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Ricci A, Dugo M, Pisanu ME, De Cecco L, Raspagliesi F, Valeri B, Veneroni S, Chirico M, Palombelli G, Daidone MG, Podo F, Canese R, Mezzanzanica D, Bagnoli M, Iorio E. Impact of Cold Ischemia on the Stability of 1H-MRS-Detected Metabolic Profiles of Ovarian Cancer Specimens. J Proteome Res 2024; 23:483-493. [PMID: 38109371 DOI: 10.1021/acs.jproteome.3c00665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Proton magnetic resonance spectroscopy (1H-MRS) of surgically collected tumor specimens may contribute to investigating cancer metabolism and the significance of the "total choline" (tCho) peak (3.2 ppm) as malignancy and therapy response biomarker. To ensure preservation of intrinsic metabolomic information, standardized handling procedures are needed. The effects of time to freeze (cold ischemia) were evaluated in (a) surgical epithelial ovarian cancer (EOC) specimens using high-resolution (HR) 1H-MRS (9.4 T) of aqueous extracts and (b) preclinical EOC samples (xenografts in SCID mice) investigated by in vivo MRI-guided 1H-MRS (4.7 T) and by HR-1H-MRS (9.4 T) of tumor extracts or intact fragments (using magic-angle-spinning (MAS) technology). No significant changes were found in the levels of 27 of 29 MRS-detected metabolites (including the tCho profile) in clinical specimens up to 2 h cold ischemia, besides an increase in lysine and a decrease in glutathione. EOC xenografts showed a 2-fold increase in free choline within 2 h cold ischemia, without further significant changes for any MRS-detected metabolite (including phosphocholine and tCho) up to 6 h. At shorter times (≤1 h), HR-MAS analyses showed unaltered tCho components, along with significant changes in lactate, glutamate, and glutamine. Our results support the view that a time to freeze of 1 h represents a safe threshold to ensure the maintenance of a reliable tCho profile in EOC specimens.
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Affiliation(s)
- Alessandro Ricci
- Notified Body 0373 Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Matteo Dugo
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy
| | - Maria Elena Pisanu
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Loris De Cecco
- Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy
| | - Francesco Raspagliesi
- Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Barbara Valeri
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Silvia Veneroni
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy
| | - Mattea Chirico
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Gianmauro Palombelli
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Maria Grazia Daidone
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy
| | - Franca Podo
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Rossella Canese
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Delia Mezzanzanica
- Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy
| | - Marina Bagnoli
- Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy
| | - Egidio Iorio
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
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Ramsden CE, Zamora D, Horowitz MS, Jahanipour J, Calzada E, Li X, Keyes GS, Murray HC, Curtis MA, Faull RM, Sedlock A, Maric D. ApoER2-Dab1 disruption as the origin of pTau-associated neurodegeneration in sporadic Alzheimer's disease. Acta Neuropathol Commun 2023; 11:197. [PMID: 38093390 PMCID: PMC10720169 DOI: 10.1186/s40478-023-01693-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023] Open
Abstract
In sporadic Alzheimer's disease (sAD) specific regions, layers and neurons accumulate hyperphosphorylated Tau (pTau) and degenerate early while others remain unaffected even in advanced disease. ApoER2-Dab1 signaling suppresses Tau phosphorylation as part of a four-arm pathway that regulates lipoprotein internalization and the integrity of actin, microtubules, and synapses; however, the role of this pathway in sAD pathogenesis is not fully understood. We previously showed that multiple ApoER2-Dab1 pathway components including ApoE, Reelin, ApoER2, Dab1, pP85αTyr607, pLIMK1Thr508, pTauSer202/Thr205 and pPSD95Thr19 accumulate together within entorhinal-hippocampal terminal zones in sAD, and proposed a unifying hypothesis wherein disruption of this pathway underlies multiple aspects of sAD pathogenesis. However, it is not yet known whether ApoER2-Dab1 disruption can help explain the origin(s) and early progression of pTau pathology in sAD. In the present study, we applied in situ hybridization and immunohistochemistry (IHC) to characterize ApoER2 expression and accumulation of ApoER2-Dab1 pathway components in five regions known to develop early pTau pathology in 64 rapidly autopsied cases spanning the clinicopathological spectrum of sAD. We found that (1) these selectively vulnerable neuron populations strongly express ApoER2; and (2) multiple ApoER2-Dab1 components representing all four arms of this pathway accumulate in abnormal neurons and neuritic plaques in mild cognitive impairment (MCI) and sAD cases and correlate with histological progression and cognitive deficits. Multiplex-IHC revealed that Dab1, pP85αTyr607, pLIMK1Thr508, pTauSer202/Thr205 and pPSD95Thr19 accumulate together within many of the same ApoER2-expressing neurons and in the immediate vicinity of ApoE/ApoJ-enriched extracellular plaques. Collective findings reveal that pTau is only one of many ApoER2-Dab1 pathway components that accumulate in multiple neuroanatomical sites in the earliest stages of sAD and provide support for the concept that ApoER2-Dab1 disruption drives pTau-associated neurodegeneration in human sAD.
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Affiliation(s)
- Christopher E Ramsden
- Lipid Peroxidation Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH (NIA/NIH), 251 Bayview Blvd., Baltimore, MD, 21224, USA.
- Intramural Program of the National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD, 20892, USA.
| | - Daisy Zamora
- Lipid Peroxidation Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH (NIA/NIH), 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Mark S Horowitz
- Lipid Peroxidation Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH (NIA/NIH), 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Jahandar Jahanipour
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, 20892, USA
| | - Elizabeth Calzada
- Lipid Peroxidation Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH (NIA/NIH), 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Xiufeng Li
- Lipid Peroxidation Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH (NIA/NIH), 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Gregory S Keyes
- Lipid Peroxidation Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH (NIA/NIH), 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Helen C Murray
- Department of Anatomy and Medical Imaging and Centre for Brain Research, Faculty of Medical and Health Science, University of Auckland, Private Bag, Auckland, 92019, New Zealand
- Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, 20892, USA
| | - Maurice A Curtis
- Department of Anatomy and Medical Imaging and Centre for Brain Research, Faculty of Medical and Health Science, University of Auckland, Private Bag, Auckland, 92019, New Zealand
| | - Richard M Faull
- Department of Anatomy and Medical Imaging and Centre for Brain Research, Faculty of Medical and Health Science, University of Auckland, Private Bag, Auckland, 92019, New Zealand
| | - Andrea Sedlock
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, 20892, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, 20892, USA
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Ramsden CE, Zamora D, Horowitz M, Jahanipour J, Keyes G, Li X, Murray HC, Curtis MA, Faull RM, Sedlock A, Maric D. ApoER2-Dab1 disruption as the origin of pTau-related neurodegeneration in sporadic Alzheimer's disease. RESEARCH SQUARE 2023:rs.3.rs-2968020. [PMID: 37461602 PMCID: PMC10350181 DOI: 10.21203/rs.3.rs-2968020/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
BACKGROUND Sporadic Alzheimer's disease (sAD) is not a global brain disease. Specific regions, layers and neurons degenerate early while others remain untouched even in advanced disease. The prevailing model used to explain this selective neurodegeneration-prion-like Tau spread-has key limitations and is not easily integrated with other defining sAD features. Instead, we propose that in humans Tau hyperphosphorylation occurs locally via disruption in ApoER2-Dab1 signaling and thus the presence of ApoER2 in neuronal membranes confers vulnerability to degeneration. Further, we propose that disruption of the Reelin/ApoE/ApoJ-ApoER2-Dab1-P85α-LIMK1-Tau-PSD95 (RAAAD-P-LTP) pathway induces deficits in memory and cognition by impeding neuronal lipoprotein internalization and destabilizing actin, microtubules, and synapses. This new model is based in part on our recent finding that ApoER2-Dab1 disruption is evident in entorhinal-hippocampal terminal zones in sAD. Here, we hypothesized that neurons that degenerate in the earliest stages of sAD (1) strongly express ApoER2 and (2) show evidence of ApoER2-Dab1 disruption through co-accumulation of multiple RAAAD-P-LTP components. METHODS We applied in situ hybridization and immunohistochemistry to characterize ApoER2 expression and accumulation of RAAAD-P-LTP components in five regions that are prone to early pTau pathology in 64 rapidly autopsied cases spanning the clinicopathological spectrum of sAD. RESULTS We found that: (1) selectively vulnerable neuron populations strongly express ApoER2; (2) numerous RAAAD-P-LTP pathway components accumulate in neuritic plaques and abnormal neurons; and (3) RAAAD-P-LTP components were higher in MCI and sAD cases and correlated with histological progression and cognitive deficits. Multiplex-IHC revealed that Dab1, pP85αTyr607, pLIMK1Thr508, pTau and pPSD95Thr19 accumulated together within dystrophic dendrites and soma of ApoER2-expressing neurons in the vicinity of ApoE/ApoJ-enriched extracellular plaques. These observations provide evidence for molecular derangements that can be traced back to ApoER2-Dab1 disruption, in each of the sampled regions, layers, and neuron populations that are prone to early pTau pathology. CONCLUSION Findings support the RAAAD-P-LTP hypothesis, a unifying model that implicates dendritic ApoER2-Dab1 disruption as the major driver of both pTau accumulation and neurodegeneration in sAD. This model provides a new conceptual framework to explain why specific neurons degenerate and identifies RAAAD-P-LTP pathway components as potential mechanism-based biomarkers and therapeutic targets for sAD.
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Affiliation(s)
| | - Daisy Zamora
- National Institute on Aging Laboratory of Clinical Investigation
| | - Mark Horowitz
- National Institute on Aging Intramural Research Program
| | | | - Gregory Keyes
- National Institute on Aging Laboratory of Clinical Investigation
| | - Xiufeng Li
- National Institute on Aging Laboratory of Clinical Investigation
| | - Helen C Murray
- The University of Auckland Faculty of Medical and Health Sciences
| | - Maurice A Curtis
- The University of Auckland Faculty of Medical and Health Sciences
| | - Richard M Faull
- The University of Auckland Faculty of Medical and Health Sciences
| | - Andrea Sedlock
- NINDS: National Institute of Neurological Disorders and Stroke
| | - Dragan Maric
- NINDS: National Institute of Neurological Disorders and Stroke
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Ramsden CE, Zamora D, Horowitz MS, Jahanipour J, Keyes GS, Li X, Murray HC, Curtis MA, Faull RM, Sedlock A, Maric D. ApoER2-Dab1 disruption as the origin of pTau-related neurodegeneration in sporadic Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.19.23290250. [PMID: 37333406 PMCID: PMC10274982 DOI: 10.1101/2023.05.19.23290250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
BACKGROUND Sporadic Alzheimer's disease (sAD) is not a global brain disease. Specific regions, layers and neurons degenerate early while others remain untouched even in advanced disease. The prevailing model used to explain this selective neurodegeneration-prion-like Tau spread-has key limitations and is not easily integrated with other defining sAD features. Instead, we propose that in humans Tau hyperphosphorylation occurs locally via disruption in ApoER2-Dab1 signaling and thus the presence of ApoER2 in neuronal membranes confers vulnerability to degeneration. Further, we propose that disruption of the Reelin/ApoE/ApoJ-ApoER2-Dab1-P85α-LIMK1-Tau-PSD95 (RAAAD-P-LTP) pathway induces deficits in memory and cognition by impeding neuronal lipoprotein internalization and destabilizing actin, microtubules, and synapses. This new model is based in part on our recent finding that ApoER2-Dab1 disruption is evident in entorhinal-hippocampal terminal zones in sAD. Here, we hypothesized that neurons that degenerate in the earliest stages of sAD (1) strongly express ApoER2 and (2) show evidence of ApoER2-Dab1 disruption through co-accumulation of multiple RAAAD-P-LTP components. METHODS We applied in situ hybridization and immunohistochemistry to characterize ApoER2 expression and accumulation of RAAAD-P-LTP components in five regions that are prone to early pTau pathology in 64 rapidly autopsied cases spanning the clinicopathological spectrum of sAD. RESULTS We found that: (1) selectively vulnerable neuron populations strongly express ApoER2; (2) numerous RAAAD-P-LTP pathway components accumulate in neuritic plaques and abnormal neurons; and (3) RAAAD-P-LTP components were higher in MCI and sAD cases and correlated with histological progression and cognitive deficits. Multiplex-IHC revealed that Dab1, pP85αTyr607, pLIMK1Thr508, pTau and pPSD95Thr19 accumulated together within dystrophic dendrites and soma of ApoER2-expressing neurons in the vicinity of ApoE/ApoJ-enriched extracellular plaques. These observations provide evidence for molecular derangements that can be traced back to ApoER2-Dab1 disruption, in each of the sampled regions, layers, and neuron populations that are prone to early pTau pathology. CONCLUSION Findings support the RAAAD-P-LTP hypothesis, a unifying model that implicates dendritic ApoER2-Dab1 disruption as the major driver of both pTau accumulation and neurodegeneration in sAD. This model provides a new conceptual framework to explain why specific neurons degenerate and identifies RAAAD-P-LTP pathway components as potential mechanism-based biomarkers and therapeutic targets for sAD.
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Affiliation(s)
- Christopher E. Ramsden
- Lipid Peroxidation Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH 251 Bayview Blvd., Baltimore, MD, 21224, USA
- Intramural Program of the National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD, 20892, USA
| | - Daisy Zamora
- Lipid Peroxidation Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH 251 Bayview Blvd., Baltimore, MD, 21224, USA
- Department of Physical Medicine and Rehabilitation, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Mark S. Horowitz
- Lipid Peroxidation Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Jahandar Jahanipour
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, 20892, USA
| | - Gregory S. Keyes
- Lipid Peroxidation Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Xiufeng Li
- Lipid Peroxidation Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Helen C. Murray
- Department of Anatomy and Medical Imaging and Centre for Brain Research, Faculty of Medical and Health Science, University of Auckland, Private Bag, Auckland, 92019, New Zealand
- Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, 20892, USA
| | - Maurice A. Curtis
- Department of Anatomy and Medical Imaging and Centre for Brain Research, Faculty of Medical and Health Science, University of Auckland, Private Bag, Auckland, 92019, New Zealand
| | - Richard M. Faull
- Department of Anatomy and Medical Imaging and Centre for Brain Research, Faculty of Medical and Health Science, University of Auckland, Private Bag, Auckland, 92019, New Zealand
| | - Andrea Sedlock
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, 20892, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, 20892, USA
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Wang S, Sun Y, Zeng T, Wu Y, Ding L, Zhang X, Zhang L, Huang X, Li H, Yang X, Ni Y, Hu Q. Impact of preanalytical freezing delay time on the stability of metabolites in oral squamous cell carcinoma tissue samples. Metabolomics 2022; 18:82. [PMID: 36282338 DOI: 10.1007/s11306-022-01943-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/11/2022] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Metabolite stability is critical for tissue metabolomics. However, changes in metabolites in tissues over time from the operating room to the laboratory remain underexplored. OBJECTIVES In this study, we evaluated the effect of postoperative freezing delay time on the stability of metabolites in normal and oral squamous cell carcinoma (OSCC) tissues. METHODS Tumor and paired normal tissues from five OSCC patients were collected after surgical resection, and samples was sequentially quenched in liquid nitrogen at 30, 40, 50, 60, 70, 80, 90 and 120 min (80 samples). Untargeted metabolic analysis by liquid chromatography-mass spectrometry/mass spectrometry in positive and negative ion modes was used to identify metabolic changes associated with delayed freezing time. The trends of metabolite changes at 30-120 and 30-60 min of delayed freezing were analyzed. RESULTS 190 metabolites in 36 chemical classes were detected. After delayed freezing for 120 min, approximately 20% of the metabolites changed significantly in normal and tumor tissues, and differences in the metabolites were found in normal and tumor tissues. After a delay of 60 min, 29 metabolites had changed significantly in normal tissues, and 84 metabolites had changed significantly in tumor tissues. In addition, we constructed three tissue freezing schemes based on the observed variation trends in the metabolites. CONCLUSION Delayed freezing of tissue samples has a certain impact on the stability of metabolites. For metabolites with significant changes, we suggest that the freezing time of tissues be reasonably selected according to the freezing schemes and the actual clinical situation.
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Affiliation(s)
- Shuai Wang
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Yawei Sun
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Tao Zeng
- State Key Lab of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Yan Wu
- Department of Oral Pathology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Liang Ding
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Xiaoxin Zhang
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Lei Zhang
- Department of Oral Pathology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Xiaofeng Huang
- Department of Oral Pathology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Huiling Li
- Department of Oral Pathology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Xihu Yang
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Yanhong Ni
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China.
| | - Qingang Hu
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China.
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China.
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Kennedy JJ, Woodcock A, Ivey RG, Lin C, Corral G, Hooper E, Martin G, Longman G, Stancik B, Cromwell EA, Whiteaker JR, Zhao L, Lorentzen TD, Thielman S, Paulovich AG. Preserving the Phosphoproteome of Clinical Biopsies Using a Quick-Freeze Collection Device. Biopreserv Biobank 2022; 20:436-445. [PMID: 36301140 PMCID: PMC9603275 DOI: 10.1089/bio.2022.0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
There is growing interest in proteomic analyses of tissue biopsies to reveal pathophysiology and identify biomarkers. The current gold standard for collecting tissue biopsies for preserving the proteome and post-translational modifications is flash freezing in liquid nitrogen (LN2). However, in many clinical settings, this is not an option due to unavailability of LN2 nor trained personnel for rapid biospecimen processing. To address this need, we developed a proof-of-concept quick-freeze prototype device to rapidly freeze biospecimens at the point-of-care to preserve the phosphoproteome without the need for LN2. Our objectives were to develop the device, demonstrate the ease of use, confirm the ability to ship through existing cold chain logistics, and evaluate the cooling performance (i.e., cool a tissue sample to <0°C in <60 seconds, below -8°C in <120 seconds, and maintain temperature <0°C for >60 minutes) in the context of preserving the proteome in a tissue biospecimen. To demonstrate feasibility, the performance of the prototype was benchmarked against flash freezing in LN2 using a murine melanoma patient-derived xenograft model subjected to total body irradiation to elicit phosphosignaling in the DNA damage response network. Tumors were harvested and quadrisected, with two parts of the tumor being snap frozen in LN2, and the remaining two parts being rapidly cooled in the prototype quick-freeze biospecimen containers. Phosphoproteins were profiled by liquid chromatography tandem mass spectrometry and quantified by targeted multiple reaction monitoring MS. Overall, the phosphoproteome was equivalent in biospecimens processed using the quick-freeze containers to those using the LN2 gold standard, although the measurements of a subset of phosphopeptides in the device-frozen specimens were more variable than LN2-frozen specimens. The prototype device forms the framework for development of a commercial device that will improve tissue biopsy preservation for measurement of important phosphosignaling molecules.
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Affiliation(s)
- Jacob J. Kennedy
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington, USA
| | | | - Richard G. Ivey
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington, USA
| | - ChenWei Lin
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington, USA
| | - Guy Corral
- Product Creation Studio, Seattle, Washington, USA
| | - Eli Hooper
- Product Creation Studio, Seattle, Washington, USA
| | | | - Gina Longman
- Product Creation Studio, Seattle, Washington, USA
| | | | - Elizabeth A. Cromwell
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington, USA
| | - Jeffrey R. Whiteaker
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington, USA
| | - Lei Zhao
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington, USA
| | - Travis D. Lorentzen
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington, USA
| | | | - Amanda G. Paulovich
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington, USA
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Ramsden CE, Keyes GS, Calzada E, Horowitz MS, Zamora D, Jahanipour J, Sedlock A, Indig FE, Moaddel R, Kapogiannis D, Maric D. Lipid Peroxidation Induced ApoE Receptor-Ligand Disruption as a Unifying Hypothesis Underlying Sporadic Alzheimer's Disease in Humans. J Alzheimers Dis 2022; 87:1251-1290. [PMID: 35466940 DOI: 10.3233/jad-220071] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Sporadic Alzheimer's disease (sAD) lacks a unifying hypothesis that can account for the lipid peroxidation observed early in the disease, enrichment of ApoE in the core of neuritic plaques, hallmark plaques and tangles, and selective vulnerability of entorhinal-hippocampal structures. OBJECTIVE We hypothesized that 1) high expression of ApoER2 (receptor for ApoE and Reelin) helps explain this anatomical vulnerability; 2) lipid peroxidation of ApoE and ApoER2 contributes to sAD pathogenesis, by disrupting neuronal ApoE delivery and Reelin-ApoER2-Dab1 signaling cascades. METHODS In vitro biochemical experiments; Single-marker and multiplex fluorescence-immunohistochemistry (IHC) in postmortem specimens from 26 individuals who died cognitively normal, with mild cognitive impairment or with sAD. RESULTS ApoE and ApoER2 peptides and proteins were susceptible to attack by reactive lipid aldehydes, generating lipid-protein adducts and crosslinked ApoE-ApoER2 complexes. Using in situ hybridization alongside IHC, we observed that: 1) ApoER2 is strongly expressed in terminal zones of the entorhinal-hippocampal 'perforant path' projections that underlie memory; 2) ApoE, lipid aldehyde-modified ApoE, Reelin, ApoER2, and the downstream Reelin-ApoER2 cascade components Dab1 and Thr19-phosphorylated PSD95 accumulated in the vicinity of neuritic plaques in perforant path terminal zones in sAD cases; 3) several ApoE/Reelin-ApoER2-Dab1 pathway markers were higher in sAD cases and positively correlated with histological progression and cognitive deficits. CONCLUSION Results demonstrate derangements in multiple ApoE/Reelin-ApoER2-Dab1 axis components in perforant path terminal zones in sAD and provide proof-of-concept that ApoE and ApoER2 are vulnerable to aldehyde-induced adduction and crosslinking. Findings provide the foundation for a unifying hypothesis implicating lipid peroxidation of ApoE and ApoE receptors in sAD.
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Affiliation(s)
- Christopher E Ramsden
- Lipid Peroxidation Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA.,Intramural Program of the National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD, USA
| | - Gregory S Keyes
- Lipid Peroxidation Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Elizabeth Calzada
- Lipid Peroxidation Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Mark S Horowitz
- Lipid Peroxidation Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Daisy Zamora
- Lipid Peroxidation Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jahandar Jahanipour
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Andrea Sedlock
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Fred E Indig
- Confocal Imaging Facility, National Institute on Aging Intramural Research Program, NIH, Baltimore, MD, USA
| | - Ruin Moaddel
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Dimitrios Kapogiannis
- Human Neuroscience Unit, Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
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8
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Buffart TE, van den Oord RAHM, van den Berg A, Hilhorst R, Bastiaensen N, Pruijt HFM, van den Brule A, Nooijen P, Labots M, de Goeij-de Haas RR, Dekker H, Piersma SR, Pham TV, van der Leij T, de Wijn R, Ruijtenbeek R, Jiménez CR, Verheul HMW. Time dependent effect of cold ischemia on the phosphoproteome and protein kinase activity in fresh-frozen colorectal cancer tissue obtained from patients. Clin Proteomics 2021; 18:8. [PMID: 33602116 PMCID: PMC7893972 DOI: 10.1186/s12014-020-09306-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/27/2020] [Indexed: 11/18/2022] Open
Abstract
Background Based on their potential to analyze aberrant cellular signaling in relation to biological function, kinase activity profiling in tumor biopsies by peptide microarrays and mass spectrometry-based phosphoproteomics may guide selection of protein kinase inhibitors in patients with cancer. Variable tissue handling procedures in clinical practice may influence protein phosphorylation status and kinase activity and therewith may hamper biomarker discovery. Here, the effect of cold ischemia time (CIT) on the stability of kinase activity and protein phosphorylation status in fresh-frozen clinical tissue samples was studied using peptide microarrays and mass spectrometry-based phosphoproteomics. Methods Biopsies of colorectal cancer resection specimens from five patients were collected and snap frozen immediately after surgery and at 6 additional time points between 0 and 180 min of CIT. Kinase activity profiling was performed for all samples using a peptide microarray. MS-based global phosphoproteomics was performed in tumors from 3 patients at 4 time points. Statistical and cluster analyses were performed to analyze changes in kinase activity and phosphoproteome resulting from CIT. Results Unsupervised cluster analysis of kinase activity and phosphoproteome data revealed that samples from the same patients cluster together. Continuous ANOVA analysis of all 7 time points for 5 patient samples resulted in 4 peptides out of 210 (2%) with significantly (p < 0.01 and fold change > 2) altered signal intensity in time. In 4 out of 5 patients tumor kinase activity was stable with CIT. MS-based phosphoproteomics resulted in the detection of 10,488 different phosphopeptides with on average 6044 phosphopeptides per tumor sample. 2715 phosphopeptides were detected in all samples at time point 0, of which 90 (3.3%) phosphopeptides showed significant changes in intensity with CIT (p < 0.01). Only two phosphopeptides were significantly changed in all time points, including one peptide (PKP3) with a fold change > 2. Conclusions The vast majority of the phosphoproteome as well as the activity of protein kinases in colorectal cancer resection tissue is stable up to 180 min of CIT and reflects tumor characteristics. However, specific changes in kinase activity with increasing CIT were observed. Therefore, stringent tissue collection procedures are advised to minimize changes in kinase activity during CIT.
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Affiliation(s)
- Tineke E Buffart
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands.,Department of Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rosanne A H M van den Oord
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands.,Department of Medical Oncology, Jeroen Bosch Hospital, 'S-Hertogenbosch, The Netherlands
| | | | - Riet Hilhorst
- PamGene International BV, 'S-Hertogenbosch, The Netherlands
| | | | - Hans F M Pruijt
- Department of Medical Oncology, Jeroen Bosch Hospital, 'S-Hertogenbosch, The Netherlands
| | - Adriaan van den Brule
- Laboratory of Molecular Diagnostics, Jeroen Bosch Hospital, 'S-Hertogenbosch, The Netherlands
| | - Peet Nooijen
- Department of Pathology, Jeroen Bosch Hospital, 'S-Hertogenbosch, The Netherlands
| | - Mariette Labots
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Henk Dekker
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Rik de Wijn
- PamGene International BV, 'S-Hertogenbosch, The Netherlands
| | - Rob Ruijtenbeek
- PamGene International BV, 'S-Hertogenbosch, The Netherlands.,GenMab BV, Utrecht, The Netherlands
| | - Connie R Jiménez
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands. .,Department of Medical Oncology, Radboud University Medical Center, Geert Grooteplein 10, 6525GA, Nijmegen, The Netherlands.
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9
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van Alphen C, Cucchi DGJ, Cloos J, Schelfhorst T, Henneman AA, Piersma SR, Pham TV, Knol JC, Jimenez CR, Janssen JJWM. The influence of delay in mononuclear cell isolation on acute myeloid leukemia phosphorylation profiles. J Proteomics 2021; 238:104134. [PMID: 33561558 DOI: 10.1016/j.jprot.2021.104134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/02/2021] [Accepted: 01/03/2021] [Indexed: 12/12/2022]
Abstract
Mass-spectrometry (MS) based phosphoproteomics is increasingly used to explore aberrant cellular signaling and kinase driver activity, aiming to improve kinase inhibitor (KI) treatment selection in malignancies. Phosphorylation is a dynamic, highly regulated post-translational modification that may be affected by variation in pre-analytical sample handling, hampering the translational value of phosphoproteomics-based analyses. Here, we investigate the effect of delay in mononuclear cell isolation on acute myeloid leukemia (AML) phosphorylation profiles. We performed MS on immuno-precipitated phosphotyrosine (pY)-containing peptides isolated from AML samples after seven pre-defined delays before sample processing (direct processing, thirty minutes, one hour, two hours, three hours, four hours and 24 h delay). Up to four hours, pY phosphoproteomics profiles show limited variation. However, in samples processed with a delay of 24 h, we observed significant change in these phosphorylation profiles, with differential phosphorylation of 22 pY phosphopeptides (p < 0.01). This includes increased phosphorylation of pY phosphopeptides of JNK and p38 kinases indicative of stress response activation. Based on these results, we conclude that processing of AML samples should be standardized at all times and should occur within four hours after sample collection. SIGNIFICANCE: Our study provides a practical time-frame in which fresh peripheral blood samples from acute myeloid patients should be processed for phosphoproteomics, in order to warrant correct interpretation of in vivo biology. We show that up to four hours of delayed processing after sample collection, pY phosphoproteomic profiles remain stable. Extended delays are associated with perturbation of phosphorylation profiles. After a delay of 24 h, JNK activation loop phosphorylation is markedly increased and may serve as a biomarker for delayed processing. These findings are relevant for biomedical acute myeloid leukemia research, as phosphoproteomic techniques are of particular interest to investigate aberrant kinase signaling in relation to disease emergence and kinase inhibitor response. With these data, we aim to contribute to reproducible research with meaningful outcomes.
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Affiliation(s)
- Carolien van Alphen
- Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, the Netherlands; OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, the Netherlands; Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - David G J Cucchi
- Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, the Netherlands
| | - Jacqueline Cloos
- Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, the Netherlands
| | - Tim Schelfhorst
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, the Netherlands; Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Alexander A Henneman
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, the Netherlands; Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Sander R Piersma
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, the Netherlands; Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Thang V Pham
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, the Netherlands; Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jaco C Knol
- Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, the Netherlands; OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, the Netherlands
| | - Connie R Jimenez
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, the Netherlands; Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
| | - Jeroen J W M Janssen
- Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, the Netherlands
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10
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Zeneyedpour L, Stingl C, Dekker LJM, Mustafa DAM, Kros JM, Luider TM. Phosphorylation Ratio Determination in Fresh-Frozen and Formalin-Fixed Paraffin-Embedded Tissue with Targeted Mass Spectrometry. J Proteome Res 2020; 19:4179-4190. [PMID: 32811146 DOI: 10.1021/acs.jproteome.0c00354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are routinely prepared and collected for diagnostics in pathology departments. These are, therefore, the most accessible research sources in pathology archives. In this study we investigated whether we can apply a targeted and quantitative parallel reaction monitoring (PRM) method for FFPE tissue samples in a sensitive and reproducible way. The feasibility of this technical approach was demonstrated for normal brain and glioblastoma multiforme tissues. Two methods were used: PRM measurement of a tryptic digest without phosphopeptide enrichment (Direct-PRM) and after Fe-NTA phosphopeptide enrichment (Fe-NTA-PRM). With these two methods, the phosphorylation ratio could be determined for four selected peptide pairs that originate from neuroblast differentiation-associated protein (AHNAK S5448-p), calcium/calmodulin-dependent protein kinase type II subunit delta (CAMK2D T337-p), eukaryotic translation initiation factor 4B (EIF4B S93-p), and epidermal growth factor receptor (EGFR S1166-p). In normal brain FFPE tissues, the Fe-NTA-PRM method enabled the quantification of targeted phosphorylated peptides with high reproducibility (CV < 14%). Our results indicate that formalin fixation does not impede relative quantification of a phospho-site and its phosphorylation ratio in FFPE tissues. The developed workflow combining these methods opens ways to study archival FFPE tissues for phosphorylation ratio determination in proteins.
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Affiliation(s)
- Lona Zeneyedpour
- Department of Neurology, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - Christoph Stingl
- Department of Neurology, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | | | - Dana A M Mustafa
- Department of Pathology, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - Johan M Kros
- Department of Pathology, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus MC, 3000 CA Rotterdam, The Netherlands
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11
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Analytical Platforms 1: Use of Cultured Cells and Fluorescent Read-Out Coupled to NormaCurve Normalization in RPPA. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019. [PMID: 31820384 DOI: 10.1007/978-981-32-9755-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
The analytic platform described in this chapter uses proteins extracted from cultured cells as an infinite source of material to set up, validate, and quality control an RPPA platform. Readout of the arrays uses near-infrared fluorescence labeling and data normalization is performed using the bioinformatics package NormaCurve.In the first part, we will describe the advantages, drawbacks, and different applications of cell line material for RPPA. In the second part, we will describe how the staining protocol, the method of readout, and the normalization method applied afterward are interconnected and should be considered together. Finally, we will describe the NormaCurve package, which is freely available, and its requirements for implementation.Four protocols are provided in this chapter: (1) Protein lysis of cell lines using a homemade Laemmli buffer, (2) RPPA staining for fluorescent readout including a signal amplification step, (3) total protein staining in the visible spectrum for normalization purposes, and (4) total protein staining in the near-infrared spectrum for normalization purposes.
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12
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Compton CC, Robb JA, Anderson MW, Berry AB, Birdsong GG, Bloom KJ, Branton PA, Crothers JW, Cushman-Vokoun AM, Hicks DG, Khoury JD, Laser J, Marshall CB, Misialek MJ, Natale KE, Nowak JA, Olson D, Pfeifer JD, Schade A, Vance GH, Walk EE, Yohe SL. Preanalytics and Precision Pathology: Pathology Practices to Ensure Molecular Integrity of Cancer Patient Biospecimens for Precision Medicine. Arch Pathol Lab Med 2019; 143:1346-1363. [PMID: 31329478 DOI: 10.5858/arpa.2019-0009-sa] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Biospecimens acquired during routine medical practice are the primary sources of molecular information about patients and their diseases that underlies precision medicine and translational research. In cancer care, molecular analysis of biospecimens is especially common because it often determines treatment choices and may be used to monitor therapy in real time. However, patient specimens are collected, handled, and processed according to routine clinical procedures during which they are subjected to factors that may alter their molecular quality and composition. Such artefactual alteration may skew data from molecular analyses, render analysis data uninterpretable, or even preclude analysis altogether if the integrity of a specimen is severely compromised. As a result, patient care and safety may be affected, and medical research dependent on patient samples may be compromised. Despite these issues, there is currently no requirement to control or record preanalytical variables in clinical practice with the single exception of breast cancer tissue handled according to the guideline jointly developed by the American Society of Clinical Oncology and College of American Pathologists (CAP) and enforced through the CAP Laboratory Accreditation Program. Recognizing the importance of molecular data derived from patient specimens, the CAP Personalized Healthcare Committee established the Preanalytics for Precision Medicine Project Team to develop a basic set of evidence-based recommendations for key preanalytics for tissue and blood specimens. If used for biospecimens from patients, these preanalytical recommendations would ensure the fitness of those specimens for molecular analysis and help to assure the quality and reliability of the analysis data.
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Affiliation(s)
- Carolyn C Compton
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - James A Robb
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Matthew W Anderson
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Anna B Berry
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - George G Birdsong
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Kenneth J Bloom
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Philip A Branton
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Jessica W Crothers
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Allison M Cushman-Vokoun
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - David G Hicks
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Joseph D Khoury
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Jordan Laser
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Carrie B Marshall
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Michael J Misialek
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Kristen E Natale
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Jan Anthony Nowak
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Damon Olson
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - John D Pfeifer
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Andrew Schade
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Gail H Vance
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Eric E Walk
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Sophia Louise Yohe
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
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Riegman PHJ, Becker KF, Zatloukal K, Pazzagli M, Schröder U, Oelmuller U. How standardization of the pre-analytical phase of both research and diagnostic biomaterials can increase reproducibility of biomedical research and diagnostics. N Biotechnol 2019; 53:35-40. [PMID: 31202859 DOI: 10.1016/j.nbt.2019.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/17/2019] [Accepted: 06/12/2019] [Indexed: 12/01/2022]
Abstract
Comparison of published biomedical studies shows that a large proportion are irreproducible, causing severe damage to society and creating an image of wasted investments. These observations are of course damaging to the biomedical research field, which is currently full of future promise. Precision medicine and disease prevention are successful, but are progressing slowly due to irreproducible study results. Although standardization is mentioned as a possible solution, it is not always clear how this could decrease or prevent irreproducible results in biomedical studies. In this article more insight is given into what quality, norms, standardization, certification, accreditation and optimized infrastructure can accomplish to reveal causes of irreproducibility and increase reproducibility when collecting biomaterials. CEN and ISO standards for the sample pre-analytical phase are currently being developed with the support of the SPIDIA4P project, and their role in increasing reproducibility in both biomedical research and diagnostics is demonstrated. In particular, it is described how standardized methods and quality assurance documentation can be exploited as tools for: 1) recognition and rejection of 'not fit for purpose' samples on the basis of detailed sample metadata, and 2) identification of methods that contribute to irreproducibility which can be adapted or replaced.
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Affiliation(s)
- P H J Riegman
- Erasmus MC Rotterdam, Pathology department, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands.
| | - K F Becker
- Technical University of Munich, Institute of Pathology, Trogerstrasse 18, 81675 Munich, Germany
| | - K Zatloukal
- Diagnostic and Research Center for Molecular BioMedicine, Institute of Pathology, Medical University of Graz, Austria
| | - M Pazzagli
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Italy
| | - U Schröder
- DIN Deutsches Institut für Normung e.V., Saatwinkler Damm 42/43, 13627 Berlin, Germany
| | - U Oelmuller
- QIAGEN GmbH, MDx Development, QIAGEN Str. 1, 40724 Hilden, Germany
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Affiliation(s)
- Albert B. Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã A. S. Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37235, United States
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15
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Cant JP, Kim JJ, Cieslar SR, Doelman J. Symposium review: Amino acid uptake by the mammary glands: Where does the control lie? J Dairy Sci 2018; 101:5655-5666. [DOI: 10.3168/jds.2017-13844] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/28/2018] [Indexed: 12/15/2022]
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16
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Wu Y, Gaskins J, Kong M, Datta S. Profiling the effects of short time-course cold ischemia on tumor protein phosphorylation using a Bayesian approach. Biometrics 2017; 74:331-341. [PMID: 28742267 DOI: 10.1111/biom.12742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 05/01/2017] [Accepted: 06/01/2017] [Indexed: 12/20/2022]
Abstract
Phosphorylated proteins provide insight into tumor etiology and are used as diagnostic, prognostic, and therapeutic markers of complex diseases. However, pre-analytic variations, such as freezing delay after biopsy acquisition, often occur in real hospital settings and potentially lead to inaccurate results. The objective of this work is to develop statistical methodology to assess the stability of phosphorylated proteins under short-time cold ischemia. We consider a hierarchical model to determine if phosphorylation abundance of a protein at a particular phosphorylation site remains constant or not during cold ischemia. When phosphorylation levels vary across time, we estimate the direction of the changes in each protein based on the maximum overall posterior probability and on the pairwise posterior probabilities, respectively. We analyze a dataset of ovarian tumor tissues that suffered cold-ischemia shock before the proteomic profiling. Gajadhar et al. (2015) applied independent clusterings for each patient because of the high heterogeneity across patients, while our proposed model shares information allowing conclusions for the entire sample population. Using the proposed model, 15 out of 32 proteins show significant changes during 1-hour cold ischemia. Through simulation studies, we conclude that our proposed methodology has a higher accuracy for detecting changes compared to an order restricted inference method. Our approach provides inference on the stability of these phosphorylated proteins, which is valuable when using these proteins as biomarkers for a disease.
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Affiliation(s)
- You Wu
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, Kentucky, U.S.A
| | - Jeremy Gaskins
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, Kentucky, U.S.A
| | - Maiying Kong
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, Kentucky, U.S.A
| | - Susmita Datta
- Department of Biostatistics, University of Florida, Gainesville, Florida, U.S.A
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17
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Thasler RMK, Berghammer AJ, Kirchner T, Slotta-Huspenina J, Becker KF, Schiergens T, Thasler WE, Wichmann HE. Federated Biobanking with Corporate Service Unit: The Munich Biobank Alliance Blueprint. Biopreserv Biobank 2016; 15:75-79. [PMID: 27991833 DOI: 10.1089/bio.2016.0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Reinhard M K Thasler
- 1 Department of General, Visceral and Transplantation Surgery, Hospital of the LMU Munich , Munich, Germany
| | | | - Thomas Kirchner
- 3 Institute for Pathology, Ludwig-Maximilians-University , Munich, Germany
| | | | | | - Tobias Schiergens
- 1 Department of General, Visceral and Transplantation Surgery, Hospital of the LMU Munich , Munich, Germany
| | - Wolfgang E Thasler
- 1 Department of General, Visceral and Transplantation Surgery, Hospital of the LMU Munich , Munich, Germany
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18
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Doucet M, Becker KF, Björkman J, Bonnet J, Clément B, Daidone MG, Duyckaerts C, Erb G, Haslacher H, Hofman P, Huppertz B, Junot C, Lundeberg J, Metspalu A, Lavitrano M, Litton JE, Moore HM, Morente M, Naimi BY, Oelmueller U, Ollier B, Parodi B, Ruan L, Stanta G, Turano P, Vaught J, Watson P, Wichmann HE, Yuille M, Zaomi M, Zatloukal K, Dagher G. Quality Matters: 2016 Annual Conference of the National Infrastructures for Biobanking. Biopreserv Biobank 2016; 15:270-276. [PMID: 27992240 DOI: 10.1089/bio.2016.0053] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Marika Doucet
- 1 BIOBANQUES Infrastructure, Inserm US13, Hôpital de la Pitié Salpêtrière , Paris, France
| | | | | | - Jacques Bonnet
- 4 Inserm U916, Institut Bergonié, Université de Bordeaux , Bordeaux, France
| | - Bruno Clément
- 1 BIOBANQUES Infrastructure, Inserm US13, Hôpital de la Pitié Salpêtrière , Paris, France .,5 Inserm UMR991, Rennes, France
| | | | | | | | | | - Paul Hofman
- 1 BIOBANQUES Infrastructure, Inserm US13, Hôpital de la Pitié Salpêtrière , Paris, France .,10 Hospital-Integrated Biobank (BB-0033-00025), FHU OncoAge, University of Nice Sophia Antipolis , Nice, France
| | | | | | - Joakim Lundeberg
- 13 Science for Life Laboratory, KTH Royal Institute of Technology , Stockholm, Sweden
| | - Andres Metspalu
- 14 Estonian Genome Center, University of Tartu , Tartu, Estonia
| | | | | | - Helen M Moore
- 17 National Cancer Institute Biorepositories and Biospecimen Research Branch (BBRB) , Rockville, Maryland
| | - Manuel Morente
- 18 Biobank Unit of the Spanish national cancer center (CNIO) , Madrid, Spain
| | | | | | - Bill Ollier
- 21 University of Manchester , Manchester, United Kingdom
| | - Barbara Parodi
- 22 Biological Resource Center of the National Institute for Cancer Research (IRCCS AOU San Martino-IST) , Genoa, Italy
| | | | | | | | - Jim Vaught
- 26 International Society for Biological and Environmental Repositories (ISBER) , Bethesda, Maryland
| | - Peter Watson
- 27 British Columbia Cancer Agency's Vancouver Island Cancer Center , Victoria, Canada
| | - H-Erich Wichmann
- 28 Helmholtz Zentrum München, Institute of Epidemiology II , Munich, Germany
| | - Martin Yuille
- 21 University of Manchester , Manchester, United Kingdom
| | - Myriam Zaomi
- 1 BIOBANQUES Infrastructure, Inserm US13, Hôpital de la Pitié Salpêtrière , Paris, France
| | | | - Georges Dagher
- 1 BIOBANQUES Infrastructure, Inserm US13, Hôpital de la Pitié Salpêtrière , Paris, France
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19
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Wheelock ÅM, Paulson L, Litton JE. The EuPA Biobank Initiative: Meeting the future challenges of biobanking in proteomics & systems medicine. J Proteomics 2016. [PMID: 26216594 DOI: 10.1016/j.jprot.2015.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
UNLABELLED In this News & Reviews Discussion, the recently launched EuPA (European Proteomics Association) Biobank Initiative is introduced in the context of current and future challenges in biobanking. The purpose of the initiative is to provide a forumand knowledge platform for integrating the extensive experiences collected by the EuPA community, and link it to the European and international biobanking communities at large. The specific impact of providing a forum and easy access to this type of information to the EuPA community is the potential of improving the quality of future sample collections and biobanks, the quality of the research produced from these sample collections, as well as the output and productivity from existing biobanks. The underutilization of biobanks has recently been identified as an emerging issue of biobankingworldwide. Measures to improve our ability to locate and access appropriate sample collections for a wide range of research purposes may enhance both the scientific quality and biobank sustainability, thereby contributing to the important task of moving our research beyond basic findings and mere publications, into clinical practice. BIOLOGICAL SIGNIFICANCE This manuscript is intended as a Discussion piece, and represents a recollection of the presentation under the “EuPA Initiative” session at HUPO/EuPA 2014 in Madrid. The launch of the EuPA (European Proteomics Association) Biobank Initiative in the context of current and future challenges in biobanking is discussed. The purpose of the initiative is to provide a forum and knowledge base for integrating the extensive experiences collected by the EuPA community, and link it to the European and international biobanking communities at large. The specific impact of providing a forumand easy access to this type of information to the EuPA community is the potential of improving the quality of future sample collections and biobanks, the quality of the research produced from these sample collections, aswell as the output and productivity fromexisting biobanks. The underutilization of biobanks has recently been identified as a challenge to the well-being and economic sustainability of biobanking worldwide. Measures to improve our ability to localize and access appropriate sample collections for validation studies and other research purposes is thus of benefit bothto scientific quality and biobank sustainability, thereby contributing to the important task of moving our research beyond basic findings and mere publications, into clinical practice. This article is part of a Special Issue entitled: HUPO 2014.
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20
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Distinct Cell- and Layer-Specific Expression Patterns and Independent Regulation of Kv2 Channel Subtypes in Cortical Pyramidal Neurons. J Neurosci 2016; 35:14922-42. [PMID: 26538660 DOI: 10.1523/jneurosci.1897-15.2015] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
UNLABELLED The Kv2 family of voltage-gated potassium channel α subunits, comprising Kv2.1 and Kv2.2, mediate the bulk of the neuronal delayed rectifier K(+) current in many mammalian central neurons. Kv2.1 exhibits robust expression across many neuron types and is unique in its conditional role in modulating intrinsic excitability through changes in its phosphorylation state, which affect Kv2.1 expression, localization, and function. Much less is known of the highly related Kv2.2 subunit, especially in forebrain neurons. Here, through combined use of cortical layer markers and transgenic mouse lines, we show that Kv2.1 and Kv2.2 are localized to functionally distinct cortical cell types. Kv2.1 expression is consistently high throughout all cortical layers, especially in layer (L) 5b pyramidal neurons, whereas Kv2.2 expression is primarily limited to neurons in L2 and L5a. In addition, L4 of primary somatosensory cortex is strikingly devoid of Kv2.2 immunolabeling. The restricted pattern of Kv2.2 expression persists in Kv2.1-KO mice, suggesting distinct cell- and layer-specific functions for these two highly related Kv2 subunits. Analyses of endogenous Kv2.2 in cortical neurons in situ and recombinant Kv2.2 expressed in heterologous cells reveal that Kv2.2 is largely refractory to stimuli that trigger robust, phosphorylation-dependent changes in Kv2.1 clustering and function. Immunocytochemistry and voltage-clamp recordings from outside-out macropatches reveal distinct cellular expression patterns for Kv2.1 and Kv2.2 in intratelencephalic and pyramidal tract neurons of L5, indicating circuit-specific requirements for these Kv2 paralogs. Together, these results support distinct roles for these two Kv2 channel family members in mammalian cortex. SIGNIFICANCE STATEMENT Neurons within the neocortex are arranged in a laminar architecture and contribute to the input, processing, and/or output of sensory and motor signals in a cell- and layer-specific manner. Neurons of different cortical layers express diverse populations of ion channels and possess distinct intrinsic membrane properties. Here, we show that the Kv2 family members Kv2.1 and Kv2.2 are expressed in distinct cortical layers and pyramidal cell types associated with specific corticostriatal pathways. We find that Kv2.1 and Kv2.2 exhibit distinct responses to acute phosphorylation-dependent regulation in brain neurons in situ and in heterologous cells in vitro. These results identify a molecular mechanism that contributes to heterogeneity in cortical neuron ion channel function and regulation.
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21
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Zahari MS, Wu X, Pinto SM, Nirujogi RS, Kim MS, Fetics B, Philip M, Barnes SR, Godfrey B, Gabrielson E, Nevo E, Pandey A. Phosphoproteomic profiling of tumor tissues identifies HSP27 Ser82 phosphorylation as a robust marker of early ischemia. Sci Rep 2015; 5:13660. [PMID: 26329039 PMCID: PMC4557083 DOI: 10.1038/srep13660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/27/2015] [Indexed: 01/06/2023] Open
Abstract
Delays between tissue collection and tissue fixation result in ischemia and ischemia-associated changes in protein phosphorylation levels, which can misguide the examination of signaling pathway status. To identify a biomarker that serves as a reliable indicator of ischemic changes that tumor tissues undergo, we subjected harvested xenograft tumors to room temperature for 0, 2, 10 and 30 minutes before freezing in liquid nitrogen. Multiplex TMT-labeling was conducted to achieve precise quantitation, followed by TiO2 phosphopeptide enrichment and high resolution mass spectrometry profiling. LC-MS/MS analyses revealed phosphorylation level changes of a number of phosphosites in the ischemic samples. The phosphorylation of one of these sites, S82 of the heat shock protein 27 kDa (HSP27), was especially abundant and consistently upregulated in tissues with delays in freezing as short as 2 minutes. In order to eliminate effects of ischemia, we employed a novel cryogenic biopsy device which begins freezing tissues in situ before they are excised. Using this device, we showed that the upregulation of phosphorylation of S82 on HSP27 was abrogated. We thus demonstrate that our cryogenic biopsy device can eliminate ischemia-induced phosphoproteome alterations, and measurements of S82 on HSP27 can be used as a robust marker of ischemia in tissues.
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Affiliation(s)
- Muhammad Saddiq Zahari
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Xinyan Wu
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Sneha M Pinto
- Institute of Bioinformatics, International Tech Park, Bangalore, 560066 India
| | | | - Min-Sik Kim
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Barry Fetics
- Robin Medical, Inc., P.O. Box 2414, Baltimore, MD 21203, USA
| | - Mathew Philip
- Robin Medical, Inc., P.O. Box 2414, Baltimore, MD 21203, USA
| | - Sheri R Barnes
- Charles River Discovery Research Services, 3300 Gateway Centre Boulevard, Morrisville NC 27560
| | - Beverly Godfrey
- Charles River Discovery Research Services, 3300 Gateway Centre Boulevard, Morrisville NC 27560
| | - Edward Gabrielson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Erez Nevo
- Robin Medical, Inc., P.O. Box 2414, Baltimore, MD 21203, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130, USA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130, USA
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22
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Thermal inactivation of enzymes and pathogens in biosamples for MS analysis. Bioanalysis 2015; 7:1885-99. [DOI: 10.4155/bio.15.122] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Protein denaturation is the common basis for enzyme inactivation and inactivation of pathogens, necessary for preservation and safe handling of biosamples for downstream analysis. While heat-stabilization technology has been used in proteomic and peptidomic research since its introduction in 2009, the advantages of using the technique for simultaneous pathogen inactivation have only recently been addressed. The time required for enzyme inactivation by heat (≈1 min) is short compared with chemical treatments, and inactivation is irreversible in contrast to freezing. Heat stabilization thus facilitates mass spectrometric studies of biomolecules with a fast conversion rate, and expands the chemical space of potential biomarkers to include more short-lived entities, such as phosphorylated proteins, in tissue samples as well as whole-blood (dried blood sample) samples.
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23
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Gündisch S, Annaratone L, Beese C, Drecol E, Marchiò C, Quaglino E, Sapino A, Becker KF, Bussolati G. Critical roles of specimen type and temperature before and during fixation in the detection of phosphoproteins in breast cancer tissues. J Transl Med 2015; 95:561-71. [PMID: 25730369 PMCID: PMC4421866 DOI: 10.1038/labinvest.2015.37] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/09/2014] [Accepted: 12/31/2014] [Indexed: 12/21/2022] Open
Abstract
The most efficient approach for therapy selection to inhibit the deregulated kinases in cancer tissues is to measure their phosphorylation status prior to the treatment. The aim of our study was to evaluate the influence of pre-analytical parameters (cold ischemia time, temperature before and during tissue fixation, and sample type) on the levels of proteins and phosphoproteins in breast cancer tissues, focusing on the PI3 kinase/AKT pathway. The BALB-neuT mouse breast cancer model expressing HER2 and pAKT proteins and human biopsy and resection specimens were analyzed. By using quantitative reverse phase protein arrays (RPPA), 9 proteins and 16 phosphoproteins relevant to breast cancer biology were assessed. Cold temperatures before and during fixation resulted in a marked improvement in the preservation of the reactivity of biological markers (eg, ER, HER2) in general and, specifically, pHER2 and pAKT. Some phosphoproteins, eg, pHER2 and pAKT, were more sensitive to prolonged cold ischemia times than others (eg, pS6RP and pSTAT5). By comparing the phosphoprotein levels in core needle biopsies with those in resection specimens, we found a marked decrease in many phosphoproteins in the latter. Cold conditions can improve the preservation of proteins and phosphoproteins in breast cancer tissues. Biopsies ≤ 1 mm in size are the preferred sample type for assessing the activity of deregulated kinases for personalized cancer treatments because the phosphoprotein levels are better preserved compared with resection specimens. Each potential new (phospho)protein biomarker should be tested for its sensitivity to pre-analytical processing prior to the development of a diagnostic assay.
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Affiliation(s)
- Sibylle Gündisch
- Institute of Pathology, Technische Universität München, Trogerstrasse, Munich, Germany
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, Via Santena, Turin, Italy
| | - Christian Beese
- Institute of Pathology, Technische Universität München, Trogerstrasse, Munich, Germany
| | - Enken Drecol
- Institute of Pathology, Technische Universität München, Trogerstrasse, Munich, Germany
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, Via Santena, Turin, Italy,Pathology Service, Azienda Ospedaliera Città della Salute e della Scienza di Torino, Via Santena, Turin, Italy
| | - Elena Quaglino
- Department of Molecular Biotechnologies and Health Sciences, University of Turin, Via Nizza, Turin, Italy
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, Via Santena, Turin, Italy,Pathology Service, Azienda Ospedaliera Città della Salute e della Scienza di Torino, Via Santena, Turin, Italy
| | - Karl-Friedrich Becker
- Institute of Pathology, Technische Universität München, Trogerstrasse, Munich, Germany,Technische Universität München, Institute of Pathology, Trogerstrasse18, Munich, D-81675, Germany. E-mail:
| | - Gianni Bussolati
- Department of Medical Sciences, University of Turin, Via Santena, Turin, Italy,Department of Medical Sciences, University of Turin, Via Santena 7, Turin 10126, Italy. E-mail:
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24
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Zhang PW, Chen L, Huang T, Zhang N, Kong XY, Cai YD. Classifying ten types of major cancers based on reverse phase protein array profiles. PLoS One 2015; 10:e0123147. [PMID: 25822500 PMCID: PMC4378934 DOI: 10.1371/journal.pone.0123147] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/24/2015] [Indexed: 12/20/2022] Open
Abstract
Gathering vast data sets of cancer genomes requires more efficient and autonomous procedures to classify cancer types and to discover a few essential genes to distinguish different cancers. Because protein expression is more stable than gene expression, we chose reverse phase protein array (RPPA) data, a powerful and robust antibody-based high-throughput approach for targeted proteomics, to perform our research. In this study, we proposed a computational framework to classify the patient samples into ten major cancer types based on the RPPA data using the SMO (Sequential minimal optimization) method. A careful feature selection procedure was employed to select 23 important proteins from the total of 187 proteins by mRMR (minimum Redundancy Maximum Relevance Feature Selection) and IFS (Incremental Feature Selection) on the training set. By using the 23 proteins, we successfully classified the ten cancer types with an MCC (Matthews Correlation Coefficient) of 0.904 on the training set, evaluated by 10-fold cross-validation, and an MCC of 0.936 on an independent test set. Further analysis of these 23 proteins was performed. Most of these proteins can present the hallmarks of cancer; Chk2, for example, plays an important role in the proliferation of cancer cells. Our analysis of these 23 proteins lends credence to the importance of these genes as indicators of cancer classification. We also believe our methods and findings may shed light on the discoveries of specific biomarkers of different types of cancers.
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Affiliation(s)
- Pei-Wei Zhang
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R. China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, P.R. China
| | - Tao Huang
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R. China
- * E-mail: (TH); (NZ); (XYK); (YDC)
| | - Ning Zhang
- Department of Biomedical Engineering, Tianjin Key Lab of BME Measurement, Tianjin University, Tianjin, P.R. China
- * E-mail: (TH); (NZ); (XYK); (YDC)
| | - Xiang-Yin Kong
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R. China
- * E-mail: (TH); (NZ); (XYK); (YDC)
| | - Yu-Dong Cai
- College of Life Science, Shanghai University, Shanghai, P.R. China
- * E-mail: (TH); (NZ); (XYK); (YDC)
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25
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Becker KF. Using tissue samples for proteomic studies-Critical considerations. Proteomics Clin Appl 2015; 9:257-67. [DOI: 10.1002/prca.201400106] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 12/08/2014] [Accepted: 01/07/2015] [Indexed: 01/09/2023]
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26
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Gajadhar AS, Johnson H, Slebos RJC, Shaddox K, Wiles K, Washington MK, Herline AJ, Levine DA, Liebler DC, White FM. Phosphotyrosine signaling analysis in human tumors is confounded by systemic ischemia-driven artifacts and intra-specimen heterogeneity. Cancer Res 2015; 75:1495-503. [PMID: 25670172 DOI: 10.1158/0008-5472.can-14-2309] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 01/05/2015] [Indexed: 01/25/2023]
Abstract
Tumor protein phosphorylation analysis may provide insight into intracellular signaling networks underlying tumor behavior, revealing diagnostic, prognostic or therapeutic information. Human tumors collected by The Cancer Genome Atlas program potentially offer the opportunity to characterize activated networks driving tumor progression, in parallel with the genetic and transcriptional landscape already documented for these tumors. However, a critical question is whether cellular signaling networks can be reliably analyzed in surgical specimens, where freezing delays and spatial sampling disparities may potentially obscure physiologic signaling. To quantify the extent of these effects, we analyzed the stability of phosphotyrosine (pTyr) sites in ovarian and colon tumors collected under conditions of controlled ischemia and in the context of defined intratumoral sampling. Cold-ischemia produced a rapid, unpredictable, and widespread impact on tumor pTyr networks within 5 minutes of resection, altering up to 50% of pTyr sites by more than 2-fold. Effects on adhesion and migration, inflammatory response, proliferation, and stress response pathways were recapitulated in both ovarian and colon tumors. In addition, sampling of spatially distinct colon tumor biopsies revealed pTyr differences as dramatic as those associated with ischemic times, despite uniform protein expression profiles. Moreover, intratumoral spatial heterogeneity and pTyr dynamic response to ischemia varied dramatically between tumors collected from different patients. Overall, these findings reveal unforeseen phosphorylation complexity, thereby increasing the difficulty of extracting physiologically relevant pTyr signaling networks from archived tissue specimens. In light of this data, prospective tumor pTyr analysis will require appropriate sampling and collection protocols to preserve in vivo signaling features.
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Affiliation(s)
- Aaron S Gajadhar
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts. David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Hannah Johnson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts. David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Robbert J C Slebos
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee. The Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Kent Shaddox
- The Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Kerry Wiles
- Cooperative Human Tissue Network Western Division, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Mary Kay Washington
- Department of Pathology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Alan J Herline
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Douglas A Levine
- Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Daniel C Liebler
- The Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee. Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts. David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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27
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Gahoi N, Ray S, Srivastava S. Array-based proteomic approaches to study signal transduction pathways: prospects, merits and challenges. Proteomics 2014; 15:218-31. [PMID: 25266292 DOI: 10.1002/pmic.201400261] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 09/17/2014] [Accepted: 09/25/2014] [Indexed: 01/17/2023]
Abstract
Very often dysfunctional aspects of various signalling networks are found to be associated with human diseases and disorders. The major characteristics of signal transduction pathways are specificity, amplification of the signal, desensitisation and integration, which is accomplished not solely, but majorly by proteins. Array-based profiling of protein-protein and other biomolecular interactions is a versatile approach, which holds immense potential for multiplex interactome mapping and provides an inclusive representation of the signal transduction pathways and networks. Protein microarrays such as analytical protein microarrays (antigen-antibody interactions, autoantibody screening), RP microarrays (interaction of a particular ligand with all the possible targets in cell), functional protein microarrays (protein-protein or protein-ligand interactions) are implemented for various applications, including analysis of protein interactions and their significance in signalling cascades. Additionally, successful amalgamation of the array-based approaches with different label-free detection techniques allows real-time analysis of interaction kinetics of multiple interaction events simultaneously. This review discusses the prospects, merits and limitations of different variants of array-based techniques and their promising applications for studying the modifications and interactions of biomolecules, and highlights the studies associated with signal transduction pathways and their impact on disease pathobiology.
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Affiliation(s)
- Nikita Gahoi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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28
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Steiner C, Ducret A, Tille JC, Thomas M, McKee TA, Rubbia-Brandt L, Scherl A, Lescuyer P, Cutler P. Applications of mass spectrometry for quantitative protein analysis in formalin-fixed paraffin-embedded tissues. Proteomics 2014; 14:441-51. [PMID: 24339433 PMCID: PMC4265304 DOI: 10.1002/pmic.201300311] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 11/04/2013] [Accepted: 11/11/2013] [Indexed: 12/12/2022]
Abstract
Proteomic analysis of tissues has advanced in recent years as instruments and methodologies have evolved. The ability to retrieve peptides from formalin-fixed paraffin-embedded tissues followed by shotgun or targeted proteomic analysis is offering new opportunities in biomedical research. In particular, access to large collections of clinically annotated samples should enable the detailed analysis of pathologically relevant tissues in a manner previously considered unfeasible. In this paper, we review the current status of proteomic analysis of formalin-fixed paraffin-embedded tissues with a particular focus on targeted approaches and the potential for this technique to be used in clinical research and clinical diagnosis. We also discuss the limitations and perspectives of the technique, particularly with regard to application in clinical diagnosis and drug discovery.
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Affiliation(s)
- Carine Steiner
- Division of Laboratory Medicine, Geneva University Hospital, Geneva, Switzerland; Human Protein Sciences Department, University of Geneva, Geneva, Switzerland; Translational Technologies and Bioinformatics, Pharma Research and Early Development, F. Hoffmann-La Roche AG, Basel, Switzerland
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29
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Mertins P, Yang F, Liu T, Mani DR, Petyuk VA, Gillette MA, Clauser KR, Qiao JW, Gritsenko MA, Moore RJ, Levine DA, Townsend R, Erdmann-Gilmore P, Snider JE, Davies SR, Ruggles KV, Fenyo D, Kitchens RT, Li S, Olvera N, Dao F, Rodriguez H, Chan DW, Liebler D, White F, Rodland KD, Mills GB, Smith RD, Paulovich AG, Ellis M, Carr SA. Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels. Mol Cell Proteomics 2014; 13:1690-704. [PMID: 24719451 DOI: 10.1074/mcp.m113.036392] [Citation(s) in RCA: 290] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Protein abundance and phosphorylation convey important information about pathway activity and molecular pathophysiology in diseases including cancer, providing biological insight, informing drug and diagnostic development, and guiding therapeutic intervention. Analyzed tissues are usually collected without tight regulation or documentation of ischemic time. To evaluate the impact of ischemia, we collected human ovarian tumor and breast cancer xenograft tissue without vascular interruption and performed quantitative proteomics and phosphoproteomics after defined ischemic intervals. Although the global expressed proteome and most of the >25,000 quantified phosphosites were unchanged after 60 min, rapid phosphorylation changes were observed in up to 24% of the phosphoproteome, representing activation of critical cancer pathways related to stress response, transcriptional regulation, and cell death. Both pan-tumor and tissue-specific changes were observed. The demonstrated impact of pre-analytical tissue ischemia on tumor biology mandates caution in interpreting stress-pathway activation in such samples and motivates reexamination of collection protocols for phosphoprotein analysis.
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Affiliation(s)
- Philipp Mertins
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
| | - Feng Yang
- ‖Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Tao Liu
- ‖Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - D R Mani
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Vladislav A Petyuk
- ‖Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Michael A Gillette
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Karl R Clauser
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Jana W Qiao
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Marina A Gritsenko
- ‖Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Ronald J Moore
- ‖Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Douglas A Levine
- **Gynecology Service/Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York 10065
| | - Reid Townsend
- ‡‡Department of Medicine, Washington University, St. Louis, Missouri 63110
| | | | | | - Sherri R Davies
- ‡‡Department of Medicine, Washington University, St. Louis, Missouri 63110
| | - Kelly V Ruggles
- §§Department of Biochemistry, New York University Langone Medical Center, New York, New York 10016
| | - David Fenyo
- §§Department of Biochemistry, New York University Langone Medical Center, New York, New York 10016
| | - R Thomas Kitchens
- ‡‡Department of Medicine, Washington University, St. Louis, Missouri 63110
| | - Shunqiang Li
- ‡‡Department of Medicine, Washington University, St. Louis, Missouri 63110
| | - Narciso Olvera
- **Gynecology Service/Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York 10065
| | - Fanny Dao
- **Gynecology Service/Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York 10065
| | - Henry Rodriguez
- ¶¶National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Daniel W Chan
- ‖‖Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland 21287
| | - Daniel Liebler
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Forest White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Karin D Rodland
- ‖Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Richard D Smith
- ‖Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | | | - Matthew Ellis
- ‡‡Department of Medicine, Washington University, St. Louis, Missouri 63110
| | - Steven A Carr
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
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