading indication was acute kidney injury (86.4%), for which rejection was the predominant diagnosis (61.4%). Direct SARS-CoV-2 viral infection was not identified. Thus, our multi-center large case series identified kidney diseases that disproportionately affect patients with COVID-19, demonstrated a high frequency of APOL1 high-risk genotypes within this group, with no evidence of direct viral infection within the kidney.
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Affiliation(s)
- Rebecca M May
- Arkana Laboratories, 10810 Executive Center Drive #100, Little Rock AR USA 72211
| | - Clarissa Cassol
- Arkana Laboratories, 10810 Executive Center Drive #100, Little Rock AR USA 72211
| | - Andrew Hannoudi
- University of Michigan, 500 S State Street, Ann Arbor, MI USA 48109
| | - Christopher P Larsen
- Arkana Laboratories, 10810 Executive Center Drive #100, Little Rock AR USA 72211
| | - Edgar Lerma
- University of Illinois at Chicago College of Medicine / Advocate Christ Medical Center, Department of Internal Medicine, 1853 W Polk St, Oak Lawn IL USA 60612
| | - Randy S Haun
- Arkana Laboratories, 10810 Executive Center Drive #100, Little Rock AR USA 72211
| | - Juarez R Braga
- University of Arkansas for Medical Sciences, Nephrology Division, 4301 W Markham St, Little Rock, AR USA 72205
| | - Samar I Hassen
- Arkana Laboratories, 10810 Executive Center Drive #100, Little Rock AR USA 72211
| | - Jon Wilson
- Arkana Laboratories, 10810 Executive Center Drive #100, Little Rock AR USA 72211
| | - Christine VanBeek
- AmeriPath Laboratories, Pathology, 225 N.E. 97(th) St #600, Oklahoma City OK USA 73114
| | - Mahesha Vankalakunti
- Manipal Hospital - Bangalore, Department of Pathology, 98 HAL Old Airport Rd, Bangalore, Karnataka India 560017
| | - Lilli Barnum
- Arkana Laboratories, 10810 Executive Center Drive #100, Little Rock AR USA 72211
| | - Patrick D Walker
- Arkana Laboratories, 10810 Executive Center Drive #100, Little Rock AR USA 72211
| | - T David Bourne
- Arkana Laboratories, 10810 Executive Center Drive #100, Little Rock AR USA 72211
| | - Nidia C Messias
- Arkana Laboratories, 10810 Executive Center Drive #100, Little Rock AR USA 72211
| | - Josephine M Ambruzs
- Arkana Laboratories, 10810 Executive Center Drive #100, Little Rock AR USA 72211
| | - Christie L Boils
- Arkana Laboratories, 10810 Executive Center Drive #100, Little Rock AR USA 72211
| | - Shree S Sharma
- Arkana Laboratories, 10810 Executive Center Drive #100, Little Rock AR USA 72211
| | - L Nicholas Cossey
- Arkana Laboratories, 10810 Executive Center Drive #100, Little Rock AR USA 72211
| | - Pravir V Baxi
- Rush University Medical Center, Nephrology Division, 1620 W. Harrison St, Chicago IL USA 60612
| | - Matthew Palmer
- University of Pennsylvania Perelman School of Medicine, Department of Pathology, 3400 Civic Center Blvd, Philadelphia PA USA 19104
| | - Jonathan Zuckerman
- University of California Los Angeles Health System, Department of Pathology and Laboratory Medicine, 140833 Le Conte Ave, Los Angeles, CA USA 90095
| | - Vighnesh Walavalkar
- UCSF Medical Center, Department of Pathology, 505 Panassus Avenue, CA USA 92103
| | - Anatoly Urisman
- UCSF Medical Center, Department of Pathology, 505 Panassus Avenue, CA USA 92103
| | - Alexander Gallan
- Medical College of Wisconsin, 9200 W. Wisconsin Avenue, WDL Building L73, Milkaukee, WI USA 53226
| | - Laith F Al-Rabadi
- University of Utah School of Medicine, 50 N Medical Drive, Salt Lake City UT 84132
| | - Roger Rodby
- Rush University Medical Center, Nephrology Division, 1620 W. Harrison St, Chicago IL USA 60612
| | - Valerie Luyckx
- University of Zurich, Department of Pathology and Molecular Biology, University Hospital Zurich, Schmelzberstrasse 8091, Zurich, Switzerland; Brigham and Women's Hospital, Renal Division, 75 Francis Street, Boston, MA USA 02115
| | - Gusavo Espino
- Albuquerque Nephrology Associates, 4333 Pan American Fwy NE, Albuquerque, NM USA 87107
| | | | - Brent Alper
- Tulane University School of Medicine, Tulane University Hypertension and Renal Center of Excellence, 6823 St. Charles Avenue, New Orleans, LA USA 70118; Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA USA 70112
| | - Son G Lam
- Nephrology and Hypertension Associated LTD, 1790 Barron Street, Oxford, MS USA 38655
| | - Ghadeer N Hannoudi
- Michigan Kidney Consultants, 44200 Woodward Ave, Suite 209, Pontiac, MI USA 48341
| | - Dwight Matthew
- Shoals Kidney & Hypertension Center, 422 East Dr Hicks Boulevard, Suite A, Florence, AL USA 35630
| | - Mark Belz
- Iowa Kidney Physicians PC, 1215 Pleasant Street, Suite 100, Des Moines, IA USA 50309
| | - Gary Singer
- Midwest Nephrology Associates, 70 Jungermann Circle, Suite 405, St. Peters, MO USA 63376
| | - Srikanth Kunaparaju
- Richmond Nephrology Associates, 7001 West Broad Street, Suite A, Richmond, VA USA 23294
| | - Deborah Price
- Nephrology Associates of NE Florida, 2 Shircliff Way DePaul Bldg Suite 700, Jacksonville, FL USA 32204
| | - Chawla Sauabh
- Northwest Indiana Nephrology, 6061 Broadway, Merrillville, IN USA 46410
| | - Chetana Rondla
- Georgia Nephrology, 595 Hurricane Shoals Road NW, Suite 100, Lawrenceville, GA USA 30046
| | - Mazen A Abdalla
- The Kidney Clinic, 2386 Clower Street, Suite C105, Snellville, GA USA 30078
| | - Marcus L Britton
- Nephrology & Hypertension Associates LTD, 1542 Medical Park Circle, Tupelo, MS USA 38801
| | - Subir Paul
- Shoals Kidney & Hypertension Center, 422 East Dr Hicks Boulevard, Suite A, Florence, AL USA 35630
| | - Uday Ranjit
- Nephrology Associates of Central Florida, 2501 N Orange Avenue #53, Orlando, FL USA 32804
| | - Prasad Bichu
- Nephrology Associates of Tidewater Ltd., Norfolk, VA USA 23510
| | | | - Yuvraj Sharma
- Henry Ford Hospital, 2799 W Grand Blvd, Detroit, MI USA 48202
| | - Ariana Gaspert
- Kantonal Hospital of Graubunden, Loestrasse 170, CH-7000, Chur, Switzerland
| | - Phillipp Grosse
- University of Zurich, Department of Pathology and Molecular Biology, University Hospital Zurich, Schmelzberstrasse 8091, Zurich, Switzerland
| | - Ian Meyer
- Mt Auburn Nephrology, 8260 Pine Road, Cincinnati OH USA 45236
| | - Brahm Vasudev
- Medical College of Wisconsin, 9200 W. Wisconsin Avenue, WDL Building L73, Milkaukee, WI USA 53226
| | - Mohamad El Kassem
- Mohamad El Kassem MD (private practice), Nephrology, Coral Springs, FL USA
| | - Juan Carlos Q Velez
- Ochsner Health System, Deparment of Nephrology, 1514 Jefferson Hwy, New Orleans LA USA 70121; Ochsner Clinical School, The University of Queensland (Australia), Department of Nephrology, St. Lucia, QLD, AUS
| | - Tiffany N Caza
- Arkana Laboratories, 10810 Executive Center Drive #100, Little Rock AR USA 72211.
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21
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Aguirre A, Urisman A, Margaretten M. Starting off on the right foot: A 22-year-old woman with leg swelling. Arthritis Care Res (Hoboken) 2021; 74:701-708. [PMID: 34197038 DOI: 10.1002/acr.24738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/27/2021] [Accepted: 06/29/2021] [Indexed: 11/08/2022]
Abstract
A previously healthy 22-year-old woman was in the second trimester of her first pregnancy when she developed new lower extremity edema. Her pregnancy course had been unremarkable, and she was receiving routine obstetric care from her family physician. One week prior to admission she developed progressive swelling in her legs.
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Affiliation(s)
- Alfredo Aguirre
- University of California, San Francisco, Department of Medicine, Division of Rheumatology
| | - Anatoly Urisman
- University of California, San Francisco, Department of Pathology
| | - Mary Margaretten
- University of California, San Francisco, Department of Medicine, Division of Rheumatology
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22
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Gu W, Talevich E, Hsu E, Qi Z, Urisman A, Federman S, Gopez A, Arevalo S, Gottschall M, Liao L, Tung J, Chen L, Lim H, Ho C, Kasowski M, Oak J, Holmes BJ, Yeh I, Yu J, Wang L, Miller S, DeRisi JL, Prakash S, Simko J, Chiu CY. Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids. Genome Med 2021; 13:98. [PMID: 34074327 PMCID: PMC8167833 DOI: 10.1186/s13073-021-00912-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 07/18/2020] [Accepted: 05/20/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) of body fluids is an emerging approach to identify occult pathogens in undiagnosed patients. We hypothesized that metagenomic testing can be simultaneously used to detect malignant neoplasms in addition to infectious pathogens. METHODS From two independent studies (n = 205), we used human data generated from a metagenomic sequencing pipeline to simultaneously screen for malignancies by copy number variation (CNV) detection. In the first case-control study, we analyzed body fluid samples (n = 124) from patients with a clinical diagnosis of either malignancy (positive cases, n = 65) or infection (negative controls, n = 59). In a second verification cohort, we analyzed a series of consecutive cases (n = 81) sent to cytology for malignancy workup that included malignant positives (n = 32), negatives (n = 18), or cases with an unclear gold standard (n = 31). RESULTS The overall CNV test sensitivity across all studies was 87% (55 of 63) in patients with malignancies confirmed by conventional cytology and/or flow cytometry testing and 68% (23 of 34) in patients who were ultimately diagnosed with cancer but negative by conventional testing. Specificity was 100% (95% CI 95-100%) with no false positives detected in 77 negative controls. In one example, a patient hospitalized with an unknown pulmonary illness had non-diagnostic lung biopsies, while CNVs implicating a malignancy were detectable from bronchoalveolar fluid. CONCLUSIONS Metagenomic sequencing of body fluids can be used to identify undetected malignant neoplasms through copy number variation detection. This study illustrates the potential clinical utility of a single metagenomic test to uncover the cause of undiagnosed acute illnesses due to cancer or infection using the same specimen.
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Affiliation(s)
- Wei Gu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94107, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA.
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA.
- Stanford Health Care, Stanford University, Stanford, CA, 94305, USA.
| | | | - Elaine Hsu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94107, USA
| | - Zhongxia Qi
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94107, USA
| | - Anatoly Urisman
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94107, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94107, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA
| | - Allan Gopez
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94107, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA
| | - Shaun Arevalo
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94107, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA
| | - Marc Gottschall
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94107, USA
| | - Linda Liao
- Stanford Health Care, Stanford University, Stanford, CA, 94305, USA
| | - Jack Tung
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Lei Chen
- Stanford Health Care, Stanford University, Stanford, CA, 94305, USA
| | - Harumi Lim
- Stanford Health Care, Stanford University, Stanford, CA, 94305, USA
| | - Chandler Ho
- Stanford Health Care, Stanford University, Stanford, CA, 94305, USA
| | - Maya Kasowski
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Jean Oak
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
- Stanford Health Care, Stanford University, Stanford, CA, 94305, USA
| | - Brittany J Holmes
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
- Stanford Health Care, Stanford University, Stanford, CA, 94305, USA
| | - Iwei Yeh
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94107, USA
| | - Jingwei Yu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94107, USA
| | - Linlin Wang
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94107, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94107, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94107, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94107, USA
| | - Sonam Prakash
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94107, USA
| | - Jeff Simko
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94107, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94107, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA.
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, 94107, USA.
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23
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Shashiprakash AK, Lutnick B, Ginley B, Govind D, Lucarelli N, Jen KY, Rosenberg AZ, Urisman A, Walavalkar V, Zuckerman JE, Delsante M, Bissonnette MLZ, Tomaszewski JE, Manthey D, Sarder P. A Distributed System Improves Inter-Observer and AI Concordance in Annotating Interstitial Fibrosis and Tubular Atrophy. Proc SPIE Int Soc Opt Eng 2021; 11603. [PMID: 34366540 DOI: 10.1117/12.2581789] [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] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Histologic examination of interstitial fibrosis and tubular atrophy (IFTA) is critical to determine the extent of irreversible kidney injury in renal disease. The current clinical standard involves pathologist's visual assessment of IFTA, which is prone to inter-observer variability. To address this diagnostic variability, we designed two case studies (CSs), including seven pathologists, using HistomicsTK- a distributed system developed by Kitware Inc. (Clifton Park, NY). Twenty-five whole slide images (WSIs) were classified into a training set of 21 and a validation set of four. The training set was composed of seven unique subsets, each provided to an individual pathologist along with four common WSIs from the validation set. In CS 1, all pathologists individually annotated IFTA in their respective slides. These annotations were then used to train a deep learning algorithm to computationally segment IFTA. In CS 2, manual and computational annotations from CS 1 were first reviewed by the annotators to improve concordance of IFTA annotation. Both the manual and computational annotation processes were then repeated as in CS1. The inter-observer concordance in the validation set was measured by Krippendorff's alpha (KA). The KA for the seven pathologists in CS1 was 0.62 with CI [0.57, 0.67], and after reviewing each other's annotations in CS2, 0.66 with CI [0.60, 0.72]. The respective CS1 and CS2 KA were 0.58 with CI [0.52, 0.64] and 0.63 with CI [0.56, 0.69] when including the deep learner as an eighth annotator. These results suggest that our designed annotation framework refines agreement of spatial annotation of IFTA and demonstrates a human-AI approach to significantly improve the development of computational models.
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Affiliation(s)
| | - Brendon Lutnick
- Department of Pathology and Anatomical Sciences, University at Buffalo - The State University of New York
| | - Brandon Ginley
- Department of Pathology and Anatomical Sciences, University at Buffalo - The State University of New York
| | - Darshana Govind
- Department of Pathology and Anatomical Sciences, University at Buffalo - The State University of New York
| | - Nicholas Lucarelli
- Department of Biomedical Engineering, University at Buffalo - The State University of New York
| | - Kuang-Yu Jen
- Department of Pathology, University of California at Davis
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine
| | - Anatoly Urisman
- Department of Pathology, University of California San Francisco
| | | | - Jonathan E Zuckerman
- Department of Pathology and Laboratory Medicine, University of California Los Angeles
| | - Marco Delsante
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Mei Lin Z Bissonnette
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - John E Tomaszewski
- Department of Biomedical Engineering, University at Buffalo - The State University of New York
| | | | - Pinaki Sarder
- Department of Pathology and Anatomical Sciences, University at Buffalo - The State University of New York
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24
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Cleary SJ, Kwaan N, Tian JJ, Calabrese DR, Mallavia B, Magnen M, Greenland JR, Urisman A, Singer JP, Hays SR, Kukreja J, Hay AM, Howie HL, Toy P, Lowell CA, Morrell CN, Zimring JC, Looney MR. Complement activation on endothelium initiates antibody-mediated acute lung injury. J Clin Invest 2020; 130:5909-5923. [PMID: 32730229 PMCID: PMC7598054 DOI: 10.1172/jci138136] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/22/2020] [Indexed: 12/11/2022] Open
Abstract
Antibodies targeting human leukocyte antigen (HLA)/major histocompatibility complex (MHC) proteins limit successful transplantation and transfusion, and their presence in blood products can cause lethal transfusion-related acute lung injury (TRALI). It is unclear which cell types are bound by these anti-leukocyte antibodies to initiate an immunologic cascade resulting in lung injury. We therefore conditionally removed MHC class I (MHC I) from likely cellular targets in antibody-mediated lung injury. Only the removal of endothelial MHC I reduced lung injury and mortality, related mechanistically to absent endothelial complement fixation and lung platelet retention. Restoration of endothelial MHC I rendered MHC I-deficient mice susceptible to lung injury. Neutrophil responses, including neutrophil extracellular trap (NET) release, were intact in endothelial MHC I-deficient mice, whereas complement depletion reduced both lung injury and NETs. Human pulmonary endothelial cells showed high HLA class I expression, and posttransfusion complement activation was increased in clinical TRALI. These results indicate that the critical source of antigen for anti-leukocyte antibodies is in fact the endothelium, which reframes our understanding of TRALI as a rapid-onset vasculitis. Inhibition of complement activation may have multiple beneficial effects of reducing endothelial injury, platelet retention, and NET release in conditions where antibodies trigger these pathogenic responses.
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Affiliation(s)
- Simon J. Cleary
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Nicholas Kwaan
- Department of Medicine, UCSF, San Francisco, California, USA
| | | | - Daniel R. Calabrese
- Department of Medicine, UCSF, San Francisco, California, USA
- Veterans Affairs Healthcare System, San Francisco, California, USA
| | - Beñat Mallavia
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Mélia Magnen
- Department of Medicine, UCSF, San Francisco, California, USA
| | - John R. Greenland
- Department of Medicine, UCSF, San Francisco, California, USA
- Veterans Affairs Healthcare System, San Francisco, California, USA
| | | | | | - Steven R. Hays
- Department of Medicine, UCSF, San Francisco, California, USA
| | | | - Ariel M. Hay
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Heather L. Howie
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Pearl Toy
- Department of Laboratory Medicine, UCSF, San Francisco, California, USA
| | | | - Craig N. Morrell
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - James C. Zimring
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Mark R. Looney
- Department of Medicine, UCSF, San Francisco, California, USA
- Department of Laboratory Medicine, UCSF, San Francisco, California, USA
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25
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Lorenzo C, Young LC, Tannka A, Urisman A, McCormick F. Abstract 3765: c-Kit mediated phosphorylation of Spred1 regulates Neurofibromin-Spred1 interaction. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3765] [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
Spred1 negatively regulates Ras/MAPK signaling following growth factor stimulation. Spred1 inhibits Ras by binding and localizing Neurofibromin, a RasGAP, to the plasma membrane to accelerate Ras GTPase activity. c-Kit, a receptor tyrosine kinase (RTK), is known to interact with Spred1 but the consequence of this interaction is unknown. Here we demonstrate that c-Kit signaling regulates Neurofibromin-Spred1 interaction. Stimulation with c-Kit ligand, SCF, results in a transient disruption in Neurofibromin-Spred1 binding which corresponds to increased Ras signaling, followed by restoration of Neurofibromin-Spred binding which corresponds to nearly basal levels of Ras signaling. Mass spectrometry analysis identified potential phosphorylation sites on Spred1 that correspond to the initial disruption and later restoration of Neurofibromin-Spred1 binding. Phosphomimetic and phosphodeficient mutants affect the interaction. Our findings provide a potential mechanism by which RTK signaling regulates negative feedback to allow transient activation and subsequent termination of Ras signaling.
Citation Format: Claire Lorenzo, Lucy C. Young, Alexandra Tannka, Anatoly Urisman, Frank McCormick. c-Kit mediated phosphorylation of Spred1 regulates Neurofibromin-Spred1 interaction [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3765.
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26
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Yan W, Markegard E, Dharmaiah S, Urisman A, Drew M, Esposito D, Scheffzek K, Nissley DV, McCormick F, Simanshu DK. Structural Insights into the SPRED1-Neurofibromin-KRAS Complex and Disruption of SPRED1-Neurofibromin Interaction by Oncogenic EGFR. Cell Rep 2020; 32:107909. [PMID: 32697994 PMCID: PMC7437355 DOI: 10.1016/j.celrep.2020.107909] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/25/2020] [Accepted: 06/24/2020] [Indexed: 02/07/2023] Open
Abstract
Sprouty-related, EVH1 domain-containing (SPRED) proteins negatively regulate RAS/mitogen-activated protein kinase (MAPK) signaling following growth factor stimulation. This inhibition of RAS is thought to occur primarily through SPRED1 binding and recruitment of neurofibromin, a RasGAP, to the plasma membrane. Here, we report the structure of neurofibromin (GTPase-activating protein [GAP]-related domain) complexed with SPRED1 (EVH1 domain) and KRAS. The structure provides insight into how the membrane targeting of neurofibromin by SPRED1 allows simultaneous interaction with activated KRAS. SPRED1 and NF1 loss-of-function mutations occur across multiple cancer types and developmental diseases. Analysis of the neurofibromin-SPRED1 interface provides a rationale for mutations observed in Legius syndrome and suggests why SPRED1 can bind to neurofibromin but no other RasGAPs. We show that oncogenic EGFR(L858R) signaling leads to the phosphorylation of SPRED1 on serine 105, disrupting the SPRED1-neurofibromin complex. The structural, biochemical, and biological results provide new mechanistic insights about how SPRED1 interacts with neurofibromin and regulates active KRAS levels in normal and pathologic conditions.
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Affiliation(s)
- Wupeng Yan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Evan Markegard
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Srisathiyanarayanan Dharmaiah
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Anatoly Urisman
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Matthew Drew
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Klaus Scheffzek
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA.
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27
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Miao J, Kyoyama H, Liu L, Chan G, Wang Y, Urisman A, Yang Y, Liu S, Xu Z, Bin H, Li H, Jablons DM, You L. Inhibition of cyclin-dependent kinase 7 down-regulates yes-associated protein expression in mesothelioma cells. J Cell Mol Med 2020; 24:1087-1098. [PMID: 31755214 PMCID: PMC6933402 DOI: 10.1111/jcmm.14841] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 09/30/2019] [Accepted: 10/20/2019] [Indexed: 01/23/2023] Open
Abstract
Cyclin-dependent kinase 7 (CDK7) is a protein kinase that plays a major role in transcription initiation. Yes-associated protein (YAP) is a main effector of the Hippo/YAP signalling pathway. Here, we investigated the role of CDK7 on YAP regulation in human malignant pleural mesothelioma (MPM). We found that in microarray samples of human MPM tissue, immunohistochemistry staining showed correlation between the expression level of CDK7 and YAP (n = 70, r = .513). In MPM cells, CDK7 expression level was significantly correlated with GTIIC reporter activity (r = .886, P = .019). Inhibition of CDK7 by siRNA decreased the YAP protein level and the GTIIC reporter activity in the MPM cell lines 211H, H290 and H2052. Degradation of the YAP protein was accelerated after CDK7 knockdown in 211H, H290 and H2052 cells. Inhibition of CDK7 reduced tumour cell migration and invasion, as well as tumorsphere formation ability. Restoration of the CDK7 gene rescued the YAP protein level and GTIIC reporter activity after siRNA knockdown in 211H and H2052 cells. Finally, we performed a co-immunoprecipitation analysis using an anti-YAP antibody and captured the CDK7 protein in 211H cells. Our results suggest that CDK7 inhibition reduces the YAP protein level by promoting its degradation and suppresses the migration and invasion of MPM cells. Cyclin-dependent kinase 7 may be a promising therapeutic target for MPM.
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Affiliation(s)
- Jinbai Miao
- Department of SurgeryThoracic Oncology LaboratoryComprehensive Cancer CenterUniversity of CaliforniaSan FranciscoCAUSA
- Department of Thoracic SurgeryBeijing Chao‐Yang HospitalAffiliated with Capital Medical UniversityBeijingChina
| | - Hiroyuki Kyoyama
- Department of SurgeryThoracic Oncology LaboratoryComprehensive Cancer CenterUniversity of CaliforniaSan FranciscoCAUSA
| | - Luwei Liu
- Department of SurgeryThoracic Oncology LaboratoryComprehensive Cancer CenterUniversity of CaliforniaSan FranciscoCAUSA
- Class of 2018Stony Brook UniversityStony BrookNYUSA
| | - Geraldine Chan
- Department of SurgeryThoracic Oncology LaboratoryComprehensive Cancer CenterUniversity of CaliforniaSan FranciscoCAUSA
- Class of 2020Medical College of WisconsinMilwaukeeWIUSA
| | - Yucheng Wang
- Department of SurgeryThoracic Oncology LaboratoryComprehensive Cancer CenterUniversity of CaliforniaSan FranciscoCAUSA
| | - Anatoly Urisman
- Department of PathologyUniversity of CaliforniaSan FranciscoCAUSA
| | - Yi‐Lin Yang
- Department of SurgeryThoracic Oncology LaboratoryComprehensive Cancer CenterUniversity of CaliforniaSan FranciscoCAUSA
| | - Shu Liu
- Department of SurgeryThoracic Oncology LaboratoryComprehensive Cancer CenterUniversity of CaliforniaSan FranciscoCAUSA
| | - Zhidong Xu
- Department of SurgeryThoracic Oncology LaboratoryComprehensive Cancer CenterUniversity of CaliforniaSan FranciscoCAUSA
| | - Hu Bin
- Department of Thoracic SurgeryBeijing Chao‐Yang HospitalAffiliated with Capital Medical UniversityBeijingChina
| | - Hui Li
- Department of Thoracic SurgeryBeijing Chao‐Yang HospitalAffiliated with Capital Medical UniversityBeijingChina
| | - David M. Jablons
- Department of SurgeryThoracic Oncology LaboratoryComprehensive Cancer CenterUniversity of CaliforniaSan FranciscoCAUSA
| | - Liang You
- Department of SurgeryThoracic Oncology LaboratoryComprehensive Cancer CenterUniversity of CaliforniaSan FranciscoCAUSA
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28
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Wang VE, Xue JY, Frederick DT, Cao Y, Lin E, Wilson C, Urisman A, Carbone DP, Flaherty KT, Bernards R, Lito P, Settleman J, McCormick F. Adaptive Resistance to Dual BRAF/MEK Inhibition in BRAF-Driven Tumors through Autocrine FGFR Pathway Activation. Clin Cancer Res 2019; 25:7202-7217. [PMID: 31515463 DOI: 10.1158/1078-0432.ccr-18-2779] [Citation(s) in RCA: 19] [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] [Received: 08/27/2018] [Revised: 03/18/2019] [Accepted: 09/06/2019] [Indexed: 01/12/2023]
Abstract
PURPOSE Combined MAPK pathway inhibition using dual BRAF and MEK inhibitors has prolonged the duration of clinical response in patients with BRAFV600E-driven tumors compared with either agent alone. However, resistance frequently arises. EXPERIMENTAL DESIGN We generated cell lines resistant to dual BRAF/MEK inhibition and utilized a pharmacologic synthetic lethal approach to identify a novel, adaptive resistance mechanism mediated through the fibroblast growth factor receptor (FGFR) pathway. RESULTS In response to drug treatment, transcriptional upregulation of FGF1 results in autocrine activation of FGFR, which potentiates extracellular signal-regulated kinases (ERK) activation. FGFR inhibition overcomes resistance to dual BRAF/MEK inhibitors in both cell lines and patient-derived xenograft (PDX) models. Abrogation of this bypass mechanism in the first-line setting enhances tumor killing and prevents the emergence of drug-resistant cells. Moreover, clinical data implicate serum FGF1 levels in disease prognosis. CONCLUSIONS Taken together, these results describe a new, adaptive resistance mechanism that is more commonly observed in the context of dual BRAF/MEK blockade as opposed to single-agent treatment and reveal the potential clinical utility of FGFR-targeting agents in combination with BRAF and MEK inhibitors as a promising strategy to forestall resistance in a subset of BRAF-driven cancers.
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Affiliation(s)
- Victoria E Wang
- Department of Medicine, University of California, San Francisco, San Francisco, California.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Jenny Y Xue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, New York.,Weill Cornell Medical College, Cornell University, New York, New York
| | | | - Yi Cao
- Discovery Oncology, Genentech, South San Francisco, California
| | - Eva Lin
- Discovery Oncology, Genentech, South San Francisco, California
| | | | - Anatoly Urisman
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - David P Carbone
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Keith T Flaherty
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Rene Bernards
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Piro Lito
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, New York.,Weill Cornell Medical College, Cornell University, New York, New York
| | - Jeff Settleman
- Discovery Oncology, Genentech, South San Francisco, California.
| | - Frank McCormick
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California.
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Castel P, Cheng A, Cuevas-Navarro A, Everman DB, Papageorge AG, Simanshu DK, Tankka A, Galeas J, Urisman A, McCormick F. RIT1 oncoproteins escape LZTR1-mediated proteolysis. Science 2019; 363:1226-1230. [PMID: 30872527 DOI: 10.1126/science.aav1444] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 02/17/2019] [Indexed: 12/11/2022]
Abstract
RIT1 oncoproteins have emerged as an etiologic factor in Noonan syndrome and cancer. Despite the resemblance of RIT1 to other members of the Ras small guanosine triphosphatases (GTPases), mutations affecting RIT1 are not found in the classic hotspots but rather in a region near the switch II domain of the protein. We used an isogenic germline knock-in mouse model to study the effects of RIT1 mutation at the organismal level, which resulted in a phenotype resembling Noonan syndrome. By mass spectrometry, we detected a RIT1 interactor, leucine zipper-like transcription regulator 1 (LZTR1), that acts as an adaptor for protein degradation. Pathogenic mutations affecting either RIT1 or LZTR1 resulted in incomplete degradation of RIT1. This led to RIT1 accumulation and dysregulated growth factor signaling responses. Our results highlight a mechanism of pathogenesis that relies on impaired protein degradation of the Ras GTPase RIT1.
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Affiliation(s)
- Pau Castel
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Alice Cheng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Antonio Cuevas-Navarro
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | - Alex G Papageorge
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, USA
| | - Alexandra Tankka
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Jacqueline Galeas
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Anatoly Urisman
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
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30
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Hsu PC, Tian B, Yang YL, Wang YC, Liu S, Urisman A, Yang CT, Xu Z, Jablons DM, You L. Cucurbitacin E inhibits the Yes‑associated protein signaling pathway and suppresses brain metastasis of human non‑small cell lung cancer in a murine model. Oncol Rep 2019; 42:697-707. [PMID: 31233205 PMCID: PMC6610039 DOI: 10.3892/or.2019.7207] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 02/20/2019] [Accepted: 06/11/2019] [Indexed: 01/08/2023] Open
Abstract
Human non-small cell lung cancer (NSCLC) is associated with an extremely poor prognosis especially for the 40% of patients who develop brain metastasis, and few treatment strategies exist. Cucurbitacin E (CuE), an oxygenated tetracyclic triterpenoid isolated from plants particularly of the family Cucurbitaceae, has shown anti-tumorigenic properties in several types of cancer, yet the mechanism remains unclear. Yes-associated protein (YAP), a main mediator of the Hippo signaling pathway, promotes tumorigenesis, drug resistance and metastasis in human NSCLC. The present study was designed to ascertain whether CuE inhibits YAP and its downstream gene expression in the human NSCLC cell lines H2030-BrM3 (K-rasG12C mutation) and PC9-BrM3 (EGFRΔexon19 mutation), which have high potential for brain metastasis. The efficacy of CuE in suppressing brain metastasis of H2030-BrM3 cells in a murine model was also investigated. It was found that after CuE treatment in H2030-BrM3 and PC9-BrM3 cells, YAP protein expression was decreased, and YAP signaling GTIIC reporter activity and expression of the downstream genes CTGF and CYR61 were significantly (P<0.01) decreased. CuE treatment also reduced the migration and invasion abilities of the H2030-BrM3 and PC9-BrM3 cells. Finally, our in vivo study showed that CuE treatment (0.2 mg/kg) suppressed H2030-BrM3 cell brain metastasis and that mice treated with CuE survived longer than the control mice treated with 10% DMSO (P=0.02). The present study is the first to demonstrate that CuE treatment inhibits YAP and the signaling downstream gene expression in human NSCLC in vitro, and suppresses brain metastasis of NSCLC in a murine model. More studies to verify the promising efficacy of CuE in inhibiting brain metastasis of NSCLC and various other cancers may be warranted.
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Affiliation(s)
- Ping-Chih Hsu
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Bo Tian
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Yi-Lin Yang
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Yu-Cheng Wang
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Shu Liu
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Anatoly Urisman
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Cheng-Ta Yang
- Department of Thoracic Medicine, Chang Gung Memorial Hospital Linkou Branch, Taoyuan 33305, Taiwan, R.O.C
| | - Zhidong Xu
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA
| | - David M Jablons
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Liang You
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA
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31
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Wong AW, Urisman A, Burlingame AL, Shokat KM. Chemically reprogramming the phospho-transfer reaction to crosslink protein kinases to their substrates. Protein Sci 2019; 28:654-662. [PMID: 30636329 PMCID: PMC6371225 DOI: 10.1002/pro.3570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/03/2019] [Accepted: 01/07/2019] [Indexed: 12/24/2022]
Abstract
The proteomic mapping of enzyme-substrate interactions is challenged by their transient nature. A method to capture interacting protein kinases in complexes with a single substrate of interest would provide a new tool for mapping kinase signaling networks. Here, we describe a nucleotide-based substrate analog capable of reprogramming the wild-type phosphoryl-transfer reaction to produce a kinase-acrylamide-based thioether crosslink to mutant substrates with a cysteine nucleophile substituted at the native phosphorylation site. A previously reported ATP-based methacrylate crosslinker (ATP-MA) was capable of mediating kinase crosslinking to short peptides but not protein substrates. Exploration of structural variants of ATP-MA to enable crosslinking of protein substrates to kinases led to the discovery that an ADP-based methacrylate (ADP-MA) crosslinker was superior to the ATP scaffold at crosslinking in vitro. The improved efficiency of ADP-MA over ATP-MA is due to reduced inhibition of the second step of the kinase-substrate crosslinking reaction by the product of the first step of the reaction. The new probe, ADP-MA, demonstrated enhanced in vitro crosslinking between the Src tyrosine kinase and its substrate Cortactin in a phosphorylation site-specific manner. The kinase-substrate crosslinking reaction can be carried out in a complex mammalian cell lysate setting, although the low abundance of endogenous kinases remains a significant challenge for efficient capture.
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Affiliation(s)
- Allison W. Wong
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCalifornia
| | - Anatoly Urisman
- Department of PathologyUniversity of California San FranciscoSan FranciscoCalifornia
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCalifornia
| | - Alma L. Burlingame
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCalifornia
| | - Kevan M. Shokat
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCalifornia
- Howard Hughes Medical InstituteUniversity of California San FranciscoSan FranciscoCalifornia
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32
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Hung LY, Sen D, Oniskey TK, Katzen J, Cohen NA, Vaughan AE, Nieves W, Urisman A, Beers MF, Krummel MF, Herbert DR. Macrophages promote epithelial proliferation following infectious and non-infectious lung injury through a Trefoil factor 2-dependent mechanism. Mucosal Immunol 2019; 12:64-76. [PMID: 30337651 PMCID: PMC6301101 DOI: 10.1038/s41385-018-0096-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [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] [Received: 08/22/2017] [Revised: 09/16/2018] [Accepted: 09/17/2018] [Indexed: 02/04/2023]
Abstract
Coordinated efforts between macrophages and epithelia are considered essential for wound healing, but the macrophage-derived molecules responsible for repair are poorly defined. This work demonstrates that lung macrophages rely upon Trefoil factor 2 to promote epithelial proliferation following damage caused by sterile wounding, Nippostrongylus brasiliensis or Bleomycin sulfate. Unexpectedly, the presence of T, B, or ILC populations was not essential for macrophage-driven repair. Instead, conditional deletion of TFF2 in myeloid-restricted CD11cCre TFF2 flox mice exacerbated lung pathology and reduced the proliferative expansion of CD45- EpCAM+ pro-SPC+ alveolar type 2 cells. TFF2 deficient macrophages had reduced expression of the Wnt genes Wnt4 and Wnt16 and reconstitution of hookworm-infected CD11cCre TFF2flox mice with rWnt4 and rWnt16 restored the proliferative defect in lung epithelia post-injury. These data reveal a previously unrecognized mechanism wherein lung myeloid phagocytes utilize a TFF2/Wnt axis as a mechanism that drives epithelial proliferation following lung injury.
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Affiliation(s)
- Li-Yin Hung
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104
| | - Debasish Sen
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Taylor K. Oniskey
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104
| | - Jeremey Katzen
- Pulmonary, Allergy, and Critical Care Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Noam A. Cohen
- Departments of Otorhinolaryngology—Head and Neck Surgery, University of Pennsylvania Perelman School of Medicine, Monell Chemical Senses Center, and Philadelphia VA Medical Center Surgical Service
| | - Andrew E. Vaughan
- Department of Biological Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104
| | - Wildaliz Nieves
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104
| | - Anatoly Urisman
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael F. Beers
- Pulmonary, Allergy, and Critical Care Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania,PENN Center for Pulmonary Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Matthew F. Krummel
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - De’Broski R. Herbert
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104
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33
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DeQuattro K, Urisman A, Margaretten M. A 36-Year-Old Man With Renal Failure, Fever, and Hypocomplementemia. Arthritis Care Res (Hoboken) 2018; 71:449-455. [PMID: 30295438 DOI: 10.1002/acr.23770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/25/2018] [Indexed: 01/05/2023]
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34
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Sahoo PK, Lee SJ, Jaiswal PB, Alber S, Kar AN, Miller-Randolph S, Taylor EE, Smith T, Singh B, Ho TSY, Urisman A, Chand S, Pena EA, Burlingame AL, Woolf CJ, Fainzilber M, English AW, Twiss JL. Axonal G3BP1 stress granule protein limits axonal mRNA translation and nerve regeneration. Nat Commun 2018; 9:3358. [PMID: 30135423 PMCID: PMC6105716 DOI: 10.1038/s41467-018-05647-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [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: 12/20/2017] [Accepted: 07/12/2018] [Indexed: 12/17/2022] Open
Abstract
Critical functions of intra-axonally synthesized proteins are thought to depend on regulated recruitment of mRNA from storage depots in axons. Here we show that axotomy of mammalian neurons induces translation of stored axonal mRNAs via regulation of the stress granule protein G3BP1, to support regeneration of peripheral nerves. G3BP1 aggregates within peripheral nerve axons in stress granule-like structures that decrease during regeneration, with a commensurate increase in phosphorylated G3BP1. Colocalization of G3BP1 with axonal mRNAs is also correlated with the growth state of the neuron. Disrupting G3BP functions by overexpressing a dominant-negative protein activates intra-axonal mRNA translation, increases axon growth in cultured neurons, disassembles axonal stress granule-like structures, and accelerates rat nerve regeneration in vivo. G3BP1 is RasGAP SH3 domain binding protein 1 that interacts with 48S pre-initiation complex when translation is stalled. Here, Twiss and colleagues show that neuronal G3BP1 can negatively regulate axonal mRNA translation, and inhibit axonal regeneration after injury.
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Affiliation(s)
- Pabitra K Sahoo
- Department of Biological Sciences, University of South Carolina, Columbia, 29208, SC, USA
| | - Seung Joon Lee
- Department of Biological Sciences, University of South Carolina, Columbia, 29208, SC, USA
| | - Poonam B Jaiswal
- Department of Cell Biology, Emory University College of Medicine, Atlanta, 30322, GA, USA
| | - Stefanie Alber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Amar N Kar
- Department of Biological Sciences, University of South Carolina, Columbia, 29208, SC, USA
| | | | - Elizabeth E Taylor
- Department of Biological Sciences, University of South Carolina, Columbia, 29208, SC, USA
| | - Terika Smith
- Department of Biological Sciences, University of South Carolina, Columbia, 29208, SC, USA
| | - Bhagat Singh
- FM Kirby Neurobiology Center and Boston Children's Hospital and Harvard Medical School, Boston, 02115, MA, USA
| | - Tammy Szu-Yu Ho
- FM Kirby Neurobiology Center and Boston Children's Hospital and Harvard Medical School, Boston, 02115, MA, USA
| | - Anatoly Urisman
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Shreya Chand
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Edsel A Pena
- Department of Statistics, University of South Carolina, Columbia, 29208, SC, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Clifford J Woolf
- FM Kirby Neurobiology Center and Boston Children's Hospital and Harvard Medical School, Boston, 02115, MA, USA
| | - Mike Fainzilber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Arthur W English
- Department of Cell Biology, Emory University College of Medicine, Atlanta, 30322, GA, USA
| | - Jeffery L Twiss
- Department of Biological Sciences, University of South Carolina, Columbia, 29208, SC, USA.
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35
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Markegard E, Mercado EL, Castel P, Silva J, Galeas J, Li K, Urisman A, McCormick F. Abstract 5520: Oncogenic RTK signaling inhibits Spred1/NF1 to sustain constitutive Ras/MAPK signaling. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5520] [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
Spred proteins negatively regulate Ras/MAPK signaling following growth factor stimulation. Inhibition of Ras primary occurs through Spreds ability to bind and localize NF1, a RasGAP and major tumor suppressor, to the plasma membrane. Spred1 and NF1 loss-of-function mutations occur across multiple cancer types including non-small cell lung carcinoma, glioblastoma, melanoma, stomach carcinoma, and uterine carcinosarcoma. Here we demonstrate that oncogenic RTK signaling leads to phosphorylation of Spred1(S105) in the EVH domain, which disrupts Spred1-NF1 binding and function. Phosphomimetic Spred1 is unable to suppress Ras-GTP following growth factor stimulation and cancer cell proliferation. The Spred1(S105) kinase is likely to be a CDK based on in vitro kinase and in vivo cell line assays. Our findings provide one potential mechanism by which oncogenic RTK signaling disrupts negative feedback to sustain constitutive Ras signaling. Furthermore, this work may elucidate a novel therapeutic target for restoring NF1-mediated inhibition of Ras.
Citation Format: Evan Markegard, Ellen L. Mercado, Pau Castel, Jillian Silva, Jacqueline Galeas, Kathy Li, Anatoly Urisman, Frank McCormick. Oncogenic RTK signaling inhibits Spred1/NF1 to sustain constitutive Ras/MAPK signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5520.
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Affiliation(s)
- Evan Markegard
- 1UCSF Helen Diller Family Comp. Cancer Ctr., San Francisco, CA
| | | | - Pau Castel
- 1UCSF Helen Diller Family Comp. Cancer Ctr., San Francisco, CA
| | - Jillian Silva
- 1UCSF Helen Diller Family Comp. Cancer Ctr., San Francisco, CA
| | | | - Kathy Li
- 3UCSF Pharmaceutical Chemistry, San Francisco, CA
| | | | - Frank McCormick
- 1UCSF Helen Diller Family Comp. Cancer Ctr., San Francisco, CA
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Ramirez JL, Urisman A, Kukreja J, Kratz JR. Surgical Management of Pulmonary Mucormycosis in Third-Trimester Pregnancy. Thorac Cardiovasc Surg Rep 2018; 7:e27-e29. [PMID: 29977735 PMCID: PMC6023714 DOI: 10.1055/s-0038-1660806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/02/2018] [Indexed: 11/06/2022] Open
Abstract
Background
Pulmonary mucormycosis is a rare fungal infection that carries a high mortality. Given the rarity of this disease, its management has not been well established.
Case Description
We report a 36-year-old female presenting with right middle and lower lobe pulmonary mucormycosis during the third trimester of pregnancy. Diagnosis was established using chest computed tomography followed by bronchoalveolar lavage and lung biopsy. Prompt initiation of amphotericin B and right middle and lower lobe lobectomy resulted in maternal survival and fetal viability.
Conclusion
This favorable outcome is attributed to extensive communication between treatment teams in addition to comprehensive surgical planning.
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Affiliation(s)
- Joel L Ramirez
- Department of Surgery, University of California, San Francisco, San Francisco, California, United States
| | - Anatoly Urisman
- Department of Pathology, University of California, San Francisco, San Francisco, California, United States
| | - Jasleen Kukreja
- Department of Surgery, University of California, San Francisco, San Francisco, California, United States
| | - Johannes R Kratz
- Department of Surgery, University of California, San Francisco, San Francisco, California, United States
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Hsu PC, Miao J, Huang Z, Yang YL, Xu Z, You J, Dai Y, Yeh CC, Chan G, Liu S, Urisman A, Yang CT, Jablons DM, You L. Inhibition of yes-associated protein suppresses brain metastasis of human lung adenocarcinoma in a murine model. J Cell Mol Med 2018; 22:3073-3085. [PMID: 29575527 PMCID: PMC5980132 DOI: 10.1111/jcmm.13582] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 10/19/2017] [Accepted: 01/19/2018] [Indexed: 12/15/2022] Open
Abstract
Yes‐associated protein (YAP) is a main mediator of the Hippo pathway and promotes cancer development and progression in human lung cancer. We sought to determine whether inhibition of YAP suppresses metastasis of human lung adenocarcinoma in a murine model. We found that metastatic NSCLC cell lines H2030‐BrM3(K‐rasG12C mutation) and PC9‐BrM3 (EGFRΔexon19 mutation) had a significantly decreased p‐YAP(S127)/YAP ratio compared to parental H2030 (K‐rasG12C mutation) and PC9 (EGFRΔexon19 mutation) cells (P < .05). H2030‐BrM3 cells had significantly increased YAP mRNA and expression of Hippo downstream genes CTGF and CYR61 compared to parental H2030 cells (P < .05). Inhibition of YAP by short hairpin RNA (shRNA) and small interfering RNA (siRNA) significantly decreased mRNA expression in downstream genes CTGF and CYR61 in H2030‐BrM3 cells (P < .05). In addition, inhibiting YAP by YAP shRNA significantly decreased migration and invasion abilities of H2030‐BrM3 cells (P < .05). We are first to show that mice inoculated with YAP shRNA‐transfected H2030‐BrM3 cells had significantly decreased metastatic tumour burden and survived longer than control mice (P < .05). Collectively, our results suggest that YAP plays an important role in promoting lung adenocarcinoma brain metastasis and that direct inhibition of YAP by shRNA suppresses H2030‐BrM3 cell brain metastasis in a murine model.
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Affiliation(s)
- Ping-Chih Hsu
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Thoracic Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Jinbai Miao
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Thoracic Surgery, Beijing Chao-Yang Hospital, Affiliated with Capital Medical University, Beijing, China
| | - Zhen Huang
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Hepatobiliary Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi-Lin Yang
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Zhidong Xu
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Joanna You
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Yuyuan Dai
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Che-Chung Yeh
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Geraldine Chan
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Shu Liu
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Anatoly Urisman
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Cheng-Ta Yang
- Department of Thoracic Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - David M Jablons
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Liang You
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
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38
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Terenzio M, Koley S, Samra N, Rishal I, Zhao Q, Sahoo PK, Urisman A, Marvaldi L, Oses-Prieto JA, Forester C, Gomes C, Kalinski AL, Di Pizio A, Doron-Mandel E, Perry RBT, Koppel I, Twiss JL, Burlingame AL, Fainzilber M. Locally translated mTOR controls axonal local translation in nerve injury. Science 2018; 359:1416-1421. [PMID: 29567716 PMCID: PMC6501578 DOI: 10.1126/science.aan1053] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [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] [Received: 03/05/2017] [Revised: 12/13/2017] [Accepted: 01/30/2018] [Indexed: 12/12/2022]
Abstract
How is protein synthesis initiated locally in neurons? We found that mTOR (mechanistic target of rapamycin) was activated and then up-regulated in injured axons, owing to local translation of mTOR messenger RNA (mRNA). This mRNA was transported into axons by the cell size-regulating RNA-binding protein nucleolin. Furthermore, mTOR controlled local translation in injured axons. This included regulation of its own translation and that of retrograde injury signaling molecules such as importin β1 and STAT3 (signal transducer and activator of transcription 3). Deletion of the mTOR 3' untranslated region (3'UTR) in mice reduced mTOR in axons and decreased local translation after nerve injury. Both pharmacological inhibition of mTOR in axons and deletion of the mTOR 3'UTR decreased proprioceptive neuronal survival after nerve injury. Thus, mRNA localization enables spatiotemporal control of mTOR pathways regulating local translation and long-range intracellular signaling.
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Affiliation(s)
- Marco Terenzio
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sandip Koley
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nitzan Samra
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ida Rishal
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Qian Zhao
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Pabitra K Sahoo
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Anatoly Urisman
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Letizia Marvaldi
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Craig Forester
- Division of Pediatric Allergy, Immunology and Bone Marrow Transplantation, University of California, San Francisco, CA 94158, USA
| | - Cynthia Gomes
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Ashley L Kalinski
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Agostina Di Pizio
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ella Doron-Mandel
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Ben-Tov Perry
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Indrek Koppel
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jeffery L Twiss
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Mike Fainzilber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
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Wang VE, Urisman A, Albacker L, Ali S, Miller V, Aggarwal R, Jablons D. Checkpoint inhibitor is active against large cell neuroendocrine carcinoma with high tumor mutation burden. J Immunother Cancer 2017; 5:75. [PMID: 28923100 PMCID: PMC5604145 DOI: 10.1186/s40425-017-0281-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [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: 06/14/2017] [Accepted: 09/01/2017] [Indexed: 01/08/2023] Open
Abstract
Background Large cell neuroendocrine tumor (LCNEC) of the lung is a rare and aggressive tumor similar to small cell lung cancer (SCLC). Thus, it is often treated similarly to SCLC in the front-line setting with a platinum doublet. However, treatment for patients beyond the first line remains undefined. Case presentation We report the case of a patient with stage IB LCNEC (PD-L1 negative but positive for PD-L1 amplification and tumor mutation burden high) who progressed after adjuvant chemotherapy after surgery and subsequent therapy with an antibody drug conjugate targeting a neuroendocrine-specific cell surface marker but achieved a significant and durable response with pembrolizumab, a humanized IgG4 monoclonal anti-PD-1 antibody. Conclusions Immunotherapy with checkpoint inhibitors is an effective treatment option for patients with metastatic LCNEC, even if PD-L1 expression is negative.
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Affiliation(s)
- Victoria E Wang
- Department of Medicine, University of California, 1600 Divisadero Street, San Francisco, California, 94115, USA.
| | - Anatoly Urisman
- Department of Pathology, University of California, San Francisco, USA
| | - Lee Albacker
- Foundation Medicine, Cambridge, Massachusetts, USA
| | - Siraj Ali
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | - Rahul Aggarwal
- Department of Medicine, University of California, 1600 Divisadero Street, San Francisco, California, 94115, USA
| | - David Jablons
- Department of Surgery, University of California, San Francisco, USA
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40
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Markegard E, Mercado EL, Silva JM, Galeas J, Trinidad MI, Urisman A, McCormick F. Abstract 1370: EGFR-mediated Spred1 phosphorylation inhibits NF1 to sustain constitutive Ras/MAPK signaling. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1370] [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
Spred proteins negatively regulate Ras/MAPK signaling following growth factor stimulation. Inhibition of Ras primary occurs through Spreds ability to bind and localize NF1, a RasGAP and major tumor suppressor, to the plasma membrane. Spred1 and NF1 loss-of-function mutations occur across multiple cancer types including non-small cell lung carcinoma, glioblastoma, melanoma, stomach carcinoma, and uterine carcinosarcoma. Here we demonstrate that EGFR signaling disrupts Spred1-NF1 binding. Mass spectrometry was performed on cells overexpressing EGFRL858R to identify potential phosphorylation sites on Spred1 and NF1 that could disrupt Spred1-NF1 binding by steric hindrance. A serine phosphorylation site on Spred1 was identified in which a phosphomimetic and phosphodeficient mutant decreased or increased Spred1-NF1 binding, respectively. Phosphomimetic Spred1 is unable to suppress Ras-GTP following EGF stimulation. Therefore, phosphorylation of Spred1 at this site by a serine kinase downstream of EGFR may disrupt Spred1-NF1 binding. To identify the Spred1 kinase we are performing an in vitro kinase assay and an unbiased CRISPRa screen. Our findings provide one potential mechanism by which EGFR signaling disrupts negative feedback to sustain constitutive Ras signaling. Furthermore, this work may elucidate a novel therapeutic target for restoring NF1-mediated inhibition of Ras.
Citation Format: Evan Markegard, Ellen L. Mercado, Jillian M. Silva, Jacqueline Galeas, Marena I. Trinidad, Anatoly Urisman, Frank McCormick. EGFR-mediated Spred1 phosphorylation inhibits NF1 to sustain constitutive Ras/MAPK signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1370. doi:10.1158/1538-7445.AM2017-1370
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Wang VE, Young L, Ali S, Miller VA, Urisman A, Wolfe J, Bivona TG, Damato B, Fogh S, Bergsland EK. A Case of Metastatic Atypical Neuroendocrine Tumor with ALK Translocation and Diffuse Brain Metastases. Oncologist 2017; 22:768-773. [PMID: 28507205 PMCID: PMC5507651 DOI: 10.1634/theoncologist.2017-0054] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/08/2017] [Indexed: 01/10/2023] Open
Abstract
A challenge in precision medicine is the identification of actionable driver mutations. Alterations can be identified within the tumor tissue, by small biopsy or fine‐needle aspirates, or by noninvasive methods, such as circulating tumor cells or circulating tumor DNA. This article presents a case of atypical neuroendocrine tumor metastatic to the bone and brain for which circulating tumor DNA analysis found an ALK translocation. A challenge in precision medicine requires identification of actionable driver mutations. Critical to such effort is the deployment of sensitive and well‐validated assays for mutation detection. Although identification of such alterations within the tumor tissue remains the gold standard, many advanced non‐small cell lung cancer cases have only limited tissue samples, derived from small biopsies or fine‐needle aspirates, available for testing. More recently, noninvasive methods using either circulating tumor cells or tumor DNA (ctDNA) have become an alternative method for identifying molecular biomarkers and screening patients eligible for targeted therapies. In this article, we present a case of a 52‐year‐old never‐smoking male who presented with widely metastatic atypical neuroendocrine tumor to the bones and the brain. Molecular genotyping using DNA harvested from a bone metastasis was unsuccessful due to limited material. Subsequent ctDNA analysis revealed an ALK translocation. The clinical significance of the mutation in this particular cancer type and therapeutic strategies are discussed. Key Points. To our knowledge, this index case represents the first reported ALK translocation identified in an atypical carcinoid tumor. Liquid biopsy such as circulating tumor DNA is a feasible alternative platform for identifying sensitizing genomic alterations. Second‐generation ALK inhibitors represent a new paradigm for treating ALK‐positive patients with brain metastases.
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Affiliation(s)
- Victoria E. Wang
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Correspondence: Victoria E. Wang, M.D., Ph.D., Department of Medicine, University of California, San Francisco, 1600 Divisadero Street, San Francisco, California 94115, USA
| | - Lauren Young
- Foundation Medicine, Cambridge, Massachusetts, USA
| | - Siraj Ali
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | - Anatoly Urisman
- Department of Medicine Pathology, University of California, San Francisco, San Francisco, California, USA
| | - John Wolfe
- Department of Pathology, Santa Rosa Memorial Hospital, Santa Rosa, California, USA
| | - Trever G. Bivona
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Bertil Damato
- Department of Medicine Ophthalmology, University of California, San Francisco, San Francisco, California, USA
| | - Shannon Fogh
- Department of Medicine Radiation Oncology, University of California, San Francisco, San Francisco, California, USA
| | - Emily K. Bergsland
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
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Brownell R, Moua T, Henry TS, Elicker BM, White D, Vittinghoff E, Jones KD, Urisman A, Aravena C, Johannson KA, Golden JA, King TE, Wolters PJ, Collard HR, Ley B. The use of pretest probability increases the value of high-resolution CT in diagnosing usual interstitial pneumonia. Thorax 2017; 72:424-429. [PMID: 28082530 DOI: 10.1136/thoraxjnl-2016-209671] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 11/30/2016] [Accepted: 12/05/2016] [Indexed: 11/03/2022]
Abstract
BACKGROUND Recent studies have suggested that non-definitive patterns on high-resolution CT (HRCT) scan provide sufficient diagnostic specificity to forgo surgical lung biopsy in the diagnosis of idiopathic pulmonary fibrosis (IPF). The objective of this study was to determine test characteristics of non-definitive HRCT patterns for identifying histopathological usual interstitial pneumonia (UIP). METHODS Patients with biopsy-proven interstitial lung disease (ILD) and non-definitive HRCT scans were identified from two academic ILD centres. Test characteristics for HRCT patterns as predictors of UIP on surgical lung biopsy were derived and validated in independent cohorts. RESULTS In the derivation cohort, 64/385 (17%) had possible UIP pattern on HRCT; 321/385 (83%) had inconsistent with UIP pattern. 113/385 (29%) patients had histopathological UIP pattern in the derivation cohort. Possible UIP pattern had a specificity of 91.2% (95% CI 87.2% to 94.3%) and a positive predictive value (PPV) of 62.5% (95% CI 49.5% to 74.3%) for UIP pattern on surgical lung biopsy. The addition of age, sex and total traction bronchiectasis score improved the PPV. Inconsistent with UIP pattern demonstrated poor PPV (22.7%, 95% CI 18.3% to 27.7%). HRCT pattern specificity was nearly identical in the validation cohort (92.7%, 95% CI 82.4% to 98.0%). The substantially higher prevalence of UIP pattern in the validation cohort improved the PPV of HRCT patterns. CONCLUSIONS A possible UIP pattern on HRCT has high specificity for UIP on surgical lung biopsy, but PPV is highly dependent on underlying prevalence. Adding clinical and radiographic features to possible UIP pattern on HRCT may provide sufficient probability of histopathological UIP across prevalence ranges to change clinical decision-making.
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Affiliation(s)
- Robert Brownell
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Teng Moua
- Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Travis S Henry
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Brett M Elicker
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Darin White
- Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric Vittinghoff
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Kirk D Jones
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Anatoly Urisman
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Carlos Aravena
- Respiratory Diseases Department, Pontifical Catholic University, Santiago, Chile
| | | | - Jeffrey A Golden
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Talmadge E King
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Paul J Wolters
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Harold R Collard
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Brett Ley
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
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Doll S, Urisman A, Oses-Prieto JA, Arnott D, Burlingame AL. Quantitative Proteomics Reveals Fundamental Regulatory Differences in Oncogenic HRAS and Isocitrate Dehydrogenase (IDH1) Driven Astrocytoma. Mol Cell Proteomics 2017; 16:39-56. [PMID: 27834733 PMCID: PMC5217781 DOI: 10.1074/mcp.m116.063883] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/04/2016] [Indexed: 12/18/2022] Open
Abstract
Glioblastoma multiformes (GBMs) are high-grade astrocytomas and the most common brain malignancies. Primary GBMs are often associated with disturbed RAS signaling, and expression of oncogenic HRAS results in a malignant phenotype in glioma cell lines. Secondary GBMs arise from lower-grade astrocytomas, have slower progression than primary tumors, and contain IDH1 mutations in over 70% of cases. Despite significant amount of accumulating genomic and transcriptomic data, the fundamental mechanistic differences of gliomagenesis in these two types of high-grade astrocytoma remain poorly understood. Only a few studies have attempted to investigate the proteome, phosphorylation signaling, and epigenetic regulation in astrocytoma. In the present study, we applied quantitative phosphoproteomics to identify the main signaling differences between oncogenic HRAS and mutant IDH1-driven glioma cells as models of primary and secondary GBM, respectively. Our analysis confirms the driving roles of the MAPK and PI3K/mTOR signaling pathways in HRAS driven cells and additionally uncovers dysregulation of other signaling pathways. Although a subset of the signaling changes mediated by HRAS could be reversed by a MEK inhibitor, dual inhibition of MEK and PI3K resulted in more complete reversal of the phosphorylation patterns produced by HRAS expression. In contrast, cells expressing mutant IDH1 did not show significant activation of MAPK or PI3K/mTOR pathways. Instead, global downregulation of protein expression was observed. Targeted proteomic analysis of histone modifications identified significant histone methylation, acetylation, and butyrylation changes in the mutant IDH1 expressing cells, consistent with a global transcriptional repressive state. Our findings offer novel mechanistic insight linking mutant IDH1 associated inhibition of histone demethylases with specific histone modification changes to produce global transcriptional repression in secondary glioblastoma. Our proteomic datasets are available for download and provide a comprehensive catalogue of alterations in protein abundance, phosphorylation, and histone modifications in oncogenic HRAS and IDH1 driven astrocytoma cells beyond the transcriptomic level.
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Affiliation(s)
- Sophia Doll
- From the ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, 94158-2517 California
| | - Anatoly Urisman
- From the ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, 94158-2517 California
| | - Juan A Oses-Prieto
- From the ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, 94158-2517 California
| | - David Arnott
- §Department of Protein Chemistry, Genentech Inc, South San Francisco, 94158-2517 California
| | - Alma L Burlingame
- From the ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, 94158-2517 California;
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44
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Urisman A, Levin RS, Gordan JD, Webber JT, Hernandez H, Ishihama Y, Shokat KM, Burlingame AL. An Optimized Chromatographic Strategy for Multiplexing In Parallel Reaction Monitoring Mass Spectrometry: Insights from Quantitation of Activated Kinases. Mol Cell Proteomics 2016; 16:265-277. [PMID: 27940637 DOI: 10.1074/mcp.m116.058172] [Citation(s) in RCA: 30] [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] [Received: 01/11/2016] [Revised: 12/01/2016] [Indexed: 01/06/2023] Open
Abstract
Reliable quantitation of protein abundances in defined sets of cellular proteins is critical to numerous biological applications. Traditional immunodetection-based methods are limited by the quality and availability of specific antibodies, especially for site-specific post-translational modifications. Targeted proteomic methods, including the recently developed parallel reaction monitoring (PRM) mass spectrometry, have enabled accurate quantitative measurements of up to a few hundred specific target peptides. However, the degree of practical multiplexing in label-free PRM workflows remains a significant limitation for the technique. Here we present a strategy for significantly increasing multiplexing in label-free PRM that takes advantage of the superior separation characteristics and retention time stability of meter-scale monolithic silica-C18 column-based chromatography. We show the utility of the approach in quantifying kinase abundances downstream of previously developed active kinase enrichment methodology based on multidrug inhibitor beads. We examine kinase activation dynamics in response to three different MAP kinase inhibitors in colorectal carcinoma cells and demonstrate reliable quantitation of over 800 target peptides from over 150 kinases in a single label-free PRM run. The kinase activity profiles obtained from these analyses reveal compensatory activation of TGF-β family receptors as a response to MAPK blockade. The gains achieved using this label-free PRM multiplexing strategy will benefit a wide array of biological applications.
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Affiliation(s)
- Anatoly Urisman
- From the ‡Department of Pathology, University of California San Francisco, San Francisco, California; .,§Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Rebecca S Levin
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California.,¶Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California
| | - John D Gordan
- ¶Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California.,‖Department of Medicine, University of California San Francisco, San Francisco, California
| | - James T Webber
- **Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California
| | - Hilda Hernandez
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Yasushi Ishihama
- ‡‡Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kevan M Shokat
- ¶Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California.,§§Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California
| | - Alma L Burlingame
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
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45
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Markegard E, Mercado EL, Galeas J, Trinidad MI, Urisman A, McCormick. F. Abstract 1874: Oncogenic EGFR signaling inhibits the Spred1-NF1 interaction to sustain constitutive Ras signaling. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-1874] [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
Spred proteins negatively regulate Ras/MAPK signaling following mitogen stimulation. Inhibition of Ras primary occurs through Spreds ability to bind and localize NF1, a RasGAP and major tumor suppressor, to the plasma membrane. Loss-of-function Spred1 and NF1 mutations occur across multiple cancer types including melanoma, non-small cell lung carcinoma, stomach carcinoma, and uterine carcinosarcoma. Here we demonstrate that oncogenic EGFR signaling disrupts Spred1-NF1 binding. Mass spectrometry was performed on cells overexpressing EGFRL858R to identify potential phosphorylation sites on Spred1 and NF1 that could disrupt Spred1-NF1 binding by steric hindrance. A serine phosphorylation site on Spred1 was identified in which a phosphomimetic and phosphodeficient mutant decreased or increased Spred1-NF1 binding, respectively. Therefore, phosphorylation of Spred1 at this site by a serine kinase downstream of oncogenic EGFR may disrupt Spred1-NF1 binding. Our findings provide one potential mechanism by which oncogenic EGFR signaling disrupts negative feedback to allow for constitutive Ras signaling. Furthermore, this work may elucidate a novel kinase therapeutic target for restoring NF1 mediated inhibition of Ras.
Citation Format: Evan Markegard, Ellen L. Mercado, Jacqueline Galeas, Marena I. Trinidad, Anatoly Urisman, Frank McCormick. Oncogenic EGFR signaling inhibits the Spred1-NF1 interaction to sustain constitutive Ras signaling. [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 1874.
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Lee S, Shang Y, Redmond SA, Urisman A, Tang AA, Li KH, Burlingame AL, Pak RA, Jovičić A, Gitler AD, Wang J, Gray NS, Seeley WW, Siddique T, Bigio EH, Lee VMY, Trojanowski JQ, Chan JR, Huang EJ. Activation of HIPK2 Promotes ER Stress-Mediated Neurodegeneration in Amyotrophic Lateral Sclerosis. Neuron 2016; 91:41-55. [PMID: 27321923 DOI: 10.1016/j.neuron.2016.05.021] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 02/16/2016] [Accepted: 05/04/2016] [Indexed: 12/13/2022]
Abstract
Persistent accumulation of misfolded proteins causes endoplasmic reticulum (ER) stress, a prominent feature in many neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). Here we report the identification of homeodomain interacting protein kinase 2 (HIPK2) as the essential link that promotes ER-stress-induced cell death via the IRE1α-ASK1-JNK pathway. ER stress, induced by tunicamycin or SOD1(G93A), activates HIPK2 by phosphorylating highly conserved serine and threonine residues (S359/T360) within the activation loop of the HIPK2 kinase domain. In SOD1(G93A) mice, loss of HIPK2 delays disease onset, reduces cell death in spinal motor neurons, mitigates glial pathology, and improves survival. Remarkably, HIPK2 activation positively correlates with TDP-43 proteinopathy in NEFH-tTA/tetO-hTDP-43ΔNLS mice, sporadic ALS and C9ORF72 ALS, and blocking HIPK2 kinase activity protects motor neurons from TDP-43 cytotoxicity. These results reveal a previously unrecognized role of HIPK2 activation in ER-stress-mediated neurodegeneration and its potential role as a biomarker and therapeutic target for ALS. VIDEO ABSTRACT.
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Affiliation(s)
- Sebum Lee
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yulei Shang
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stephanie A Redmond
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA; Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Anatoly Urisman
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Amy A Tang
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ryan A Pak
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ana Jovičić
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jinhua Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School & Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Nathanael S Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School & Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - William W Seeley
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Teepu Siddique
- Division of Neuromuscular Medicine and Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Eileen H Bigio
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Virginia M-Y Lee
- Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Disease Research, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Disease Research, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jonah R Chan
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA; Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eric J Huang
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA; Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Pathology Service 113B, VA Medical Center, San Francisco, CA 94121, USA.
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Hung LY, Sen D, Oniskey TK, Nieves W, Urisman A, Krummel MF, Herbert DR. Macrophage-Dependent Regeneration of Pulmonary Epithelia Requires Trefoil Factor 2 for Wnt Expression. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.68.10] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Coordination between epithelial and myeloid cell lineages may facilitate tissue repair, but mechanistic evidence is lacking. Independently of Type 2 cytokines (interleukin-4/13), and T, B or ILC populations, lung macrophages promoted epithelial proliferation following injury caused by Nippostrongylus brasiliensis or bleomycin sulfate. Multiple myeloid populations up-regulated Trefoil factor 2 (TFF2) following lung injury and CD11c-driven Tff2 deletion impaired the proliferative expansion of pro-SpC+ distal lung epithelial progenitors. Direct interactions between macrophages and damaged epithelia resulted Wnt production, which accelerated epithelial proliferation, trans-epithelial resistance, and barrier function in a TFF2-dependent manner. In summary, the current study demonstrates that TFF2 is a regenerative cytokine expressed by macrophages to facilitate repair of infectious or non-infectious lung damage.
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Fujita-Sato S, Galeas J, Truitt M, Pitt C, Urisman A, Bandyopadhyay S, Ruggero D, McCormick F. Enhanced MET Translation and Signaling Sustains K-Ras-Driven Proliferation under Anchorage-Independent Growth Conditions. Cancer Res 2015; 75:2851-62. [PMID: 25977330 DOI: 10.1158/0008-5472.can-14-1623] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 05/01/2015] [Indexed: 01/04/2023]
Abstract
Oncogenic K-Ras mutation occurs frequently in several types of cancers, including pancreatic and lung cancers. Tumors with K-Ras mutation are resistant to chemotherapeutic drugs as well as molecular targeting agents. Although numerous approaches are ongoing to find effective ways to treat these tumors, there are still no effective therapies for K-Ras mutant cancer patients. Here we report that K-Ras mutant cancers are more dependent on K-Ras in anchorage-independent culture conditions than in monolayer culture conditions. In seeking to determine mechanisms that contribute to the K-Ras dependency in anchorage-independent culture conditions, we discovered the involvement of Met in K-Ras-dependent, anchorage-independent cell growth. The Met signaling pathway is enhanced and plays an indispensable role in anchorage-independent growth even in cells in which Met is not amplified. Indeed, Met expression is elevated under anchorage-independent growth conditions and is regulated by K-Ras in a MAPK/ERK kinase (MEK)-dependent manner. Remarkably, in spite of a global downregulation of mRNA translation during anchorage-independent growth, we find that Met mRNA translation is specifically enhanced under these conditions. Importantly, ectopic expression of an active Met mutant rescues K-Ras ablation-derived growth suppression, indicating that K-Ras-mediated Met expression drives "K-Ras addiction" in anchorage-independent conditions. Our results indicate that enhanced Met expression and signaling is essential for anchorage-independent growth of K-Ras mutant cancer cells and suggests that pharmacological inhibitors of Met could be effective for K-Ras mutant tumor patients.
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Affiliation(s)
- Saori Fujita-Sato
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California. Oncology Research Laboratories, Daiichi Sankyo Co., Ltd., Tokyo, Japan
| | - Jacqueline Galeas
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Morgan Truitt
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Cameron Pitt
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Anatoly Urisman
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Sourav Bandyopadhyay
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Davide Ruggero
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California.
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Affiliation(s)
- Anatoly Urisman
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Kirk Jones
- Department of Pathology, University of California San Francisco, San Francisco, California
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Wiita AP, Ziv E, Wiita PJ, Urisman A, Julien O, Burlingame AL, Weissman JS, Wells JA. Global cellular response to chemotherapy-induced apoptosis. eLife 2013; 2:e01236. [PMID: 24171104 PMCID: PMC3808542 DOI: 10.7554/elife.01236] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 09/23/2013] [Indexed: 12/28/2022] Open
Abstract
How cancer cells globally struggle with a chemotherapeutic insult before succumbing to apoptosis is largely unknown. Here we use an integrated systems-level examination of transcription, translation, and proteolysis to understand these events central to cancer treatment. As a model we study myeloma cells exposed to the proteasome inhibitor bortezomib, a first-line therapy. Despite robust transcriptional changes, unbiased quantitative proteomics detects production of only a few critical anti-apoptotic proteins against a background of general translation inhibition. Simultaneous ribosome profiling further reveals potential translational regulation of stress response genes. Once the apoptotic machinery is engaged, degradation by caspases is largely independent of upstream bortezomib effects. Moreover, previously uncharacterized non-caspase proteolytic events also participate in cellular deconstruction. Our systems-level data also support co-targeting the anti-apoptotic regulator HSF1 to promote cell death by bortezomib. This integrated approach offers unique, in-depth insight into apoptotic dynamics that may prove important to preclinical evaluation of any anti-cancer compound. DOI:http://dx.doi.org/10.7554/eLife.01236.001 Many cancer treatments work by causing cancer cells to enter an advanced stage of a process known as programmed cell death or apoptosis. When a cell begins apoptosis, it takes a series of metabolic steps–such as fragmenting its DNA or reducing its volume–that eventually kills it. The cancer cells in tumours are able to grow because they are able to avoid apoptosis. When cancer cells are treated with cytotoxic drugs they do not die immediately but try to stave off the effect of the drug. However, we still know relatively little about what happens at the molecular levels as cancer cells struggle to avoid apoptosis. Now Wiita et al. have combined two methods for studying cancer cells–deep sequencing of RNA and quantitative proteomics–to simultaneously observe a variety of processes, including the transcription of genes to produce messenger RNA (mRNA) molecules, the translation of these mRNA molecules to produce proteins, and the proteolysis (or breakdown) of these proteins when the cells were subjected to chemotherapy. Wiita et al. studied how human myeloma cells responded to bortezomib, a drug that is used to treat various blood cancers, and found that ribosomes–the complex molecular machines that perform the translation step– reacted to the chemotherapy by preferentially translating certain mRNA molecules in order to produce a set of proteins that protect the cell. Developing drugs to inhibit the effects of these stress-response proteins could make the cancer cells more responsive to existing anticancer drugs. When this effort to stay alive is ultimately unsuccessful, the destruction of proteins appears surprisingly unrelated to the previous attempts that were made to protect the cell. With further work the “global cellular response” approach developed by Wiita et al. could lead to the discovery of new drug targets, improve our understanding of drug resistance in chemotherapy, and provide new ways to monitor how patients respond to treatment. DOI:http://dx.doi.org/10.7554/eLife.01236.002
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Affiliation(s)
- Arun P Wiita
- Department of Pharmaceutical Chemistry , University of California, San Francisco , San Francisco , United States ; Department of Laboratory Medicine , University of California, San Francisco , San Francisco , United States
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