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Munoz-Zuluaga CA, Heymann JJ, Solomon JP, Patel A, Siddiqui MT, Scognamiglio T, Gokozan HN. Use of the Afirma Xpression Atlas for cytologically indeterminate, Afirma Genomic Sequencing Classifier suspicious thyroid nodules: Clinicopathologic analysis with postoperative molecular testing. Am J Clin Pathol 2024; 161:463-468. [PMID: 38104250 DOI: 10.1093/ajcp/aqad169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023] Open
Abstract
OBJECTIVES Afirma has recently introduced its Xpression Atlas (XA) as an adjunct to its Genomic Sequencing Classifier (GSC) for risk stratification of cytologically indeterminate thyroid nodules. We evaluated the performance of Afirma XA and associated pathologic findings for Afirma GSC suspicious nodules. METHODS Intradepartmental records of thyroid fine-needle aspirations (FNAs) from January 2021 to December 2022 were identified and reviewed for patient and nodule characteristics, FNA findings, molecular test results, and final surgical pathology, if available. RESULTS Material for Afirma GSC testing was collected in 624 thyroid FNAs, and 148 (24%) were classified as cytologically indeterminate. Afirma GSC testing was successful in 132 (89%) of those cases, of which 35 (27%) were Afirma GSC suspicious. Afirma XA testing was positive in 11 cases (11/35 [31%]). Eight (73%) patients underwent surgery that revealed 7 patients with papillary thyroid carcinoma and 1 patient with noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) (risk of malignancy: 100% [8/8]). Among the 24 patients with negative Afirma XA results, 19 (79%) underwent surgery, revealing 5 patients with malignancy and 3 patients with NIFTP (risk of malignancy: 42% [8/19]). Overall, the risk of malignancy for Afirma GSC suspicious nodules was 59% (16/27). CONCLUSIONS Afirma XA improved risk stratification of thyroid disease with a high risk of malignancy in Afirma GSC suspicious nodules. A negative Afirma XA result, however, should not be used as a rule-out test.
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Affiliation(s)
- Carlos A Munoz-Zuluaga
- Divisions of Cytopathology, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
- Divisions of Head and Neck Pathology, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
| | - Jonas J Heymann
- Divisions of Cytopathology, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
| | - James P Solomon
- Divisions of Molecular and Genomic Pathology, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
| | - Ami Patel
- Divisions of Cytopathology, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
| | - Momin T Siddiqui
- Divisions of Cytopathology, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
| | - Theresa Scognamiglio
- Divisions of Head and Neck Pathology, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
| | - Hamza N Gokozan
- Divisions of Cytopathology, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
- Divisions of Head and Neck Pathology, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
- Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, US
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2
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Gokozan HN, Mostyka M, Scognamiglio T, Solomon JP, Beg S, Stern E, Goyal A, Siddiqui MT, Heymann JJ. Diagnostic interobserver agreement for thyroid fine-needle aspirates: Effects of reviewer experience and molecular diagnostics. Am J Clin Pathol 2024:aqae043. [PMID: 38656386 DOI: 10.1093/ajcp/aqae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
OBJECTIVES Few cytologically indeterminate thyroid fine-needle aspirations (FNAs) harbor BRAF V600E. Here, we assess interobserver agreement for The Bethesda System for Reporting Thyroid Cytopathology (TBSRTC) category III (atypia of undetermined significance [AUS]) FNAs harboring BRAF V600E and contrast their features with those harboring non-BRAF V600E alterations, with attention to cytopathology experience. METHODS Seven reviewers evaluated 5 AUS thyroid FNAs harboring BRAF V600E. To blind reviewers, cases were intermixed with 19 FNAs falling within other TBSRTC categories and in which genetic alterations other than BRAF V600E had been identified (24 FNAs total). Interobserver agreement against both "index" and most popular ("mode") diagnoses was calculated. Four additional BRAF V600E cases were independently reviewed. RESULTS Reviewers included 3 trainees and 3 American Board of Pathology (board)-certified cytopathologists. Board-certified cytopathologists, whose experience ranged from 2 to more than 15 subspecialty practice years, had known AUS rates. BRAF V600E was identified in 5 of 260 (2%) AUS FNAs. Interobserver agreement was higher among cytopathologists with more experience. Mode diagnosis differed from index diagnosis in 6 of 11 cases harboring RAS-like alterations; mode diagnosis was AUS in 4 of 5 BRAF V600E FNAs. CONCLUSIONS Atypia of undetermined significance of thyroid FNAs harboring BRAF V600E is uncommon yet relatively reproducible, particularly among pathologists with experience. It is advisable to sequence BRAF across V600 in such cases.
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Affiliation(s)
- Hamza N Gokozan
- Department of Pathology and Laboratory Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
| | - Maria Mostyka
- Department of Pathology and Laboratory Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
| | - Theresa Scognamiglio
- Department of Pathology and Laboratory Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
| | - James P Solomon
- Department of Pathology and Laboratory Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
| | - Shaham Beg
- Department of Pathology and Laboratory Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
| | - Evan Stern
- Department of Pathology and Laboratory Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
| | - Abha Goyal
- Department of Pathology and Laboratory Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
| | - Momin T Siddiqui
- Department of Pathology and Laboratory Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
| | - Jonas J Heymann
- Department of Pathology and Laboratory Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical College, New York, NY, US
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Solomon JP. Practical Considerations for Oncogenic Fusion Detection and Reporting in Solid Tumors. J Appl Lab Med 2024; 9:116-123. [PMID: 38167769 DOI: 10.1093/jalm/jfad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/15/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Chromosomal rearrangements that result in oncogenic fusions can hold tremendous clinical significance in solid tumors, often with diagnostic or treatment implications. CONTENT Traditionally, low-throughput methods such as fluorescence in situ hybridization were used to identify fusions in the clinical laboratory. With the rise of next-generation sequencing techniques and the broad adoption of comprehensive genomic profiling, the practice of screening for fusions as part of an oncologic workup has evolved. RNA sequencing methods are increasingly used, as these comprehensive high-throughput assays have many advantages over traditional techniques. Several RNA sequencing platforms are available, each with benefits and drawbacks. Regardless of the approach, systematic evaluation of the RNA sequencing results and the fusions identified by the assay should be performed. Assessment of fusion events relies upon evaluation of quality evidence, structural evidence, and functional evidence to ensure accurate fusion reporting and interpretation. SUMMARY Given the clinical significance of gene fusions in oncology, understanding the variety of assays available for fusion detection, their benefits and drawbacks, and how they are used in the identification and interpretation of gene fusions is important for the modern precision oncology practice.
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Affiliation(s)
- James P Solomon
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States
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4
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Wang C, Yantiss RK, Lieberman MD, Tubito-Massarano F, Qin L, Yemelyanova A, Solomon JP, Hissong E. A Rare PDGFRA Exon 15 Germline Mutation Identified in a Patient With Phenotypic Manifestations Concerning for GIST-Plus Syndrome: A Case Report and Review of Literature. Int J Surg Pathol 2023; 31:1139-1145. [PMID: 36802986 DOI: 10.1177/10668969231152588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Molecular alterations in PDGFRA are well-described as drivers of sporadic gastrointestinal stromal tumors (GISTs) and inflammatory fibroid polyps (IFPs). However, a small number of families with germline PDGFRA mutations in exons 12, 14, and 18 have been reported, forming the basis of an autosomal dominant inherited disorder with incomplete penetrance and variable expressivity, now referred to as PDGFRA-mutant syndrome or GIST-plus syndrome. Phenotypic manifestations of this rare syndrome include multiple gastrointestinal GISTS, IFPs, fibrous tumors, and other variable features. Herein, we report the case of a 58-year-old female who presented with a gastric GIST and numerous small intestinal IFPs, found to harbor a previously undescribed germline PDGFRA exon 15 p.G680R mutation. Somatic tumor testing was performed on the GIST, a duodenal IFP, and an ileal IFP utilizing a targeted next-generation sequencing panel, revealing additional and distinct secondary PDGFRA exon 12 somatic mutations in each of the 3 tumors. Our findings raise important considerations regarding mechanisms of tumor development in patients with underlying germline PDGFRA alterations and highlight the potential utility of expanding currently available germline and somatic testing panels to include exons outside the typical hotspot regions.
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Affiliation(s)
- Chiyun Wang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, University of Ottawa, Ottawa, ON, Canada
| | - Rhonda K Yantiss
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | | | - Lihui Qin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Anna Yemelyanova
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - James P Solomon
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Erika Hissong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
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5
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Slocum CC, Park HJ, Baek I, Catalano J, Wells MT, Liechty B, Mathew S, Song W, Solomon JP, Pisapia DJ. Towards a single-assay approach: a combined DNA/RNA sequencing panel eliminates diagnostic redundancy and detects clinically-relevant fusions in neuropathology. Acta Neuropathol Commun 2022; 10:167. [PMCID: PMC9670552 DOI: 10.1186/s40478-022-01466-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/20/2022] [Indexed: 11/18/2022] Open
Abstract
AbstractSince the introduction of integrated histological and molecular diagnoses by the 2016 World Health Organization (WHO) Classification of Tumors of the Nervous System, an increasing number of molecular markers have been found to have prognostic significance in infiltrating gliomas, many of which have now become incorporated as diagnostic criteria in the 2021 WHO Classification. This has increased the applicability of targeted-next generation sequencing in the diagnostic work-up of neuropathology specimens and in addition, raises the question of whether targeted sequencing can, in practice, reliably replace older, more traditional diagnostic methods such as immunohistochemistry and fluorescence in-situ hybridization. Here, we demonstrate that the Oncomine Cancer Gene Mutation Panel v2 assay targeted-next generation sequencing panel for solid tumors is not only superior to IHC in detecting mutation in IDH1/2 and TP53 but can also predict 1p/19q co-deletion with high sensitivity and specificity relative to fluorescence in-situ hybridization by looking at average copy number of genes sequenced on 1p, 1q, 19p, and 19q. Along with detecting the same molecular data obtained from older methods, targeted-next generation sequencing with an RNA sequencing component provides additional information regarding the presence of RNA based alterations that have diagnostic significance and possible therapeutic implications. From this work, we advocate for expanded use of targeted-next generation sequencing over more traditional methods for the detection of important molecular alterations as a part of the standard diagnostic work up for CNS neoplasms.
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Solomon JP, Yang SR, Choudhury NJ, Ptashkin RN, Eslamdoost N, Falcon CJ, Martin A, Plodkowski A, Wilhelm C, Shen R, Ladanyi M, Berger M, Zhang Y, Drilon A, Arcila ME. Bioinformatically Expanded Next-Generation Sequencing Analysis Optimizes Identification of Therapeutically Relevant MET Copy Number Alterations in >50,000 Tumors. Clin Cancer Res 2022; 28:4649-4659. [PMID: 36044468 PMCID: PMC9633455 DOI: 10.1158/1078-0432.ccr-22-1321] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/07/2022] [Accepted: 08/29/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE Clinical relevance thresholds and laboratory methods are poorly defined for MET amplification, a targetable biomarker across malignancies. EXPERIMENTAL DESIGN The utility of next-generation sequencing (NGS) in assessing MET copy number alterations was determined in >50,000 solid tumors. Using fluorescence in situ hybridization as reference, we validated and optimized NGS analysis. RESULTS Incorporating read-depth and focality analyses achieved 91% concordance, 97% sensitivity, and 89% specificity. Tumor heterogeneity, neoplastic cell proportions, and genomic focality affected MET amplification assessment. NGS methodology showed superiority in capturing overall amplification status in heterogeneous tumors and defining amplification focality among other genomic alterations. MET copy gains and amplifications were found in 408 samples across 23 malignancies. Total MET copy number inversely correlated with amplified segment size. High-level/focal amplification was enriched in certain genomic subgroups and associated with targeted therapy response. CONCLUSIONS Leveraging our integrated bioinformatic approach, targeted therapy benefit was observed across diverse MET amplification contexts.
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Affiliation(s)
- James P. Solomon
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Soo-Ryum Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Noura J. Choudhury
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan N. Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nasrin Eslamdoost
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christina J. Falcon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Axel Martin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew Plodkowski
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Clare Wilhelm
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronglai Shen
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria E. Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Correspondence: Maria E. Arcila, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065. Phone: 212-639-7879;
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7
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Gokozan HN, Dilcher TL, Alperstein SA, Qiu Y, Mostyka M, Scognamiglio T, Solomon JP, Song W, Rennert H, Beg S, Stern E, Goyal A, Siddiqui MT, Heymann JJ. Combining molecular testing and the Bethesda category III:VI ratio for thyroid fine‐needle aspirates: A quality‐assurance metric for evaluating diagnostic performance in a cytopathology laboratory. Cancer Cytopathol 2021; 130:259-274. [DOI: 10.1002/cncy.22542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/23/2021] [Accepted: 12/01/2021] [Indexed: 01/21/2023]
Affiliation(s)
- Hamza N. Gokozan
- Division of Cytopathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
- Division of Head and Neck Pathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Thomas L. Dilcher
- Division of Cytopathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Susan A. Alperstein
- Division of Cytopathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Yuqing Qiu
- Department of Population Health Sciences New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Maria Mostyka
- Division of Head and Neck Pathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Theresa Scognamiglio
- Division of Head and Neck Pathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - James P. Solomon
- Clinical Genomics Laboratory Department of Pathology and Laboratory Medicine New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Wei Song
- Clinical Genomics Laboratory Department of Pathology and Laboratory Medicine New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Hanna Rennert
- Division of Molecular and Genomic Pathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Shaham Beg
- Division of Cytopathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Evan Stern
- Division of Cytopathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Abha Goyal
- Division of Cytopathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Momin T. Siddiqui
- Division of Cytopathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Jonas J. Heymann
- Division of Cytopathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
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8
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Park HJ, Baek I, Cheang G, Solomon JP, Song W. Comparison of RNA-Based Next-Generation Sequencing Assays for the Detection of NTRK Gene Fusions. J Mol Diagn 2021; 23:1443-1451. [PMID: 34756276 DOI: 10.1016/j.jmoldx.2021.07.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/28/2021] [Accepted: 07/16/2021] [Indexed: 12/29/2022] Open
Abstract
Recently, the US Food and Drug Administration approved several targeted therapies directed against oncogenic fusions. One of the most effective such targeted therapies is Vitrakvi (larotrectinib), highly specific oral tropomyosin receptor kinase inhibitor indicated for the treatment of patients with any solid tumor harboring a fusion involving one of the neurotrophic receptor tyrosine kinase (NTRK) genes. Although several diagnostic approaches can be used to detect these NTRK fusions, RNA-based next-generation sequencing remains one of the most sensitive methods, as it can directly detect the transcribed end product of gene fusion at the mRNA level. In this study, performance characteristics of three RNA-based next-generation sequencing assays with distinct mechanisms and chemistries were investigated: anchored multiplex PCR, amplicon-based multiplex PCR, and hybrid capture-based enrichment method. Analytical sensitivity analysis shows that the amplicon-based multiplex PCR method has the lowest limit of detection. However, both hybrid-capture and anchored multiplex PCR methods can detect NTRK fusions with uncommon or novel fusion partners, which is challenging for the amplicon-based multiplex method. As for clinical sensitivity, all three methods were highly concordant in detecting NTRK fusions in patient samples. Additionally, they all presented equivalent high-level performance in specificity, suggesting that all three platforms can detect NTRK fusions in clinical samples with similar performance characteristics.
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Affiliation(s)
- Hyeon J Park
- Department of Laboratory Medicine and Pathology, Weill Cornell Medicine, New York, New York
| | - Inji Baek
- Department of Laboratory Medicine and Pathology, Weill Cornell Medicine, New York, New York
| | - Gloria Cheang
- Department of Laboratory Medicine and Pathology, Weill Cornell Medicine, New York, New York
| | - James P Solomon
- Department of Laboratory Medicine and Pathology, Weill Cornell Medicine, New York, New York
| | - Wei Song
- Department of Laboratory Medicine and Pathology, Weill Cornell Medicine, New York, New York.
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9
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Hissong E, Baek I, Costa V, Beneck D, Saxena A, Solomon JP, Song W. Identification of a Microsatellite Stable, EGFR-Mutant Lung Adenocarcinoma Developing in a Patient With Lynch Syndrome. JCO Precis Oncol 2020; 4:818-822. [PMID: 35050755 DOI: 10.1200/po.20.00074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Erika Hissong
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY
| | - Inji Baek
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY
| | - Victoria Costa
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY
| | - Debra Beneck
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY
| | - Ashish Saxena
- Department of Medicine New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY
| | - James P Solomon
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY
| | - Wei Song
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY
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10
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Abstract
Due to the efficacy of tropomyosin receptor kinase (TRK) inhibitor therapy and the recent Food and Drug Administration approval of larotrectinib, it is now clinically important to accurately and efficiently identify patients with neurotrophic TRK (NTRK) fusion-driven cancer. These oncogenic fusions occur when the kinase domain of NTRK1, NTRK2 or NTRK3 fuse with any of a number of N-terminal partners. NTRK fusions are characteristic of a few rare types of cancer, such as secretory carcinoma of the breast or salivary gland and infantile fibrosarcoma, but they are also infrequently seen in some common cancers, such as melanoma, glioma and carcinomas of the thyroid, lung and colon. There are multiple methods for identifying NTRK fusions, including pan-TRK immunohistochemistry, fluorescence in situ hybridisation and sequencing methods, and the advantages and drawbacks of each are reviewed here. While testing algorithms will obviously depend on availability of various testing modalities and economic considerations for each individual laboratory, we propose triaging specimens based on histology and other molecular findings to most efficiently identify tumours harbouring these treatable oncogenic fusions.
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Affiliation(s)
- J P Solomon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - R Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - J F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - M Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
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11
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Rosen EY, Goldman DA, Hechtman JF, Benayed R, Schram AM, Cocco E, Shifman S, Gong Y, Kundra R, Solomon JP, Bardelli A, Scaltriti M, Drilon A, Iasonos A, Taylor BS, Hyman DM. Abstract 16: Landscape and outcome of TRK fusion-positive Cancers. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.advprecmed20-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
TRK inhibitors achieve marked tumor-agnostic efficacy in TRK fusion-positive cancers and consequently are now an established standard of care. Little is known, however, about the demographics, clinical outcomes, response to alternative standard therapies, or genomic characteristics of TRK fusion-positive cancers. Utilizing a center-wide screening program involving more than 26,000 prospectively sequenced patients, genomic and clinical data from all cases with identified TRK fusions were extracted. An integrated analysis was performed of genomic, therapeutic, and phenomic outcomes. In total, we identified 76 cases with confirmed TRK fusions (0.27% overall prevalence) involving 48 unique rearrangements and 17 distinct cancer types. The presence of a TRK fusion was associated with depletion of concurrent oncogenic drivers (p=4.4E-7) and lower tumor mutation burden (p=4.2E-9), with the exception of colorectal cancer where TRK fusions co-occur with microsatellite instability (MSI-H). Longitudinal profiling in a subset of patients indicated that TRK fusions were present in all sampled timepoints in 82% (14/17) of cases. Progression-free survival on first-line therapy, excluding TRK inhibitors, administered for advanced disease was 9.6 months (95% CI: 4.8-13.2). The best ORR achieved with chemotherapy containing-regimens across all lines of therapy was 63% (95% CI: 41-81). Among 12 patients treated with checkpoint inhibitors, the only response observed was in an MSI-H colorectal patient. TRK fusion-positive cancers can respond to alternative standards of care, although efficacy of immunotherapy in the absence of other predictive biomarkers (MSI-H) appears limited. TRK fusions are present in tumors with simple genomes lacking in concurrent drivers that may partially explain the tumor-agnostic efficacy of TRK inhibitors.
Citation Format: Ezra Y. Rosen, Debra A. Goldman, Jaclyn F. Hechtman, Ryma Benayed, Alison M. Schram, Emiliano Cocco, Sophie Shifman, Yixiao Gong, Ritika Kundra, James P. Solomon, Alberto Bardelli, Maurizio Scaltriti, Alexander Drilon, Alexia Iasonos, Barry S. Taylor, David M. Hyman. Landscape and outcome of TRK fusion-positive Cancers [abstract]. In: Proceedings of the AACR Special Conference on Advancing Precision Medicine Drug Development: Incorporation of Real-World Data and Other Novel Strategies; Jan 9-12, 2020; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(12_Suppl_1):Abstract nr 16.
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Affiliation(s)
- Ezra Y. Rosen
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | | | - Ryma Benayed
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | | | | | - Yixiao Gong
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Ritika Kundra
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
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12
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Rosen EY, Goldman DA, Hechtman JF, Benayed R, Schram AM, Cocco E, Shifman S, Gong Y, Kundra R, Solomon JP, Bardelli A, Scaltriti M, Drilon A, Iasonos A, Taylor BS, Hyman DM. TRK Fusions Are Enriched in Cancers with Uncommon Histologies and the Absence of Canonical Driver Mutations. Clin Cancer Res 2019; 26:1624-1632. [PMID: 31871300 DOI: 10.1158/1078-0432.ccr-19-3165] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/14/2019] [Accepted: 12/19/2019] [Indexed: 01/19/2023]
Abstract
PURPOSE TRK inhibitors achieve marked tumor-agnostic efficacy in TRK fusion-positive cancers and consequently are now an established standard of care. Little is known, however, about the demographics, outcomes, response to alternative standard therapies, or genomic characteristics of TRK fusion-positive cancers. EXPERIMENTAL DESIGN Utilizing a center-wide screening program involving more than 26,000 prospectively sequenced patients, genomic and clinical data from all cases with TRK fusions were extracted. An integrated analysis was performed of genomic, therapeutic, and phenomic outcomes. RESULTS We identified 76 cases with confirmed TRK fusions (0.28% overall prevalence) involving 48 unique rearrangements and 17 cancer types. The presence of a TRK fusion was associated with depletion of concurrent oncogenic drivers (P < 0.001) and lower tumor mutation burden (P < 0.001), with the exception of colorectal cancer where TRK fusions cooccur with microsatellite instability (MSI-H). Longitudinal profiling in a subset of patients indicated that TRK fusions were present in all sampled timepoints in 82% (14/17) of cases. Progression-free survival on first-line therapy, excluding TRK inhibitors, administered for advanced disease was 9.6 months [95% confidence interval (CI), 4.8-13.2]. The best overall response rate achieved with chemotherapy containing-regimens across all lines of therapy was 63% (95% CI, 41-81). Among 12 patients treated with checkpoint inhibitors, a patient with MSI-H colorectal cancer had the only observed response. CONCLUSIONS TRK fusion-positive cancers can respond to alternative standards of care, although efficacy of immunotherapy in the absence of other predictive biomarkers (MSI-H) appears limited. TRK fusions are present in tumors with simple genomes lacking in concurrent drivers that may partially explain the tumor-agnostic efficacy of TRK inhibitors.
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Affiliation(s)
- Ezra Y Rosen
- Department of Medicine, Memorial Sloan Kettering, New York, New York
| | - Debra A Goldman
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering, New York, New York
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Emiliano Cocco
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering, New York, New York
| | - Sophie Shifman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering, New York, New York
| | - Yixiao Gong
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering, New York, New York
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering, New York, New York
| | - James P Solomon
- Department of Pathology, Memorial Sloan Kettering, New York, New York
| | - Alberto Bardelli
- Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy.,Department of Oncology, University of Torino, Candiolo, Italy
| | - Maurizio Scaltriti
- Department of Pathology, Memorial Sloan Kettering, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering, New York, New York
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Alexia Iasonos
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Barry S Taylor
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering, New York, New York.,Weill Cornell Medical College, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering, New York, New York.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering, New York, New York
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering, New York, New York. .,Weill Cornell Medical College, New York, New York
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13
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Solomon JP, Hechtman JF. Detection of NTRK Fusions: Merits and Limitations of Current Diagnostic Platforms. Cancer Res 2019; 79:3163-3168. [PMID: 31196931 DOI: 10.1158/0008-5472.can-19-0372] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/15/2019] [Accepted: 03/27/2019] [Indexed: 12/13/2022]
Abstract
Oncogenic fusions involving NTRK1, NTRK2, and NTRK3 with various partners are diagnostic of infantile fibrosarcoma and secretory carcinoma yet also occur in lower frequencies across many types of malignancies. Recently, targeted small molecular inhibitor therapy has been shown to induce a durable response in a high percentage of patients with NTRK fusion-positive cancers, which has made the detection of NTRK fusions critical. Several techniques for NTRK fusion diagnosis exist, including pan-Trk IHC, FISH, reverse transcription PCR, DNA-based next-generation sequencing (NGS), and RNA-based NGS. Each of these assays has unique features, advantages, and limitations, and familiarity with these assays is critical to appropriately screen for NTRK fusions. Here, we review the details of each existing methodology.
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Affiliation(s)
- James P Solomon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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Abstract
Although there have been many recent discoveries in the molecular alterations associated with urothelial carcinoma, current understanding of this disease lags behind many other malignancies. Historically, a two-pathway model had been applied to distinguish low- and high-grade urothelial carcinoma, although significant overlap and increasing complexity of molecular alterations has been recently described. In many cases, mutations in HRAS and FGFR3 that affect the MAPK and PI3K pathways seem to be associated with noninvasive low-grade papillary tumors, whereas mutations in TP53 and RB that affect the G1-S transition of the cell cycle are associated with high-grade in situ and invasive carcinoma. However, recent large-scale analyses have identified overlap in these pathways relative to morphology, and in addition, many other variants in a wide variety of oncogenes and tumor-suppressor genes have been identified. New technologies including next-generation sequencing have enabled more detailed analysis of urothelial carcinoma, and several groups have proposed molecular classification systems based on these data, although consensus is elusive. This article reviews the current understanding of alterations affecting oncogenes and tumor-suppressor genes associated with urothelial carcinoma, and their application in the context of morphology and classification schema.
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Affiliation(s)
- James P Solomon
- Department of Pathology, University of California, San Diego, 200 West Arbor Drive, La Jolla, CA 92103, USA
| | - Donna E Hansel
- Division of Anatomic Pathology, Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA 92093, USA.
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15
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Solomon JP, Lowenthal BM, Kader AK, Parsons JK, Flaig TW, Siefker-Radtke AO, Dyrskjøt L, Hansel DE. Challenges in the Diagnosis of Urothelial Carcinoma Variants: Can Emerging Molecular Data Complement Pathology Review? Urology 2017; 102:7-16. [DOI: 10.1016/j.urology.2016.10.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 09/12/2016] [Accepted: 10/07/2016] [Indexed: 11/17/2022]
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16
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Solomon JP, Dell'Aquila M, Fadare O, Hasteh F. Her2/neu Status Determination in Breast Cancer: A Single Institutional Experience Using a Dual-Testing Approach With Immunohistochemistry and Fluorescence In Situ Hybridization. Am J Clin Pathol 2017; 147:432-437. [PMID: 28340220 DOI: 10.1093/ajcp/aqw224] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES According to current guidelines, either immunohistochemistry (IHC) or in situ hybridization (ISH) can be used to determine human epidermal growth factor receptor 2 (Her2/neu) status in breast carcinoma. While the guidelines explicitly delineate result interpretation, there is no consensus on the most appropriate testing algorithm. METHODS The Her2/neu statuses of 369 consecutive cases of invasive breast cancer (from 351 patients) were assessed in a dual-testing algorithm that uses both IHC and fluorescence ISH (FISH). FISH was performed using dual-color HER2/ chromosome enumeration probe 17 ( CEP17 ) probes, and if equivocal results were obtained, reflex testing using HER2/lissencephaly gene 1 ( LIS1 ) probes was used. Results from both modalities were scored and reported using American Society of Clinical Oncology/College of American Pathologists 2013 criteria. RESULTS Sixty-one (16.5%) of the 369 tumors were found to be Her2/neu positive by at least one modality. The overall concordance between IHC and FISH results was 97.6%. Six of the 369 tumors were reclassified as Her2/neu positive after a negative IHC result. FISH was also able to identify significantly more Her2/neu-positive cases than IHC. CONCLUSIONS The commonly used reflex strategy based on IHC results may deny potentially beneficial targeted therapy for a small cohort of patients, which should be considered as testing guidelines are formulated and the cost-benefit analyses of various testing algorithms are assessed.
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Affiliation(s)
- James P Solomon
- From the Department of Pathology, University of California San Diego, La Jolla
| | - Marie Dell'Aquila
- From the Department of Pathology, University of California San Diego, La Jolla
| | - Oluwole Fadare
- From the Department of Pathology, University of California San Diego, La Jolla
| | - Farnaz Hasteh
- From the Department of Pathology, University of California San Diego, La Jolla
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17
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Solomon JP, Page LJ, Balch WE, Kelly JW. Gelsolin amyloidosis: genetics, biochemistry, pathology and possible strategies for therapeutic intervention. Crit Rev Biochem Mol Biol 2012; 47:282-96. [PMID: 22360545 DOI: 10.3109/10409238.2012.661401] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein misassembly into aggregate structures, including cross-β-sheet amyloid fibrils, is linked to diseases characterized by the degeneration of post-mitotic tissue. While amyloid fibril deposition in the extracellular space certainly disrupts cellular and tissue architecture late in the course of amyloid diseases, strong genetic, pathological and pharmacologic evidence suggests that the process of amyloid fibril formation itself, known as amyloidogenesis, likely causes these maladies. It seems that the formation of oligomeric aggregates during the amyloidogenesis process causes the proteotoxicity and cytotoxicity characteristic of these disorders. Herein, we review what is known about the genetics, biochemistry and pathology of familial amyloidosis of Finnish type (FAF) or gelsolin amyloidosis. Briefly, autosomal dominant D187N or D187Y mutations compromise Ca(2+) binding in domain 2 of gelsolin, allowing domain 2 to sample unfolded conformations. When domain 2 is unfolded, gelsolin is subject to aberrant furin endoproteolysis as it passes through the Golgi on its way to the extracellular space. The resulting C-terminal 68 kDa fragment (C68) is susceptible to extracellular endoproteolytic events, possibly mediated by a matrix metalloprotease, affording 8 and 5 kDa amyloidogenic fragments of gelsolin. These amyloidogenic fragments deposit systemically, causing a variety of symptoms including corneal lattice dystrophy and neurodegeneration. The first murine model of the disease recapitulates the aberrant processing of mutant plasma gelsolin, amyloid deposition, and the degenerative phenotype. We use what we have learned from our biochemical studies, as well as insight from mouse and human pathology to propose therapeutic strategies that may halt the progression of FAF.
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Affiliation(s)
- James P Solomon
- Departments of Chemistry and Molecular and Experimental Medicine, The Skaggs Institute for Chemical Biology, La Jolla, CA, USA
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18
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Solomon JP, Bourgault S, Powers ET, Kelly JW. Heparin binds 8 kDa gelsolin cross-β-sheet oligomers and accelerates amyloidogenesis by hastening fibril extension. Biochemistry 2011; 50:2486-98. [PMID: 21348501 DOI: 10.1021/bi101905n] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Glycosaminoglycans (GAGs) are highly sulfated linear polysaccharides prevalent in the extracellular matrix, and they associate with virtually all amyloid deposits in vivo. GAGs accelerate the aggregation of many amyloidogenic peptides in vitro, but little mechanistic evidence is available to explain why. Herein, spectroscopic methods demonstrate that GAGs do not affect the secondary structure of the monomeric 8 kDa amyloidogenic fragment of human plasma gelsolin. Moreover, monomerized 8 kDa gelsolin does not bind to heparin under physiological conditions. In contrast, 8 kDa gelsolin cross-β-sheet oligomers and amyloid fibrils bind strongly to heparin, apparently because of electrostatic interactions between the negatively charged polysaccharide and a positively charged region of the 8 kDa gelsolin assemblies. Our observations are consistent with a scaffolding mechanism whereby cross-β-sheet oligomers, upon formation, bind to GAGs, accelerating the fibril extension phase of amyloidogenesis, possibly by concentrating and orienting the oligomers to more efficiently form amyloid fibrils. Notably, heparin decreases the 8 kDa gelsolin concentration necessary for amyloid fibril formation, likely a consequence of fibril stabilization through heparin binding. Because GAG overexpression, which is common in amyloidosis, may represent a strategy for minimizing cross-β-sheet oligomer toxicity by transforming them into amyloid fibrils, the mechanism described herein for GAG-mediated acceleration of 8 kDa gelsolin amyloidogenesis provides a starting point for therapeutic strategy development. The addition of GAG mimetics, small molecule sulfonates shown to reduce the amyloid load in animal models of amyloidosis, to a heparin-accelerated 8 kDa gelsolin aggregation reaction mixture neither significantly alters the rate of amyloidogenesis nor prevents oligomers from binding to GAGs, calling into question their commonly accepted mechanism.
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Affiliation(s)
- James P Solomon
- Department of Chemistry and Molecular and Experimental Medicine and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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19
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Bourgault S, Solomon JP, Reixach N, Kelly JW. Sulfated glycosaminoglycans accelerate transthyretin amyloidogenesis by quaternary structural conversion. Biochemistry 2011; 50:1001-15. [PMID: 21194234 DOI: 10.1021/bi101822y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Glycosaminoglycans (GAGs), which are found in association with all extracellular amyloid deposits in humans, are known to accelerate the aggregation of various amyloidogenic proteins in vitro. However, the precise molecular mechanism(s) by which GAGs accelerate amyloidogenesis remains elusive. Herein, we show that sulfated GAGs, especially heparin, accelerate transthyretin (TTR) amyloidogenesis by quaternary structural conversion. The clustering of sulfate groups on heparin and its polymeric nature are essential features for accelerating TTR amyloidogenesis. Heparin does not influence TTR tetramer stability or TTR dissociation kinetics, nor does it alter the folded monomer-misfolded monomer equilibrium directly. Instead, heparin accelerates the conversion of preformed TTR oligomers into larger aggregates. The more rapid disappearance of monomeric TTR in the presence of heparin likely reflects the fact that the monomer-misfolded amyloidogenic monomer-oligomer-TTR fibril equilibria are all linked, a hypothesis that is strongly supported by the light scattering data. TTR aggregates prepared in the presence of heparin exhibit a higher resistance to trypsin and proteinase K proteolysis and a lower exposure of hydrophobic side chains comprising hydrophobic clusters, suggesting an active role for heparin in amyloidogenesis. Our data suggest that heparin accelerates TTR aggregation by a scaffold-based mechanism, in which the sulfate groups comprising GAGs interact primarily with TTR oligomers through electrostatic interactions, concentrating and orienting the oligomers, facilitating the formation of higher molecular weight aggregates. This model raises the possibility that GAGs may play a protective role in human amyloid diseases by interacting with proteotoxic oligomers and promoting their association into less toxic amyloid fibrils.
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Affiliation(s)
- Steve Bourgault
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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Murray AN, Solomon JP, Wang YJ, Balch WE, Kelly JW. Discovery and characterization of a mammalian amyloid disaggregation activity. Protein Sci 2010; 19:836-46. [PMID: 20162625 DOI: 10.1002/pro.363] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The formation of amyloid, a cross-beta-sheet fibrillar aggregate, is associated with a variety of aging-associated degenerative diseases. Herein, we report the existence of a mammalian amyloid disaggregase activity that is present in all tissues and cell types tested. Homogenates from mammalian tissues and cell lines are able to disaggregate amyloid fibrils composed of amyloid beta (A beta)(1-40) or the 8 kDa plasma gelsolin fragment. The mammalian disaggregase activity is sensitive to proteinase K digestion and can be uncoupled from proteolysis activity using a protease inhibitor cocktail. Amyloid disaggregation and proteolysis activities are remarkably resistant to changes in temperature and pH. Identification and manipulation of the proteins responsible for the amyloid disaggregation/degradation activities offers the possibility of ameliorating aggregation-associated diseases.
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Affiliation(s)
- Amber N Murray
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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21
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Solomon JP, Yonemoto IT, Murray AN, Price JL, Powers ET, Balch WE, Kelly JW. The 8 and 5 kDa fragments of plasma gelsolin form amyloid fibrils by a nucleated polymerization mechanism, while the 68 kDa fragment is not amyloidogenic. Biochemistry 2009; 48:11370-80. [PMID: 19904968 PMCID: PMC2907741 DOI: 10.1021/bi901368e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Familial amyloidosis of Finnish type (FAF), or gelsolin amyloidosis, is a systemic amyloid disease caused by a mutation (D187N/Y) in domain 2 of human plasma gelsolin, resulting in domain 2 misfolding within the secretory pathway. When D187N/Y gelsolin passes through the Golgi, furin endoproteolysis within domain 2 occurs as a consequence of the abnormal conformations that enable furin to bind and cleave, resulting in the secretion of a 68 kDa C-terminal fragment (amino acids 173-755, C68). The C68 fragment is cleaved upon secretion from the cell by membrane type 1 matrix metalloprotease (MT1-MMP), affording the 8 and 5 kDa fragments (amino acids 173-242 and 173-225, respectively) comprising the amyloid fibrils in FAF patients. Herein, we show that the 8 and 5 kDa gelsolin fragments form amyloid fibrils by a nucleated polymerization mechanism. In addition to demonstrating the expected concentration dependence of a nucleated polymerization reaction, the addition of preformed amyloid fibrils, or "seeds", was shown to bypass the requirement for the formation of a high-energy nucleus, accelerating 8 and 5 kDa D187N gelsolin amyloidogenesis. The C68 fragment can form small oligomers, but not amyloid fibrils, even when seeded with preformed 8 kDa fragment plasma gelsolin fibrils. Because the 68 kDa fragment of gelsolin does not form amyloid fibrils in vitro or in a recently published transgenic mouse model of FAF, we propose that administration of an MT1-MMP inhibitor could be an effective strategy for the treatment of FAF.
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Affiliation(s)
- James P. Solomon
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - Isaac T. Yonemoto
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - Amber N. Murray
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - Joshua L. Price
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - Evan T. Powers
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - William E. Balch
- Departments of Cell Biology and Chemical Physiology and the Institute for Childhood and Neglected Diseases, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - Jeffery W. Kelly
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 USA
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