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Berg WA, Berg JM, Bandos AI, Vargo A, Chough DM, Lu AH, Ganott MA, Kelly AE, Nair BE, Hartman JY, Waheed U, Hakim CM, Harnist KS, Reginella RF, Shinde DD, Carlin BA, Cohen CS, Wallace LP, Sumkin JH, Zuley ML. Addition of Contrast-enhanced Mammography to Tomosynthesis for Breast Cancer Detection in Women with a Personal History of Breast Cancer: Prospective TOCEM Trial Interim Analysis. Radiology 2024; 311:e231991. [PMID: 38687218 PMCID: PMC11070607 DOI: 10.1148/radiol.231991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 03/09/2024] [Accepted: 03/19/2024] [Indexed: 05/02/2024]
Abstract
Background Digital breast tomosynthesis (DBT) is often inadequate for screening women with a personal history of breast cancer (PHBC). The ongoing prospective Tomosynthesis or Contrast-Enhanced Mammography, or TOCEM, trial includes three annual screenings with both DBT and contrast-enhanced mammography (CEM). Purpose To perform interim assessment of cancer yield, stage, and recall rate when CEM is added to DBT in women with PHBC. Materials and Methods From October 2019 to December 2022, two radiologists interpreted both examinations: Observer 1 reviewed DBT first and then CEM, and observer 2 reviewed CEM first and then DBT. Effects of adding CEM to DBT on incremental cancer detection rate (ICDR), cancer type and node status, recall rate, and other performance characteristics of the primary radiologist decisions were assessed. Results Among the participants (mean age at entry, 63.6 years ± 9.6 [SD]), 1273, 819, and 227 women with PHBC completed year 1, 2, and 3 screening, respectively. For observer 1, year 1 cancer yield was 20 of 1273 (15.7 per 1000 screenings) for DBT and 29 of 1273 (22.8 per 1000 screenings; ICDR, 7.1 per 1000 screenings [95% CI: 3.2, 13.4]) for DBT plus CEM (P < .001). Year 2 plus 3 cancer yield was four of 1046 (3.8 per 1000 screenings) for DBT and eight of 1046 (7.6 per 1000 screenings; ICDR, 3.8 per 1000 screenings [95% CI: 1.0, 7.6]) for DBT plus CEM (P = .001). Year 1 recall rate for observer 1 was 103 of 1273 (8.1%) for (incidence) DBT alone and 187 of 1273 (14.7%) for DBT plus CEM (difference = 84 of 1273, 6.6% [95% CI: 5.3, 8.1]; P < .001). Year 2 plus 3 recall rate was 40 of 1046 (3.8%) for DBT and 92 of 1046 (8.8%) for DBT plus CEM (difference = 52 of 1046, 5.0% [95% CI: 3.7, 6.3]; P < .001). In 18 breasts with cancer detected only at CEM after integration of both observers, 13 (72%) cancers were invasive (median tumor size, 0.6 cm) and eight of nine (88%) with staging were N0. Among 1883 screenings with adequate reference standard, there were three interval cancers (one at the scar, two in axillae). Conclusion CEM added to DBT increased early breast cancer detection each year in women with PHBC, with an accompanying approximately 5.0%-6.6% recall rate increase. Clinical trial registration no. NCT04085510 © RSNA, 2024 Supplemental material is available for this article.
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Affiliation(s)
- Wendie A. Berg
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Jeremy M. Berg
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Andriy I. Bandos
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Adrienne Vargo
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Denise M. Chough
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Amy H. Lu
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Marie A. Ganott
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Amy E. Kelly
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Bronwyn E. Nair
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Jamie Y. Hartman
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | | | - Christiane M. Hakim
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Kimberly S. Harnist
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Ruthane F. Reginella
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Dilip D. Shinde
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Bea A. Carlin
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Cathy S. Cohen
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Luisa P. Wallace
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Jules H. Sumkin
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
| | - Margarita L. Zuley
- From the Departments of Radiology (W.A.B., A.V., D.M.C., A.H.L.,
M.A.G., A.E.K., B.E.N., J.Y.H., U.W., C.M.H., K.S.H., R.F.R., D.D.S., B.A.C.,
C.S.C., L.P.W., J.H.S., M.L.Z.) and Computational and Systems Biology (J.M.B.),
University of Pittsburgh School of Medicine, 300 Halket St, Pittsburgh, PA
15213; Department of Radiology, UPMC Magee-Womens Hospital, Pittsburgh, Pa
(W.A.B., A.V., D.M.C., A.H.L., M.A.G., C.M.H., D.D.S., C.S.C., J.H.S., M.L.Z.);
and Department of Biostatistics, University of Pittsburgh School of Public
Health, Pittsburgh, Pa (A.I.B.)
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2
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Berg WA, Zuley ML, Chang TS, Gizienski TA, Chough DM, Böhm-Vélez M, Sharek DE, Straka MR, Hakim CM, Hartman JY, Harnist KS, Tyma CS, Kelly AE, Waheed U, Houshmand G, Nair BE, Shinde DD, Lu AH, Bandos AI, Berg JM, Lettiere NB, Ganott MA. Prospective Multicenter Diagnostic Performance of Technologist-Performed Screening Breast Ultrasound After Tomosynthesis in Women With Dense Breasts (the DBTUST). J Clin Oncol 2023; 41:2403-2415. [PMID: 36626696 PMCID: PMC10150890 DOI: 10.1200/jco.22.01445] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 10/25/2022] [Accepted: 11/19/2022] [Indexed: 01/11/2023] Open
Abstract
PURPOSE To assess diagnostic performance of digital breast tomosynthesis (DBT) alone or combined with technologist-performed handheld screening ultrasound (US) in women with dense breasts. METHODS In an institutional review board-approved, Health Insurance Portability and Accountability Act-compliant multicenter protocol in western Pennsylvania, 6,179 women consented to three rounds of annual screening, interpreted by two radiologist observers, and had appropriate follow-up. Primary analysis was based on first observer results. RESULTS Mean participant age was 54.8 years (range, 40-75 years). Across 17,552 screens, there were 126 cancer events in 125 women (7.2/1,000; 95% CI, 5.9 to 8.4). In year 1, DBT-alone cancer yield was 5.0/1,000, and of DBT+US, 6.3/1,000, difference 1.3/1,000 (95% CI, 0.3 to 2.1; P = .005). In years 2 + 3, DBT cancer yield was 4.9/1,000, and of DBT+US, 5.9/1,000, difference 1.0/1,000 (95% CI, 0.4 to 1.5; P < .001). False-positive rate increased from 7.0% for DBT in year 1 to 11.5% for DBT+US and from 5.9% for DBT in year 2 + 3 to 9.7% for DBT+US (P < .001 for both). Nine cancers were seen only by double reading DBT and one by double reading US. Ten interval cancers (0.6/1,000 [95% CI, 0.2 to 0.9]) were identified. Despite reduction in specificity, addition of US improved receiver operating characteristic curves, with area under receiver operating characteristic curve increasing from 0.83 for DBT alone to 0.92 for DBT+US in year 1 (P = .01), with smaller improvements in subsequent years. Of 6,179 women, across all 3 years, 172/6,179 (2.8%) unique women had a false-positive biopsy because of DBT as did another 230/6,179 (3.7%) women because of US (P < .001). CONCLUSION Overall added cancer detection rate of US screening after DBT was modest at 19/17,552 (1.1/1,000; CI, 0.5- to 1.6) screens but potentially overcomes substantial increases in false-positive recalls and benign biopsies.
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Affiliation(s)
- Wendie A. Berg
- Department of Radiology, University of Pittsburgh School of Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Margarita L. Zuley
- Department of Radiology, University of Pittsburgh School of Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | | | - Terri-Ann Gizienski
- Department of Radiology, University of Pittsburgh School of Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Denise M. Chough
- Department of Radiology, University of Pittsburgh School of Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | | | | | | | - Christiane M. Hakim
- Department of Radiology, University of Pittsburgh School of Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Jamie Y. Hartman
- Department of Radiology, University of Pittsburgh School of Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Kimberly S. Harnist
- Department of Radiology, University of Pittsburgh School of Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Cathy S. Tyma
- Department of Radiology, University of Pittsburgh School of Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA
- Department of Radiology, New York University Grossman School of Medicine, New York, NY
| | - Amy E. Kelly
- Department of Radiology, University of Pittsburgh School of Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Uzma Waheed
- Department of Radiology, University of Pittsburgh School of Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA
- Department of Radiology, Stanford University School of Medicine, Stanford, CA
| | - Golbahar Houshmand
- Department of Radiology, University of Pittsburgh School of Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA
- Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Bronwyn E. Nair
- Department of Radiology, University of Pittsburgh School of Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Dilip D. Shinde
- Department of Radiology, University of Pittsburgh School of Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Amy H. Lu
- Department of Radiology, University of Pittsburgh School of Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Andriy I. Bandos
- Department of Biostatistics, University of Pittsburgh School of Public Health, Pittsburgh, PA
| | - Jeremy M. Berg
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Nicole B. Lettiere
- Department of Radiology, University of Pittsburgh School of Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA
- ICON-Amgen, Pittsburgh, PA
| | - Marie A. Ganott
- Department of Radiology, University of Pittsburgh School of Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA
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3
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Spenner JM, Berg JM. Exploring the use of cobalt(II) dipolar shifts in refining the structure of a zinc finger peptide. J Inorg Biochem 2022; 235:111912. [PMID: 35850025 DOI: 10.1016/j.jinorgbio.2022.111912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/13/2022] [Accepted: 07/03/2022] [Indexed: 10/17/2022]
Abstract
The uses of dipolar shifts due to cobalt(II) substituted for zinc(II) in a consensus zinc finger peptide for refining the NMR-determined structure were examined. Substantial differences between the calculated and observed chemical shift differences between the cobalt(II) and zinc(II) complexes were observed when these dipolar shifts were not used as constraints in the structure refinement. However, inclusion of these constraints resulted in excellent agreement with minor adjustments in the structure and a slight improvement in the precision of the structure determination. Other calculations revealed that the dipolar shifts were not adequate to determine the overall folded structure by themselves, but were useful in increasing the accuracy and precision of a structure determined based only on nuclear Overhauser effects constraints involving only backbone atoms.
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Affiliation(s)
- Jonathan M Spenner
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeremy M Berg
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
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Kovacs JA, Berg JM. Special issue in memory of Richard H. Holm. J Inorg Biochem 2022; 236:111948. [DOI: 10.1016/j.jinorgbio.2022.111948] [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: 10/31/2022]
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5
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Berg JM. Misleading portrayal of children's asthma study. Science 2021; 374:414. [PMID: 34672736 DOI: 10.1126/science.abm4776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Jeremy M Berg
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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Lee CS, Berg JM, Berg WA. Cancer Yield Exceeds 2% for BI-RADS 3 Probably Benign Findings in Women Older Than 60 Years in the National Mammography Database. Radiology 2021; 299:550-558. [PMID: 33787333 DOI: 10.1148/radiol.2021204031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Background Breast Imaging Reporting and Data System (BI-RADS) category 3 (BR3) (probably benign) mammographic assessments are reserved for imaging findings known to have likelihood of malignancy of 2% or less. Purpose To determine the effect of age, finding type, and prior mammography on cancer yield for BR3 findings in the National Mammography Database (NMD). Materials and Methods This HIPAA-compliant retrospective cohort institutional review board-exempt study evaluated women recalled from screening mammography followed by BR3 assessment at diagnostic evaluation from January 2009 to March 2018 and from 471 NMD facilities. Only the first BR3 occurrence was included for women with biopsy or imaging follow-up of at least 2 years. Women with a history of breast cancer or who underwent biopsy at time of initial BR3 assessment were excluded. Women were stratified by age in 10-year intervals. Cancer yield was calculated for each age group, with (for presumed new findings) and without prior mammographic comparison, and by lesion type, where available. Linear regression with weighted-age binning was performed to assess for differences between groups; P < .05 was indicative of a significant difference. Results A total of 1 380 652 (18.2%) women were recalled after screening mammography, of whom 157 130 (11.4%) were given a BR3 assessment within 90 days after screening. Of these, 43 628 women (median age, 55 years; age range, 25-90 years) had adequate follow-up for analysis. Cancer yield increased with increasing age decile, ranging from 0.51% (six of 1167) in women aged 30-39 years to 4.63% (41 of 885) in women aged 80-90 years; cancer yield exceeded 2% at and after age 59.7 years for baseline findings and at and after age 53.6 years for presumed new findings, although there was no effect on stage distribution. Cancer yield for baseline BR3 masses was 10 of 2111 (0.47% [95% CI: 0.24, 0.90]) versus 47 of 3003 (1.57% [95% CI: 1.16, 2.09]) with prior comparisons (P < .001); cancer yield for baseline calcifications was eight of 929 (0.86% [95% CI: 0.40, 1.76]) versus 84 of 2999 (2.80% [95% CI: 2.23, 3.47]) with prior comparisons (P < .001). Difference in cancer yield was 0.51% (95% CI: 0.16, 0.86) between women with and women without prior comparison at the same age (P = .006). Conclusion Cancer yield exceeded the 2% threshold for women aged 60 years or older and reached 4.6% for women aged 80-89 years. Breast Imaging Reporting and Data System 3 findings in women with a prior comparison had higher cancer yield than in those without a prior comparison at the same age. © RSNA, 2021 Online supplemental material is available for this article.
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Affiliation(s)
- Cindy S Lee
- From the Department of Radiology, New York University Langone Medical Center, 765 Stewart Ave, Garden City, NY 11530 (C.S.L.); Departments of Computational and Systems Biology (J.M.B.) and Radiology (W.A.B.), University of Pittsburgh School of Medicine, Pittsburgh, Pa; and Magee-Womens Hospital of University of Pittsburgh Medical Center, Pittsburgh, Pa (W.A.B.)
| | - Jeremy M Berg
- From the Department of Radiology, New York University Langone Medical Center, 765 Stewart Ave, Garden City, NY 11530 (C.S.L.); Departments of Computational and Systems Biology (J.M.B.) and Radiology (W.A.B.), University of Pittsburgh School of Medicine, Pittsburgh, Pa; and Magee-Womens Hospital of University of Pittsburgh Medical Center, Pittsburgh, Pa (W.A.B.)
| | - Wendie A Berg
- From the Department of Radiology, New York University Langone Medical Center, 765 Stewart Ave, Garden City, NY 11530 (C.S.L.); Departments of Computational and Systems Biology (J.M.B.) and Radiology (W.A.B.), University of Pittsburgh School of Medicine, Pittsburgh, Pa; and Magee-Womens Hospital of University of Pittsburgh Medical Center, Pittsburgh, Pa (W.A.B.)
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Berg WA, Berg JM, Sickles EA, Burnside ES, Zuley ML, Rosenberg RD, Lee CS. Cancer Yield and Patterns of Follow-up for BI-RADS Category 3 after Screening Mammography Recall in the National Mammography Database. Radiology 2020; 296:32-41. [PMID: 32427557 DOI: 10.1148/radiol.2020192641] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Background The literature supports the use of short-interval follow-up as an alternative to biopsy for lesions assessed as probably benign, Breast Imaging Reporting and Data System (BI-RADS) category 3, with an expected malignancy rate of less than 2%. Purpose To assess outcomes from 6-, 12-, and 24-month follow-up of probably benign findings first identified at recall from screening mammography in the National Mammography Database (NMD). Materials and Methods This retrospective study included women recalled from screening mammography with BI-RADS category 3 assessment at additional evaluation from January 2009 through March 2018 from 471 NMD facilities. Only the first BI-RADS category 3 occurrence for women aged 25 years or older with no personal history of breast cancer was analyzed, with biopsy or 2-year imaging follow-up. Cancer yield and positive predictive value of biopsies performed (PPV3) were determined at each follow-up. Results Among 45 202 women (median age, 55 years; range, 25-90 years) with a BI-RADS category 3 lesion, 1574 (3.5%) underwent biopsy at the time of lesion detection, yielding 72 cancers (cancer yield, 4.6%; 72 of 1574 women). For the remaining 43 628 women who accepted surveillance, 922 were seen within 90 days (with 78 lesions biopsied and 12 [15%] classified as malignant). The women still in surveillance (31 465 of 43 381 women [72.5%]) underwent follow-up mammography at 6 months. Of 3001 (9.5%) lesions biopsied, 456 (15.2%) were malignant (cancer yield, 1.5%; 456 of 31 465 women; 95% confidence interval [CI]: 1.3%, 1.6%). Among 18 748 of 25 997 women (72.1%) in surveillance who underwent follow-up at 12 months, 1219 (6.5%) underwent biopsy with 230 (18.9%) malignant lesions found (cancer yield, 1.2%; 230 of 18 748 women; 95% CI: 1.1%, 1.4%). Through 2-year follow-up, the biopsy rate was 11.2% (4894 of 43 628 women) with a cancer yield of 1.86% (810 malignancies found among 43 628 women; 95% CI: 1.73%, 1.98%) and a PPV3 of 16.6% (810 malignancies found among 4894 women). Conclusion In the National Mammography Database, Breast Imaging Reporting and Data System (BI-RADS) category 3 use is appropriate, with 1.86% cumulative cancer yield through 2-year follow-up. Of 810 malignancies, 468 (57.8%) were diagnosed at or before 6 months, validating necessity of short-interval follow-up of mammographic BI-RADS category 3 findings. © RSNA, 2020 Online supplemental material is available for this article. See also the editorial by Moy in this issue.
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Affiliation(s)
- Wendie A Berg
- From the Departments of Radiology (W.A.B., M.L.Z.) and Computational and Systems Biology (J.M.B.), University of Pittsburgh School of Medicine, Pittsburgh, Pa; Magee-Women's Hospital of University of Pittsburgh Medical Center, 300 Halket St, Pittsburgh, PA 15213 (W.A.B., M.L.Z.); Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, Calif (E.A.S.); Department of Radiology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wis (E.S.B.); Radiology Associates of Albuquerque, Albuquerque, NM (R.D.R.); and Department of Radiology, New York University Langone Medical Center, New York, NY (C.S.L.).,The views expressed in this article represent those of the author(s), and do not necessarily represent the official views of the American College of Radiology's National
Radiology Data Registry or the American College of Radiology
| | - Jeremy M Berg
- From the Departments of Radiology (W.A.B., M.L.Z.) and Computational and Systems Biology (J.M.B.), University of Pittsburgh School of Medicine, Pittsburgh, Pa; Magee-Women's Hospital of University of Pittsburgh Medical Center, 300 Halket St, Pittsburgh, PA 15213 (W.A.B., M.L.Z.); Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, Calif (E.A.S.); Department of Radiology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wis (E.S.B.); Radiology Associates of Albuquerque, Albuquerque, NM (R.D.R.); and Department of Radiology, New York University Langone Medical Center, New York, NY (C.S.L.).,The views expressed in this article represent those of the author(s), and do not necessarily represent the official views of the American College of Radiology's National
Radiology Data Registry or the American College of Radiology
| | - Edward A Sickles
- From the Departments of Radiology (W.A.B., M.L.Z.) and Computational and Systems Biology (J.M.B.), University of Pittsburgh School of Medicine, Pittsburgh, Pa; Magee-Women's Hospital of University of Pittsburgh Medical Center, 300 Halket St, Pittsburgh, PA 15213 (W.A.B., M.L.Z.); Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, Calif (E.A.S.); Department of Radiology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wis (E.S.B.); Radiology Associates of Albuquerque, Albuquerque, NM (R.D.R.); and Department of Radiology, New York University Langone Medical Center, New York, NY (C.S.L.).,The views expressed in this article represent those of the author(s), and do not necessarily represent the official views of the American College of Radiology's National
Radiology Data Registry or the American College of Radiology
| | - Elizabeth S Burnside
- From the Departments of Radiology (W.A.B., M.L.Z.) and Computational and Systems Biology (J.M.B.), University of Pittsburgh School of Medicine, Pittsburgh, Pa; Magee-Women's Hospital of University of Pittsburgh Medical Center, 300 Halket St, Pittsburgh, PA 15213 (W.A.B., M.L.Z.); Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, Calif (E.A.S.); Department of Radiology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wis (E.S.B.); Radiology Associates of Albuquerque, Albuquerque, NM (R.D.R.); and Department of Radiology, New York University Langone Medical Center, New York, NY (C.S.L.).,The views expressed in this article represent those of the author(s), and do not necessarily represent the official views of the American College of Radiology's National
Radiology Data Registry or the American College of Radiology
| | - Margarita L Zuley
- From the Departments of Radiology (W.A.B., M.L.Z.) and Computational and Systems Biology (J.M.B.), University of Pittsburgh School of Medicine, Pittsburgh, Pa; Magee-Women's Hospital of University of Pittsburgh Medical Center, 300 Halket St, Pittsburgh, PA 15213 (W.A.B., M.L.Z.); Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, Calif (E.A.S.); Department of Radiology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wis (E.S.B.); Radiology Associates of Albuquerque, Albuquerque, NM (R.D.R.); and Department of Radiology, New York University Langone Medical Center, New York, NY (C.S.L.).,The views expressed in this article represent those of the author(s), and do not necessarily represent the official views of the American College of Radiology's National
Radiology Data Registry or the American College of Radiology
| | - Robert D Rosenberg
- From the Departments of Radiology (W.A.B., M.L.Z.) and Computational and Systems Biology (J.M.B.), University of Pittsburgh School of Medicine, Pittsburgh, Pa; Magee-Women's Hospital of University of Pittsburgh Medical Center, 300 Halket St, Pittsburgh, PA 15213 (W.A.B., M.L.Z.); Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, Calif (E.A.S.); Department of Radiology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wis (E.S.B.); Radiology Associates of Albuquerque, Albuquerque, NM (R.D.R.); and Department of Radiology, New York University Langone Medical Center, New York, NY (C.S.L.).,The views expressed in this article represent those of the author(s), and do not necessarily represent the official views of the American College of Radiology's National
Radiology Data Registry or the American College of Radiology
| | - Cindy S Lee
- From the Departments of Radiology (W.A.B., M.L.Z.) and Computational and Systems Biology (J.M.B.), University of Pittsburgh School of Medicine, Pittsburgh, Pa; Magee-Women's Hospital of University of Pittsburgh Medical Center, 300 Halket St, Pittsburgh, PA 15213 (W.A.B., M.L.Z.); Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, Calif (E.A.S.); Department of Radiology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wis (E.S.B.); Radiology Associates of Albuquerque, Albuquerque, NM (R.D.R.); and Department of Radiology, New York University Langone Medical Center, New York, NY (C.S.L.).,The views expressed in this article represent those of the author(s), and do not necessarily represent the official views of the American College of Radiology's National
Radiology Data Registry or the American College of Radiology
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Affiliation(s)
- Isaac Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
| | - Jeremy M Berg
- Editor-in-Chief, Science, Washington, DC 20005, USA.
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Berg JM, Smith OM. Editorial retraction. Sci Transl Med 2018; 10:10/471/eaaw2634. [PMID: 30541789 DOI: 10.1126/scitranslmed.aaw2634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Berg JM, Smith OM. Editorial retraction. Sci Transl Med 2017; 9:9/393/eaan8388. [DOI: 10.1126/scitranslmed.aan8388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Chandran UR, Medvedeva OP, Barmada MM, Blood PD, Chakka A, Luthra S, Ferreira A, Wong KF, Lee AV, Zhang Z, Budden R, Scott JR, Berndt A, Berg JM, Jacobson RS. TCGA Expedition: A Data Acquisition and Management System for TCGA Data. PLoS One 2016; 11:e0165395. [PMID: 27788220 PMCID: PMC5082933 DOI: 10.1371/journal.pone.0165395] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 10/11/2016] [Indexed: 11/19/2022] Open
Abstract
Background The Cancer Genome Atlas Project (TCGA) is a National Cancer Institute effort to profile at least 500 cases of 20 different tumor types using genomic platforms and to make these data, both raw and processed, available to all researchers. TCGA data are currently over 1.2 Petabyte in size and include whole genome sequence (WGS), whole exome sequence, methylation, RNA expression, proteomic, and clinical datasets. Publicly accessible TCGA data are released through public portals, but many challenges exist in navigating and using data obtained from these sites. We developed TCGA Expedition to support the research community focused on computational methods for cancer research. Data obtained, versioned, and archived using TCGA Expedition supports command line access at high-performance computing facilities as well as some functionality with third party tools. For a subset of TCGA data collected at University of Pittsburgh, we also re-associate TCGA data with de-identified data from the electronic health records. Here we describe the software as well as the architecture of our repository, methods for loading of TCGA data to multiple platforms, and security and regulatory controls that conform to federal best practices. Results TCGA Expedition software consists of a set of scripts written in Bash, Python and Java that download, extract, harmonize, version and store all TCGA data and metadata. The software generates a versioned, participant- and sample-centered, local TCGA data directory with metadata structures that directly reference the local data files as well as the original data files. The software supports flexible searches of the data via a web portal, user-centric data tracking tools, and data provenance tools. Using this software, we created a collaborative repository, the Pittsburgh Genome Resource Repository (PGRR) that enabled investigators at our institution to work with all TCGA data formats, and to interrogate these data with analysis pipelines, and associated tools. WGS data are especially challenging for individual investigators to use, due to issues with downloading, storage, and processing; having locally accessible WGS BAM files has proven invaluable. Conclusion Our open-source, freely available TCGA Expedition software can be used to create a local collaborative infrastructure for acquiring, managing, and analyzing TCGA data and other large public datasets.
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Affiliation(s)
- Uma R. Chandran
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States of America
| | - Olga P. Medvedeva
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - M. Michael Barmada
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA, United States of America
- Center for Simulation and Modeling, University of Pittsburgh, Pittsburgh, PA, United States of America
- UPMC Corporate Services, Pittsburgh, PA, United States of America
| | - Philip D. Blood
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Anish Chakka
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States of America
| | - Soumya Luthra
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States of America
| | - Antonio Ferreira
- Center for Simulation and Modeling, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Kim F. Wong
- Center for Simulation and Modeling, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Adrian V. Lee
- University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States of America
- Department of Pharmacology and Cell Biology, University of Pittsburgh, Pittsburgh, PA, United States of America
- Magee-Women’s Research Institute, Pittsburgh, PA, United States of America
| | - Zhihui Zhang
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Robert Budden
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - J. Ray Scott
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Annerose Berndt
- UPMC Corporate Services, Pittsburgh, PA, United States of America
| | - Jeremy M. Berg
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Rebecca S. Jacobson
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States of America
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
- * E-mail:
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Stern AM, Schurdak ME, Bahar I, Berg JM, Taylor DL. A Perspective on Implementing a Quantitative Systems Pharmacology Platform for Drug Discovery and the Advancement of Personalized Medicine. J Biomol Screen 2016; 21:521-34. [PMID: 26962875 PMCID: PMC4917453 DOI: 10.1177/1087057116635818] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Drug candidates exhibiting well-defined pharmacokinetic and pharmacodynamic profiles that are otherwise safe often fail to demonstrate proof-of-concept in phase II and III trials. Innovation in drug discovery and development has been identified as a critical need for improving the efficiency of drug discovery, especially through collaborations between academia, government agencies, and industry. To address the innovation challenge, we describe a comprehensive, unbiased, integrated, and iterative quantitative systems pharmacology (QSP)-driven drug discovery and development strategy and platform that we have implemented at the University of Pittsburgh Drug Discovery Institute. Intrinsic to QSP is its integrated use of multiscale experimental and computational methods to identify mechanisms of disease progression and to test predicted therapeutic strategies likely to achieve clinical validation for appropriate subpopulations of patients. The QSP platform can address biological heterogeneity and anticipate the evolution of resistance mechanisms, which are major challenges for drug development. The implementation of this platform is dedicated to gaining an understanding of mechanism(s) of disease progression to enable the identification of novel therapeutic strategies as well as repurposing drugs. The QSP platform will help promote the paradigm shift from reactive population-based medicine to proactive personalized medicine by focusing on the patient as the starting and the end point.
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Affiliation(s)
- Andrew M. Stern
- Department of Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Mark E. Schurdak
- Department of Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
- The University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
- The University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Jeremy M. Berg
- Department of Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
- University of Pittsburgh Institute for Personalized Medicine, Pittsburgh, PA, USA
| | - D. Lansing Taylor
- Department of Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
- The University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
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Berg JM, Berg WA. No myth: Benefits of breast screening. Nature 2016; 529:283. [DOI: 10.1038/529283b] [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: 11/09/2022]
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Oguro-Ando A, Rosensweig C, Herman E, Nishimura Y, Werling D, Bill BR, Berg JM, Gao F, Coppola G, Abrahams BS, Geschwind DH. Increased CYFIP1 dosage alters cellular and dendritic morphology and dysregulates mTOR. Mol Psychiatry 2015; 20:1069-78. [PMID: 25311365 PMCID: PMC4409498 DOI: 10.1038/mp.2014.124] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 07/18/2014] [Accepted: 08/21/2014] [Indexed: 12/22/2022]
Abstract
Rare maternally inherited duplications at 15q11-13 are observed in ~1% of individuals with an autism spectrum disorder (ASD), making it among the most common causes of ASD. 15q11-13 comprises a complex region, and as this copy number variation encompasses many genes, it is important to explore individual genotype-phenotype relationships. Cytoplasmic FMR1-interacting protein 1 (CYFIP1) is of particular interest because of its interaction with Fragile X mental retardation protein (FMRP), its upregulation in transformed lymphoblastoid cell lines from patients with duplications at 15q11-13 and ASD and the presence of smaller overlapping deletions of CYFIP1 in patients with schizophrenia and intellectual disability. Here, we confirm that CYFIP1 is upregulated in transformed lymphoblastoid cell lines and demonstrate its upregulation in the post-mortem brain from 15q11-13 duplication patients for the first time. To investigate how increased CYFIP1 dosage might predispose to neurodevelopmental disease, we studied the consequence of its overexpression in multiple systems. We show that overexpression of CYFIP1 results in morphological abnormalities including cellular hypertrophy in SY5Y cells and differentiated mouse neuronal progenitors. We validate these results in vivo by generating a BAC transgenic mouse, which overexpresses Cyfip1 under the endogenous promotor, observing an increase in the proportion of mature dendritic spines and dendritic spine density. Gene expression profiling on embryonic day 15 suggested the dysregulation of mammalian target of rapamycin (mTOR) signaling, which was confirmed at the protein level. Importantly, similar evidence of mTOR-related dysregulation was seen in brains from 15q11-13 duplication patients with ASD. Finally, treatment of differentiated mouse neuronal progenitors with an mTOR inhibitor (rapamycin) rescued the morphological abnormalities resulting from CYFIP1 overexpression. Together, these data show that CYFIP1 overexpression results in specific cellular phenotypes and implicate modulation by mTOR signaling, further emphasizing its role as a potential convergent pathway in some forms of ASD.
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Affiliation(s)
- A Oguro-Ando
- Programs in Neurogenetics, Department of. Neurology and Program in Neurobehavioral Genetics and Center for Autism Research and Treatment, Semel Institute for Neuroscience and Behavior, David Geffen School of Medicine, University of California at Los Angeles, 2309 Gonda Bldg, 695 Charles E. Young Dr. South Los Angeles, CA 90095-1761
,Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - C Rosensweig
- Programs in Neurogenetics, Department of. Neurology and Program in Neurobehavioral Genetics and Center for Autism Research and Treatment, Semel Institute for Neuroscience and Behavior, David Geffen School of Medicine, University of California at Los Angeles, 2309 Gonda Bldg, 695 Charles E. Young Dr. South Los Angeles, CA 90095-1761
| | - E Herman
- Programs in Neurogenetics, Department of. Neurology and Program in Neurobehavioral Genetics and Center for Autism Research and Treatment, Semel Institute for Neuroscience and Behavior, David Geffen School of Medicine, University of California at Los Angeles, 2309 Gonda Bldg, 695 Charles E. Young Dr. South Los Angeles, CA 90095-1761
| | - Y Nishimura
- Programs in Neurogenetics, Department of. Neurology and Program in Neurobehavioral Genetics and Center for Autism Research and Treatment, Semel Institute for Neuroscience and Behavior, David Geffen School of Medicine, University of California at Los Angeles, 2309 Gonda Bldg, 695 Charles E. Young Dr. South Los Angeles, CA 90095-1761
| | - D Werling
- Programs in Neurogenetics, Department of. Neurology and Program in Neurobehavioral Genetics and Center for Autism Research and Treatment, Semel Institute for Neuroscience and Behavior, David Geffen School of Medicine, University of California at Los Angeles, 2309 Gonda Bldg, 695 Charles E. Young Dr. South Los Angeles, CA 90095-1761
| | - BR Bill
- Programs in Neurogenetics, Department of. Neurology and Program in Neurobehavioral Genetics and Center for Autism Research and Treatment, Semel Institute for Neuroscience and Behavior, David Geffen School of Medicine, University of California at Los Angeles, 2309 Gonda Bldg, 695 Charles E. Young Dr. South Los Angeles, CA 90095-1761
| | - JM Berg
- Programs in Neurogenetics, Department of. Neurology and Program in Neurobehavioral Genetics and Center for Autism Research and Treatment, Semel Institute for Neuroscience and Behavior, David Geffen School of Medicine, University of California at Los Angeles, 2309 Gonda Bldg, 695 Charles E. Young Dr. South Los Angeles, CA 90095-1761
| | - F Gao
- Programs in Neurogenetics, Department of. Neurology and Program in Neurobehavioral Genetics and Center for Autism Research and Treatment, Semel Institute for Neuroscience and Behavior, David Geffen School of Medicine, University of California at Los Angeles, 2309 Gonda Bldg, 695 Charles E. Young Dr. South Los Angeles, CA 90095-1761
| | - G Coppola
- Programs in Neurogenetics, Department of. Neurology and Program in Neurobehavioral Genetics and Center for Autism Research and Treatment, Semel Institute for Neuroscience and Behavior, David Geffen School of Medicine, University of California at Los Angeles, 2309 Gonda Bldg, 695 Charles E. Young Dr. South Los Angeles, CA 90095-1761
,Semel Institute, David Geffen School of Medicine, University of California at Los Angeles, 2309 Gonda Bldg, 695 Charles E. Young Dr. South, Los Angeles, CA 90095-1761
| | - BS Abrahams
- Programs in Neurogenetics, Department of. Neurology and Program in Neurobehavioral Genetics and Center for Autism Research and Treatment, Semel Institute for Neuroscience and Behavior, David Geffen School of Medicine, University of California at Los Angeles, 2309 Gonda Bldg, 695 Charles E. Young Dr. South Los Angeles, CA 90095-1761
| | - DH Geschwind
- Programs in Neurogenetics, Department of. Neurology and Program in Neurobehavioral Genetics and Center for Autism Research and Treatment, Semel Institute for Neuroscience and Behavior, David Geffen School of Medicine, University of California at Los Angeles, 2309 Gonda Bldg, 695 Charles E. Young Dr. South Los Angeles, CA 90095-1761
,Dept. of Human Genetics, David Geffen School of Medicine, University of California at Los Angeles, 2309 Gonda Bldg, 695 Charles E. Young Dr. South, Los Angeles, CA 90095-1761
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16
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Levine AS, Alpern RJ, Andrews NC, Antman K, Balser JR, Berg JM, Davis PB, Fitz JG, Golden RN, Goldman L, Jameson JL, Lee VS, Polonsky KS, Rappley MD, Reece EA, Rothman PB, Schwinn DA, Shapiro LJ, Spiegel AM. Research in academic medical centers: Two threats to sustainable support. Sci Transl Med 2015; 7:289fs22. [DOI: 10.1126/scitranslmed.aac5200] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Reductions in federal support and clinical revenue jeopardize biomedical research and, in turn, clinical medicine.
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Affiliation(s)
- Arthur S. Levine
- Senior Vice Chancellor for the Health Sciences, John and Gertrude Petersen Dean, School of Medicine, and Professor of Medicine and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Robert J. Alpern
- Dean and Ensign Professor, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nancy C. Andrews
- Dean and Vice Chancellor for Academic Affairs, Duke University School of Medicine, Durham, NC 27710, USA
| | - Karen Antman
- Provost, Boston University Medical Campus, Dean, School of Medicine, Boston, MA 02118, USA
| | - Jeffrey R. Balser
- Vice Chancellor for Health Affairs, Dean, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Jeremy M. Berg
- Associate Senior Vice Chancellor for Science Strategy and Planning in the Health Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Pamela B. Davis
- Dean, Case Western Reserve University School of Medicine, Senior Vice President for Medical Affairs, Case Western Reserve University, Cleveland, OH 44106, USA
| | - J. Gregory Fitz
- Executive Vice President for Academic Affairs and Provost, Dean, UT Southwestern Medical School, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Robert N. Golden
- Dean, School of Medicine and Public Health, Vice Chancellor for Medicine Affairs, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Lee Goldman
- Executive Vice President and Dean of the Faculties of Health Sciences and Medicine, Chief Executive, Columbia University Medical Center, New York, NY 10032, USA
| | - J. Larry Jameson
- Executive Vice President, University of Pennsylvania for the Health System, Dean, Raymond and Ruth Perelman School of Medicine University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vivian S. Lee
- Dean, School of Medicine, A. Lorris Betz Senior Vice-President for Health Sciences, CEO, University of Utah Health Care, Salt Lake City, UT 84132, USA
| | - Kenneth S. Polonsky
- Richard T. Crane Distinguished Service Professor, Dean of the Division of the Biological Sciences and the Pritzker School of Medicine, Executive Vice President of Medical Affairs, The University of Chicago, Chicago, IL 60637, USA
| | - Marsha D. Rappley
- Dean, Michigan State University College of Human Medicine, East Lansing, MI 48824, USA
| | - E. Albert Reece
- Vice President for Medical Affairs, University of Maryland, John Z. and Akiko K. Bowers Distinguished Professor, and Dean, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Paul B. Rothman
- Dean of the Medical Faculty, CEO, Johns Hopkins Medicine, Baltimore, MD 21205, USA
| | - Debra A. Schwinn
- Dean, Roy J. and Lucille A. Carver College of Medicine, Professor of Anesthesiology, Pharmacology & Biochemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Larry J. Shapiro
- Spencer T. and Ann W. Olin Distinguished Professor, Executive Vice Chancellor for Medical Affairs, and Dean, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Allen M. Spiegel
- The Marilyn and Stanley M. Katz Dean, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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17
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Abstract
The development of robust science policy depends on use of the best available data, rigorous analysis, and inclusion of a wide range of input. While director of the National Institute of General Medical Sciences (NIGMS), I took advantage of available data and emerging tools to analyze training time distribution by new NIGMS grantees, the distribution of the number of publications as a function of total annual National Institutes of Health support per investigator, and the predictive value of peer-review scores on subsequent scientific productivity. Rigorous data analysis should be used to develop new reforms and initiatives that will help build a more sustainable American biomedical research enterprise.
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Affiliation(s)
- Jeremy M Berg
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
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18
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19
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Namuswe F, Berg JM. Secondary interactions involving zinc-bound ligands: roles in structural stabilization and macromolecular interactions. J Inorg Biochem 2011; 111:146-9. [PMID: 22196020 DOI: 10.1016/j.jinorgbio.2011.10.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 10/07/2011] [Accepted: 10/26/2011] [Indexed: 10/14/2022]
Abstract
A large number of proteins contain bound zinc ions. These zinc ions are frequently coordinated by a combination of histidine and cysteine residues. In addition to atoms that coordinate directly to the zinc ions, these side chains have groups that can donate or accept hydrogen bonds from other groups. These secondary interactions can help stabilize the zinc-binding sites, can contribute to protein folding and stability, and, on occasion, can participate in interactions with other macromolecules. Five examples of these secondary interactions are discussed: carbonic anhydrase (where secondary interactions involving histidine residues stabilize the zinc-binding site thermodynamically and kinetically), retroviral nucleocapsid proteins and TRAF proteins (where cysteinate sulfur to peptide NH hydrogen bonds contribute to the structural relationships between adjacent domains), and nucleic acid binding proteins, Zif268 and TIS11 where secondary interactions participate in protein-nucleic acid interactions.
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Affiliation(s)
- Frances Namuswe
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases/NIH, Bethesda, MD 20892, United States
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20
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Wang R, Ilangovan U, Leal BZ, Robinson AK, Amann BT, Tong CV, Berg JM, Hinck AP, Kim CA. Identification of nucleic acid binding residues in the FCS domain of the polycomb group protein polyhomeotic. Biochemistry 2011; 50:4998-5007. [PMID: 21351738 DOI: 10.1021/bi101487s] [Citation(s) in RCA: 8] [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: 12/31/2022]
Abstract
Polycomb group (PcG) proteins maintain the silent state of developmentally important genes. Recent evidence indicates that noncoding RNAs also play an important role in targeting PcG proteins to chromatin and PcG-mediated chromatin organization, although the molecular basis for how PcG and RNA function in concert remains unclear. The Phe-Cys-Ser (FCS) domain, named for three consecutive residues conserved in this domain, is a 30-40-residue Zn(2+) binding motif found in a number of PcG proteins. The FCS domain has been shown to bind RNA in a non-sequence specific manner, but how it does so is not known. Here, we present the three-dimensional structure of the FCS domain from human Polyhomeotic homologue 1 (HPH1, also known as PHC1) determined using multidimensional nuclear magnetic resonance methods. Chemical shift perturbations upon addition of RNA and DNA resulted in the identification of Lys 816 as a potentially important residue required for nucleic acid binding. The role played by this residue in Polyhomeotic function was demonstrated in a transcription assay conducted in Drosophila S2 cells. Mutation of the Arg residue to Ala in the Drosophila Polyhomeotic (Ph) protein, which is equivalent to Lys 816 in HPH1, was unable to repress transcription of a reporter gene to the level of wild-type Ph. These results suggest that direct interaction between the Ph FCS domain and nucleic acids is required for Ph-mediated repression.
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Affiliation(s)
- Renjing Wang
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, MSC 7760, San Antonio, Texas 78229-3990, United States
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21
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Affiliation(s)
- R M Long
- National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland, USA.
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22
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Guerrerio AL, Berg JM. Design of single-stranded nucleic acid binding peptides based on nucleocapsid CCHC-box zinc-binding domains. J Am Chem Soc 2010; 132:9638-43. [PMID: 20586464 DOI: 10.1021/ja910942v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The solution structures of nucleocapsid (NC)-like CCHC zinc-binding domains bound to nucleic acid targets have revealed that these domains bind guanosine residues within single-stranded nucleic acids. Here, we have performed initial studies examining the potential use of NC-like CCHC zinc-binding domains as modules to construct single-stranded nucleic acid binding peptides. The affinity for guanosine-containing single-stranded deoxyribooligonucleotides increases with the number of CCHC domains in the peptide. The length of the linker between domains affects the spacing of guanosine residues in oligonucleotides that are preferentially bound. These studies provide a proof of principle that NC-like CCHC zinc-binding domains can be utilized as a basis for designing peptides that bind specific single-stranded nucleic acid sequences.
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Affiliation(s)
- Anthony L Guerrerio
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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23
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Abstract
Most proteins are targeted to the peroxisomal matrix by virtue of a peroxisomal targeting signal-1 (PTS1), a short carboxy-terminal sequence specifically recognized by the PTS1 receptor Pex5p. We had previously developed a model that allowed the estimation of the affinities of many PTS1 sequences within the human proteome for Pex5p that revealed a wide range of predicted affinities. We have now experimentally determined the affinities of the PTS1-containing peptides from 42 proteins from the human proteome for Pex5p and show that these range over 4 orders of magnitude. These affinities correlate reasonably well with the predicted values and are substantially more precise. In an attempt to provide a possible explanation for the wide range of PTS1-Pex5p affinities, we compared these affinities with mRNA levels (as a proxy for rates of protein production) of the genes encoding these proteins in 79 human tissues and cell types. We note that high affinity PTS1-Pex5p interactions tend to correspond to proteins encoded by genes expressed at relatively low levels, whereas lower affinity PTS1-Pex5p interactions tend to correspond to proteins encoded by genes exhibiting higher levels and wider ranges of expression. Further analysis revealed that these relationships are consistent with the notion that a relatively uniform pool of protein-Pex5p complexes is maintained for appropriate peroxisome assembly.
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Affiliation(s)
- Debdip Ghosh
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
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24
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Jantz D, Berg JM. Probing the DNA-binding affinity and specificity of designed zinc finger proteins. Biophys J 2010; 98:852-60. [PMID: 20197039 DOI: 10.1016/j.bpj.2009.11.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 10/30/2009] [Accepted: 11/02/2009] [Indexed: 11/17/2022] Open
Abstract
Engineered transcription factors and endonucleases based on designed Cys(2)His(2) zinc finger domains have proven to be effective tools for the directed regulation and modification of genes. The introduction of this technology into both research and clinical settings necessitates the development of rapid and accurate means of evaluating both the binding affinity and binding specificity of designed zinc finger domains. Using a fluorescence anisotropy-based DNA-binding assay, we examined the DNA-binding properties of two engineered zinc finger proteins that differ by a single amino acid. We demonstrate that the protein with the highest affinity for a particular DNA site need not be the protein that binds that site with the highest degree of specificity. Moreover, by comparing the binding characteristics of the two proteins at varying salt concentrations, we show that the ionic strength makes significant and variable contributions to both affinity and specificity. These results have significant implications for zinc finger design as they highlight the importance of considering affinity, specificity, and environmental requirements in designing a DNA-binding domain for a particular application.
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Affiliation(s)
- Derek Jantz
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
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25
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Davis AM, Berg JM. Homodimerization and heterodimerization of minimal zinc(II)-binding-domain peptides of T-cell proteins CD4, CD8alpha, and Lck. J Am Chem Soc 2009; 131:11492-7. [PMID: 19624124 DOI: 10.1021/ja9028928] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metal-mediated protein oligomerization is an emerging mode of protein-protein interaction. The C-terminal cytosolic domains of T-cell coreceptors CD4 and CD8alpha form zinc-bridged heterodimers with the N-terminal region of the kinase Lck, with each protein contributing two cysteinate ligands to the complex. Using size exclusion chromatography, (1)H NMR, and UV/visible absorption spectroscopy with cobalt(II) as a spectroscopic probe, we demonstrate that small peptides derived from these regions form metal-bridged heterodimers but also homodimers, in contrast to previous reports. The Lck-CD4 and Lck-CD8alpha cobalt(II)-bridged heterodimer complexes are more stable than the corresponding (Lck)(2)cobalt(II) complex by factors of 11 +/- 4 and 22 +/- 9, respectively. These studies were aided by the discovery that cobalt(II) complexes with a cobalt(II)(-Cys-X-X-Cys-)(-Cys-X-Cys-) chromophore show unusual optical spectra with one component of the visible d-d ((4)A(2)-to-(4)T(1)(P)) transition red-shifted and well separated from the other components. These results provide insights into the basis of specificity of metal-bridged complex formation and on the potential biological significance of metal-bridged homodimers in T-cells.
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Affiliation(s)
- Alisa M Davis
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive & Kidney Disorders, National Institutes of Health, Bethesda, Maryland 20892, USA
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26
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Martin GG, Hostetler HA, McIntosh AL, Tichy SE, Williams BJ, Russell DH, Berg JM, Spencer TA, Ball J, Kier AB, Schroeder F. Structure and Function of the Sterol Carrier Protein-2 N-Terminal Presequence. Biochemistry 2008. [DOI: 10.1021/bi801129n] [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: 11/29/2022]
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27
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Martin GG, Hostetler HA, McIntosh AL, Tichy SE, Williams BJ, Russell DH, Berg JM, Spencer TA, Ball J, Kier AB, Schroeder F. Structure and function of the sterol carrier protein-2 N-terminal presequence. Biochemistry 2008; 47:5915-34. [PMID: 18465878 PMCID: PMC2474712 DOI: 10.1021/bi800251e] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although sterol carrier protein-2 (SCP-2) is encoded as a precursor protein (proSCP-2), little is known regarding the structure and function of the 20-amino acid N-terminal presequence. As shown herein, the presequence contains significant secondary structure and alters SCP-2: (i) secondary structure (CD), (ii) tertiary structure (aqueous exposure of Trp shown by UV absorbance, fluorescence, and fluorescence quenching), (iii) ligand binding site [Trp response to ligands, peptide cross-linked by photoactivatable free cholesterol (FCBP)], (iv) selectivity for interaction with anionic phospholipid-rich membranes, (v) interaction with a peroxisomal import protein [FRET studies of Pex5p(C) binding], the N-terminal presequence increased SCP-2's affinity for Pex5p(C) by 10-fold, and (vi) intracellular targeting in living and fixed cells (confocal microscopy). Nearly 5-fold more SCP-2 than proSCP-2 colocalized with plasma membrane lipid rafts and caveolae (AF488-CTB); 2.8-fold more SCP-2 than proSCP-2 colocalized with a mitochondrial marker (Mitotracker), but nearly 2-fold less SCP-2 than proSCP-2 colocalized with peroxisomes (AF488 antibody to PMP70). These data indicate the importance of the N-terminal presequence in regulating SCP-2 structure, cholesterol localization within the ligand binding site, membrane association, and, potentially, intracellular targeting.
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Affiliation(s)
- Gregory G. Martin
- Department of Physiology and Pharmacology, Texas A&M University, TVMC, College Station, TX 77843-4466
| | - Heather A. Hostetler
- Department of Physiology and Pharmacology, Texas A&M University, TVMC, College Station, TX 77843-4466
| | - Avery L. McIntosh
- Department of Physiology and Pharmacology, Texas A&M University, TVMC, College Station, TX 77843-4466
| | - Shane E. Tichy
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3255
| | - Brad J. Williams
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3255
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3255
| | - Jeremy M. Berg
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | | | - Judith Ball
- Department of Pathobiology, Texas A&M University, College Station, TX 77843-4467
| | - Ann B. Kier
- Department of Pathobiology, Texas A&M University, College Station, TX 77843-4467
| | - Friedhelm Schroeder
- Department of Physiology and Pharmacology, Texas A&M University, TVMC, College Station, TX 77843-4466
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28
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Norvell JC, Berg JM. [Protein structure initiative]. Tanpakushitsu Kakusan Koso 2008; 53:655-657. [PMID: 18409559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- John C Norvell
- National Institute of General Medical Sciences, National Institutes of Health, USA
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29
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Affiliation(s)
- John C Norvell
- NIGMS, NIH, 45 Center Drive MSC 6200, Bethesda, MD 20892-6200, USA.
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31
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Maynard EL, Berg JM. Quantitative analysis of peroxisomal targeting signal type-1 binding to wild-type and pathogenic mutants of Pex5p supports an affinity threshold for peroxisomal protein targeting. J Mol Biol 2007; 368:1259-66. [PMID: 17399738 DOI: 10.1016/j.jmb.2007.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [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: 12/29/2006] [Accepted: 03/02/2007] [Indexed: 11/26/2022]
Abstract
Peroxisomal biogenesis disorders (PBDs) are caused by mutations in 12 distinct genes that encode the components of the peroxisome assembly machinery. Three mutations in the gene encoding Pex5p, the peroxisomal targeting signal type-1 (PTS1) receptor, have been reported, each associated with a disorder of the Zellweger spectrum of different severity. Here, we report studies of the affinities of mutated forms of Pex5p for a series of PTS1 peptides and conclude that PTS1-affinity reductions are correlated with disease severity and cell biological phenotype. A quantitative model has been developed that allows estimation of the dissociation constants for complexes with a wide range of PTS1 sequences bound to wild-type and mutant Pex5p. In the context of this model, the binding measurements suggest that no PTS1-containing proteins are targeted by Pex5p(N489K) and only a relatively small subset of PTS1-containing proteins with the highest affinity for Pex5p are targeted to peroxisomes by Pex5p(S563W). Furthermore, the results of the analysis are consistent with an approximate dissociation constant threshold near 500 nM required for efficient protein targeting to peroxisomes.
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Affiliation(s)
- Ernest L Maynard
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
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33
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Berg JM. Opportunities for chemical biologists: a view from the National Institutes of Health. ACS Chem Biol 2006; 1:547-8. [PMID: 17168545 DOI: 10.1021/cb6003993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The most exciting and vibrant areas of research often lie at the interfaces between disciplines that have traditionally been separate. In the case of the chemical and biological sciences, such interfaces have been fruitfully explored for more than a century. The fields of pharmacology, biochemistry, and biophysical chemistry are relatively mature, yet they are still quite active and full of challenging problems and opportunities for new discoveries. These fields are integral to biomedical research and have had a tremendous impact on human health.
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Affiliation(s)
- Jeremy M Berg
- National Institute of General Medical Sciences, 45 Center Drive, 2As-12, Bethesda, Maryland 20892, USA.
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34
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Alexander DF, Alving BM, Battey JF, Berg JM, Collins FS, Fauci AS, Gallin JI, Grady PA, Hodes RJ, Hrynkow SH, Insel TR, Jones JF, Katz SI, Landis SC, Li TK, Lindberg DA, Nabel EG, Niederhuber JE, Pettigrew RI, Rodgers GP, Ruffin J, Scarpa A, Schwartz DA, Sieving PA, Straus SE, Tabak LA, Volkow ND. Response to: "Rescuing the NIH before it is too late". J Clin Invest 2006; 116:1462-3. [PMID: 16648877 PMCID: PMC1449952 DOI: 10.1172/jci28894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We, the directors of the 27 NIH institutes and centers, wanted to respond to the points made by Andrew Marks in his recent editorial. While we appreciate that the scientific community has concerns, the current initiatives and directions of the NIH have been developed through planning processes that reflect openness and continued constituency input, all aimed at assessing scientific opportunities and addressing public health needs.
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35
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Schwab JM, Berg JM. Chemical Biology and the NIH. ACS Chem Biol 2006. [DOI: 10.1021/cb0600052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John M. Schwab
- Division of Pharmacology, Physiology, and Biological Chemistry
- National Institute of General Medical Sciences, National Institutes of Health, 45 Center Drive, Bethesda, Maryland 20892
| | - Jeremy M. Berg
- National Institute of General Medical Sciences, National Institutes of Health, 45 Center Drive, Bethesda, Maryland 20892
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36
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Mani M, Smith J, Kandavelou K, Berg JM, Chandrasegaran S. Binding of two zinc finger nuclease monomers to two specific sites is required for effective double-strand DNA cleavage. Biochem Biophys Res Commun 2005; 334:1191-1197. [PMID: 16043120 PMCID: PMC4170802 DOI: 10.1016/j.bbrc.2005.07.021] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Accepted: 07/11/2005] [Indexed: 11/20/2022]
Abstract
Custom-designed zinc finger nucleases (ZFNs) are becoming powerful tools in gene targeting-the process of replacing a gene within a genome by homologous recombination. Here, we have studied the DNA cleavage by one such ZFN, DeltaQNK-FN, in order to gain insight into how ZFNs cleave DNA and how two inverted sites promote double-strand cleavage. DNA cleavage by DeltaQNK-FN is greatly facilitated when two DeltaQNK-binding sites are close together in an inverted orientation. Substrate cleavage was not first order with respect to the concentration of DeltaQNK-FN, indicating that double-strand cleavage requires dimerization of the FokI cleavage domain. Rates of DNA cleavage decrease as the substrate concentrations increase, suggesting that the DeltaQNK-FN molecules are effectively "trapped" in a 1:1 complex on DNA when the DNA is in excess. The physical association of two ZFN monomers on DNA was monitored by using the biotin-pull-down assay, which showed that the formation of DeltaQNK-FN active complex required both binding of the two DeltaQNK-FN molecules to specific DNA sites and divalent metal ions.
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Affiliation(s)
- Mala Mani
- Department of Environmental Health Sciences, The Johns Hopkins University School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205-2179, USA
| | - Jeff Smith
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - Karthikeyan Kandavelou
- Department of Environmental Health Sciences, The Johns Hopkins University School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205-2179, USA
| | - Jeremy M. Berg
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - Srinivasan Chandrasegaran
- Department of Environmental Health Sciences, The Johns Hopkins University School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205-2179, USA
- Corresponding author. Fax: +1 410 955 0299., (S. Chandrasegaran)
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37
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Abstract
The metal binding properties of peptides corresponding to metal-binding sites spanning regions that normally function as linkers in tandem arrays of metal-binding domain-containing proteins were examined. For a peptide with two His residues from one TFIIIA-like zinc finger domain, a canonical TFIIIA-like linker, and two Cys residues from an adjacent zinc domain, the dissociation constant for the 1:1 peptide to cobalt(II) was found to be 15 +/- 10 microM, compared with 60 nM for the corresponding zinc finger domains themselves. Peptides overlapping two sets of metal-binding domains from human TRAF (tumor necrosis factor receptor-associated factor) proteins were examined. In one case, the affinity of the presumed metal-binding domain and that for the linker region were comparable, while in the second case, the affinity of the linker peptide was higher than that for the corresponding presumed metal-binding domain peptide. These studies revealed that cobalt(II) affinities in the micromolar range can occur even for peptides that do not correspond to natural zinc-binding domains and that the degree of distinction between authentic metal-binding domains and the corresponding linker-spanning peptides may be modest, at least for single domain peptide models.
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Affiliation(s)
- Karen R Thickman
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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Chisholm-Brause CJ, Berg JM, Little KM, Matzner RA, Morris DE. Uranyl sorption by smectites: spectroscopic assessment of thermodynamic modeling. J Colloid Interface Sci 2004; 277:366-82. [PMID: 15341848 DOI: 10.1016/j.jcis.2004.04.047] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [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: 03/15/2004] [Accepted: 04/23/2004] [Indexed: 10/26/2022]
Abstract
Batch sorption experiments and thermodynamic modeling of the interaction of UO2(2+) and its hydrolysis products with two smectitic clay minerals, the reference material SWy-1 [McKinley et al., Clays Clay Miner. 43 (1995) 586] and the soil isolate LK-1 [Turner et al., Geochim. Cosmochim. Acta 30 (1996) 3399], have established a conceptual framework for uranyl/smectite surface complexation based on general reactions between aqueous uranyl species and the reactive sites on the mineral surfaces. In this report, we have formulated and spectroscopically tested a set of hypotheses based on this conceptual framework using samples prepared under similar or identical conditions to evaluate the agreement between surface complexation/speciation as enumerated by spectroscopic characterization and that elaborated by the surface complexation model. Both steady-state and time-resolved optical emission spectral data are presented for uranyl on both smectite minerals as well as on the analogue phases SiO2 and Al(OH)3 spanning the pH range from approximately 4 to 8 and the background electrolyte concentrations from approximately 0.001 to 0.1 M. The spectral data enable the explicit identification of an outer-sphere exchange-site population of the hydrated cation [UO2(OH2)5(2+) ] in SWy-1. Spectral data also clearly establish the existence of inner-sphere surface complexes on the analogue phases and on the amphoteric clay crystallite edge sites [aluminol (>Al-OH) and silanol (>Si-OH)]. Based on the spectral characteristics of these uranyl edge-site populations, it is possible to readily infer for the SiO2, Al(OH)3, and SWy-1 samples the evolution in surface speciation with increasing pH to more hydrolyzed uranyl-surface complexes consistent with the conceptual model. The spectral domain characteristics of the edge-site populations on LK-1 with increasing pH suggest that there is no change in the hydrolysis of the uranyl-surface species. However, emission lifetime data are interpreted as indicating a shift in the surface speciation of the same uranyl-surface species from aluminol sites to silanol sites with pH increase. This observation is also consistent with the conceptual framework of the model. Data are also reported for Eu3+/smectite samples to provide additional insight into the exchange site populations. The emission spectra for Eu3+ in the basal-plane exchange sites differs significantly between SWy-1 and LK-1 samples reflecting a difference in the basal plane spacing between these two minerals, but the emission lifetime data suggest that the Eu3+ cation remains fully hydrated in both systems. The overall general description of surface speciation of uranyl on these mineral phases as enumerated by spectroscopy is in good accord with that derived from the conceptual thermodynamic model, lending added confidence to our understanding and descriptions of surface complexation behavior in this complex geochemical system.
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Affiliation(s)
- C J Chisholm-Brause
- Department of Applied Science, College of William and Mary, Applied Research Center, 12050 Jefferson Avenue, Newport News, VA 23606, USA.
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Abstract
The majority of proteins targeted to the peroxisomal lumen contain a C-terminal peroxisomal targeting signal-1 (PTS1) that is bound by the peroxin Pex5p. The PTS1 is generally regarded as a C-terminal tripeptide that adheres to the consensus (S/A/C)(K/R/H)(L/M). Previously, we studied the binding affinity of peptides of the form YQX(-3)X(-2)X(-1) to the peptide-binding domain of human Pex5p (referred to as Pex5p-C). Optimal affinity was found for YQSKL, which bound with an affinity of 200 +/- 40 nM. To extend this work, we investigated the properties of a peptide containing the last 9 residues of acyl-CoA oxidase (RHYLKPLQSKL) and discovered that it binds to Pex5p-C with a dissociation constant of 1.4 +/- 0.4 nM, 180 times tighter than YQSKL. Further analysis revealed that the enhanced affinity is primarily due to the presence of leucine in the (-5) position. In addition, a peptide corresponding to the luciferase C-terminus (YKGGKSKL) was found to bind Pex5p-C about 20 times tighter than YQSKL. The majority of this effect results from having lysine in position (-4). Catalase contains a noncanonical PTS1 (-AREKANL). The affinity of YQANL was found to be 3600 +/- 400 nM. This relatively weak binding is consistent with previous unsuccessful attempts to direct chloramphenicol acetyltransferase to the peroxisome by fusing -ANL to its C-terminus (-GGA-ANL). The peptides YKANL, YEKANL, YREKANL, and YAREKANL all bound Pex5p-C with higher affinities than did YQANL, but the affinities are still lower than peptides that correspond to functional targeting signals in other contexts. Because both catalase and Pex5p are tetramers (as opposed to the monomeric Pex5p-C and the peptides used in our studies), multidentate effects on binding affinity between Pex5p and other oligomeric proteins should be considered. Our study provides direct thermodynamic data revealing that peptide binding to Pex5p-C binding is favored by lysine in the (-4) position and leucine in the (-5) position. Our results suggest that peptides or proteins with optimized residues in the (-4) and/or (-5) positions can bind to Pex5p with affinities that are at least two orders of magnitude greater than that of YQSKL, and that this stabilization can compensates for otherwise weakly binding PTS1s.
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Affiliation(s)
- Ernest L Maynard
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Abstract
Zinc(II) and cobalt(II) binding to a series of zinc finger peptides with different charged residue pairs across from one another in a beta-sheet were examined. Previous studies revealed a narrow range of interaction free energies (<0.5 kcal/mol) between these residues. Here, isothermal titration calorimetry studies were performed, revealing a range of over 3 kcal/mol in relative binding enthalpies. Double mutant cycle analysis revealed a range of interaction enthalpies ranging from -3.1 to -3.4 kcal/mol for the Arg-Asp pair to -0.8 kcal/mol for the Lys-Glu pair. The large range of interaction enthalpies coupled with the small range of interaction free energies reveals substantial entropy-enthalpy compensation. The magnitudes of the effects are consistent with the formation of a structurally rigid Arg-Asp contact ion pair but less direct and more mobile interactions involving the other combinations.
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Affiliation(s)
- Cheryl A Blasie
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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Guerrerio AL, Berg JM. Metal ion affinities of the zinc finger domains of the metal responsive element-binding transcription factor-1 (MTF1). Biochemistry 2004; 43:5437-44. [PMID: 15122909 DOI: 10.1021/bi0358418] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metal response element (MRE) binding transcription factor-1 (MTF1) is a six Cys(2)His(2) zinc finger-containing transcription factor required for basal and zinc-induced transcription of metallothionein genes. The cobalt(II) and zinc(II) affinities of a protein fragment comprising the six zinc finger domains have been examined to reveal apparent dissociation constants (for the six domains collectively) of 0.5 +/- 0.2 microM for cobalt(II) and 31 +/- 14 pM for zinc(II). Two approaches have been used to determine the metal ion affinities of the individual domains. First, the six domains have been examined as single domain peptides revealing dissociation constants ranging from 0.3 to 1.7 microM for cobalt(II). The domains fall into two sets with peptides corresponding to domains 2, 3, and 4 showing relatively high affinity (K(d)(Co(II)) 0.3-0.5 microM) and peptides corresponding to domains 1, 5, and 6 showing lower affinity (K(d)(Co(II)) 1.6-1.7 microM). Second, we examined the affinity of each domain in the context of the six zinc finger domain protein by individually mutating one metal-binding His residue to Cys to allow independent monitoring of the cobalt(II) occupancy of each site. The affinity of each domain was higher in this context than as a single domain peptide with affinities (corrected for the effect of the mutation) ranging from 0.02 to 0.5 microM. The increase in affinity for the individual domains ranged from factors of 1.1 to 20. The order of affinities (from higher to lowest) was observed to be 4 > 2 approximately 5 > 6 approximately 3 approximately 1. These results reveal that none of the Cys(2)His(2) zinc finger domains of MTF1 have dramatically low metal ion affinities, certainly none low enough to respond to changes in free zinc ion concentrations in the micromolar range. Nonetheless, the metal ion affinities of some domains do differ by a factor of 25 with domains at both the amino- and carboxyl-termini showing lower intrinsic affinities for metal ions than the central domains.
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Affiliation(s)
- Anthony L Guerrerio
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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Abstract
Cys(2)His(2) zinc finger proteins make up the largest class of transcription factors encoded in the genomes of higher eukaryotes. Recent studies of the Ikaros transcription factor demonstrated that this zinc finger protein undergoes cell cycle-dependent changes in association with DNA that seem to be due to phosphorylation of Thr or Ser residues in the linker regions connecting adjacent zinc finger domains. The high degree of conservation of this linker sequence within the Cys(2)His(2) superfamily suggested a common mechanism for the cell cycle-dependent modulation of DNA-binding affinity throughout this large class of transcription factors. The effects of linker phosphorylation on DNA-binding affinity were investigated through a direct comparison of the DNA-binding properties of four synthetic zinc finger proteins produced by native chemical ligation. The four proteins, comprising three zinc finger domains joined by two consensus Thr-Gly-Glu-Lys-Pro linkers, correspond to all four possible combinations of linker Thr phosphorylation states. Fluorescence-based DNA-binding studies of a specific DNA-binding site revealed that phosphorylation of a single linker reduced binding affinity approximately 40-fold, whereas phosphorylation of both linkers reduced binding affinity 130-fold. These results with purified components demonstrate that linker phosphorylation does, indeed, produce a significant reduction in DNA-binding affinity and support a model wherein a single cell cycle-dependent Ser/Thr kinase could simultaneously inactivate a large number of zinc finger transcription factors.
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Affiliation(s)
- Derek Jantz
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Berg JM, Lippard SJ. Bioinorganic chemistry. Curr Opin Chem Biol 2004. [DOI: 10.1016/j.cbpa.2004.02.014] [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: 10/26/2022]
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Fields S, Morimoto RI, Berg JM, Zakian VA, Reyes GR. New Members Appointed to NAGMS Council. J Investig Med 2004. [DOI: 10.1177/108155890405200404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
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Affiliation(s)
- Derek Jantz
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, USA
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Berkovits-Cymet HJ, Amann BT, Berg JM. Solution Structure of a CCHHC Domain of Neural Zinc Finger Factor-1 and Its Implications for DNA Binding. Biochemistry 2004; 43:898-903. [PMID: 14744132 DOI: 10.1021/bi035159d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure of a CCHHC zinc-binding domain from neural zinc finger factor-1 (NZF-1) has been determined in solution though the use of NMR methods. This domain is a member of a family of domains that have the Cys-X(4)-Cys-X(4)-His-X(7)-His-X(5)-Cys consensus sequence. The structure determination reveals a novel fold based around a zinc(II) ion coordinated to three Cys residues and the second of the two conserved His residues. The other His residue is stacked between the metal-coordinated His residue and a relatively conserved aromatic residue. Analysis of His to Gln sequence variants reveals that both His residues are required for the formation of a well-defined structure, but neither is required for high-affinity metal binding at a tetrahedral site. The structure suggests that a two-domain protein fragment and a double-stranded DNA binding site may interact with a common two-fold axis relating the two domains and the two half-sites of the DNA-inverted repeat.
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Affiliation(s)
- Holly J Berkovits-Cymet
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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Berg JM. Jeremy M. Berg, PhD, Named New Director of National Institute of General Medical Sciences. J Investig Med 2004. [DOI: 10.1177/108155890405200107] [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: 01/09/2023]
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Michel SL, Amann BT, Guerrerio AL, Berg JM. Regulation of tumor necrosis factor alpha (TNFα) mRNA by NUP-475, a novel zinc binding protein. J Inorg Biochem 2003. [DOI: 10.1016/s0162-0134(03)80524-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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