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Amorrortu RP, Zhao Y, Keenan RJ, Gilbert SM, Rollison DE. Factors Associated with Self-reported COVID-19 Infection and Hospitalization among Patients Seeking Care at a Comprehensive Cancer Center. J Racial Ethn Health Disparities 2023:10.1007/s40615-023-01855-4. [PMID: 37917235 DOI: 10.1007/s40615-023-01855-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND COVID-19 infection severity differs by race and ethnicity, but its long-term effect on cancer-related outcomes is unknown. Therefore, information on COVID-19 history is critical to ascertain among new cancer patients in order to advance research on its impact on cancer outcomes and potentially related health disparities. METHODS A cross-sectional study was conducted among 16,025 new patients seeking care at Moffitt Cancer Center (MCC) between 2021 and 2022. Patient self-reported histories of COVID-19 infection and other pre-existing health conditions were obtained from electronic questionnaires administered to all new MCC patients. Associations between demographics and COVID-19 infection and hospitalization were examined. RESULTS A total of 1,971 patients (12.3%) reported ever having COVID-19. Self-reported COVID-19 history was significantly more prevalent in Hispanic vs. non-Hispanic patients (OR = 1.24, 1.05-1.45) and less prevalent in Asian versus White patients (OR = 0.49, 95% 0.33-0.70). Among patients who ever had COVID-19, 10.6% reported a COVID-19-related hospitalization. Males had higher odds of a COVID-19 related hospitalization than females (OR = 1.50, 95% CI = 1.09-2.05), as did Black/African American patients (OR = 2.11, 95% CI = 1.18-3.60) and patients of races other than Black/African American and Asian (OR = 2.61, 95% CI = 1.43-4.54) compared to White patients. Hispanic patients also experienced higher odds of hospitalization (OR = 2.06, 95% CI-1.29- 3.23) compared with non-Hispanic patients of all races in a sensitivity analysis that combined race/ethnicity. Pre-existing lung and breathing problems were associated with higher odds of being hospitalized with COVID-19 (OR = 2.38, 95% CI = 1.61-3.48), but these and other health conditions did not explain the observed associations between race and COVID-19 hospitalization. CONCLUSIONS Higher rates of COVID-19 hospitalization were observed among patients identifying as Black/African American or Hispanic independent of pre-existing health conditions. Future studies evaluating long-term effects of COVID-19 should carefully examine potential racial/ethnic disparities in cancer outcomes.
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Affiliation(s)
- Rossybelle P Amorrortu
- Department of Cancer Epidemiology, Moffitt Cancer Center, 12902 Magnolia Drive, CSB 8th 8108, Tampa, FL, 33612, USA
| | - Yayi Zhao
- Department of Cancer Epidemiology, Moffitt Cancer Center, 12902 Magnolia Drive, CSB 8th 8108, Tampa, FL, 33612, USA
| | - Robert J Keenan
- Department of Thoracic Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Scott M Gilbert
- Department of Health Outcomes and Behavior, Moffitt Cancer Center, Tampa, FL, USA
- Department of Genitourinary Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Dana E Rollison
- Department of Cancer Epidemiology, Moffitt Cancer Center, 12902 Magnolia Drive, CSB 8th 8108, Tampa, FL, 33612, USA.
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2
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Rollison DE, Gonzalez BD, Turner K, Jim HSL, Zhao Y, Amorrortu RP, Howard R, Ghia KM, Ngo B, Reisman P, Moore C, Perkins R, Keenan RJ, Sallman DA, Naso CM, Robinson EJ, Vadaparampil ST, Simmons VN, Schabath MB, Gilbert SM. Examining disparities in large-scale patient-reported data capture using digital tools among cancer patients at clinical intake. Cancer Med 2023; 12:19033-19046. [PMID: 37596773 PMCID: PMC10557830 DOI: 10.1002/cam4.6459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/19/2023] [Accepted: 08/06/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND Patient-reported data can improve quality of healthcare delivery and patient outcomes. Moffitt Cancer Center ("Moffitt") administers the Electronic Patient Questionnaire (EPQ) to collect data on demographics, including sexual orientation and gender identity (SOGI), medical history, cancer risk factors, and quality of life. Here we investigated differences in EPQ completion by demographic and cancer characteristics. METHODS An analysis including 146,142 new adult patients at Moffitt in 2009-2020 was conducted using scheduling, EPQ and cancer registry data. EPQ completion was described by calendar year and demographics. Logistic regression was used to estimate associations between demographic/cancer characteristics and EPQ completion. More recently collected information on SOGI were described. RESULTS Patient portal usage (81%) and EPQ completion rates (79%) were consistently high since 2014. Among patients in the cancer registry, females were more likely to complete the EPQ than males (odds ratio [OR] = 1.17, 95% confidence interval [CI] = 1.14-1.20). Patients ages 18-64 years were more likely to complete the EPQ than patients aged ≥65. Lower EPQ completion rates were observed among Black or African American patients (OR = 0.59, 95% CI = 0.56-0.63) as compared to Whites and among patients whose preferred language was Spanish (OR = 0.40, 95% CI = 0.36-0.44) or another language as compared to English. Furthermore, patients with localized (OR = 1.16, 95% CI = 1.12-1.19) or regional (OR = 1.16, 95% CI = 1.12-1.20) cancer were more likely to complete the EPQ compared to those with metastatic disease. Less than 3% of patients self-identified as being lesbian, gay, or bisexual and <0.1% self-identified as transgender, genderqueer, or other. CONCLUSIONS EPQ completion rates differed across demographics highlighting opportunities for targeted process improvement. Healthcare organizations should evaluate data acquisition methods to identify potential disparities in data completeness that can impact quality of clinical care and generalizability of self-reported data.
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Affiliation(s)
- Dana E. Rollison
- Department of Cancer EpidemiologyMoffitt Cancer CenterTampaFloridaUSA
| | - Brian D. Gonzalez
- Department of Health Outcomes and BehaviorMoffitt Cancer CenterTampaFloridaUSA
| | - Kea Turner
- Department of Health Outcomes and BehaviorMoffitt Cancer CenterTampaFloridaUSA
| | - Heather S. L. Jim
- Department of Health Outcomes and BehaviorMoffitt Cancer CenterTampaFloridaUSA
| | - Yayi Zhao
- Department of Cancer EpidemiologyMoffitt Cancer CenterTampaFloridaUSA
| | | | - Rachel Howard
- Department of Health InformaticsMoffitt Cancer CenterTampaFloridaUSA
| | - Kavita M. Ghia
- Collaborative Data Services Core, Moffitt Cancer CenterTampaFloridaUSA
| | - Bryan Ngo
- Department of Business Intelligence and AnalyticsMoffitt Cancer CenterTampaFloridaUSA
| | - Phillip Reisman
- Department of Health InformaticsMoffitt Cancer CenterTampaFloridaUSA
| | - Colin Moore
- Department of Clinical InformaticsMoffitt Cancer CenterTampaFloridaUSA
| | - Randa Perkins
- Department of Clinical InformaticsMoffitt Cancer CenterTampaFloridaUSA
| | - Robert J. Keenan
- Department of Thoracic OncologyMoffitt Cancer CenterTampaFloridaUSA
| | - David A. Sallman
- Department of Malignant HematologyMoffitt Cancer CenterTampaFloridaUSA
| | - Cristina M. Naso
- Department of Virtual HealthMoffitt Cancer CenterTampaFloridaUSA
| | - Edmondo J. Robinson
- Center for Digital HealthMoffitt Cancer CenterTampaFloridaUSA
- Department of Internal and Hospital MedicineMoffitt Cancer CenterTampaFloridaUSA
| | | | - Vani N. Simmons
- Department of Health Outcomes and BehaviorMoffitt Cancer CenterTampaFloridaUSA
| | | | - Scott M. Gilbert
- Department of Health Outcomes and BehaviorMoffitt Cancer CenterTampaFloridaUSA
- Department of Genitourinary OncologyMoffitt Cancer CenterTampaFloridaUSA
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Smalinskaitė L, Kim MK, Lewis AJO, Keenan RJ, Hegde RS. Mechanism of an intramembrane chaperone for multipass membrane proteins. Nature 2022; 611:161-166. [PMID: 36261528 PMCID: PMC7614104 DOI: 10.1038/s41586-022-05336-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 09/12/2022] [Indexed: 01/29/2023]
Abstract
Multipass membrane proteins play numerous roles in biology and include receptors, transporters, ion channels and enzymes1,2. How multipass proteins are co-translationally inserted and folded at the endoplasmic reticulum is not well understood2. The prevailing model posits that each transmembrane domain (TMD) of a multipass protein successively passes into the lipid bilayer through a front-side lateral gate of the Sec61 protein translocation channel3-9. The PAT complex, an intramembrane chaperone comprising Asterix and CCDC47, engages early TMDs of multipass proteins to promote their biogenesis by an unknown mechanism10. Here, biochemical and structural analysis of intermediates during multipass protein biogenesis showed that the nascent chain is not engaged with Sec61, which is occluded and latched closed by CCDC47. Instead, Asterix binds to and redirects the substrate to a location behind Sec61, where the PAT complex contributes to a multipass translocon surrounding a semi-enclosed, lipid-filled cavity11. Detection of multiple TMDs in this cavity after their emergence from the ribosome suggests that multipass proteins insert and fold behind Sec61. Accordingly, biogenesis of several multipass proteins was unimpeded by inhibitors of the Sec61 lateral gate. These findings elucidate the mechanism of an intramembrane chaperone and suggest a new framework for multipass membrane protein biogenesis at the endoplasmic reticulum.
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Affiliation(s)
- Luka Smalinskaitė
- MRC Laboratory of Molecular Biology, Cell Biology Division, Cambridge, UK
| | - Min Kyung Kim
- MRC Laboratory of Molecular Biology, Cell Biology Division, Cambridge, UK
| | - Aaron J O Lewis
- MRC Laboratory of Molecular Biology, Cell Biology Division, Cambridge, UK
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Cell Biology Division, Cambridge, UK.
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Giuliano AR, Lancet JE, Pilon-Thomas S, Dong N, Jain AG, Tan E, Ball S, Tworoger SS, Siegel EM, Whiting J, Mo Q, Cubitt CL, Dukes CW, Hensel JA, Keenan RJ, Hwu P. Evaluation of Antibody Response to SARS-CoV-2 mRNA-1273 Vaccination in Patients With Cancer in Florida. JAMA Oncol 2022; 8:748-754. [PMID: 35266953 PMCID: PMC8914884 DOI: 10.1001/jamaoncol.2022.0001] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Importance Patients with cancer experience high rates of morbidity and mortality after SARS-CoV-2 infection. Immune response to mRNA-1273 vaccination across multiple cancer types and treatments remains to be established. Objective To quantitate antibody responses after mRNA-1273 vaccination among patients with solid tumors and hematologic cancer and to assess clinical and treatment factors associated with vaccine response. Design, Setting, and Participants This cohort study included patients with cancer who were aged 18 years or older, spoke English or Spanish, had received their first mRNA-1273 dose between January 12 and 25, 2021, and agreed to blood tests before and after vaccination. Exposures Receipt of 1 and 2 mRNA-1273 SARS-CoV-2 vaccine doses. Main Outcomes and Measures Seroconversion after each vaccine dose and IgG levels against SARS-CoV-2 spike protein obtained immediately before the first and second vaccine doses and 57 days (plus or minus 14 days) after the first vaccine dose. Cancer diagnoses and treatments were ascertained by medical record review. Serostatus was assessed via enzyme-linked immunosorbent assay. Paired t tests were applied to examine days 1, 29, and 57 SARS-CoV-2 antibody levels. Binding antibody IgG geometric mean titers were calculated based on log10-transformed values. Results The 515 participants were a mean (SD) age of 64.5 (11.4) years; 262 (50.9%) were women; and 32 (6.2%) were Hispanic individuals and 479 (93.0%) White individuals; race and ethnicity data on 4 (0.7%) participants were missing. Seropositivity after vaccine dose 2 was 90.3% (465; 95% CI, 87.4%-92.7%) among patients with cancer, was significantly lower among patients with hematologic cancer (84.7% [255]; 95% CI, 80.1%-88.6%) vs solid tumors (98.1% [210]; 95% CI, 95.3%-99.5%), and was lowest among patients with lymphoid cancer (70.0% [77]; 95% CI, 60.5%-78.4%). Patients receiving a vaccination within 6 months after anti-CD20 monoclonal antibody treatment had a significantly lower seroconversion (6.3% [1]; 95% CI, 0.2%-30.2%) compared with those treated 6 to 24 months earlier (53.3% [8]; 95% CI, 26.6%-78.7%) or those who never received anti-CD20 treatment (94.2% [456]; 95% CI, 91.7%-96.1%). Low antibody levels after vaccination were observed among patients treated with anti-CD20 within 6 months before vaccination (GM, 15.5 AU/mL; 95% CI, 9.8-24.5 AU/mL), patients treated with small molecules (GM, 646.7 AU/mL; 95% CI, 441.9-946.5 AU/mL), and patients with low lymphocyte (GM, 547.4 AU/mL; 95% CI, 375.5-797.7 AU/mL) and IgG (GM, 494.7 AU/mL; 95% CI, 304.9-802.7 AU/mL) levels. Conclusions and Relevance This cohort study found that the mRNA-1273 SARS-CoV-2 vaccine induced variable antibody responses that differed by cancer diagnosis and treatment received. These findings suggest that patients with hematologic cancer and those who are receiving immunosuppressive treatments may need additional vaccination doses.
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Affiliation(s)
| | | | | | - Ning Dong
- Moffitt Cancer Center, Tampa, Florida
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5
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Abstract
Roughly one quarter of all genes code for integral membrane proteins that are inserted into the plasma membrane of prokaryotes or the endoplasmic reticulum membrane of eukaryotes. Multiple pathways are used for the targeting and insertion of membrane proteins on the basis of their topological and biophysical characteristics. Multipass membrane proteins span the membrane multiple times and face the additional challenges of intramembrane folding. In many cases, integral membrane proteins require assembly with other proteins to form multi-subunit membrane protein complexes. Recent biochemical and structural analyses have provided considerable clarity regarding the molecular basis of membrane protein targeting and insertion, with tantalizing new insights into the poorly understood processes of multipass membrane protein biogenesis and multi-subunit protein complex assembly.
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Affiliation(s)
- Ramanujan S Hegde
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Robert J Keenan
- Gordon Center for Integrative Science, The University of Chicago, Chicago, IL, USA.
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McGilvray PT, Anghel SA, Sundaram A, Zhong F, Trnka MJ, Fuller JR, Hu H, Burlingame AL, Keenan RJ. An ER translocon for multi-pass membrane protein biogenesis. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321092072] [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: 11/10/2022] Open
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McGilvray PT, Anghel SA, Sundaram A, Zhong F, Trnka MJ, Fuller JR, Hu H, Burlingame AL, Keenan RJ. An ER translocon for multi-pass membrane protein biogenesis. eLife 2020; 9:e56889. [PMID: 32820719 PMCID: PMC7505659 DOI: 10.7554/elife.56889] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [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: 03/13/2020] [Accepted: 08/20/2020] [Indexed: 12/23/2022] Open
Abstract
Membrane proteins with multiple transmembrane domains play critical roles in cell physiology, but little is known about the machinery coordinating their biogenesis at the endoplasmic reticulum. Here we describe a ~ 360 kDa ribosome-associated complex comprising the core Sec61 channel and five accessory factors: TMCO1, CCDC47 and the Nicalin-TMEM147-NOMO complex. Cryo-electron microscopy reveals a large assembly at the ribosome exit tunnel organized around a central membrane cavity. Similar to protein-conducting channels that facilitate movement of transmembrane segments, cytosolic and luminal funnels in TMCO1 and TMEM147, respectively, suggest routes into the central membrane cavity. High-throughput mRNA sequencing shows selective translocon engagement with hundreds of different multi-pass membrane proteins. Consistent with a role in multi-pass membrane protein biogenesis, cells lacking different accessory components show reduced levels of one such client, the glutamate transporter EAAT1. These results identify a new human translocon and provide a molecular framework for understanding its role in multi-pass membrane protein biogenesis.
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Affiliation(s)
- Philip T McGilvray
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - S Andrei Anghel
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
- Department of Molecular Genetics and Cell Biology, The University of ChicagoChicagoUnited States
| | - Arunkumar Sundaram
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - Frank Zhong
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
- Department of Molecular Genetics and Cell Biology, The University of ChicagoChicagoUnited States
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - James R Fuller
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - Hong Hu
- Center for Research Informatics, The University of ChicagoChicagoUnited States
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
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O'Donnell JP, Phillips BP, Yagita Y, Juszkiewicz S, Wagner A, Malinverni D, Keenan RJ, Miller EA, Hegde RS. The architecture of EMC reveals a path for membrane protein insertion. eLife 2020; 9:e57887. [PMID: 32459176 PMCID: PMC7292650 DOI: 10.7554/elife.57887] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [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: 04/15/2020] [Accepted: 05/26/2020] [Indexed: 12/29/2022] Open
Abstract
Approximately 25% of eukaryotic genes code for integral membrane proteins that are assembled at the endoplasmic reticulum. An abundant and widely conserved multi-protein complex termed EMC has been implicated in membrane protein biogenesis, but its mechanism of action is poorly understood. Here, we define the composition and architecture of human EMC using biochemical assays, crystallography of individual subunits, site-specific photocrosslinking, and cryo-EM reconstruction. Our results suggest that EMC's cytosolic domain contains a large, moderately hydrophobic vestibule that can bind a substrate's transmembrane domain (TMD). The cytosolic vestibule leads into a lumenally-sealed, lipid-exposed intramembrane groove large enough to accommodate a single substrate TMD. A gap between the cytosolic vestibule and intramembrane groove provides a potential path for substrate egress from EMC. These findings suggest how EMC facilitates energy-independent membrane insertion of TMDs, explain why only short lumenal domains are translocated by EMC, and constrain models of EMC's proposed chaperone function.
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Affiliation(s)
| | - Ben P Phillips
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Yuichi Yagita
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | | | | | | | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
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9
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Spiess PE, Greene J, Keenan RJ, Paculdo D, Letson GD, Peabody JW. Meeting the challenge of the 2019 novel coronavirus disease in patients with cancer. Cancer 2020; 126:3174-3175. [PMID: 32324273 PMCID: PMC7264676 DOI: 10.1002/cncr.32919] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/25/2020] [Accepted: 04/02/2020] [Indexed: 12/27/2022]
Abstract
The alarming situation of the 2019 novel coronavirus disease (COVID‐19) is contrasted by the limited efforts to curb the spread and impact of the disease among patients with cancer. This commentary proposes a simple 5‐part strategy plus rapidly expanded use of telemedicine to anticipate and deal with COVID‐19 and, by extension, future epidemics in patients with cancer.
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Affiliation(s)
- Philippe E Spiess
- Genitourinary Oncology Program, Moffitt Cancer Center, Tampa, Florida
| | - John Greene
- Infectious Disease Program, Moffitt Cancer Center, Tampa, Florida
| | - Robert J Keenan
- Thoracic Oncology Program, Moffitt Cancer Center, Tampa, Florida
| | | | | | - John W Peabody
- QURE Healthcare, San Francisco, California.,University of California San Francisco, San Francisco, California.,University of California Los Angeles, Los Angeles, California
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10
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Anghel SA, McGilvray PT, Hegde RS, Keenan RJ. Identification of Oxa1 Homologs Operating in the Eukaryotic Endoplasmic Reticulum. Cell Rep 2019; 21:3708-3716. [PMID: 29281821 PMCID: PMC5868721 DOI: 10.1016/j.celrep.2017.12.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [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: 05/17/2017] [Revised: 10/18/2017] [Accepted: 12/01/2017] [Indexed: 12/23/2022] Open
Abstract
Members of the evolutionarily conserved Oxa1/Alb3/YidC family mediate membrane protein biogenesis at the mitochondrial inner membrane, chloroplast thylakoid membrane, and bacterial plasma membrane, respectively. Despite their broad phylogenetic distribution, no Oxa1/Alb3/YidC homologs are known to operate in eukaryotic cells outside the endosymbiotic organelles. Here, we present bioinformatic evidence that the tail-anchored protein insertion factor WRB/Get1, the “endoplasmic reticulum (ER) membrane complex” subunit EMC3, and TMCO1 are ER-resident homologs of the Oxa1/Alb3/YidC family. Topology mapping and co-evolution-based modeling demonstrate that Get1, EMC3, and TMCO1 share a conserved Oxa1-like architecture. Biochemical analysis of human TMCO1, the only homolog not previously linked to membrane protein biogenesis, shows that it associates with the Sec translocon and ribosomes. These findings suggest a specific biochemical function for TMCO1 and define a superfamily of proteins—the “Oxa1 superfamily”—whose shared function is to facilitate membrane protein biogenesis.
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Affiliation(s)
- S Andrei Anghel
- Department of Biochemistry and Molecular Biology , The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Cell and Molecular Biology Graduate Program , The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Philip T McGilvray
- Department of Biochemistry and Molecular Biology , The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology , The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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11
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Nguyen DT, Fontaine JP, Robinson LA, Keenan RJ, Toloza EM. Pulmonary Lobectomy Is Not Inferior to Pneumonectomy for Stage-II (N1) Non-Small Cell Lung Cancer. J Am Coll Surg 2018. [DOI: 10.1016/j.jamcollsurg.2018.08.266] [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: 11/25/2022]
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12
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Mateja A, Keenan RJ. A structural perspective on tail-anchored protein biogenesis by the GET pathway. Curr Opin Struct Biol 2018; 51:195-202. [PMID: 30173121 DOI: 10.1016/j.sbi.2018.07.009] [Citation(s) in RCA: 23] [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: 05/14/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/16/2022]
Abstract
Many tail-anchored (TA) membrane proteins are targeted to and inserted into the endoplasmic reticulum (ER) by the `guided entry of tail-anchored proteins' (GET) pathway. This post-translational pathway uses transmembrane-domain selective cytosolic chaperones for targeting, and a dedicated membrane protein complex for insertion. The past decade has seen rapid progress towards defining the molecular basis of TA protein biogenesis by the GET pathway. Here we review the mechanisms underlying each step of the pathway, emphasizing recent structural work and highlighting key questions that await future studies.
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Affiliation(s)
- Agnieszka Mateja
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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13
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Affiliation(s)
- Tawee Tanvetyanon
- Thoracic Oncology Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Robert J Keenan
- Thoracic Oncology Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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14
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Zalisko BE, Chan C, Denic V, Rock RS, Keenan RJ. Tail-Anchored Protein Insertion by a Single Get1/2 Heterodimer. Cell Rep 2018; 20:2287-2293. [PMID: 28877464 DOI: 10.1016/j.celrep.2017.08.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/27/2017] [Accepted: 08/07/2017] [Indexed: 01/19/2023] Open
Abstract
The Get1/2 transmembrane complex drives the insertion of tail-anchored (TA) proteins from the cytosolic chaperone Get3 into the endoplasmic reticulum membrane. Mechanistic insight into how Get1/2 coordinates this process is confounded by a lack of understanding of the basic architecture of the complex. Here, we define the oligomeric state of full-length Get1/2 in reconstituted lipid bilayers by combining single-molecule and bulk fluorescence measurements with quantitative in vitro insertion analysis. We show that a single Get1/2 heterodimer is sufficient for insertion and demonstrate that the conserved cytosolic regions of Get1 and Get2 bind asymmetrically to opposing subunits of the Get3 homodimer. Altogether, our results define a simplified model for how Get1/2 and Get3 coordinate TA protein insertion.
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Affiliation(s)
- Benjamin E Zalisko
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Charlene Chan
- Department of Molecular and Cellular Biology, Northwest Labs, Harvard University, Cambridge, MA 02138, USA
| | - Vladimir Denic
- Department of Molecular and Cellular Biology, Northwest Labs, Harvard University, Cambridge, MA 02138, USA.
| | - Ronald S Rock
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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15
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Wohlever ML, Mateja A, McGilvray PT, Day KJ, Keenan RJ. Msp1 Is a Membrane Protein Dislocase for Tail-Anchored Proteins. Mol Cell 2017; 67:194-202.e6. [PMID: 28712723 DOI: 10.1016/j.molcel.2017.06.019] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 05/09/2017] [Accepted: 06/16/2017] [Indexed: 11/18/2022]
Abstract
Mislocalized tail-anchored (TA) proteins of the outer mitochondrial membrane are cleared by a newly identified quality control pathway involving the conserved eukaryotic protein Msp1 (ATAD1 in humans). Msp1 is a transmembrane AAA-ATPase, but its role in TA protein clearance is not known. Here, using purified components reconstituted into proteoliposomes, we show that Msp1 is both necessary and sufficient to drive the ATP-dependent extraction of TA proteins from the membrane. A crystal structure of the Msp1 cytosolic region modeled into a ring hexamer suggests that active Msp1 contains a conserved membrane-facing surface adjacent to a central pore. Structure-guided mutagenesis of the pore residues shows that they are critical for TA protein extraction in vitro and for functional complementation of an msp1 deletion in yeast. Together, these data provide a molecular framework for Msp1-dependent extraction of mislocalized TA proteins from the outer mitochondrial membrane.
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Affiliation(s)
- Matthew L Wohlever
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Agnieszka Mateja
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Philip T McGilvray
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Kasey J Day
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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16
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Srivastava R, Zalisko BE, Keenan RJ, Howell SH. The GET System Inserts the Tail-Anchored Protein, SYP72, into Endoplasmic Reticulum Membranes. Plant Physiol 2017; 173:1137-1145. [PMID: 27923985 PMCID: PMC5291014 DOI: 10.1104/pp.16.00928] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 12/04/2016] [Indexed: 05/25/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana) genome encodes homologs of the Guided Entry of Tail (GET)-anchored protein system for the posttranslational insertion of tail-anchored (TA) proteins into endoplasmic reticulum (ER) membranes. In yeast, TA proteins are loaded onto the cytosolic targeting factor Get3 and are then delivered to the membrane-associated Get1/2 complex for insertion into ER membranes. The role of the GET system in Arabidopsis was investigated by monitoring the membrane insertion of a tail-anchored protein, SYP72, a syntaxin. SYP72 bound to yeast Get3 in vitro, forming a Get3-SYP72 fusion complex that could be inserted into yeast GET1/2-containing proteoliposomes. The Arabidopsis GET system functioned in vivo to insert TA proteins into ER membranes as demonstrated by the fact that the YFP-tagged SYP72 localized to the ER in wild-type plants but accumulated as cytoplasmic inclusions in get1, get3, or get4 mutants. The GET mutants get1 and get3 were less tolerant of ER stress agents and showed symptoms of ER stress even under unstressed conditions. Hence, the GET system is responsible for the insertion of TA proteins into the ER in Arabidopsis, and mutants with GET dysfunctions are more susceptible to ER stress.
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Affiliation(s)
- Renu Srivastava
- Plant Sciences Institute and Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50010 (R.S., S.H.H.); and
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637 (B.E.Z., R.J.K.)
| | - Benjamin E Zalisko
- Plant Sciences Institute and Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50010 (R.S., S.H.H.); and
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637 (B.E.Z., R.J.K.)
| | - Robert J Keenan
- Plant Sciences Institute and Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50010 (R.S., S.H.H.); and
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637 (B.E.Z., R.J.K.)
| | - Stephen H Howell
- Plant Sciences Institute and Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50010 (R.S., S.H.H.); and
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637 (B.E.Z., R.J.K.)
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17
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Nguyen DT, Fontaine JP, Robinson LA, Keenan RJ, Toloza EM. P1.17: Improved Survival for Stage-2 (N1) Pulmonary Adenocarcinoma and Squamous Cell Carcinoma After Pulmonary Lobectomy. J Thorac Oncol 2016. [DOI: 10.1016/j.jtho.2016.08.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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18
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Nguyen DT, Fontaine JP, Robinson LA, Keenan RJ, Toloza EM. P1.22: Temporal Survival Improvement for Stage-II (T3N0M0) Lung Adenocarcinoma After Pulmonary Lobectomy. J Thorac Oncol 2016. [DOI: 10.1016/j.jtho.2016.08.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Sharma P, Keenan RJ, Sexton WJ. Mass in Solitary Intrathoracic Kidney Within Bochdalek Hernia. Urology 2016; 97:e15-e16. [PMID: 27554626 DOI: 10.1016/j.urology.2016.08.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/01/2016] [Accepted: 08/12/2016] [Indexed: 11/19/2022]
Abstract
Bochdalek hernia is a congenital defect in the diaphragm posterolaterally that allows abdominal contents to enter the thorax. Herniation and development of an intrathoracic kidney associated with this condition are uncommon, with an incidence less than 0.25%. Intrathoracic kidney is also the rarest form of renal ectopia, consisting of less than 5% of cases. We present a series of images from a case of a 55-year-old female with a right renal mass suspicious for malignancy in a solitary right intrathoracic kidney within Bochdalek hernia, who underwent an open right partial nephrectomy for definitive diagnosis and treatment.
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Affiliation(s)
- Pranav Sharma
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL.
| | - Robert J Keenan
- Department of Thoracic Oncology, Quality, H. Lee Moffitt Cancer Center, Tampa, FL
| | - Wade J Sexton
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL
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20
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Itakura E, Zavodszky E, Shao S, Wohlever ML, Keenan RJ, Hegde RS. Ubiquilins Chaperone and Triage Mitochondrial Membrane Proteins for Degradation. Mol Cell 2016; 63:21-33. [PMID: 27345149 PMCID: PMC4942676 DOI: 10.1016/j.molcel.2016.05.020] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/04/2016] [Accepted: 05/16/2016] [Indexed: 12/14/2022]
Abstract
We investigated how mitochondrial membrane proteins remain soluble in the cytosol until their delivery to mitochondria or degradation at the proteasome. We show that Ubiquilin family proteins bind transmembrane domains in the cytosol to prevent aggregation and temporarily allow opportunities for membrane targeting. Over time, Ubiquilins recruit an E3 ligase to ubiquitinate bound clients. The attached ubiquitin engages Ubiquilin's UBA domain, normally bound to an intramolecular UBL domain, and stabilizes the Ubiquilin-client complex. This conformational change precludes additional chances at membrane targeting for the client, while simultaneously freeing Ubiquilin's UBL domain for targeting to the proteasome. Loss of Ubiquilins by genetic ablation or sequestration in polyglutamine aggregates leads to accumulation of non-inserted mitochondrial membrane protein precursors. These findings define Ubiquilins as a family of chaperones for cytosolically exposed transmembrane domains and explain how they use ubiquitin to triage clients for degradation via coordinated intra- and intermolecular interactions.
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Affiliation(s)
- Eisuke Itakura
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Department of Biology, Faculty of Science, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Eszter Zavodszky
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sichen Shao
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Matthew L Wohlever
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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21
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Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AMJJ, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Christopher Fromme J, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJB, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FRNC, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P. Data publication with the structural biology data grid supports live analysis. Nat Commun 2016; 7:10882. [PMID: 26947396 PMCID: PMC4786681 DOI: 10.1038/ncomms10882] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [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: 10/16/2015] [Accepted: 01/28/2016] [Indexed: 11/26/2022] Open
Abstract
Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.
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Affiliation(s)
- Peter A. Meyer
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
| | - Stephanie Socias
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
| | - Jason Key
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
| | - Elizabeth Ransey
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
| | - Emily C. Tjon
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
| | - Alejandro Buschiazzo
- Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
- Department of Structural Biology & Chemistry, Institut Pasteur, 75015 Paris, France
| | - Ming Lei
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chris Botka
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - James Withrow
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700S. Cass Avenue, Argonne, Illinois 60439, USA
| | - David Neau
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700S. Cass Avenue, Argonne, Illinois 60439, USA
| | - Kanagalaghatta Rajashankar
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700S. Cass Avenue, Argonne, Illinois 60439, USA
| | - Karen S. Anderson
- Departments of Pharmacology and Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Richard H. Baxter
- Department of Chemistry, Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Stephen C. Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
| | - Titus J. Boggon
- Departments of Pharmacology and Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | | | - Dominika Borek
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Tom J. Brett
- Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Chung-I Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Walter J. Chazin
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Kevin D. Corbett
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210, USA
| | - Sean Crosson
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, Missouri 63104, USA
| | - Catherine L. Drennan
- Departments of Chemistry and Biology and the Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Michael J. Eck
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Brandt F. Eichman
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Qing R. Fan
- Departments of Pharmacology and Pathology and Cell Biology, Columbia University, New York, New York 10032, USA
| | - Adrian R. Ferré-D'Amaré
- Laboratory of RNA Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland 20892, USA
| | - J. Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - K. Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Stephen C. Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ekaterina E. Heldwein
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada K7M 3G5
| | - Robert J. Keenan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Andrew C. Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
| | - Marc Kvansakul
- Department of Biochemistry and Genetics, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Jason S. McLellan
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA
| | - Yorgo Modis
- Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Yunsun Nam
- University of Texas, Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Zbyszek Otwinowski
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Emil F. Pai
- Departments of Biochemistry, Medical Biophysics and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
- Campbell Family Institute for Cancer Research, Ontario Cancer Institute/University Health Network, Toronto, Ontario, Canada M5G 2M9
| | - Pedro José Barbosa Pereira
- IBMC—Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4150 Porto, Portugal
| | - Carlo Petosa
- Université Grenoble Alpes/CNRS/CEA, Institut de Biologie Structurale, 38027 Grenoble, France
| | - C. S. Raman
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, USA
| | - Tom A. Rapoport
- Howard Hughes Medical Institute and Harvard Medical School, Department of Cell Biology, Boston, Massachusetts 02115, USA
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland 20892, USA
- National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA
| | - Michael K. Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Gabby Rudenko
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Thomas U. Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Yousif Shamoo
- Department of BioSciences, Rice University, Houston, Texas 77005, USA
| | - Holger Sondermann
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
| | - Yizhi J. Tao
- Department of BioSciences, Rice University, Houston, Texas 77005, USA
| | - Niraj H. Tolia
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Kenneth D. Westover
- Departments of Biochemistry and Radiation Oncology, University of Texas, Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Ian Foster
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, and Department of Computer Science, University of Chicago, Chicago, Illinois 60637, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Filipe R. N C. Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147 USA
| | - Tom Kirchhausen
- Program in Cellular and Molecular Medicine and Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Departments of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kay Diederichs
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Mercè Crosas
- Institute for Quantitative Social Science, Harvard University, Cambridge, Massachusetts, 02138, USA
| | - Piotr Sliz
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
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22
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Dominik PK, Borowska MT, Dalmas O, Kim SS, Perozo E, Keenan RJ, Kossiakoff AA. Conformational Chaperones for Structural Studies of Membrane Proteins Using Antibody Phage Display with Nanodiscs. Structure 2015; 24:300-9. [PMID: 26749445 DOI: 10.1016/j.str.2015.11.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/20/2015] [Accepted: 11/23/2015] [Indexed: 01/18/2023]
Abstract
A major challenge in membrane biophysics is to define the mechanistic linkages between a protein's conformational transitions and its function. We describe a novel approach to stabilize transient functional states of membrane proteins in native-like lipid environments allowing for their structural and biochemical characterization. This is accomplished by combining the power of antibody Fab-based phage display selection with the benefits of embedding membrane protein targets in lipid-filled nanodiscs. In addition to providing a stabilizing lipid environment, nanodiscs afford significant technical advantages over detergent-based formats. This enables the production of a rich pool of high-performance Fab binders that can be used as crystallization chaperones, as fiducial markers for single-particle cryoelectron microscopy, and as probes of different conformational states. Moreover, nanodisc-generated Fabs can be used to identify detergents that best mimic native membrane environments for use in biophysical studies.
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Affiliation(s)
- Pawel K Dominik
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Marta T Borowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Olivier Dalmas
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Sangwoo S Kim
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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23
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Borowska MT, Dominik PK, Anghel SA, Kossiakoff AA, Keenan RJ. A YidC-like Protein in the Archaeal Plasma Membrane. Structure 2015; 23:1715-1724. [PMID: 26256539 PMCID: PMC4558205 DOI: 10.1016/j.str.2015.06.025] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 05/29/2015] [Accepted: 06/21/2015] [Indexed: 01/08/2023]
Abstract
Cells possess specialized machinery to direct the insertion of membrane proteins into the lipid bilayer. In bacteria, the essential protein YidC inserts certain proteins into the plasma membrane, and eukaryotic orthologs are present in the mitochondrial inner membrane and the chloroplast thylakoid membrane. The existence of homologous insertases in archaea has been proposed based on phylogenetic analysis. However, limited sequence identity, distinct architecture, and the absence of experimental data have made this assignment ambiguous. Here we describe the 3.5-Å crystal structure of an archaeal DUF106 protein from Methanocaldococcus jannaschii (Mj0480), revealing a lipid-exposed hydrophilic surface presented by a conserved YidC-like fold. Functional analysis reveals selective binding of Mj0480 to ribosomes displaying a stalled YidC substrate, and a direct interaction between the buried hydrophilic surface of Mj0480 and the nascent chain. These data provide direct experimental evidence that the archaeal DUF106 proteins are YidC/Oxa1/Alb3-like insertases of the archaeal plasma membrane.
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Affiliation(s)
- Marta T Borowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - S Andrei Anghel
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA.
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24
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Mateja A, Paduch M, Chang HY, Szydlowska A, Kossiakoff AA, Hegde RS, Keenan RJ. Protein targeting. Structure of the Get3 targeting factor in complex with its membrane protein cargo. Science 2015; 347:1152-5. [PMID: 25745174 PMCID: PMC4413028 DOI: 10.1126/science.1261671] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Tail-anchored (TA) proteins are a physiologically important class of membrane proteins targeted to the endoplasmic reticulum by the conserved guided-entry of TA proteins (GET) pathway. During transit, their hydrophobic transmembrane domains (TMDs) are chaperoned by the cytosolic targeting factor Get3, but the molecular nature of the functional Get3-TA protein targeting complex remains unknown. We reconstituted the physiologic assembly pathway for a functional targeting complex and showed that it comprises a TA protein bound to a Get3 homodimer. Crystal structures of Get3 bound to different TA proteins showed an α-helical TMD occupying a hydrophobic groove that spans the Get3 homodimer. Our data elucidate the mechanism of TA protein recognition and shielding by Get3 and suggest general principles of hydrophobic domain chaperoning by cellular targeting factors.
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Affiliation(s)
- Agnieszka Mateja
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Hsin-Yang Chang
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Anna Szydlowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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25
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Bestul AJ, Christensen JR, Grzegorzewska AP, Burke TA, Sees JA, Carroll RT, Sirotkin V, Keenan RJ, Kovar DR. Fission yeast profilin is tailored to facilitate actin assembly by the cytokinesis formin Cdc12. Mol Biol Cell 2014; 26:283-93. [PMID: 25392301 PMCID: PMC4294675 DOI: 10.1091/mbc.e13-05-0281] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The evolutionarily conserved small actin-monomer binding protein profilin is believed to be a housekeeping factor that maintains a general pool of unassembled actin. However, despite similar primary sequences, structural folds, and affinities for G-actin and poly-L-proline, budding yeast profilin ScPFY fails to complement fission yeast profilin SpPRF temperature-sensitive mutant cdc3-124 cells. To identify profilin's essential properties, we built a combinatorial library of ScPFY variants containing either WT or SpPRF residues at multiple positions and carried out a genetic selection to isolate variants that support life in fission yeast. We subsequently engineered ScPFY(9-Mut), a variant containing nine substitutions in the actin-binding region, which complements cdc3-124 cells. ScPFY(9-Mut), but not WT ScPFY, suppresses severe cytokinesis defects in cdc3-124 cells. Furthermore, the major activity rescued by ScPFY(9-Mut) is the ability to enhance cytokinesis formin Cdc12-mediated actin assembly in vitro, which allows cells to assemble functional contractile rings. Therefore an essential role of profilin is to specifically facilitate formin-mediated actin assembly for cytokinesis in fission yeast.
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Affiliation(s)
- Andrew J Bestul
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Jenna R Christensen
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | | | - Thomas A Burke
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Jennifer A Sees
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Robert T Carroll
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Vladimir Sirotkin
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
| | - David R Kovar
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637 Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
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26
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Grogan EL, Deppen SA, Ballman KV, Andrade GM, Verdial FC, Aldrich MC, Chen CL, Decker PA, Harpole DH, Cerfolio RJ, Keenan RJ, Jones DR, D'Amico TA, Shrager JB, Meyers BF, Putnam JB. Accuracy of fluorodeoxyglucose-positron emission tomography within the clinical practice of the American College of Surgeons Oncology Group Z4031 trial to diagnose clinical stage I non-small cell lung cancer. Ann Thorac Surg 2014; 97:1142-8. [PMID: 24576597 DOI: 10.1016/j.athoracsur.2013.12.043] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 12/04/2013] [Accepted: 12/18/2013] [Indexed: 01/24/2023]
Abstract
BACKGROUND Fluorodeoxyglucose-positron emission tomography (FDG-PET) is recommended for diagnosis and staging of non-small cell lung cancer (NSCLC). Meta-analyses of FDG-PET diagnostic accuracy demonstrated sensitivity of 96% and specificity of 78% but were performed in select centers, introducing potential bias. This study evaluates the accuracy of FDG-PET to diagnose NSCLC and examines differences across enrolling sites in the national American College of Surgeons Oncology Group (ACOSOG) Z4031 trial. METHODS Between 2004 and 2006, 959 eligible patients with clinical stage I (cT1-2 N0 M0) known or suspected NSCLC were enrolled in the Z4031 trial, and with a baseline FDG-PET available for 682. Final diagnosis was determined by pathologic examination. FDG-PET avidity was categorized into avid or not avid by radiologist description or reported maximum standard uptake value. FDG-PET diagnostic accuracy was calculated for the entire cohort. Accuracy differences based on preoperative size and by enrolling site were examined. RESULTS Preoperative FDG-PET results were available for 682 participants enrolled at 51 sites in 39 cities. Lung cancer prevalence was 83%. FDG-PET sensitivity was 82% (95% confidence interval, 79 to 85) and specificity was 31% (95% confidence interval, 23% to 40%). Positive and negative predictive values were 85% and 26%, respectively. Accuracy improved with lesion size. Of 80 false-positive scans, 69% were granulomas. False-negative scans occurred in 101 patients, with adenocarcinoma being the most frequent (64%), and 11 were 10 mm or less. The sensitivity varied from 68% to 91% (p=0.03), and the specificity ranged from 15% to 44% (p=0.72) across cities with more than 25 participants. CONCLUSIONS In a national surgical population with clinical stage I NSCLC, FDG-PET to diagnose lung cancer performed poorly compared with published studies.
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Affiliation(s)
- Eric L Grogan
- Veterans Affairs Medical Center, Nashville, Tennessee; Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee; Institute for Medicine and Public Health, Vanderbilt University, Nashville, Tennessee.
| | - Stephen A Deppen
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee; Institute for Medicine and Public Health, Vanderbilt University, Nashville, Tennessee
| | - Karla V Ballman
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Gabriela M Andrade
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Francys C Verdial
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee; Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Chiu L Chen
- Center for Quantitative Sciences, Mayo Clinic, Rochester, Minnesota
| | - Paul A Decker
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - David H Harpole
- Department of Surgery, Duke University, Durham, North Carolina
| | | | - Robert J Keenan
- Department of Surgery, Allegheny General Hospital, Pittsburgh, Pennsylvania
| | - David R Jones
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Joseph B Shrager
- Department of Surgery, Stanford University, Stanford, California
| | - Bryan F Meyers
- Department of Surgery, Washington University, St. Louis, Missouri
| | - Joe B Putnam
- Veterans Affairs Medical Center, Nashville, Tennessee; Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
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27
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Grogan EL, Deppen SA, Chen H, Ballman KV, Verdial FC, Aldrich MC, Decker PA, Harpole DH, Cerfolio RJ, Keenan RJ, Jones DR, D'Amico TA, Shrager JB, Meyers BF, Putnam JB. Abstract LB-296: FDG-PET avidity negatively impacts survival in pStage I NSCLC in the ACOSOG Z4031 trial. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-lb-296] [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
Background: Fluoro-deoxyglucose positron emission tomography (FDG-PET) scans are used for diagnosis and staging of known or suspected non-small cell lung cancer (NSCLC). Single institution studies examining the impact of avidity on survival have reported mixed results. The purpose of this study is to evaluate the association between FDG-PET avidity and survival in the national prospective ACOSOG Z4031 trial in patients with pathological Stage I NSCLC.
Methods: Between 2004 and 2006, 1074 patients with known or suspected clinical stage I (cT1-2N0M0) NSCLC were enrolled in the ACOSOG Z4031 trial and underwent surgical resection. FDG-PET results were abstracted from radiology interpretations included in the case report forms. FDG-PET avidity was categorized based on either radiologist description or reported maximum standard uptake value (SUV). The four categories were: 1) not avid and not cancerous (SUV=0), 2) low avidity and likely not cancerous (SUV>0 and <2.5), 3) avid and probably cancerous (SUV≥2.5 and <5) and 4) highly avid and likely cancerous (SUV≥5). The lesion was classified as avid if in categories 3 or 4. The final diagnosis was determined by pathological examination and all cause mortality was reported. Cox proportional hazard regression was used to assess the impact of FDG-PET avidity on survival. The covariates used in the model included pStage, gender, age, race, and preoperative lesion size. Kaplan-Meier survival curves were calculated and the log-rank test was used to determine differences in survival based on FDG-PET avidity.
Results: There were 51 enrolling sites in 39 cities with 969 eligible participants. Preoperative FDG-PET results were available for 540 participants with NSCLC and 81% had FDG-PET avid or highly avid lesions. 400 patients had pStage I NSCLC and the 5 year survival was 70% with 95%CI (65%, 75%). FDG-PET avidity, male gender, age, and lesion size negatively impacted survival. FDG-PET avidity in pStage I disease still negatively impacted survival (p=0.03) when controlling for lesion size. The 5 year survival for Stage I disease was 80% with 95%CI (68%, 88%) in FDG-PET negative patients and 67% with 95% CI (61%, 72%) in FDG-PET positive patients (p=0.02).
Conclusions: In a national surgical population with pathological stage I NSCLC, FDG-PET avidity negatively impacted five year survival, independently of lesion size. Further work should be done to determine if chemotherapy would be beneficial in patients with PET avid lesions and pStage I NSCLC.
Citation Format: Eric L. Grogan, Stephen A. Deppen, Heidi Chen, Karla V. Ballman, Francys C. Verdial, Melinda C. Aldrich, Paul A. Decker, David H. Harpole, Robert J. Cerfolio, Robert J. Keenan, David R. Jones, Thomas A. D'Amico, Joseph B. Shrager, Bryan F. Meyers, Joe B. Putnam. FDG-PET avidity negatively impacts survival in pStage I NSCLC in the ACOSOG Z4031 trial. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-296. doi:10.1158/1538-7445.AM2013-LB-296
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28
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Abstract
Eukaryotic tail-anchored (TA) membrane proteins are inserted into the endoplasmic reticulum by a post-translational TRC40 pathway, but no comparable pathway is known in other domains of life. The crystal structure of an archaebacterial TRC40 sequence homolog bound to ADP•AlF(4) (-) reveals characteristic features of eukaryotic TRC40, including a zinc-mediated dimer and a large hydrophobic groove. Moreover, archaeal TRC40 interacts with the transmembrane domain of TA substrates and directs their membrane insertion. Thus, the TRC40 pathway is more broadly conserved than previously recognized.
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Affiliation(s)
- John Sherrill
- Department of Biochemistry & Molecular Biology, The University of Chicago, Gordon Center for Integrative Science, Room W238, Chicago, IL 60637, USA
| | - Malaiyalam Mariappan
- Cell Biology and Metabolism Program, National Institute of Child Health and Human Development, National Institutes of Health, Room 101, Building 18T, 18 Library Drive, Bethesda, MD 20892, USA
| | - Pawel Dominik
- Department of Biochemistry & Molecular Biology, The University of Chicago, Gordon Center for Integrative Science, Room W238, Chicago, IL 60637, USA
| | - Ramanujan S. Hegde
- Cell Biology and Metabolism Program, National Institute of Child Health and Human Development, National Institutes of Health, Room 101, Building 18T, 18 Library Drive, Bethesda, MD 20892, USA
| | - Robert J. Keenan
- Department of Biochemistry & Molecular Biology, The University of Chicago, Gordon Center for Integrative Science, Room W238, Chicago, IL 60637, USA
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29
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Mariappan M, Mateja A, Dobosz M, Bove E, Hegde RS, Keenan RJ. The mechanism of membrane-associated steps in tail-anchored protein insertion. Nature 2011; 477:61-6. [PMID: 21866104 PMCID: PMC3760497 DOI: 10.1038/nature10362] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 07/13/2011] [Indexed: 12/23/2022]
Abstract
Tail-anchored (TA) membrane proteins destined for the endoplasmic reticulum are chaperoned by cytosolic targeting factors that deliver them to a membrane receptor for insertion. Although a basic framework for TA protein recognition is now emerging, the decisive targeting and membrane insertion steps are not understood. Here we reconstitute the TA protein insertion cycle with purified components, present crystal structures of key complexes between these components and perform mutational analyses based on the structures. We show that a committed targeting complex, formed by a TA protein bound to the chaperone ATPase Get3, is initially recruited to the membrane through an interaction with Get2. Once the targeting complex has been recruited, Get1 interacts with Get3 to drive TA protein release in an ATPase-dependent reaction. After releasing its TA protein cargo, the now-vacant Get3 recycles back to the cytosol concomitant with ATP binding. This work provides a detailed structural and mechanistic framework for the minimal TA protein insertion cycle.
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Affiliation(s)
- Malaiyalam Mariappan
- Cell Biology and Metabolism Program, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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30
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Abstract
Fluorescent proteins (FPs) are invaluable tools for biomedical research. Useful FPs have desirable fluorescence properties such as brightness and photostability, but a limitation is that many orange, red, and far-red FPs are cytotoxic when expressed in the cytosol. This cytotoxicity stems from aggregation. To reduce aggregation, we engineered the surface of DsRed-Express to generate DsRed-Express2, a highly soluble tetrameric FP that is noncytotoxic in bacterial and mammalian cells. Directed evolution of DsRed-Express2 yielded the color variants E2-Orange, E2-Red/Green, and E2-Crimson. These variants can be used to label whole cells for single- and multi-color experiments employing microscopy or flow cytometry. Methods are described for reducing the higher-order aggregation of oligomeric FPs and for analyzing FP cytotoxicity in Escherichia coli and HeLa cells.
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Affiliation(s)
- Rita L. Strack
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th St., Chicago, IL 60637
| | - Robert J. Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th St., Chicago, IL 60637
| | - Benjamin S. Glick
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 E. 58th St., Chicago, IL 60637
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31
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Abstract
Like GFP, the fluorescent protein DsRed has a chromophore that forms autocatalytically within the folded protein, but the mechanism of DsRed chromophore formation has been unclear. It was proposed that an initial oxidation generates a green chromophore, and that a final oxidation yields the red chromophore. However, this model does not adequately explain why a mature DsRed sample contains a mixture of green and red chromophores. We present evidence that the maturation pathway for DsRed branches upstream of chromophore formation. After an initial oxidation step, a final oxidation to form the acylimine of the red chromophore is in kinetic competition with a dehydration to form the green chromophore. This scheme explains why green and red chromophores are alternative end points of the maturation pathway.
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Affiliation(s)
- Rita L Strack
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
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32
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Mariappan M, Li X, Stefanovic S, Sharma A, Mateja A, Keenan RJ, Hegde RS. A ribosome-associating factor chaperones tail-anchored membrane proteins. Nature 2010; 466:1120-4. [PMID: 20676083 PMCID: PMC2928861 DOI: 10.1038/nature09296] [Citation(s) in RCA: 222] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2010] [Accepted: 06/18/2010] [Indexed: 12/21/2022]
Abstract
Hundreds of proteins are inserted post-translationally into the endoplasmic reticulum (ER) membrane by a single carboxy-terminal transmembrane domain (TMD). During targeting through the cytosol, the hydrophobic TMD of these tail-anchored (TA) proteins requires constant chaperoning to prevent aggregation or inappropriate interactions. A central component of this targeting system is TRC40, a conserved cytosolic factor that recognizes the TMD of TA proteins and delivers them to the ER for insertion. The mechanism that permits TRC40 to find and capture its TA protein cargos effectively in a highly crowded cytosol is unknown. Here we identify a conserved three-protein complex composed of Bat3, TRC35 and Ubl4A that facilitates TA protein capture by TRC40. This Bat3 complex is recruited to ribosomes synthesizing membrane proteins, interacts with the TMDs of newly released TA proteins, and transfers them to TRC40 for targeting. Depletion of the Bat3 complex allows non-TRC40 factors to compete for TA proteins, explaining their mislocalization in the analogous yeast deletion strains. Thus, the Bat3 complex acts as a TMD-selective chaperone that effectively channels TA proteins to the TRC40 insertion pathway.
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Affiliation(s)
- Malaiyalam Mariappan
- Cell Biology and Metabolism Program, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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33
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Mateja A, Szlachcic A, Downing M, Dobosz M, Mariappan M, Hegde RS, Keenan RJ. Tail-Anchored Membrane Protein Recognition by Get3. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.2715] [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: 10/19/2022] Open
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34
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Strack RL, Hein B, Bhattacharyya D, Hell SW, Keenan RJ, Glick BS. Correction to A Rapidly Maturing Far-Red Derivative of DsRed-Express2 for Whole-Cell Labeling. Biochemistry 2009. [DOI: 10.1021/bi901587v] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Strack RL, Hein B, Bhattacharyya D, Hell SW, Keenan RJ, Glick BS. A rapidly maturing far-red derivative of DsRed-Express2 for whole-cell labeling. Biochemistry 2009; 48:8279-81. [PMID: 19658435 PMCID: PMC2861903 DOI: 10.1021/bi900870u] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 07/17/2009] [Indexed: 11/30/2022]
Abstract
Fluorescent proteins (FPs) with far-red excitation and emission are desirable for multicolor labeling and live-animal imaging. We describe E2-Crimson, a far-red derivative of the tetrameric FP DsRed-Express2. Unlike other far-red FPs, E2-Crimson is noncytotoxic in bacterial and mammalian cells. E2-Crimson is brighter than other far-red FPs and matures substantially faster than other red and far-red FPs. Approximately 40% of the E2-Crimson fluorescence signal is remarkably photostable. With an excitation maximum at 611 nm, E2-Crimson is the first FP that is efficiently excited with standard far-red lasers. We show that E2-Crimson has unique applications for flow cytometry and stimulated emission depletion (STED) microscopy.
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Affiliation(s)
- Rita L. Strack
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| | - Birka Hein
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37070 Göttingen, Germany
| | - Dibyendu Bhattacharyya
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, Illinois 60637
| | - Stefan W. Hell
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37070 Göttingen, Germany
| | - Robert J. Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| | - Benjamin S. Glick
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, Illinois 60637
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36
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Landreneau RJ, Cerfolio RJ, McKenna RJ, Schuchert MJ, Miller DL, Jaklitsch MT, Wee JO, Keenan RJ, Luketich JD, deHoyas A, Ding Z, Johnson JL. In Vitro Tumor Response Rates and Population Treatment Response Rates for Non–Small-Cell Lung Cancer. Clin Lung Cancer 2009. [DOI: 10.3816/clc.2009.n.062] [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: 11/20/2022]
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37
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Mateja A, Szlachcic A, Downing ME, Dobosz M, Mariappan M, Hegde RS, Keenan RJ. The structural basis of tail-anchored membrane protein recognition by Get3. Nature 2009; 461:361-6. [PMID: 19675567 DOI: 10.1038/nature08319] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 07/27/2009] [Indexed: 11/09/2022]
Abstract
Targeting of newly synthesized membrane proteins to the endoplasmic reticulum is an essential cellular process. Most membrane proteins are recognized and targeted co-translationally by the signal recognition particle. However, nearly 5% of membrane proteins are 'tail-anchored' by a single carboxy-terminal transmembrane domain that cannot access the co-translational pathway. Instead, tail-anchored proteins are targeted post-translationally by a conserved ATPase termed Get3. The mechanistic basis for tail-anchored protein recognition or targeting by Get3 is not known. Here we present crystal structures of yeast Get3 in 'open' (nucleotide-free) and 'closed' (ADP.AlF(4)(-)-bound) dimer states. In the closed state, the dimer interface of Get3 contains an enormous hydrophobic groove implicated by mutational analyses in tail-anchored protein binding. In the open state, Get3 undergoes a striking rearrangement that disrupts the groove and shields its hydrophobic surfaces. These data provide a molecular mechanism for nucleotide-regulated binding and release of tail-anchored proteins during their membrane targeting by Get3.
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Affiliation(s)
- Agnieszka Mateja
- Department of Biochemistry & Molecular Biology, The University of Chicago, Gordon Center for Integrative Science, Room W238, 929 East 57th Street, Chicago, Illinois 60637, USA
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38
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Strack RL, Bhattacharyya D, Glick BS, Keenan RJ. Noncytotoxic orange and red/green derivatives of DsRed-Express2 for whole-cell labeling. BMC Biotechnol 2009; 9:32. [PMID: 19344508 PMCID: PMC2678115 DOI: 10.1186/1472-6750-9-32] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 04/03/2009] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Whole-cell labeling is a common application of fluorescent proteins (FPs), but many red and orange FPs exhibit cytotoxicity that limits their use as whole-cell labels. Recently, a tetrameric red FP called DsRed-Express2 was engineered for enhanced solubility and was shown to be noncytotoxic in bacterial and mammalian cells. Our goal was to create derivatives of this protein with different spectral properties. RESULTS Building on previous studies of DsRed mutants, we created two DsRed-Express2 derivatives: E2-Orange, an orange FP, and E2-Red/Green, a dual-color FP with both red and green emission. We show that these new FPs retain the low cytotoxicity of DsRed-Express2. In addition, we show that these new FPs are useful as second or third colors for flow cytometry and fluorescence microscopy. CONCLUSION E2-Orange and E2-Red/Green will facilitate the production of healthy, stably fluorescent cell lines and transgenic organisms for multi-color labeling studies.
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Affiliation(s)
- Rita L Strack
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.
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39
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Strack RL, Strongin DE, Bhattacharyya D, Tao W, Berman A, Broxmeyer HE, Keenan RJ, Glick BS. A noncytotoxic DsRed variant for whole-cell labeling. Nat Methods 2008; 5:955-7. [PMID: 18953349 DOI: 10.1038/nmeth.1264] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 09/23/2008] [Indexed: 11/09/2022]
Abstract
A common application of fluorescent proteins is to label whole cells, but many RFPs are cytotoxic when used with standard high-level expression systems. We engineered a rapidly maturing tetrameric fluorescent protein called DsRed-Express2 that has minimal cytotoxicity. DsRed-Express2 exhibits strong and stable expression in bacterial and mammalian cells, and it outperforms other available RFPs with regard to photostability and phototoxicity.
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Affiliation(s)
- Rita L Strack
- Department of Biochemistry and Molecular Biology, The University of Chicago, Gordon Center W238, Chicago, Illinois 60637, USA
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40
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Zenati M, Pham SM, Keenan RJ, Griffith BP. Extracorporeal membrane oxygenation for lung transplant recipients with primary severe donor lung dysfunction. Transpl Int 2008. [DOI: 10.1111/j.1432-2277.1996.tb00884.x] [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: 11/30/2022]
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41
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Schnitzler CE, Keenan RJ, McCord R, Matysik A, Christianson LM, Haddock SHD. Spectral diversity of fluorescent proteins from the anthozoan Corynactis californica. Mar Biotechnol (NY) 2008; 10:328-342. [PMID: 18330643 DOI: 10.1007/s10126-007-9072-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Revised: 11/15/2007] [Accepted: 11/19/2007] [Indexed: 05/26/2023]
Abstract
Color morphs of the temperate, nonsymbiotic corallimorpharian Corynactis californica show variation in pigment pattern and coloring. We collected seven distinct color morphs of C. californica from subtidal locations in Monterey Bay, California, and found that tissue- and color-morph-specific expression of at least six different genes is responsible for this variation. Each morph contains at least three to four distinct genetic loci that code for these colors, and one morph contains at least five loci. These genes encode a subfamily of new GFP-like proteins, which fluoresce across the visible spectrum from green to red, while sharing between 75% to 89% pairwise amino-acid identity. Biophysical characterization reveals interesting spectral properties, including a bright yellow protein, an orange protein, and a red protein exhibiting a "fluorescent timer" phenotype. Phylogenetic analysis indicates that the FP genes from this species evolved together but that diversification of anthozoan fluorescent proteins has taken place outside of phylogenetic constraints, especially within the Corallimorpharia. The discovery of more examples of fluorescent proteins in a non-bioluminescent, nonsymbiotic anthozoan highlights possibilities of adaptive ecological significance unrelated to light regulation for algal symbionts. The patterns and colors of fluorescent proteins in C. californica and similar species may hold meaning for organisms that possess the visual pigments to distinguish them.
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Affiliation(s)
- Christine E Schnitzler
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA 95039, USA
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Strongin DE, Bevis B, Khuong N, Downing ME, Strack RL, Sundaram K, Glick BS, Keenan RJ. Structural rearrangements near the chromophore influence the maturation speed and brightness of DsRed variants. Protein Eng Des Sel 2007; 20:525-34. [PMID: 17962222 DOI: 10.1093/protein/gzm046] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
The red fluorescent protein DsRed has been extensively engineered for use as an in vivo research tool. In fast maturing DsRed variants, the chromophore maturation half-time is approximately 40 min, compared to approximately 12 h for wild-type DsRed. Further, DsRed has been converted from a tetramer into a monomer, a task that entailed mutating approximately 20% of the amino acids. These engineered variants of DsRed have proven extremely valuable for biomedical research, but the structural basis for the improved characteristics has not been thoroughly investigated. Here we present a 1.7 A crystal structure of the fast maturing tetrameric variant DsRed.T4. We also present a biochemical characterization and 1.6 A crystal structure of the monomeric variant DsRed.M1, also known as DsRed-Monomer. Analysis of the crystal structures suggests that rearrangements of Ser69 and Glu215 contribute to fast maturation, and that positioning of the Lys70 side chain modulates fluorescence quantum yield. Despite the 45 mutations in DsRed.M1 relative to wild-type DsRed, there is a root-mean-square deviation of only 0.3 A between the two structures. We propose that novel intramolecular interactions in DsRed.M1 partially compensate for the loss of intermolecular interactions found in the tetramer.
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Affiliation(s)
- Daniel E Strongin
- Department of Molecular Genetics and Cell Biology, University of Chicago, IL 60637, USA
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Abstract
GAT is an N-acetyltransferase from Bacillus licheniformis that was optimized by gene shuffling for acetylation of the broad spectrum herbicide, glyphosate, forming the basis of a novel mechanism of glyphosate tolerance in transgenic plants (Castle, L. A., Siehl, D. L., Gorton, R., Patten, P. A., Chen, Y. H., Bertain, S., Cho, H. J., Duck, N., Wong, J., Liu, D., and Lassner, M. W. (2004) Science 304, 1151-1154). The 1.6-A resolution crystal structure of an optimized GAT variant in ternary complex with acetyl coenzyme A and a competitive inhibitor, 3-phosphoglyerate, defines GAT as a member of the GCN5-related family of N-acetyltransferases. Four active site residues (Arg-21, Arg-73, Arg-111, and His-138) contribute to a positively charged substrate-binding site that is conserved throughout the GAT subfamily. Structural and kinetic data suggest that His-138 functions as a catalytic base via substrate-assisted deprotonation of the glyphosate secondary amine, whereas another active site residue, Tyr-118, functions as a general acid. Although the physiological substrate is unknown, native GAT acetylates D-2-amino-3-phosphonopropionic acid with a kcat/Km of 1500 min-1 mM-1. Kinetic data show preferential binding of short analogs to native GAT and progressively better binding of longer analogs to optimized variants. Despite a 200-fold increase in kcat and a 5.4-fold decrease in Km for glyphosate, only 4 of the 21 substitutions present in R7 GAT lie in the active site. Single-site revertants constructed at these positions suggest that glyphosate binding is optimized through substitutions that increase the size of the substrate-binding site. The large improvement in kcat is likely because of the cooperative effects of additional substitutions located distal to the active site.
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Affiliation(s)
- Daniel L Siehl
- Pioneer Hi-Bred International, Redwood City, California 94063, USA.
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Meyers BF, Downey RJ, Decker PA, Keenan RJ, Siegel BA, Cerfolio RJ, Landreneau RJ, Reed CE, Balfe DM, Dehdashti F, Ballman KV, Rusch VW, Putnam JB. The utility of positron emission tomography in staging of potentially operable carcinoma of the thoracic esophagus: results of the American College of Surgeons Oncology Group Z0060 trial. J Thorac Cardiovasc Surg 2007; 133:738-45. [PMID: 17320575 DOI: 10.1016/j.jtcvs.2006.09.079] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Revised: 08/09/2006] [Accepted: 09/26/2006] [Indexed: 02/08/2023]
Abstract
OBJECTIVES The American College of Surgeons Oncology Group trial Z0060 is a prospective multi-institutional trial with a primary objective to evaluate whether positron emission tomography (PET) with F-18 fluorodeoxyglucose (FDG) detects evidence of metastastic disease that precludes esophagectomy in patients with esophageal cancer who are surgical candidates after routine staging. METHODS Patients with resectable, biopsy-proven carcinoma were enrolled after computed tomography of chest and abdomen demonstrated no evidence of metastasis. FDG-PET was performed according to specified standards. FDG-PET findings suggesting metastases required confirmation and patients without metastases on PET were expected to proceed to surgery. RESULTS A total of 262 patients were registered. Of these, 199 were deemed eligible and of these, 189 patients were evaluable. Seventy-three patients were ineligible or unevaluable. Reasons for ineligibility included nonresectable disease by routine staging (39), missing or outdated staging procedures (12), PET technical protocol violations (10), no cancer (4), pre-PET induction therapy (3), claustrophobia (1), and other causes (4). There were 145 (78%) patients who went on to have surgery, 42 (22%) who did not, and 2 patients for whom the surgical status was not determined. The reasons for no resection included the following: M1 disease found by PET and confirmed (9), M1 disease found by PET and not confirmed (2), M1 disease at exploration not found by PET (7), decline or death before surgery (10), patient refusal of surgery (7), unresectable local tumor at exploration (5), and extensive N1 disease precluding operation (2). Eight (4.2%) patients undergoing resection had a recurrence in the first 6 months. CONCLUSIONS Although 22% of eligible patients did not undergo esophagectomy, FDG-PET after standard clinical staging for esophageal carcinoma identified confirmed M1b disease in at least 4.8% (95% confidence interval: 2.2%-8.9%) of patients before resection. Unconfirmed PET evidence of M1 disease and regional adenopathy (N1 disease) led to definitive nonsurgical or induction therapy in additional patients.
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Affiliation(s)
- Bryan F Meyers
- Department of Surgery, Washington University School of Medicine, St. Louis, Mo
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Abstract
Given the discomfort of thoracic surgical incisions, thoracic surgeons must understand and use contemporary multimodality pain treatments. Acute postthoracotomy pain not only causes psychologic distress to the patient but also has detrimental effects on pulmonary function and postoperative mobility, leading to increased morbidity. By choosing the most appropriate and least traumatic surgical incision, adhering to meticulous surgical techniques, and avoiding intercostal nerve injury or rib fractures, surgeons can minimize postoperative pain. Aggressive perioperative and postoperative pain management is best accomplished with use of an epidural anesthetic and covering breakthrough pain with an IV-PCA. Alternatively, an infusion system for continuous administration of local anesthetics directly in the subpleural plane, posterior to the intercostal incision, also provides excellent pain control. Again, use of an IV-PCA as adjuvant therapy is recommended. With careful planning, severe pain and its negative impact on thoracic surgical patients can be prevented.
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Affiliation(s)
- Richard P Koehler
- Department of Cardiovascular and Thoracic Surgery, Allegheny General Hospital, 320 East North Avenue, South Tower, 14th Floor, Pittsburgh, PA 15212, USA
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Birdas TJ, Koehler RPM, Colonias A, Trombetta M, Maley RH, Landreneau RJ, Keenan RJ. Sublobar Resection With Brachytherapy Versus Lobectomy for Stage Ib Nonsmall Cell Lung Cancer. Ann Thorac Surg 2006; 81:434-8; discussion 438-9. [PMID: 16427827 DOI: 10.1016/j.athoracsur.2005.08.052] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2005] [Revised: 08/23/2005] [Accepted: 08/25/2005] [Indexed: 10/25/2022]
Abstract
BACKGROUND We have previously shown that intraoperative brachytherapy decreases the local recurrences associated with sublobar resections for small stage Ia nonsmall-cell lung cancer (NSCLC). In this report, we present the outcomes of sublobar resection with brachytherapy compared with lobectomy in patients with stage Ib tumors. METHODS We retrospectively reviewed 167 stage Ib NSCLC patients: 126 underwent lobectomy and 41 sublobar resection with (125)I brachytherapy over the resection staple line. Endpoints were perioperative outcomes, incidence of recurrence, and disease-free and overall survival. RESULTS Patients undergoing sublobar resections had significantly worse preoperative pulmonary function. Hospital mortality, nonfatal complications, and median length of stay were similar in the two groups. Median follow-up was 25.1 months. Local recurrence in sublobar resection patients was 2 of 41 (4.8%), similar to the lobectomy group: 4 of 126 (3.2%; p = 0.6). At 4 years, both groups had equivalent disease-free survival (sublobar group, 43.0%; median, 37.7 months; and lobectomy group, 42.8%; median 41.8 months, p = 0.57) and overall survival (sublobar group, 54.1%; median, 50.2 months; and lobectomy group, 51.8%; median, 56.9 months; p = 0.38). CONCLUSIONS Sublobar resection with brachytherapy reduced local recurrence rates to the equivalent of lobectomy in patients with stage Ib NSCLC, and resulted in similar perioperative outcomes and disease-free and overall survival, despite being used in patients with compromised lung function. We recommend the addition of intraoperative brachytherapy to sublobar resections in stage Ib patients who cannot tolerate a lobectomy.
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Affiliation(s)
- Thomas J Birdas
- Department of Cardiothoracic Surgery, Allegheny General Hospital, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.
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Abstract
The success of structural studies performed on an individual target in small scale or on many targets in the system-wide scale of structural genomics depends critically on three parameters: (i) obtaining an expression system capable of producing large quantities of the macromolecule(s) of interest, (ii) purifying this material in soluble form, and (iii) obtaining diffraction-quality crystals suitable for x-ray analysis. The attrition rate caused by these constraints is often quite high. Here, we present a strategy that addresses each of these three parameters simultaneously. Using DNA shuffling to introduce functional sequence variability into a protein of interest, we screened crude lysate supernatants for soluble variants that retain enzymatic activity. Crystallization trials performed on three WT and eight shuffled enzymes revealed two variants that crystallized readily. One of these was used to determine the high-resolution structure of the enzyme by x-ray analysis. The sequence diversity introduced through shuffling efficiently samples crystal packing space by modifying the surface properties of the enzyme. The approach demonstrated here does not require guidance as to the type of mutation necessary for improvements in expression, solubility, or crystallization. The method is scaleable and can be applied in situations where a single protein is being studied or in high-throughput structural genomics programs. Furthermore, it should be readily applied to structural studies of soluble proteins, membrane proteins, and macromolecular complexes.
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Affiliation(s)
- Robert J Keenan
- Pioneer Hi-Bred International, Inc., Verdia Campus, 700A Bay Road, Redwood City, CA 94063, USA.
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Fernando HC, Santos RS, Benfield JR, Grannis FW, Keenan RJ, Luketich JD, Close JM, Landreneau RJ. Lobar and sublobar resection with and without brachytherapy for small stage IA non–small cell lung cancer. J Thorac Cardiovasc Surg 2005; 129:261-7. [DOI: 10.1016/j.jtcvs.2004.09.025] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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50
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Birdas TJ, Beckart DH, Keenan RJ. Contralateral spontaneous pneumothorax after pneumonectomy: thoracoscopic management with cardiopulmonary bypass. Interact Cardiovasc Thorac Surg 2005; 4:27-9. [PMID: 17670349 DOI: 10.1510/icvts.2004.093294] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Spontaneous contralateral pneumothorax after pneumonectomy is a rare condition. Management can be quite challenging, as surgical intervention other than tube thoracostomy poses significant risks. We report a case of spontaneous pneumothorax that did not resolve with conventional management, necessitating thoracoscopic bleb resection with the use of cardiopulmonary bypass.
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Affiliation(s)
- Thomas J Birdas
- Department of Cardiothoracic Surgery, Allegheny General Hospital, 320 East North Avenue, South Tower, 14th Floor, Pittsburgh, PA 15212, USA.
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