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Xu J, Park KJ, Rehrauer WM, Weisman PS. Mesonephric-like adenocarcinoma of the ovary with squamoid morular metaplasia, aberrant β-catenin expression, and concurrent FGFR2 and CTNNB1 mutations: a case report. Virchows Arch 2024; 484:147-150. [PMID: 36856760 DOI: 10.1007/s00428-023-03522-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023]
Abstract
In general, endometrioid-defining features such as squamoid morular metaplasia are not thought to be associated with mesonephric adenocarcinoma (MA) and mesonephric-like adenocarcinoma (MLA). Here, we report a case of FGFR2-mutated ovarian MLA with squamoid morular metaplasia accompanied by aberrant nuclear and cytoplasmic β-catenin expression and CTNNB1 mutation. Histologically, the tumor showed classical MLA histology, including well-formed glands with intraluminal eosinophilic secretions and cells with papillary thyroid carcinoma-like nuclei. Squamoid morular metaplasia was intimately associated with the tumor. Glandular epithelial elements, including those immediately associated with the squamoid morules, were negative for ER, but positive for both GATA3 and PAX8; aberrant β-catenin expression was limited to the squamoid morules. This case illustrates the ability of mesonephric neoplasia to exhibit histological features previously thought to be restricted to an endometrioid phenotype.
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Affiliation(s)
- Jin Xu
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Kay J Park
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William M Rehrauer
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Paul S Weisman
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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2
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Rehrauer WM, Yang DT. Laboratory-Developed Tests: A Critical Bridge During the COVID-19 Pandemic. WMJ 2023; 122:432-433. [PMID: 38180940] [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: 01/07/2024]
Affiliation(s)
- William M Rehrauer
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health and University of Wisconsin Hospitals and Clinics, Madison, Wisconsin
| | - David T Yang
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health and University of Wisconsin Hospitals and Clinics, Madison, Wisconsin,
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3
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Feichtinger S, Lazar AA, Luebbe MA, Accola MA, Jung-Hynes BD, Anderson PJ, Koglin KM, Schliesman KS, Ehlenbach W, Smith J, Chen DJ, Rehrauer WM, Bailey AL. Case report: isolation of Hydrogenophaga from septic blood culture following near-death drowning in lakewater. Access Microbiol 2023; 5:000533.v4. [PMID: 37841090 PMCID: PMC10569664 DOI: 10.1099/acmi.0.000533.v4] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 08/14/2023] [Indexed: 10/17/2023] Open
Abstract
A patient suffered a non-fatal wet drowning in a freshwater lake and developed bacteraemia several days later. Blood culture grew a Gram-negative rod that could not be identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). 16S ribosomal RNA sequencing of the isolate identified the microbe as Hydrogenophaga laconesensis - an environmental microbe commonly found in freshwater. The recovery of multiple pathogenic micro-organisms (although not H. laconesensis ) from culture of respiratory specimens prompted the initiation of antibiotic therapy with cefepime and, later, vancomycin. The patient's clinical course gradually improved over the course of 2 weeks and she was ultimately discharged home with minimal sequelae. To our knowledge, this is the first evidence of human infection with bacteria in the genus Hydrogenophaga . Hydrogenophaga may be considered in cases of freshwater near-drowning, and MALDI-TOF MS databases should be updated to include H. laconesensis .
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Affiliation(s)
- Stuart Feichtinger
- Department of Anesthesiology, Division of Critical Care, University of Wisconsin–Madison School of Medicine and Public Health, Madison, WI, USA
| | - Angela A. Lazar
- University of Wisconsin Hospitals and Clinics, Clinical Laboratories, Madison, WI, USA
| | - Megan A. Luebbe
- University of Wisconsin Hospitals and Clinics, Clinical Laboratories, Madison, WI, USA
| | - Molly A. Accola
- University of Wisconsin Hospitals and Clinics, Clinical Laboratories, Madison, WI, USA
| | | | - Patti J. Anderson
- University of Wisconsin Hospitals and Clinics, Clinical Laboratories, Madison, WI, USA
| | - Kelly M. Koglin
- University of Wisconsin Hospitals and Clinics, Clinical Laboratories, Madison, WI, USA
| | - Karen S. Schliesman
- University of Wisconsin Hospitals and Clinics, Clinical Laboratories, Madison, WI, USA
| | - William Ehlenbach
- Department of Medicine, University of Wisconsin–Madison School of Medicine and Public Health, Madison, WI, USA
| | - Jeannina Smith
- Department of Medicine, University of Wisconsin–Madison School of Medicine and Public Health, Madison, WI, USA
| | - Derrick J. Chen
- University of Wisconsin Hospitals and Clinics, Clinical Laboratories, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison School of Medicine and Public Health, Madison, WI, USA
| | - William M. Rehrauer
- University of Wisconsin Hospitals and Clinics, Clinical Laboratories, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison School of Medicine and Public Health, Madison, WI, USA
| | - Adam L. Bailey
- University of Wisconsin Hospitals and Clinics, Clinical Laboratories, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison School of Medicine and Public Health, Madison, WI, USA
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4
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Gormley JP, Selvaggi SM, Rehrauer WM, Kucher ET. A simplified molecular method to detect high-risk HPV using the Aptima HPV assay on head and neck FNA smears. Cancer Cytopathol 2023; 131:171-178. [PMID: 36287090 DOI: 10.1002/cncy.22662] [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: 06/23/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Fine-needle aspiration is used as a diagnostic tool in head and neck oropharyngeal squamous cell carcinoma and its metastases. Prognosis and treatment rely on the presence or absence of the human papilloma virus. The purpose of this study was to validate the performance of the Aptima HPV assay using Hema-Diff stained fine-needle aspiration smears in the diagnosis of human papilloma virus-related oropharyngeal squamous cell carcinoma using a simplified method to obtain tumor cells for testing. METHODS Patients with a diagnosis of squamous cell carcinoma and positive p16 immunohistochemical staining were identified. Aptima Specimen Transport Media was used to remove tumor cells from the Hema-Diff stained slides using a moistened swab. The selected cells were tested for high risk-human papilloma virus using the Aptima HPV assay and Aptima HPV 16 18/45 genotype assay. The results were compared with the p16 immunohistochemical staining of the related cell block and surgical specimens. RESULTS Twenty-one of the 21 (100%) p16-positive cases were found to be positive for high risk-human papilloma virus, whereas 20 of 21 (95%) negative cases were found to be negative for high risk-human papilloma virus using the Aptima HPV assay. CONCLUSION The Aptima HPV assay can be used to detect high-risk human papilloma virus in Hema-Diff stained fine-needle aspiration smears of oropharyngeal squamous cell carcinoma with a sensitivity of 100% and a specificity of 95%. This provides a valuable alternative to p16 immunohistochemical staining of cell block sections that often lack appropriate numbers of tumor cells.
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Affiliation(s)
- Joseph P Gormley
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Suzanne M Selvaggi
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - William M Rehrauer
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Erek T Kucher
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
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5
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Torio EA, Ressler VT, Kincaid VA, Hurst R, Hall MP, Encell LP, Zimmerman K, Forsyth SK, Rehrauer WM, Accola MA, Hsu CC, Machleidt T, Dart ML. Development of a rapid, simple, and sensitive point-of-care technology platform utilizing ternary NanoLuc. Front Microbiol 2022; 13:970233. [PMID: 36386626 PMCID: PMC9643700 DOI: 10.3389/fmicb.2022.970233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/06/2022] [Indexed: 12/02/2022] Open
Abstract
Point-of-care tests are highly valuable in providing fast results for medical decisions for greater flexibility in patient care. Many diagnostic tests, such as ELISAs, that are commonly used within clinical laboratory settings require trained technicians, laborious workflows, and complex instrumentation hindering their translation into point-of-care applications. Herein, we demonstrate the use of a homogeneous, bioluminescent-based, split reporter platform that enables a simple, sensitive, and rapid method for analyte detection in clinical samples. We developed this point-of-care application using an optimized ternary, split-NanoLuc luciferase reporter system that consists of two small reporter peptides added as appendages to analyte-specific affinity reagents. A bright, stable bioluminescent signal is generated as the affinity reagents bind to the analyte, allowing for proximity-induced complementation between the two reporter peptides and the polypeptide protein, in addition to the furimazine substrate. Through lyophilization of the stabilized reporter system with the formulated substrate, we demonstrate a shelf-stable, all-in-one, add-and-read analyte-detection system for use in complex sample matrices at the point-of-care. We highlight the modularity of this platform using two distinct SARS-CoV-2 model systems: SARS-CoV-2 N-antigen detection for active infections and anti-SARS-CoV-2 antibodies for immunity status detection using chemically conjugated or genetically fused affinity reagents, respectively. This technology provides a simple and standardized method to develop rapid, robust, and sensitive analyte-detection assays with flexible assay formatting making this an ideal platform for research, clinical laboratory, as well as point-of-care applications utilizing a simple handheld luminometer.
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Affiliation(s)
| | | | | | - Robin Hurst
- Promega Corporation, Madison, WI, United States
| | - Mary P Hall
- Promega Corporation, Madison, WI, United States
| | | | | | | | - William M Rehrauer
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
- University of Wisconsin Hospital and Clinics, Clinical Laboratories, Madison, WI, United States
| | - Molly A Accola
- University of Wisconsin Hospital and Clinics, Clinical Laboratories, Madison, WI, United States
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6
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Matson DR, Accola MA, Henderson L, Shao X, Frater-Rubsam L, Horner VL, Rehrauer WM, Weisman P, Xu J. A "Null" Pattern of p16 Immunostaining in Endometrial Serous Carcinoma: An Under-recognized and Important Aberrant Staining Pattern. Int J Gynecol Pathol 2022; 41:378-388. [PMID: 34380970 PMCID: PMC8831662 DOI: 10.1097/pgp.0000000000000817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The ability to distinguish endometrial serous carcinoma (SC) from high-grade endometrioid adenocarcinoma is of great importance given their differences in prognosis and management. In practice, this distinction typically relies upon the use of a focused immunohistochemical panel including p53, p16, and mismatch repair proteins. The expression of p16 is characteristically strong and diffuse in SCs, and weak and/or patchy in many high-grade endometrioid adenocarcinomas. Here, we report a subset of SCs that are entirely negative for p16 immunostaining, a pattern we refer to as "p16 null." This pattern was identified in 2 of 63 cases of SC diagnosed at our institution-1 with histologically classic features and 1 with ambiguous high-grade histologic features. These tumors otherwise showed a SC signature by immunohistochemical and demonstrated an SC pattern of genetic mutations. No mutation in the gene for p16, cyclin-dependent kinase inhibitor 2A (CDKN2A), was identified in either case. However, molecular correlates for the absent p16 expression were present, including homozygous deletion of CDKN2A in one case and hemizygous deletion of CDKN2A with promotor hypermethylation of the remaining allele in the other case. To our knowledge, this constitutes the first report conclusively demonstrating the existence of a small subset of SCs that are completely negative by p16 immunohistochemistry, and the molecular lesions responsible for this pattern. In the context of an otherwise clinically and histologically classic example of SC, we endorse this "null" p16 staining pattern as an alternative aberrant staining pattern that should not deter one from committing to this diagnosis.
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Affiliation(s)
- Daniel R. Matson
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, 600 Highland Ave, Madison, WI 53792
| | - Molly A. Accola
- UW Health Clinical Laboratories, University of Wisconsin Hospitals and Clinics, 600 Highland Avenue, Madison, WI, 53792
| | - Les Henderson
- Wisconsin State Laboratory of Hygiene, 460 Henry Mall, Madison, WI 53706
| | - Xiangqiang Shao
- Wisconsin State Laboratory of Hygiene, 460 Henry Mall, Madison, WI 53706
| | - Leah Frater-Rubsam
- Wisconsin State Laboratory of Hygiene, 460 Henry Mall, Madison, WI 53706
| | - Vanessa L. Horner
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, 600 Highland Ave, Madison, WI 53792
- Wisconsin State Laboratory of Hygiene, 460 Henry Mall, Madison, WI 53706
| | - William M. Rehrauer
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, 600 Highland Ave, Madison, WI 53792
| | - Paul Weisman
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, 600 Highland Ave, Madison, WI 53792
| | - Jin Xu
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, 600 Highland Ave, Madison, WI 53792
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7
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Ramuta MD, Newman CM, Brakefield SF, Stauss MR, Wiseman RW, Kita-Yarbro A, O'Connor EJ, Dahal N, Lim A, Poulsen KP, Safdar N, Marx JA, Accola MA, Rehrauer WM, Zimmer JA, Khubbar M, Beversdorf LJ, Boehm EC, Castañeda D, Rushford C, Gregory DA, Yao JD, Bhattacharyya S, Johnson MC, Aliota MT, Friedrich TC, O'Connor DH, O'Connor SL. SARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings. medRxiv 2022. [PMID: 35378751 PMCID: PMC8978944 DOI: 10.1101/2022.03.29.22272716] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two years after the emergence of SARS-CoV-2, there is still a need for better ways to assess the risk of transmission in congregate spaces. We deployed active air samplers to monitor the presence of SARS-CoV-2 in real-world settings across communities in the Upper Midwestern states of Wisconsin and Minnesota. Over 29 weeks, we collected 527 air samples from 15 congregate settings and detected 106 SARS-CoV-2 positive samples, demonstrating SARS-CoV-2 can be detected in air collected from daily and weekly sampling intervals. We expanded the utility of air surveillance to test for 40 other respiratory pathogens. Surveillance data revealed differences in timing and location of SARS-CoV-2 and influenza A virus detection in the community. In addition, we obtained SARS-CoV-2 genome sequences from air samples to identify variant lineages. Collectively, this shows air surveillance is a scalable, cost-effective, and high throughput alternative to individual testing for detecting respiratory pathogens in congregate settings.
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8
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Braun KM, Moreno GK, Buys A, Somsen ED, Bobholz M, Accola MA, Anderson L, Rehrauer WM, Baker DA, Safdar N, Lepak AJ, O’Connor DH, Friedrich TC. Viral Sequencing to Investigate Sources of SARS-CoV-2 Infection in US Healthcare Personnel. Clin Infect Dis 2021; 73:e1329-e1336. [PMID: 33857303 PMCID: PMC8083259 DOI: 10.1093/cid/ciab281] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Healthcare personnel (HCP) are at increased risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We posit that current infection control guidelines generally protect HCP from SARS-CoV-2 infection in a healthcare setting. METHODS In this retrospective case series, we used viral genomics to investigate the likely source of SARS-CoV-2 infection in HCP at a major academic medical institution in the Upper Midwest of the United States between 25 March and 27 December 2020. We obtained limited epidemiological data through informal interviews and review of the electronic health record and combined this information with healthcare-associated viral sequences and viral sequences collected in the broader community to infer the most likely source of infection in HCP. RESULTS We investigated SARS-CoV-2 infection clusters involving 95 HCP and 137 possible patient contact sequences. The majority of HCP infections could not be linked to a patient or coworker (55 of 95 [57.9%]) and were genetically similar to viruses circulating concurrently in the community. We found that 10.5% of HCP infections (10 of 95) could be traced to a coworker. Strikingly, only 4.2% (4 of 95) could be traced to a patient source. CONCLUSIONS Infections among HCP add further strain to the healthcare system and put patients, HCP, and communities at risk. We found no evidence for healthcare-associated transmission in the majority of HCP infections evaluated. Although we cannot rule out the possibility of cryptic healthcare-associated transmission, it appears that HCP most commonly become infected with SARS-CoV-2 via community exposure. This emphasizes the ongoing importance of mask wearing, physical distancing, robust testing programs, and rapid distribution of vaccines.
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Affiliation(s)
- Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Ashley Buys
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Elizabeth D Somsen
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Max Bobholz
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Molly A Accola
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - Laura Anderson
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - William M Rehrauer
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - David A Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Nasia Safdar
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Alexander J Lepak
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - David H O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
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9
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Newman CM, Ramuta MD, McLaughlin MT, Wiseman RW, Karl JA, Dudley DM, Stauss MR, Maddox RJ, Weiler AM, Bliss MI, Fauser KN, Haddock LA, Shortreed CG, Haj AK, Accola MA, Heffron AS, Bussan HE, Reynolds MR, Harwood OE, Moriarty RV, Stewart LM, Crooks CM, Prall TM, Neumann EK, Somsen ED, Burmeister CB, Hall KL, Rehrauer WM, Friedrich TC, O'Connor SL, O'Connor DH. Initial Evaluation of a Mobile SARS-CoV-2 RT-LAMP Testing Strategy. J Biomol Tech 2021; 32:137-147. [PMID: 35035293 PMCID: PMC8730517 DOI: 10.7171/jbt.21-32-03-009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) control in the United States remains hampered, in part, by testing limitations. We evaluated a simple, outdoor, mobile, colorimetric reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay workflow where self-collected saliva is tested for SARS-CoV-2 RNA. From July 16, 2020, to November 19, 2020, surveillance samples (n = 4704) were collected from volunteers and tested for SARS-CoV-2 at 5 sites. Twenty-one samples tested positive for SARS-CoV-2 by RT-LAMP; 12 were confirmed positive by subsequent quantitative reverse-transcription polymerase chain reaction (qRT-PCR) testing, whereas 8 tested negative for SARS-CoV-2 RNA, and 1 could not be confirmed because the donor did not consent to further molecular testing. We estimated the false-negative rate of the RT-LAMP assay only from July 16, 2020, to September 17, 2020 by pooling residual heat-inactivated saliva that was unambiguously negative by RT-LAMP into groups of 6 or fewer and testing for SARS-CoV-2 RNA by qRT-PCR. We observed a 98.8% concordance between the RT-LAMP and qRT-PCR assays, with only 5 of 421 RT-LAMP-negative pools (2493 total samples) testing positive in the more-sensitive qRT-PCR assay. Overall, we demonstrate a rapid testing method that can be implemented outside the traditional laboratory setting by individuals with basic molecular biology skills and that can effectively identify asymptomatic individuals who would not typically meet the criteria for symptom-based testing modalities.
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Affiliation(s)
- Christina M Newman
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Mitchell D Ramuta
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew T McLaughlin
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Roger W Wiseman
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Julie A Karl
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Dawn M Dudley
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Robert J Maddox
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Andrea M Weiler
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Mason I Bliss
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Luis A Haddock
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Cecilia G Shortreed
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Amelia K Haj
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly A Accola
- University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Anna S Heffron
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Hailey E Bussan
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew R Reynolds
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Olivia E Harwood
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Ryan V Moriarty
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Laurel M Stewart
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Chelsea M Crooks
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Trent M Prall
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Emma K Neumann
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth D Somsen
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Corrie B Burmeister
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Kristi L Hall
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - William M Rehrauer
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Thomas C Friedrich
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Shelby L O'Connor
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - David H O'Connor
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
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10
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Braun KM, Moreno GK, Wagner C, Accola MA, Rehrauer WM, Baker DA, Koelle K, O’Connor DH, Bedford T, Friedrich TC, Moncla LH. Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks. PLoS Pathog 2021; 17:e1009849. [PMID: 34424945 PMCID: PMC8412271 DOI: 10.1371/journal.ppat.1009849] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/02/2021] [Accepted: 07/29/2021] [Indexed: 02/08/2023] Open
Abstract
The emergence of divergent SARS-CoV-2 lineages has raised concern that novel variants eliciting immune escape or the ability to displace circulating lineages could emerge within individual hosts. Though growing evidence suggests that novel variants arise during prolonged infections, most infections are acute. Understanding how efficiently variants emerge and transmit among acutely-infected hosts is therefore critical for predicting the pace of long-term SARS-CoV-2 evolution. To characterize how within-host diversity is generated and propagated, we combine extensive laboratory and bioinformatic controls with metrics of within- and between-host diversity to 133 SARS-CoV-2 genomes from acutely-infected individuals. We find that within-host diversity is low and transmission bottlenecks are narrow, with very few viruses founding most infections. Within-host variants are rarely transmitted, even among individuals within the same household, and are rarely detected along phylogenetically linked infections in the broader community. These findings suggest that most variation generated within-host is lost during transmission.
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Affiliation(s)
- Katarina M. Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Gage K. Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Cassia Wagner
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Molly A. Accola
- University of Wisconsin School of Medicine and Public Health and the William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, United States of America
| | - William M. Rehrauer
- University of Wisconsin School of Medicine and Public Health and the William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, United States of America
| | - David A. Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Louise H. Moncla
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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11
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Juang DS, Juang TD, Dudley DM, Newman CM, Accola MA, Rehrauer WM, Friedrich TC, O'Connor DH, Beebe DJ. Oil immersed lossless total analysis system for integrated RNA extraction and detection of SARS-CoV-2. Nat Commun 2021; 12:4317. [PMID: 34262053 PMCID: PMC8280165 DOI: 10.1038/s41467-021-24463-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 06/10/2021] [Indexed: 12/03/2022] Open
Abstract
The COVID-19 pandemic exposed difficulties in scaling current quantitative PCR (qPCR)-based diagnostic methodologies for large-scale infectious disease testing. Bottlenecks include lengthy multi-step processes for nucleic acid extraction followed by qPCR readouts, which require costly instrumentation and infrastructure, as well as reagent and plastic consumable shortages stemming from supply chain constraints. Here we report an Oil Immersed Lossless Total Analysis System (OIL-TAS), which integrates RNA extraction and detection onto a single device that is simple, rapid, cost effective, and requires minimal supplies and infrastructure to perform. We validated the performance of OIL-TAS using contrived SARS-CoV-2 viral particle samples and clinical nasopharyngeal swab samples. OIL-TAS showed a 93% positive predictive agreement (n = 57) and 100% negative predictive agreement (n = 10) with clinical SARS-CoV-2 qPCR assays in testing clinical samples, highlighting its potential to be a faster, cheaper, and easier-to-deploy alternative for infectious disease testing. Bottlenecks in qPCR-based COVID-19 diagnostics include the lengthy multistep process and reagent shortages. Here the authors report OIL-TAS which integrates RNA extraction and detection into a single device.
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Affiliation(s)
- Duane S Juang
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Terry D Juang
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Dawn M Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Christina M Newman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly A Accola
- UW Health Clinical Laboratories, University of Wisconsin Hospital and Clinics, Madison, WI, USA
| | - William M Rehrauer
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.,UW Health Clinical Laboratories, University of Wisconsin Hospital and Clinics, Madison, WI, USA
| | - Thomas C Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.,Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - David J Beebe
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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12
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Cordes AK, Rehrauer WM, Accola MA, Wölk B, Hilfrich B, Heim A. Fully automated detection and differentiation of pandemic and endemic coronaviruses (NL63, 229E, HKU1, OC43 and SARS-CoV-2) on the hologic panther fusion. J Med Virol 2021; 93:4438-4445. [PMID: 33350484 DOI: 10.1002/jmv.26749] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 12/18/2022]
Abstract
The hologic panther fusion (PF) platform provides fully automated CE marked diagnostics for respiratory viruses, including the recently discovered severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) by a transcription mediated amplification (TMA) assay, but not for the endemic human coronaviruses (hCoV). Therefore, a laboratory developed test (LDT) comprising a multiplexed reverse transcription polymerase chain reaction (RT-PCR) protocol that detects and differentiates the four hCoV NL63, 229E, HKU1, and OC43 was adapted on the PF. The novel CE marked Aptima SARS-CoV-2 TMA and the LDT for hCoV were validated with 321 diagnostic specimens from the upper and lower respiratory tract in comparison to two SARS-CoV-2 RT-PCRs (PF E-gene RT-PCR and genesig RT-PCR, 157 specimens) or the R-GENE hCoV/hParaFlu RT-PCR (164 specimens), respectively. For the endemic hCoV, results were 96.3% concordant with two specimens discordantly positive in the PF and four specimens discordantly positive in the R-GENE assay. All discordantly positive samples had Ct values between 33 and 39. The PF hCoV LDT identified 23 hCoV positive specimens as NL63, 15 as 229E, 15 as HKU1, and 25 as OC43. The Aptima SARS-CoV-2 TMA gave 99.4% concordant results compared to the consensus results with a single specimen discordantly positive. Moreover, 36 samples from proficiency testing panels were detected and typed correctly by both novel methods. In conclusion, the SARS-CoV-2 TMA and the LDT for hCoV enhanced the diagnostic spectrum of the PF for all coronaviruses circulating globally for a multitude of diagnostic materials from the upper and lower respiratory tract.
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Affiliation(s)
- Anne K Cordes
- Institute of Virology, Medical School Hannover, Hannover, Germany
| | - William M Rehrauer
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Molly A Accola
- Molecular Diagnostics, Clinical Labs, University of Wisconsin Hospital, Madison, Wisconsin, USA
| | - Benno Wölk
- LADR Medical Laboratory Dr Kramer and Colleagues, Geesthacht, Germany
| | | | - Albert Heim
- Institute of Virology, Medical School Hannover, Hannover, Germany
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13
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Newman CM, Ramuta MD, McLaughlin MT, Wiseman RW, Karl JA, Dudley DM, Stauss MR, Maddox RJ, Weiler AM, Bliss MI, Fauser KN, Haddock LA, Shortreed CG, Haj AK, Accola MA, Heffron AS, Bussan HE, Reynolds MR, Harwood OE, Moriarty RV, Stewart LM, Crooks CM, Prall TM, Neumann EK, Somsen ED, Burmeister CB, Hall KL, Rehrauer WM, Friedrich TC, O’Connor SL, O’Connor DH. Initial evaluation of a mobile SARS-CoV-2 RT-LAMP testing strategy. medRxiv 2021:2020.07.28.20164038. [PMID: 33655260 PMCID: PMC7924282 DOI: 10.1101/2020.07.28.20164038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) control in the United States remains hampered, in part, by testing limitations. We evaluated a simple, outdoor, mobile, colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay workflow where self-collected saliva is tested for SARS-CoV-2 RNA. From July 16 to November 19, 2020, 4,704 surveillance samples were collected from volunteers and tested for SARS-CoV-2 at 5 sites. A total of 21 samples tested positive for SARS-CoV-2 by RT-LAMP; 12 were confirmed positive by subsequent quantitative reverse-transcription polymerase chain reaction (qRT-PCR) testing, while 8 were negative for SARS-CoV-2 RNA, and 1 could not be confirmed because the donor did not consent to further molecular testing. We estimated the RT-LAMP assay's false-negative rate from July 16 to September 17, 2020 by pooling residual heat-inactivated saliva that was unambiguously negative by RT-LAMP into groups of 6 or less and testing for SARS-CoV-2 RNA by qRT-PCR. We observed a 98.8% concordance between the RT-LAMP and qRT-PCR assays, with only 5 of 421 RT-LAMP negative pools (2,493 samples) testing positive in the more sensitive qRT-PCR assay. Overall, we demonstrate a rapid testing method that can be implemented outside the traditional laboratory setting by individuals with basic molecular biology skills and can effectively identify asymptomatic individuals who would not typically meet the criteria for symptom-based testing modalities.
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Affiliation(s)
- Christina M. Newman
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Mitchell D. Ramuta
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew T. McLaughlin
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Roger W. Wiseman
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Julie A. Karl
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Dawn M. Dudley
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | - Mason I. Bliss
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Luis A. Haddock
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Cecilia G. Shortreed
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Amelia K. Haj
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly A. Accola
- University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Anna S. Heffron
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Hailey E. Bussan
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew R. Reynolds
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Olivia E. Harwood
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Ryan V. Moriarty
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Laurel M. Stewart
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Chelsea M. Crooks
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Trent M. Prall
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Emma K. Neumann
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth D. Somsen
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Corrie B. Burmeister
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Kristi L. Hall
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - William M. Rehrauer
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Thomas C. Friedrich
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Shelby L. O’Connor
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - David H. O’Connor
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
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14
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Dudley DM, Newman CM, Weiler AM, Ramuta MD, Shortreed CG, Heffron AS, Accola MA, Rehrauer WM, Friedrich TC, O’Connor DH. Optimizing direct RT-LAMP to detect transmissible SARS-CoV-2 from primary nasopharyngeal swab samples. PLoS One 2020; 15:e0244882. [PMID: 33382861 PMCID: PMC7775089 DOI: 10.1371/journal.pone.0244882] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/17/2020] [Indexed: 12/31/2022] Open
Abstract
SARS-CoV-2 testing is crucial to controlling the spread of this virus, yet shortages of nucleic acid extraction supplies and other key reagents have hindered the response to COVID-19 in the US. Several groups have described loop-mediated isothermal amplification (LAMP) assays for SARS-CoV-2, including testing directly from nasopharyngeal swabs and eliminating the need for reagents in short supply. Frequent surveillance of individuals attending work or school is currently unavailable to most people but will likely be necessary to reduce the ~50% of transmission that occurs when individuals are nonsymptomatic. Here we describe a fluorescence-based RT-LAMP test using direct nasopharyngeal swab samples and show consistent detection in clinically confirmed primary samples with a limit of detection (LOD) of ~625 copies/μl, approximately 100-fold lower sensitivity than qRT-PCR. While less sensitive than extraction-based molecular methods, RT-LAMP without RNA extraction is fast and inexpensive. Here we also demonstrate that adding a lysis buffer directly into the RT-LAMP reaction improves the sensitivity of some samples by approximately 10-fold. Furthermore, purified RNA in this assay achieves a similar LOD to qRT-PCR. These results indicate that high-throughput RT-LAMP testing could augment qRT-PCR in SARS-CoV-2 surveillance programs, especially while the availability of qRT-PCR testing and RNA extraction reagents is constrained.
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Affiliation(s)
- Dawn M. Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Christina M. Newman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Mitchell D. Ramuta
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Cecilia G. Shortreed
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Anna S. Heffron
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Molly A. Accola
- University of Wisconsin Hospitals and Clinics, Madison, Wisconsin, United States of America
| | - William M. Rehrauer
- University of Wisconsin Hospitals and Clinics, Madison, Wisconsin, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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15
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Moreno GK, Braun KM, Riemersma KK, Martin MA, Halfmann PJ, Crooks CM, Prall T, Baker D, Baczenas JJ, Heffron AS, Ramuta M, Khubbar M, Weiler AM, Accola MA, Rehrauer WM, O'Connor SL, Safdar N, Pepperell CS, Dasu T, Bhattacharyya S, Kawaoka Y, Koelle K, O'Connor DH, Friedrich TC. Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread. Nat Commun 2020; 11:5558. [PMID: 33144575 PMCID: PMC7609670 DOI: 10.1038/s41467-020-19346-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/06/2020] [Indexed: 12/25/2022] Open
Abstract
Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties following the statewide "Safer at Home" order, which went into effect 25 March 2020. Our results suggest patterns of SARS-CoV-2 transmission may vary substantially even in nearby communities. Understanding these local patterns will enable better targeting of public health interventions.
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Affiliation(s)
- Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Kasen K Riemersma
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael A Martin
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Chelsea M Crooks
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Trent Prall
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - David Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - John J Baczenas
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Anna S Heffron
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Mitchell Ramuta
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Manjeet Khubbar
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, USA
| | - Andrea M Weiler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly A Accola
- University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- The William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - William M Rehrauer
- University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- The William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Shelby L O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Nasia Safdar
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Caitlin S Pepperell
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Trivikram Dasu
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, USA
| | | | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Katia Koelle
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA.
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16
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Moreno GK, Braun KM, Riemersma KK, Martin MA, Halfmann PJ, Crooks CM, Prall T, Baker D, Baczenas JJ, Heffron AS, Ramuta M, Khubbar M, Weiler AM, Accola MA, Rehrauer WM, O'Connor SL, Safdar N, Pepperell CS, Dasu T, Bhattacharyya S, Kawaoka Y, Koelle K, O'Connor DH, Friedrich TC. Distinct patterns of SARS-CoV-2 transmission in two nearby communities in Wisconsin, USA. medRxiv 2020:2020.07.09.20149104. [PMID: 32676620 PMCID: PMC7359545 DOI: 10.1101/2020.07.09.20149104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties, and limited viral transmission between counties, following the statewide Safer-at-Home public health order, which went into effect 25 March 2020. Our results suggest that early containment efforts suppressed the spread of SARS-CoV-2 within Wisconsin.
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Affiliation(s)
- Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Kasen K Riemersma
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Michael A Martin
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, United States of America
- Department of Biology, Emory University, Atlanta, GA, United States of America
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Chelsea M Crooks
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Trent Prall
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - David Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - John J Baczenas
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Anna S Heffron
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Mitchell Ramuta
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Manjeet Khubbar
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, United States of America
| | - Andrea M Weiler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Molly A Accola
- University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of 26 America and the William S. Middleton Memorial Veterans Hospital
| | - William M Rehrauer
- University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of 26 America and the William S. Middleton Memorial Veterans Hospital
| | - Shelby L O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Nasia Safdar
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of 28 Medicine and Public Health, Madison, WI
| | - Caitlin S Pepperell
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of 28 Medicine and Public Health, Madison, WI
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 30 Madison, WI, United States of America
| | - Trivikram Dasu
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, United States of America
| | - Sanjib Bhattacharyya
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, United States of America
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Katia Koelle
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, United States of America
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
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17
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Abstract
Patient: Male, 70-year-old Final Diagnosis: Actinomucor elegans Symptoms: Bleeding • dizziness • eschar Medication: — Clinical Procedure: Culture • MALDI • sequencing • tooth extraction Specialty: Infectious Diseases
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Affiliation(s)
- Phillip A Kubica
- Department of Pathology and Laboratory Medicine, University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - William M Rehrauer
- Department of Pathology and Laboratory Medicine, University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Alana K Sterkel
- Department of Pathology and Laboratory Medicine, University of Wisconsin Hospitals and Clinics, Madison, WI, USA
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18
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Stoffel M, Rysavy MB, Rose SL, Laffin J, Rehrauer WM, Reza Hafez G, Flynn C. Multiple concurrent unusual neoplasms presenting in a patient with familial adenomatous polyposis: A case report and review of the literature. Human Pathology: Case Reports 2018. [DOI: 10.1016/j.ehpc.2018.07.004] [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: 10/28/2022] Open
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19
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Matson DR, Accola MA, Rehrauer WM, Huang W. An atypical case of Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC)-associated renal cell carcinoma identified by next-generation sequencing. Human Pathology: Case Reports 2018. [DOI: 10.1016/j.ehpc.2017.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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20
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Hartley CP, Mahajan AM, Selvaggi SM, Rehrauer WM. FNA smears of pancreatic ductal adenocarcinoma are superior to formalin-fixed paraffin-embedded tissue as a source of DNA: Comparison of targeted KRAS amplification and genotyping in matched preresection and postresection samples. Cancer Cytopathol 2017; 125:838-847. [PMID: 29024530 DOI: 10.1002/cncy.21935] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/01/2017] [Accepted: 09/13/2017] [Indexed: 12/24/2022]
Abstract
BACKGROUND The current study was conducted to compare DNA yield, including normalization to nuclear area, DNA amplification functionality, and detection of KRAS mutations between matched fine-needle aspiration (FNA) specimens and pancreatic resections diagnostic of pancreatic ductal adenocarcinoma. METHODS A retrospective sample of 30 matched single FNA smears and macrodissected formalin-fixed, paraffin-embedded (FFPE) curls (2 5-μm curls) were compared by measuring the following: nuclear area (via digital image analysis), DNA yield (via NanoDrop spectrophotometry and Quantus fluorometry), and polymerase chain reaction threshold cycles for KRAS amplifications. Variants in KRAS codons 12/13 and 61 were detected by fluorescent melt curve analyses, followed by Sanger DNA sequencing. RESULTS Despite a similar nuclear area, FNA smears yielded greater DNA per nuclear area via 2 DNA quantification methods. KRAS codon 12 mutations were detected in 23 of 30 FNA specimens (77%) compared with 17 of 30 matched FFPE specimens (57%), for a concordance rate of 74%. No KRAS codon 13 or 61 mutations were detected. CONCLUSIONS FNA specimens are a more optimal source of DNA, and represent an important resource in the preresection and postresection molecular analysis of pancreatic ductal adenocarcinoma. Cancer Cytopathol 2017;125:838-47. © 2017 American Cancer Society.
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Affiliation(s)
- Christopher P Hartley
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Aparna M Mahajan
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Suzanne M Selvaggi
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - William M Rehrauer
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
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21
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Matson DR, Accola MA, Rehrauer WM, Corliss RF. Fatal Myocarditis Following Treatment with the PD-1 Inhibitor Nivolumab. J Forensic Sci 2017; 63:954-957. [DOI: 10.1111/1556-4029.13633] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/06/2017] [Accepted: 08/07/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Daniel R. Matson
- Department of Pathology and Laboratory Medicine; University of Wisconsin School of Medicine and Public Health; UWHC - Rm A4/204 - 3224 600 Highland Avenue Madison WI 53792
| | - Molly A. Accola
- University of Wisconsin Hospitals and Clinics; UWHC - Mailcode 2472 600 Highland Avenue Madison WI 53792
| | - William M. Rehrauer
- University of Wisconsin School of Medicine and Public Health; UWHC - Mailcode 2472 600 Highland Avenue Madison WI 53792
| | - Robert F. Corliss
- University of Wisconsin School of Medicine and Public Health; UWHC - L5/151 CSC - 8550 600 Highland Avenue Madison WI 53792
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22
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Burkard ME, Deming DA, Parsons BM, Kenny PA, Schuh MR, Leal T, Uboha N, Lang JM, Thompson MA, Warren R, Bauman J, Mably MS, Laffin J, Paschal CR, Lager AM, Lee K, Matkowskyj KA, Buehler DG, Rehrauer WM, Kolesar J. Implementation and Clinical Utility of an Integrated Academic-Community Regional Molecular Tumor Board. JCO Precis Oncol 2017; 1:1600022. [PMID: 32913980 DOI: 10.1200/po.16.00022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Purpose Precision oncology develops and implements evidence-based personalized therapies that are based on specific genetic targets within each tumor. However, a major challenge that remains is the provision of a standardized, up-to-date, and evidenced-based precision medicine initiative across a geographic region. Materials and Methods We developed a statewide molecular tumor board that integrates academic and community oncology practices. The Precision Medicine Molecular Tumor Board (PMMTB) has three components: a biweekly Web-based teleconference tumor board meeting provided as a free clinical service, an observational research registry, and a monthly journal club to establish and revise evidence-based guidelines for off-label therapies. The PMMTB allows for flexible and rapid implementation of treatment, uniformity in practice, and the ability to track outcomes. Results We describe the implementation of the PMMTB and its first year of activity. Seventy-seven patient cases were presented, 48 were enrolled in a registry, and 38 had recommendations and clinical follow-up. The 38 subjects had diverse solid tumors (lung, 45%; GI, 21%; breast, 13%; other, 21%). Of these subjects, targeted therapy was recommended for 32 (84%). Clinical trials were identified for 24 subjects (63%), and nontrial targeted medicines for 16 (42%). Nine subjects (28%) received recommended therapy with a response rate of 17% (one of six) and a clinical benefit rate (partial response + stable disease) of 38% (three of eight). Although clinical trials often were identified, patients rarely enrolled. Conclusion The PMMTB provides a model for a regional molecular tumor board with clinical utility. This work highlights the need for outcome registries and improved access to clinical trials to pragmatically implement precision oncology.
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Affiliation(s)
- Mark E Burkard
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Dustin A Deming
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Benjamin M Parsons
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Paraic A Kenny
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Marissa R Schuh
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Ticiana Leal
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Nataliya Uboha
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Joshua M Lang
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Michael A Thompson
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Ruth Warren
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Jordan Bauman
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Mary S Mably
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Jennifer Laffin
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Catherine R Paschal
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Angela M Lager
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Kristy Lee
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Kristina A Matkowskyj
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Darya G Buehler
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - William M Rehrauer
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
| | - Jill Kolesar
- , , , , , , , , , , , , , , and , University of Wisconsin-Madison; , University of Wisconsin School of Medicine and Public Health; , UW Health; , William S. Middleton VA Medical Center, Madison; and , Gundersen Health System, La Crosse; , Aurora Health Care, Milwaukee; and , Green Bay Oncology, Green Bay, WI
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23
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Matson DR, Xu J, Huffman L, Barroilhet L, Accola M, Rehrauer WM, Weisman P. KRAS and GNAS Co-Mutation in Metastatic Low-Grade Appendiceal Mucinous Neoplasm (LAMN) to the Ovaries: A Practical Role for Next-Generation Sequencing. Am J Case Rep 2017; 18:558-562. [PMID: 28526814 PMCID: PMC5447665 DOI: 10.12659/ajcr.903581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Patient: Female, 49 Final Diagnosis: Metastatic LAMN Symptoms: Abdominal discomfort Medication: — Clinical Procedure: Laparoscopic total abdominal hysterectomy • bilateral salpingo-oophorectomy • complete supracolic omentectomy • appendectomy Specialty: Oncology
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Affiliation(s)
- Daniel R Matson
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Jin Xu
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Laura Huffman
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Lisa Barroilhet
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Molly Accola
- University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - William M Rehrauer
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Paul Weisman
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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24
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Rosenbaum JN, Guo Z, Baus RM, Werner H, Rehrauer WM, Lloyd RV. INSM1: A Novel Immunohistochemical and Molecular Marker for Neuroendocrine and Neuroepithelial Neoplasms. Am J Clin Pathol 2015; 144:579-91. [PMID: 26386079 DOI: 10.1309/ajcpgzwxxbsnl4vd] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
OBJECTIVES Neuroendocrine neoplasms (NENs) are heterogeneous neoplasms, which are sometimes malignant, although predicting metastasis is difficult. INSM1 is a transcription factor expressed transiently in embryonic neuroendocrine (NE) tissue, thought to coordinate termination of cell division with differentiation of NE and neuroepithelial cells. In adult tissues, INSM1 has been identified in multiple tumors of NE or neuroepithelial origin but has not been thoroughly investigated as a potential neoplastic marker. METHODS We evaluated INSM1 as a semiquantitative immunohistochemical (IHC) marker for NE and neuroepithelial neoplasms and as a quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) marker for gastrointestinal NENs (GI-NENs). RESULTS Using IHC, we found in normal adult tissue that INSM1 expression was highly restricted to nuclei of NE cells and tissues. INSM1 was not detected in any adult nonneoplastic, non-NE tissue. In neoplastic tissue, INSM1 was detectable by IHC in 88.3% of 129 NEN specimens. In contrast, INSM1 was detected by IHC in only one of 27 neoplasms without a neuroepithelial or NE component. Using qRT-PCR, we evaluated INSM1 gene expression in 113 GI-NEN specimens. CONCLUSIONS INSM1 expression was significantly increased in neoplastic vs nonneoplastic tissue. Furthermore, among midgut GI-NENs, neoplasms with known metastases showed significantly higher expression than those that had not yet metastasized.
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Affiliation(s)
- Jason N Rosenbaum
- From the Department of Pathology and Laboratory Medicine, University of Wisconsin Hospital and Clinics, Madison.
| | - Zhenying Guo
- From the Department of Pathology and Laboratory Medicine, University of Wisconsin Hospital and Clinics, Madison
| | - Rebecca M Baus
- From the Department of Pathology and Laboratory Medicine, University of Wisconsin Hospital and Clinics, Madison
| | - Helen Werner
- From the Department of Pathology and Laboratory Medicine, University of Wisconsin Hospital and Clinics, Madison
| | - William M Rehrauer
- From the Department of Pathology and Laboratory Medicine, University of Wisconsin Hospital and Clinics, Madison
| | - Ricardo V Lloyd
- From the Department of Pathology and Laboratory Medicine, University of Wisconsin Hospital and Clinics, Madison
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25
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Chapman-Fredricks JR, Cioffi-Lavina M, Accola MA, Rehrauer WM, Garcia-Buitrago MT, Gomez-Fernandez C, Ganjei-Azar P, Jordà M. High-Risk Human Papillomavirus DNA Detected in Primary Squamous Cell Carcinoma of Urinary Bladder. Arch Pathol Lab Med 2013; 137:1088-93. [DOI: 10.5858/arpa.2012-0122-oa] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—We reported previously that more than one-third (37%) of primary bladder squamous cell carcinomas (SCCs) demonstrate diffuse p16 immunoreactivity independent of gender. This observation made us question whether p16 overexpression in bladder carcinoma is due to human papillomavirus (HPV)–dependent mechanisms.
Objectives.—To determine whether the presence of high-risk HPV (HR-HPV) DNA could be detected in these tumor cells.
Design.—Fourteen cases of primary bladder SCC, which were positive for p16 by immunohistochemistry, were probed for the detection of HR-HPV by in situ hybridization and the signal amplification Invader assay. Samples positive for detection of HR-HPV by Invader assay were amplified by using HR-HPV type-specific primers, and amplification products were DNA sequenced.
Results.—Detection of HR-HPV by the in situ hybridization method was negative in all cases (0 of 14). However, in 3 of 14 cases (21.4%), the presence of HR-HPV DNA was detected with the Cervista HPV HR Invader assay, which was followed by identification of genotype. All positive cases were confirmed by using HR-HPV type-specific amplification followed by DNA sequencing. Identified HR-HPV genotypes included HPV 16 (2 cases) and HPV 35 (1 case).
Conclusions.—High-risk HPV DNA is detectable in a subset of primary bladder SCCs. Based on the well-documented carcinogenic potential of HR-HPV, there is a necessity for additional studies to investigate the role of HR-HPV in bladder carcinogenesis.
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Affiliation(s)
- Jennifer Rose Chapman-Fredricks
- From the Department of Pathology & Laboratory Medicine, University of Miami, Miami, Florida (Drs Chapman-Fredricks, Cioffi-Lavina, Garcia-Buitrago, Gomez-Fernandez, Ganjei-Azar, and Jordà); the Clinical Molecular Diagnostics Laboratory, University of Wisconsin Hospital and Clinics, Madison (Dr Accola); and the Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison (Dr Rehrauer)
| | - Maureen Cioffi-Lavina
- From the Department of Pathology & Laboratory Medicine, University of Miami, Miami, Florida (Drs Chapman-Fredricks, Cioffi-Lavina, Garcia-Buitrago, Gomez-Fernandez, Ganjei-Azar, and Jordà); the Clinical Molecular Diagnostics Laboratory, University of Wisconsin Hospital and Clinics, Madison (Dr Accola); and the Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison (Dr Rehrauer)
| | - Molly A. Accola
- From the Department of Pathology & Laboratory Medicine, University of Miami, Miami, Florida (Drs Chapman-Fredricks, Cioffi-Lavina, Garcia-Buitrago, Gomez-Fernandez, Ganjei-Azar, and Jordà); the Clinical Molecular Diagnostics Laboratory, University of Wisconsin Hospital and Clinics, Madison (Dr Accola); and the Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison (Dr Rehrauer)
| | - William M. Rehrauer
- From the Department of Pathology & Laboratory Medicine, University of Miami, Miami, Florida (Drs Chapman-Fredricks, Cioffi-Lavina, Garcia-Buitrago, Gomez-Fernandez, Ganjei-Azar, and Jordà); the Clinical Molecular Diagnostics Laboratory, University of Wisconsin Hospital and Clinics, Madison (Dr Accola); and the Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison (Dr Rehrauer)
| | - Monica T. Garcia-Buitrago
- From the Department of Pathology & Laboratory Medicine, University of Miami, Miami, Florida (Drs Chapman-Fredricks, Cioffi-Lavina, Garcia-Buitrago, Gomez-Fernandez, Ganjei-Azar, and Jordà); the Clinical Molecular Diagnostics Laboratory, University of Wisconsin Hospital and Clinics, Madison (Dr Accola); and the Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison (Dr Rehrauer)
| | - Carmen Gomez-Fernandez
- From the Department of Pathology & Laboratory Medicine, University of Miami, Miami, Florida (Drs Chapman-Fredricks, Cioffi-Lavina, Garcia-Buitrago, Gomez-Fernandez, Ganjei-Azar, and Jordà); the Clinical Molecular Diagnostics Laboratory, University of Wisconsin Hospital and Clinics, Madison (Dr Accola); and the Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison (Dr Rehrauer)
| | - Parvin Ganjei-Azar
- From the Department of Pathology & Laboratory Medicine, University of Miami, Miami, Florida (Drs Chapman-Fredricks, Cioffi-Lavina, Garcia-Buitrago, Gomez-Fernandez, Ganjei-Azar, and Jordà); the Clinical Molecular Diagnostics Laboratory, University of Wisconsin Hospital and Clinics, Madison (Dr Accola); and the Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison (Dr Rehrauer)
| | - Mercè Jordà
- From the Department of Pathology & Laboratory Medicine, University of Miami, Miami, Florida (Drs Chapman-Fredricks, Cioffi-Lavina, Garcia-Buitrago, Gomez-Fernandez, Ganjei-Azar, and Jordà); the Clinical Molecular Diagnostics Laboratory, University of Wisconsin Hospital and Clinics, Madison (Dr Accola); and the Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison (Dr Rehrauer)
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26
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Chao BH, Traynor AM, Yang DT, Zhang C, Pier T, Kim K, Rehrauer WM, Cannon DM, Cannon GM, Bye T, Tibbetts RS. Automated quantitative analyses (AQUA) of cyclic-AMP-response-element-binding protein (CREB), phosphorylated CREB (pCREB), and ataxia-telangiectasia-mutated protein kinase (ATM) protein expression in patients (pts) undergoing thoracic radiation for locally advanced non-small cell lung cancer (NSCLC). J Clin Oncol 2012. [DOI: 10.1200/jco.2012.30.15_suppl.e13537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e13537 Background: Increased protein expression of CREB, a DNA damage-regulated transcription factor, has been associated with poor survival in advanced NSCLC. We have demonstrated that exposure of cancer cell lines to low dose ionizing radiation (IR) increased pCREB on a Ser133 residue. However, exposure to high dose IR correlated with pCREB on Ser121 by ATM, a master regulator of the cellular DNA damage response. This unusual bimodal response of CREB to IR, reflected by activation at low doses and attenuation at high doses, suggested that CREB may control cell fate decisions in response to DNA damage. We hypothesized that patterns of protein expression of CREB, pCREB Ser133, and ATM would predict treatment response in pts who have undergone radiotherapy for locally advanced NSCLC. Methods: Diagnostic tumor specimens were obtained from pts who underwent thoracic radiation in a clinical trial for locally advanced NSCLC. Protein expression of CREB, pCREB Ser133, and ATM was assessed by AQUA. Wilcoxon rank sum test was used to assess differences in protein expression. Univariate regression was conducted to evaluate protein expression and clinical outcomes. Kruskal Wallis test was used to assess protein expression and pneumonitis. Results: Sufficient tumor tissue was available for 35 of 79 pts enrolled. Best responses in 6 months included 12% CR, 73% PR, 9% SD, and 6% PD. Pre-treatment protein expression per AQUA analyses of CREB, pCREB Ser133, and ATM were not statistically associated with time to in-field progression, time to out-of-field progression, time to distant metastasis, best response, pneumonitis, or overall survival. Unexpectedly, increased expression of pCREB Ser133 was associated with durable anti-tumor response to radiation at a median duration of 14.6 months (p=0.03). Conclusions: Protein expression per AQUA of CREB, pCREB Ser133, and ATM did not confirm our hypotheses, possibly related to our limited sample size. Further analysis of the role of CREB in response to IR in cancer pts is ongoing.
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Affiliation(s)
- Bo H. Chao
- University of Wisconsin Carbone Cancer Center, Madison, WI
| | | | - David T Yang
- University of Wisconsin Carbone Cancer Center, Madison, WI
| | - Chong Zhang
- University of Wisconsin Carbone Cancer Center, Madison, WI
| | - Thomas Pier
- University of Wisconsin Carbone Cancer Center, Madison, WI
| | - KyungMann Kim
- University of Wisconsin Carbone Cancer Center, Madison, WI
| | | | | | | | - Tyler Bye
- University of Wisconsin Carbone Cancer Center, Madison, WI
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Bhattacharya D, Accola MA, Ansari IH, Striker R, Rehrauer WM. Naturally occurring genotype 2b/1a hepatitis C virus in the United States. Virol J 2011; 8:458. [PMID: 21967740 PMCID: PMC3205070 DOI: 10.1186/1743-422x-8-458] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 10/03/2011] [Indexed: 12/20/2022] Open
Abstract
Background Hepatitis C Virus (HCV) infected patients are frequently repeatedly exposed to the virus, but very few recombinants between two genotypes have been reported. Findings We describe the discovery of an HCV recombinant using a method developed in a United States clinical lab for HCV genotyping that employs sequencing of both 5' and 3' portions of the HCV genome. Over twelve months, 133 consecutive isolates were analyzed, and a virus from one patient was found with discordant 5' and 3' sequences suggesting it was a genotype 2b/1a recombinant. We ruled out a mixed infection and mapped a recombination point near the NS2/3 cleavage site. Conclusions This unique HCV recombinant virus described shares some features with other recombinant viruses although it is the only reported recombinant of a genotype 2 with a subtype 1a. This recombinant represents a conundrum for current clinical treatment guidelines, including treatment with protease inhibitors. This recombinant is also challenging to detect by the most commonly employed methods of genotyping that are directed primarily at the 5' structural portion of the HCV genome.
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Affiliation(s)
- Dipankar Bhattacharya
- University of Wisconsin-Madison, School of Medicine and Public Health, Department of Medicine, Madison, WI 53706, USA
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28
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Bauer M, Su G, He R, Rehrauer WM, Kendziorski CM, Casper TC, Jonat W, Friedl A. Heterogeneity of gene expression in stromal fibroblasts of breast carcinomas and normal breast. Cancer Res 2009. [DOI: 10.1158/0008-5472.sabcs-105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Abstract #105
Background: The cancer microenvironment plays a critical role in tumor development and progression. Cancer associated fibroblasts (CAF) constitute a significant component of the tumor stroma and participate in reciprocal communication with the tumor cells. Information on differential gene expression specifically in stromal fibroblasts is sparse and data describing the variability of gene expression in CAF and normal fibroblasts (NF) is currently lacking. The purpose of this study was to identify genes differentially expressed in CAF and matched NF and to analyze the heterogeneity of gene expression profiles in the two cell types.
 Materials and methods: Fibroblast cell cultures were established from 6 patients with primary invasive breast cancer. Gene expression profiles were generated using oligonucleotide microarrays (Affymetrix HG-U133 Plus 2.0). Differentially expressed genes were ranked using Empirical Bayes modeling. A cut-off value of 0.005 was chosen for the posterior probability of equivalent expression. Lists of overexpressed genes were generated after eliminating genes with less than two-fold overexpression.
 Results: 17 genes were overexpressed in CAF compared to NF with known functions in paracrine and intracellular signaling, transcription regulation and extracellular matrix production. Using the same posterior probability cut-off, we identified 7 genes which were expressed at least two-fold higher in NF than in CAF. These genes have purported roles in steroid hormone metabolism, transcription, migration and cell signaling. Using semiquantitative RT-PCR and immunohistochemistry, we confirmed the over- and underexpression of a subset of 10 differentially expressed genes. The heterogeneity of gene expression in CAF vs. NF was compared with F-tests to determine variances. The estimated probability of NF gene expression variance being higher than CAF gene expression variance was 0.547 with a 95% confidence interval of 0.543 to 0.551 (p<0.0001), indicating that gene expression is more variable in NF than in CAF. By ranking the q-values of individual genes we identified 3 known genes, which show a significant difference in variance between CAF and NF (p<0.05).
 Conclusion: Altered gene expression in fibroblasts likely contributes to tumor growth and progression by enhancing ECM production, promoting stromal-epithelial paracrine signaling and altering steroid hormone metabolism. The inter-individual heterogeneity of gene expression in NF may indicate that the mammary stroma varies between individuals, supporting the hypothesis that the ability of the stroma to act as a barrier to cancer development and tumor progression may also be variable. Conversely, the heterogeneous gene expression in NF may be a reflection of a relative synchronization and uniformity of gene expression in CAF.
Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 105.
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Affiliation(s)
- M Bauer
- 1 Gynecology and Obstetrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - G Su
- 2 Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
| | - R He
- 2 Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
| | - WM Rehrauer
- 2 Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
| | - CM Kendziorski
- 3 Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
| | - TC Casper
- 3 Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
| | - W Jonat
- 1 Gynecology and Obstetrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - A Friedl
- 2 Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
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29
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Kaizu M, Borchardt GJ, Glidden CE, Fisk DL, Loffredo JT, Watkins DI, Rehrauer WM. Molecular typing of major histocompatibility complex class I alleles in the Indian rhesus macaque which restrict SIV CD8+ T cell epitopes. Immunogenetics 2007; 59:693-703. [PMID: 17641886 DOI: 10.1007/s00251-007-0233-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Accepted: 05/21/2007] [Indexed: 01/09/2023]
Abstract
The utility of the rhesus macaque as an animal model in both HIV vaccine development and pathogenesis studies necessitates the development of accurate and efficient major histocompatibility complex (MHC) genotyping technologies. In this paper, we describe the development and application of allele-specific polymerase chain reaction (PCR) amplification for the simultaneous detection of eight MHC class I alleles from the rhesus macaque (Macaca mulatta) of Indian descent. These alleles were selected, as they have been implicated in the restriction of CD8(+) T cell epitopes of simian immunodeficiency virus (SIV). Molecular typing of Mamu-A 01, Mamu-A 02, Mamu-A 08, Mamu-A 11, Mamu-B 01, Mamu-B 03, Mamu-B 04, and Mamu-B 17 was conducted in a high throughput fashion using genomic DNA. Our amplification strategy included a conserved internal control target to minimize false negative results and can be completed in less than 5 h. We have genotyped over 4,000 animals to establish allele frequencies from colonies all over the western hemisphere. The ability to identify MHC-defined rhesus macaques will greatly enhance investigation of the immune responses, which are responsible for the control of viral replication. Furthermore, application of this technically simple and accurate typing method should facilitate selection, utilization, and breeding of rhesus macaques for AIDS virus pathogenesis and vaccine studies.
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Affiliation(s)
- Masahiko Kaizu
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA
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Loffredo JT, Maxwell J, Qi Y, Glidden CE, Borchardt GJ, Soma T, Bean AT, Beal DR, Wilson NA, Rehrauer WM, Lifson JD, Carrington M, Watkins DI. Mamu-B*08-positive macaques control simian immunodeficiency virus replication. J Virol 2007; 81:8827-32. [PMID: 17537848 PMCID: PMC1951344 DOI: 10.1128/jvi.00895-07] [Citation(s) in RCA: 238] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Certain major histocompatibility complex (MHC) class I alleles are associated with the control of human immunodeficiency virus and simian immunodeficiency virus (SIV) replication. We have designed sequence-specific primers for detection of the rhesus macaque MHC class I allele Mamu-B*08 by PCR and screened a cohort of SIV-infected macaques for this allele. Analysis of 196 SIV(mac)239-infected Indian rhesus macaques revealed that Mamu-B*08 was significantly overrepresented in elite controllers; 38% of elite controllers were Mamu-B*08 positive compared to 3% of progressors (P = 0.00001). Mamu-B*08 was also associated with a 7.34-fold decrease in chronic phase viremia (P = 0.002). Mamu-B*08-positive macaques may, therefore, provide a good model to understand the correlates of MHC class I allele-associated immune protection and viral containment in human elite controllers.
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Affiliation(s)
- John T Loffredo
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 555 Science Drive, Madison, WI 53711, USA
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31
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Loffredo JT, Sidney J, Piaskowski S, Szymanski A, Furlott J, Rudersdorf R, Reed J, Peters B, Hickman-Miller HD, Bardet W, Rehrauer WM, O'Connor DH, Wilson NA, Hildebrand WH, Sette A, Watkins DI. The high frequency Indian rhesus macaque MHC class I molecule, Mamu-B*01, does not appear to be involved in CD8+ T lymphocyte responses to SIVmac239. J Immunol 2005; 175:5986-97. [PMID: 16237093 DOI: 10.4049/jimmunol.175.9.5986] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Although the SIV-infected Indian rhesus macaque (Macaca mulatta) is the animal model most widely used for studying HIV infection, our current understanding of the functional macaque MHC class I molecules is limited. To date, SIV-derived CD8+ T lymphocyte epitopes from only three high frequency macaque MHC class I molecules have been extensively characterized. In this study, we defined the peptide-binding properties of the high frequency Indian rhesus macaque class I molecule, Mamu-B*01 ( approximately 26%). We first identified a preliminary binding motif by eluting and sequencing endogenously bound Mamu-B*01 ligands. We further characterized the peptide-binding characteristics using panels of single amino acid substitution analogs. Using this detailed motif, 507 peptides derived from SIV(mac)239 were identified and tested for their Mamu-B*01 binding capacity. Surprisingly, only 11 (2.2%) of these motif-containing peptides bound with IC50 values < or =500 nM. We assessed the immunogenicity of these peptides using freshly isolated PBMC from ten Mamu-B*01+ SIV-infected rhesus macaques in IFN-gamma ELISPOT and IFN-gamma/TNF-alpha intracellular cytokine staining assays. Lymphocytes from these SIV-infected macaques responded to none of these peptides. Furthermore, there was no sequence variation indicative of escape in the regions of the virus that encoded these peptides. Additionally, we could not confirm previous reports of SIV-derived Mamu-B*01-restricted epitopes in the Env and Gag proteins. Our results suggest that the high frequency MHC class I molecule, Mamu-B*01, is not involved in SIV-specific CD8+ T lymphocyte responses.
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Affiliation(s)
- John T Loffredo
- Wisconsin National Primate Research Center (WNPRC), University of Wisconsin, Madison, WI 53715, USA
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32
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O'Connor DH, McDermott AB, Krebs KC, Dodds EJ, Miller JE, Gonzalez EJ, Jacoby TJ, Yant L, Piontkivska H, Pantophlet R, Burton DR, Rehrauer WM, Wilson N, Hughes AL, Watkins DI. A dominant role for CD8+-T-lymphocyte selection in simian immunodeficiency virus sequence variation. J Virol 2004; 78:14012-22. [PMID: 15564508 PMCID: PMC533930 DOI: 10.1128/jvi.78.24.14012-14022.2004] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CD8(+) T lymphocytes (CD8-TL) select viral escape variants in both human immunodeficiency virus and simian immunodeficiency virus (SIV) infections. The frequency of CD8-TL viral escape as well as the contribution of escape to overall virus diversification has not been assessed. We quantified CD8-TL selection in SIV infections by sequencing viral genomes from 35 SIVmac239-infected animals at the time of euthanasia. Here we show that positive selection for sequences encoding 46 known CD8-TL epitopes is comparable to the positive selection observed for the variable loops of env. We also found that >60% of viral variation outside of the viral envelope occurs within recognized CD8-TL epitopes. Therefore, we conclude that CD8-TL selection is the dominant cause of SIV diversification outside of the envelope.
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Affiliation(s)
- David H O'Connor
- Wisconsin Primate Research Center, Department of Pathology, Laboratoty of Medicine, University of Wisconsin, 1300 University Ave., Madison, WI 53706, USA
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33
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O'Connor DH, Mothe BR, Weinfurter JT, Fuenger S, Rehrauer WM, Jing P, Rudersdorf RR, Liebl ME, Krebs K, Vasquez J, Dodds E, Loffredo J, Martin S, McDermott AB, Allen TM, Wang C, Doxiadis GG, Montefiori DC, Hughes A, Burton DR, Allison DB, Wolinsky SM, Bontrop R, Picker LJ, Watkins DI. Major histocompatibility complex class I alleles associated with slow simian immunodeficiency virus disease progression bind epitopes recognized by dominant acute-phase cytotoxic-T-lymphocyte responses. J Virol 2003; 77:9029-40. [PMID: 12885919 PMCID: PMC167227 DOI: 10.1128/jvi.77.16.9029-9040.2003] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Certain major histocompatibility complex class I (MHC-I) alleles are associated with delayed disease progression in individuals infected with human immunodeficiency virus (HIV) and in macaques infected with simian immunodeficiency virus (SIV). However, little is known about the influence of these MHC alleles on acute-phase cellular immune responses. Here we follow 51 animals infected with SIV(mac)239 and demonstrate a dramatic association between Mamu-A*01 and -B*17 expression and slowed disease progression. We show that the dominant acute-phase cytotoxic T lymphocyte (CTL) responses in animals expressing these alleles are largely directed against two epitopes restricted by Mamu-A*01 and one epitope restricted by Mamu-B*17. One Mamu-A*01-restricted response (Tat(28-35)SL8) and the Mamu-B*17-restricted response (Nef(165-173)IW9) typically select for viral escape variants in early SIV(mac)239 infection. Interestingly, animals expressing Mamu-A*1 and -B*17 have less variation in the Tat(28-35)SL8 epitope during chronic infection than animals that express only Mamu-A*01. Our results show that MHC-I alleles that are associated with slow progression to AIDS bind epitopes recognized by dominant CTL responses during acute infection and underscore the importance of understanding CTL responses during primary HIV infection.
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Affiliation(s)
- David H O'Connor
- Wisconsin Regional Primate Research Center and Department of Pathology and Laboratory Medicine, Madison, Wisconsin, USA
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34
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Rehrauer WM, Bruck I, Woodgate R, Goodman MF, Kowalczykowski SC. Modulation of RecA nucleoprotein function by the mutagenic UmuD'C protein complex. J Biol Chem 1998; 273:32384-7. [PMID: 9829966 DOI: 10.1074/jbc.273.49.32384] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RecA, UmuC, and UmuD' proteins are essential for error-prone, replicative bypass of DNA lesions. Normally, RecA protein mediates homologous pairing of DNA. We show that purified Umu(D')2C blocks this recombination function. Biosensor measurements establish that the mutagenic complex binds to the RecA nucleoprotein filament with a stoichiometry of one Umu(D')2C complex for every two RecA monomers. Furthermore, Umu(D')2C competitively inhibits LexA repressor cleavage but not ATPase activity, implying that Umu(D')2C binds in or proximal to the helical groove of the RecA nucleoprotein filament. This binding reduces joint molecule formation and even more severely impedes DNA heteroduplex formation by RecA protein, ultimately blocking all DNA pairing activity and thereby abridging participation in recombination function. Thus, Umu(D')2C restricts the activities of the RecA nucleoprotein filament and presumably, in this manner, recruits it for mutagenic repair function. This modulation by Umu(D')2C is envisioned as a key event in the transition from a normal mode of genomic maintenance by "error-free" recombinational repair, to one of "error-prone" DNA replication.
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Affiliation(s)
- W M Rehrauer
- Division of Biological Sciences, Sections of Microbiology and of Molecular and Cellular Biology, University of California, Davis, California 95616-8665, USA
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35
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Harmon FG, Rehrauer WM, Kowalczykowski SC. Interaction of Escherichia coli RecA protein with LexA repressor. II. Inhibition of DNA strand exchange by the uncleavable LexA S119A repressor argues that recombination and SOS induction are competitive processes. J Biol Chem 1996; 271:23874-83. [PMID: 8798618] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The Escherichia coli RecA protein is involved in SOS induction, DNA repair, and homologous recombination. In vitro, RecA protein serves as a co-protease to cleave LexA repressor, the repressor of the SOS regulon; in addition, RecA protein promotes homologous pairing and DNA strand exchange, steps important to homologous recombination and DNA repair. To determine if these two functions of RecA protein are competing or parallel, the effect of uncleavable LexA S119A repressor on RecA protein-dependent activities was examined. LexA S119A repressor inhibits both the single-stranded DNA (ssDNA)-dependent ATP hydrolysis and DNA strand exchange activities of RecA protein. As for wild-type LexA repressor (Rehrauer, W. M., Lavery, P. E., Palmer, E. L., Singh, R. N., and Kowalczykowski, S. C. (1996) J. Biol. Chem. 271, 23865-23873), inhibition of ATP hydrolysis is dependent upon the presence of E. coli single-stranded DNA binding (SSB) protein, arguing that LexA repressor affects the competition between RecA protein and SSB protein for ssDNA binding sites. In contrast, inhibition of DNA strand exchange activity is SSB protein-independent, suggesting that LexA S119A repressor blocks a site required for DNA strand exchange. These results imply that there is a common site on the RecA protein filament for secondary DNA and LexA repressor binding and raise the possibility that the recombination and co-protease activities of the RecA protein filament are competitive.
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Affiliation(s)
- F G Harmon
- Division of Biological Sciences, Sections of Microbiology and of Molecular and Cellular Biology, University of California, Davis, California 95616-8665, USA
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36
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Rehrauer WM, Lavery PE, Palmer EL, Singh RN, Kowalczykowski SC. Interaction of Escherichia coli RecA protein with LexA repressor. I. LexA repressor cleavage is competitive with binding of a secondary DNA molecule. J Biol Chem 1996; 271:23865-73. [PMID: 8798617] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Essential to the two distinct cellular events of genetic recombination and SOS induction in Escherichia coli, RecA protein promotes the homologous pairing and exchange of DNA strands and the proteolytic cleavage of the LexA repressor, respectively. Since both of these activities require single-stranded DNA (ssDNA) and ATP, the inter-relationship between these reactions was investigated and found to display many parallels. The extent of active complex formed between RecA protein and M13 ssDNA, as measured by both ATP hydrolysis and LexA proteolysis, is stimulated in a similar manner by either a reduction in magnesium ion concentration or the presence of single-stranded DNA binding (SSB) protein. However, unexpectedly, SSB protein inhibits both LexA proteolysis and ATP hydrolysis (in assays containing repressor) at concentrations of RecA protein that are substoichiometric to the ssDNA, arguing that LexA repressor affects the competition between RecA and SSB proteins for limited ssDNA binding sites. Additionally, attenuation of LexA repressor cleavage in the presence of double-stranded DNA or by an excess of ssDNA suggests that interaction of the RecA nucleoprotein filament with either LexA repressor or a secondary DNA molecule is mutually exclusive. The significance of these results is discussed in the context of both the regulation of inducible responses to DNA damage, and the competitive relationship between the processes of SOS induction and genetic recombination.
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Affiliation(s)
- W M Rehrauer
- Department of Molecular Biology, Northwestern University Medical School, Chicago, Illinois 60611, USA
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37
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Rehrauer WM, Lavery PE, Palmer EL, Singh RN, Kowalczykowski SC. Interaction of Escherichia coli RecA Protein with LexA Repressor. J Biol Chem 1996. [DOI: 10.1074/jbc.271.39.23865] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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39
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Abstract
Photochemical cross-linking has been used to identify residues in the Escherichia coli RecA protein that are proximal to and may directly mediate binding of DNA. Ultraviolet irradiation promotes specific and efficient cross-linking of the RecA protein to poly(deoxythymidylic) acid. Cross-linked peptides remaining covalently attached to the polynucleotide following proteolytic digestion with trypsin correspond to amino acids 61-72, 178-183, and 233-243 of the RecA protein primary sequence. Their location and surface accessibility in the crystal structure, along with the behavior of various recA mutants, support the assignment of the cross-linked regions to the DNA binding site(s) of the RecA protein. Functional overlap of amino acids 61-72 with an element of the ATP binding site suggests a structural mechanism by which nucleotide cofactors allosterically affect the RecA nucleoprotein filament.
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Affiliation(s)
- W M Rehrauer
- Department of Molecular Biology, Northwestern University Medical School, Chicago, Illinois 60611, USA
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40
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Abstract
Homologous recombination is a fundamental biological process. Biochemical understanding of this process is most advanced for Escherichia coli. At least 25 gene products are involved in promoting genetic exchange. At present, this includes the RecA, RecBCD (exonuclease V), RecE (exonuclease VIII), RecF, RecG, RecJ, RecN, RecOR, RecQ, RecT, RuvAB, RuvC, SbcCD, and SSB proteins, as well as DNA polymerase I, DNA gyrase, DNA topoisomerase I, DNA ligase, and DNA helicases. The activities displayed by these enzymes include homologous DNA pairing and strand exchange, helicase, branch migration, Holliday junction binding and cleavage, nuclease, ATPase, topoisomerase, DNA binding, ATP binding, polymerase, and ligase, and, collectively, they define biochemical events that are essential for efficient recombination. In addition to these needed proteins, a cis-acting recombination hot spot known as Chi (chi: 5'-GCTGGTGG-3') plays a crucial regulatory function. The biochemical steps that comprise homologous recombination can be formally divided into four parts: (i) processing of DNA molecules into suitable recombination substrates, (ii) homologous pairing of the DNA partners and the exchange of DNA strands, (iii) extension of the nascent DNA heteroduplex; and (iv) resolution of the resulting crossover structure. This review focuses on the biochemical mechanisms underlying these steps, with particular emphases on the activities of the proteins involved and on the integration of these activities into likely biochemical pathways for recombination.
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Affiliation(s)
- S C Kowalczykowski
- Division of Biological Sciences, University of California, Davis 95616-8665
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Rehrauer WM, Kowalczykowski SC. Alteration of the nucleoside triphosphate (NTP) catalytic domain within Escherichia coli recA protein attenuates NTP hydrolysis but not joint molecule formation. J Biol Chem 1993; 268:1292-7. [PMID: 8419331] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The hydrolysis of the nucleoside triphosphates, such as ATP or GTP, plays a central role in a variety of biochemical processes; but, in most cases, the specific mechanism of energy transduction is unclear. DNA strand exchange promoted by the Escherichia coli recA protein is normally associated with ATP hydrolysis. However, we advanced the idea that the observed ATP hydrolysis is not obligatorily linked to the exchange of DNA strands (Menetski, J. P., Bear, D. G., and Kowalczykowski, S. C. (1990) Proc. Natl. Acad. Sci. U. S. A. 87, 21-25); instead, ATP binding resulting in an allosteric transition to an active form of the recA protein is sufficient. In this paper, we extend this conclusion by introducing a mutation within a highly conserved region of the recA protein that, on the basis of sequence similarity, is proposed to interact with the pyrophosphate moiety of a bound NTP molecule. The conservative substitution of an arginine for the invariant lysine at position 72 reduces NTP hydrolysis by approximately 600-850-fold. This mutation does not significantly alter the capacity of the mutant recA (K72R) protein either to bind nucleotide cofactors and single-stranded DNA or to respond allosterically to nucleotide cofactor binding. Despite the dramatic attenuation in NTP hydrolysis, the recA (K72R) protein retains the ability to promote homologous pairing and extensive exchange of DNA strands (up to 1.5 kilobase pairs). These results both identify a component of the catalytic domain for NTP hydrolysis and demonstrate that the recA protein-promoted pairing and exchange of DNA strands mechanistically require the allosteric transition induced by NTP cofactor binding, but not the energy educed from NTP hydrolysis.
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Affiliation(s)
- W M Rehrauer
- Department of Cell, Molecular, and Structural Biology, Northwestern University Medical School, Chicago, Illinois 60611
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