1
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Brar N, Lawrence L, Fung E, Zehnder JL, Greenberg PL, Mannis GN, Zhang TY, Gratzinger D, Oak J, Silva O, Kurzer J, Tan B, Menke JR, Fernandez-Pol S. p53 immunohistochemistry as an ancillary tool for rapid assessment of residual disease in TP53-mutated acute myeloid leukemia and myelodysplastic syndromes. Am J Clin Pathol 2024:aqae034. [PMID: 38643353 DOI: 10.1093/ajcp/aqae034] [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: 11/07/2023] [Accepted: 03/02/2024] [Indexed: 04/22/2024] Open
Abstract
OBJECTIVES Measurable residual disease flow cytometry (MRD-FC) and molecular studies are the most sensitive methods for detecting residual malignant populations after therapy for TP53-mutated acute myeloid leukemia and myelodysplastic neoplasms (TP53+ AML/MDS). However, their sensitivity is limited in suboptimal aspirates or when the immunophenotype of the neoplastic blasts overlaps with erythroids or normal maturing myeloid cells. In this study, we set out to determine if p53 immunohistochemistry (IHC) correlates with MRD-FC and next-generation sequencing (NGS) in the posttherapy setting and to determine the utility of p53 IHC to detect residual disease in the setting of negative or equivocal MRD-FC. METHODS We retrospectively identified 28 pre- and posttherapy bone marrow biopsy specimens from 9 patients with TP53+ AML/MDS and a p53 overexpressor phenotype by IHC (strong 3+ staining at initial diagnosis). Next-generation sequencing and/or MRD-FC results were collected for each specimen. RESULTS Using a threshold of more than ten 2-3+ cells in any one 400× field, p53 IHC detected residual disease with a sensitivity of 94% and a specificity of 89%. The threshold used in this study showed a high degree of concordance among 6 blinded pathologists (Fleiss κ = 0.97). CONCLUSIONS Our study suggests that p53 IHC can be used as a rapid tool (within 24 hours) to aid in the detection of residual disease that may complement MRD-FC or NGS in cases in which the flow cytometry immunophenotype is equivocal and/or the bone marrow aspirate is suboptimal.
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Affiliation(s)
- Nivaz Brar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
| | - Lauren Lawrence
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
| | - Eula Fung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford, CA, US
| | - Peter L Greenberg
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford, CA, US
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, US
| | - Gabriel N Mannis
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford, CA, US
| | - Tian Y Zhang
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford, CA, US
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, US
| | - Dita Gratzinger
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
| | - Jean Oak
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
| | - Oscar Silva
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
| | - Jason Kurzer
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
| | - Brent Tan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
| | - Joshua R Menke
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
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2
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Fei F, Kunder CA, Ho C, Zehnder JL, Tomasello G, Fung E, Suarez CJ. Diagnostic impact of RNA-based next-generation sequencing fusion panel for solid tumors: A single-institution experience. Am J Clin Pathol 2024; 161:329-341. [PMID: 38001052 DOI: 10.1093/ajcp/aqad148] [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: 07/02/2023] [Accepted: 10/06/2023] [Indexed: 11/26/2023] Open
Abstract
OBJECTIVES Gene rearrangements frequently act as oncogenic driver mutations and determine the onset and progression of cancer. RNA-based next-generation sequencing (NGS) is being used with increasing frequency for solid tumors. The purpose of our study is to investigate the feasibility and utility of an RNA-based NGS fusion panel for solid tumors. METHODS We conducted a retrospective, single-institution review of fusion panels requested between May 2022 and March 2023. Demographic, clinical, pathologic, and molecular findings of the patients were reviewed. The utility of the RNA-based NGS fusion panel for the pathologic diagnosis of solid tumors was assessed. RESULTS Our study included 345 cases, and a fusion event was identified in 24.3% (78/321) of cases. Among the 110 cases submitted for diagnostic purposes, a fusion event was detected in 42.7% (47/110) of cases. The results led to refinement or clarification of the initial diagnosis in 31.9% (15/47) of cases and agreement or support for the initial diagnosis in 59.6% (28/47) of cases. Furthermore, our study indicated that the overall cellularity (tumor and normal tissue) of the tested specimen influences the success of the testing process. CONCLUSIONS In summary, this study demonstrated the feasibility and utility of an RNA-based NGS fusion panel for a wide variety of solid tumors in the appropriate clinicopathologic context. These findings warrant further validation in larger studies involving multiple institutional patient cohorts.
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Affiliation(s)
- Fei Fei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
- Department of Pathology, City of Hope Medical Center, Duarte, CA, US
| | - Christian A Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
| | - Chandler Ho
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
| | - Gianna Tomasello
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
| | - Eula Fung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
| | - Carlos J Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, US
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3
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Zhang H, Villar-Prados A, Bussel JB, Zehnder JL. The highs and lows of cyclic thrombocytopenia. Br J Haematol 2024; 204:56-67. [PMID: 38083878 PMCID: PMC10906350 DOI: 10.1111/bjh.19239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 01/11/2024]
Abstract
Cyclic thrombocytopenia (CTP) is characterized by periodic platelet oscillation with substantial amplitude. Most CTP cases have a thrombocytopenic background and are often misdiagnosed as immune thrombocytopenia with erratically effective treatment choices. CTP also occurs during hydroxyurea treatment in patients with myeloproliferative diseases. While the aetiology of CTP remains uncertain, here we evaluate historical, theoretical and clinical findings to provide a framework for understanding CTP pathophysiology. CTP retains the intrinsic oscillatory factors defined by the homeostatic regulation of platelet count, presenting as reciprocal platelet/thrombopoietin oscillations and stable oscillation periodicity. Moreover, CTP patients possess pathogenic factors destabilizing the platelet homeostatic system thereby creating opportunities for external perturbations to initiate and sustain the exaggerated platelet oscillations. Beyond humoral and cell-mediated autoimmunity, we propose recently uncovered germline and somatic genetic variants, such as those of MPL, STAT3 or DNMT3A, as pathogenic factors in thrombocytopenia-related CTP. Likewise, the JAK2 V617F or BCR::ABL1 translocation that drives underlying myeloproliferative diseases may also play a pathogenic role in hydroxyurea-induced CTP, where hydroxyurea treatment can serve as both a trigger and a pathogenic factor of platelet oscillation. Elucidating the pathogenic landscape of CTP provides an opportunity for targeted therapeutic approaches in the future.
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Affiliation(s)
- Haiyu Zhang
- Department of Pathology. Stanford University School of Medicine, Stanford, California, 94305
| | - Alejandro Villar-Prados
- Department of Medicine, Division of Hematology and Oncology. Stanford University School of Medicine, Stanford, California, 94305
| | - James B. Bussel
- Department of Pediatrics. Division of Oncology/Hematology, New York Presbyterian Hospital/Weill Cornell Medical College, New York, NY, 10065
| | - James L. Zehnder
- Department of Pathology and Department of Medicine, Division of Hematology. Stanford University School of Medicine, Stanford, California, 94305
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4
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Zehnder JL, Bussel JB, Cooper N. The role of genetics in refractory immune thrombocytopenia. Br J Haematol 2023; 203:62-64. [PMID: 37735556 DOI: 10.1111/bjh.19110] [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: 06/15/2023] [Accepted: 07/31/2023] [Indexed: 09/23/2023]
Abstract
Patients with refractory immune thrombocytopenia (rITP) have increased morbidity and mortality. Currently, there is limited understanding of the cause of refractoriness and no markers to help direct novel treatment options. Understanding the reason(s) for refractoriness is crucial to determining novel treatment options. The pathogenesis underlying rITP has generally been thought to be an underlying genetic predisposition with an environmental trigger. Familial ITP remains rare, and there are few twin studies, suggesting that a simple genetic cause is unlikely. However, genetic mutations provide the background for several autoimmune diseases. In this review, we explore the evidence of either an inherited genetic cause of rITP or an acquired mutation, in particular one resulting in clonal expansion of cytotoxic T cells.
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Affiliation(s)
- James L Zehnder
- Department of Pathology and Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - James B Bussel
- Division of Hematology/Oncology, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Nichola Cooper
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK
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5
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Luo RY, Pfaffroth C, Yang S, Hoang K, Yeung PSW, Zehnder JL, Shi RZ. Study of β 1-transferrin and β 2-transferrin using microprobe-capture in-emitter elution and high-resolution mass spectrometry. Sci Rep 2023; 13:14974. [PMID: 37696850 PMCID: PMC10495423 DOI: 10.1038/s41598-023-42064-7] [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: 03/10/2023] [Accepted: 09/05/2023] [Indexed: 09/13/2023] Open
Abstract
Cerebrospinal fluid (CSF) leak can be diagnosed in clinical laboratories by detecting a diagnostic marker β2-transferrin (β2-Tf) in secretion samples. β2-Tf and the typical transferrin (Tf) proteoform in serum, β1-transferrin (β1-Tf), are Tf glycoforms. An innovative affinity capture technique for sample preparation, called microprobe-capture in-emitter elution (MPIE), was incorporated with high-resolution mass spectrometry (HR-MS) to study the Tf glycoforms and the primary structures of β1-Tf and β2-Tf. To implement MPIE, an analyte is first captured on the surface of a microprobe, and subsequently eluted from the microprobe inside an electrospray emitter. The capture process is monitored in real-time via next-generation biolayer interferometry (BLI). When electrospray is established from the emitter to a mass spectrometer, the analyte is immediately ionized via electrospray ionization (ESI) for HR-MS analysis. Serum, CSF, and secretion samples were analyzed using MPIE-ESI-MS. Based on the MPIE-ESI-MS results, the primary structures of β1-Tf and β2-Tf were elucidated. As Tf glycoforms, β1-Tf and β2-Tf share the amino acid sequence but contain varying N-glycans: (1) β1-Tf, the major serum-type Tf, has two G2S2 N-glycans on Asn413 and Asn611; and (2) β2-Tf, the major brain-type Tf, has an M5 N-glycan on Asn413 and a G0FB N-glycan on Asn611. The resolving power of the innovative MPIE-ESI-MS method was demonstrated in the study of β2-Tf as well as β1-Tf. Knowing the N-glycan structures on β2-Tf allows for the design of more novel test methods for β2-Tf in the future.
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Affiliation(s)
- Ruben Yiqi Luo
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Clinical Laboratories, Stanford Health Care, 3375 Hillview Ave, Palo Alto, CA, 94304, USA.
| | - Christopher Pfaffroth
- Clinical Laboratories, Stanford Health Care, 3375 Hillview Ave, Palo Alto, CA, 94304, USA
| | - Samuel Yang
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kevin Hoang
- Clinical Laboratories, Stanford Health Care, 3375 Hillview Ave, Palo Alto, CA, 94304, USA
| | - Priscilla S-W Yeung
- Department of Pathology, Stanford University, Stanford, CA, USA
- Clinical Laboratories, Stanford Health Care, 3375 Hillview Ave, Palo Alto, CA, 94304, USA
| | - James L Zehnder
- Department of Pathology, Stanford University, Stanford, CA, USA
- Clinical Laboratories, Stanford Health Care, 3375 Hillview Ave, Palo Alto, CA, 94304, USA
| | - Run-Zhang Shi
- Department of Pathology, Stanford University, Stanford, CA, USA
- Clinical Laboratories, Stanford Health Care, 3375 Hillview Ave, Palo Alto, CA, 94304, USA
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6
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Fei F, Stehr H, Zehnder JL. Genomic landscape of T-large granular lymphocyte leukemia and chronic lymphoproliferative disorder of NK cells: a single institution experience. Leuk Lymphoma 2023; 64:1536-1544. [PMID: 37330635 DOI: 10.1080/10428194.2023.2220450] [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: 03/20/2023] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/19/2023]
Abstract
LGLL is a rare and chronic lymphoproliferative disorder including T-LGLL and CLPD-NK. Here, we investigated the genomic profiles of LGLL with a focus on STAT3 and STAT5B mutations in a cohort of 49 patients (41 T-LGLL, 8 CLPD-NK). Our study indicated that STAT3 was identified in 38.8% (19/49) of all patients, while STAT5B occurred in only 8.2% (4/49) of patients. We found that STAT3 mutations were associated with lower ANC in T-LGLL patients. The average number of pathogenic/likely pathogenic mutations in STAT3/STAT5B-mutated patients was significantly higher than that in WT patients (1.78 ± 1.17 vs 0.65 ± 1.36, p = 0.0032). Additionally, TET2-only mutated T-LGLL (n = 5) had a significant reduction in platelet values compared with the WT (n = 16) or STAT3-only mutated T-LGLL (n = 12) (p < 0.05). In conclusion, we compared the somatic mutational landscape between STAT3/STAT5B WT and mutated patients and correlate with their distinct clinical characteristics.
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Affiliation(s)
- Fei Fei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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7
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Malik A, Sayed AA, Han P, Tan MMH, Watt E, Constantinescu-Bercu A, Cocker ATH, Khoder A, Saputil RC, Thorley E, Teklemichael A, Ding Y, Hart ACJ, Zhang H, Mitchell WA, Imami N, Crawley JTB, Salles-Crawley II, Bussel JB, Zehnder JL, Adams S, Zhang BM, Cooper N. The role of CD8+ T-cell clones in immune thrombocytopenia. Blood 2023; 141:2417-2429. [PMID: 36749920 PMCID: PMC10329190 DOI: 10.1182/blood.2022018380] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 02/09/2023] Open
Abstract
Immune thrombocytopenia (ITP) is traditionally considered an antibody-mediated disease. However, a number of features suggest alternative mechanisms of platelet destruction. In this study, we use a multidimensional approach to explore the role of cytotoxic CD8+ T cells in ITP. We characterized patients with ITP and compared them with age-matched controls using immunophenotyping, next-generation sequencing of T-cell receptor (TCR) genes, single-cell RNA sequencing, and functional T-cell and platelet assays. We found that adults with chronic ITP have increased polyfunctional, terminally differentiated effector memory CD8+ T cells (CD45RA+CD62L-) expressing intracellular interferon gamma, tumor necrosis factor α, and granzyme B, defining them as TEMRA cells. These TEMRA cells expand when the platelet count falls and show no evidence of physiological exhaustion. Deep sequencing of the TCR showed expanded T-cell clones in patients with ITP. T-cell clones persisted over many years, were more prominent in patients with refractory disease, and expanded when the platelet count was low. Combined single-cell RNA and TCR sequencing of CD8+ T cells confirmed that the expanded clones are TEMRA cells. Using in vitro model systems, we show that CD8+ T cells from patients with ITP form aggregates with autologous platelets, release interferon gamma, and trigger platelet activation and apoptosis via the TCR-mediated release of cytotoxic granules. These findings of clonally expanded CD8+ T cells causing platelet activation and apoptosis provide an antibody-independent mechanism of platelet destruction, indicating that targeting specific T-cell clones could be a novel therapeutic approach for patients with refractory ITP.
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Affiliation(s)
- Amna Malik
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Anwar A. Sayed
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Medical Microbiology and Immunology, Taibah University, Medina, Saudi Arabia
| | - Panpan Han
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
- Department of Hematology, Shandong Province Hospital, Shandong First Medical University, Jinan, China
| | - Michelle M. H. Tan
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Eleanor Watt
- Specialist Integrated Haematology and Malignancy Diagnostic Service–Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Adela Constantinescu-Bercu
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | | | - Ahmad Khoder
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Rocel C. Saputil
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Emma Thorley
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Ariam Teklemichael
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Yunchuan Ding
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Alice C. J. Hart
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Haiyu Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Wayne A. Mitchell
- Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Nesrina Imami
- Centre for Immunology and Vaccinology, Imperial College London, London, United Kingdom
| | - James T. B. Crawley
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Isabelle I. Salles-Crawley
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Vascular Biology Research Centre, Molecular and Clinical Sciences Research Institute, St. George’s, University of London, London, United Kingdom
| | - James B. Bussel
- Department of Pediatrics, Weill Cornell Medicine, New York, NY
| | - James L. Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Stuart Adams
- Specialist Integrated Haematology and Malignancy Diagnostic Service–Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Bing M. Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Nichola Cooper
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
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8
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Kumar J, Patel S, Chang A, Mukherjee S, Small C, Gollapudi S, Butzmann A, Jangam D, Weinberg OK, George TI, Zehnder JL, Ohgami RS. Smoking status in acute myeloid leukemia is associated with worse overall survival and independent of prior nonhematopoietic malignancies, cytogenetic abnormalities, and WHO category. Hum Pathol 2023; 135:45-53. [PMID: 36921727 DOI: 10.1016/j.humpath.2023.03.005] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
Acute myeloid leukemia (AML) is an aggressive hematopoietic malignancy with several patient- and disease-associated variables known to impact prognosis. Tobacco smoking is an environmental factor associated with a greater incidence of AML, but there have been limited studies that evaluated smoking toward overall survival. We retrospectively searched for AML cases and collected clinical and diagnostic data for each case. We also used an independent next-generation sequencing (NGS) data set to assess for a distinct mutational signature associated with smoking. When stratified by smoking status, there was a greater number of males, patients aged ≥60 years, and patients with ≥2 comorbidities within the smoking category (P < .05). Survival analysis demonstrated decreased survival probability in the smokers, male smokers, smokers with 1 other comorbidity, and smokers without a prior history of nonhematopoietic malignancy (P < .05) as compared to nonsmokers. Smoking was associated with a decrease in survival within the World Health Organization categories of AML, not otherwise specified (AML NOS; P = .035) and AML with recurrent genetic abnormalities (AML RGA; P = .002). Multivariate analysis showed that patients who were smokers had a greater hazard ratio than nonsmokers after adjusting for the other covariates. Our findings demonstrated that smoking was independently associated with decreased overall survival after adjusting for other potentially confounding factors. In addition, our results suggest that a mutational signature can be recognized using NGS data in a subset of AML patients who smoke.
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Affiliation(s)
- Jyoti Kumar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065 United States.
| | - Samit Patel
- Department of Pharmacy, Stanford University School of Medicine, Stanford, CA, 94305 United States
| | - Abraham Chang
- Department of Pharmacy, Stanford University School of Medicine, Stanford, CA, 94305 United States
| | - Soham Mukherjee
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143 United States
| | - Corinn Small
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143 United States
| | - Sumanth Gollapudi
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143 United States
| | - Alexandra Butzmann
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143 United States
| | - Diwash Jangam
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305 United States
| | - Olga K Weinberg
- Department of Pathology, University of Texas Southwestern, Dallas, TX, 75235 United States
| | - Tracy I George
- Department of Pathology, University of Utah Health, Salt Lake City, UT, 84132 United States
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305 United States
| | - Robert S Ohgami
- Department of Pathology, University of Utah Health, Salt Lake City, UT, 84132 United States
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9
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Tung JK, Jangam D, Ho CC, Fung E, Khodadoust MS, Kim YH, Zehnder JL, Stehr H, Zhang BM. Minimal/Measurable Residual Disease (MRD) Monitoring in Patients with Lymphoid Neoplasms by High-Throughput Sequencing of the T-Cell Receptor. J Mol Diagn 2023; 25:331-341. [PMID: 36870603 DOI: 10.1016/j.jmoldx.2023.02.002] [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] [Received: 04/12/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 03/06/2023] Open
Abstract
High-throughput sequencing of the T-cell receptor beta (TRB) and gamma (TRG) loci is increasingly utilized due to its high sensitivity, specificity, and versatility in the diagnosis of various T-cell malignancies. Application of these technologies for tracking disease burden can be valuable in detecting recurrence, determining response to therapy, guiding future management of patients, and establishing endpoints for clinical trials. In this study, the performance of the commercially available LymphoTrack high-throughput sequencing assay was assessed for determining residual disease burden in patients with various T-cell malignancies seen at the authors' institution. A custom bioinformatics pipeline and database was also developed to facilitate minimal/measurable residual disease analysis and clinical reporting. This assay demonstrated excellent test performance characteristics, achieving a sensitivity of 1 of 100,000 T-cell equivalents for the DNA inputs evaluated and high concordance with orthogonal testing methods. This assay was further utilized to correlate disease burden in several patients, demonstrating its potential utility for monitoring patients with T-cell malignancies.
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Affiliation(s)
- Jack K Tung
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Diwash Jangam
- Molecular Pathology Laboratory, Stanford Health Care, Stanford, California
| | - Chandler C Ho
- Molecular Pathology Laboratory, Stanford Health Care, Stanford, California
| | - Eula Fung
- Molecular Pathology Laboratory, Stanford Health Care, Stanford, California
| | - Michael S Khodadoust
- Department of Dermatology, Stanford University School of Medicine, Stanford, California; Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, California
| | - Youn H Kim
- Department of Dermatology, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Bing M Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
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10
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Luo RY, Wong C, Xia JQ, Glader BE, Shi RZ, Zehnder JL. Neutral-Coating Capillary Electrophoresis Coupled with High-Resolution Mass Spectrometry for Top-Down Identification of Hemoglobin Variants. Clin Chem 2023; 69:56-67. [PMID: 36308334 DOI: 10.1093/clinchem/hvac171] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/30/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Identification of hemoglobin (Hb) variants is of significant value in the clinical diagnosis of hemoglobinopathy. However, conventional methods for identification of Hb variants in clinical laboratories can be inadequate due to the lack of structural characterization. We describe the use of neutral-coating capillary electrophoresis coupled with high-resolution mass spectrometry (CE-HR-MS) to achieve high-performance top-down identification of Hb variants. METHODS An Orbitrap Q-Exactive Plus mass spectrometer was coupled with an ECE-001 capillary electrophoresis (CE) unit through an EMASS-II ion source. A PS1 neutral-coating capillary was used for CE. Samples of red blood cells were lysed in water and diluted in 10 mM ammonium formate buffer for analysis. Deconvolution of raw mass spectrometry data was carried out to merge multiple charge states and isotopic peaks of an analyte to obtain its monoisotopic mass. RESULTS The neutral-coating CE could baseline separate individual Hb subunits dissociated from intact Hb forms, and the HR-MS could achieve both intact-protein analysis and top-down analysis of analytes. A number of patient samples that contain Hb subunit variants were analyzed, and the variants were successfully identified using the CE-HR-MS method. CONCLUSIONS The CE-HR-MS method has been demonstrated as a useful tool for top-down identification of Hb variants. With the ability to characterize the primary structures of Hb subunits, the CE-HR-MS method has significant advantages to complement or partially replace the conventional methods for the identification of Hb variants.
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Affiliation(s)
- Ruben Yiqi Luo
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.,Clinical Laboratories, Stanford Health Care, Palo Alto, CA, USA
| | - Carolyn Wong
- Clinical Laboratories, Stanford Health Care, Palo Alto, CA, USA
| | | | - Bertil E Glader
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.,Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Run-Zhang Shi
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.,Clinical Laboratories, Stanford Health Care, Palo Alto, CA, USA
| | - James L Zehnder
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.,Clinical Laboratories, Stanford Health Care, Palo Alto, CA, USA
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11
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Testa S, Kumar J, Goodell AJ, Zehnder JL, Alexander KM, Sidana S, Arai S, Witteles RM, Liedtke M. Prevalence, mutational spectrum and clinical implications of clonal hematopoiesis of indeterminate potential in plasma cell dyscrasias. Semin Oncol 2022; 49:465-475. [PMID: 36503855 DOI: 10.1053/j.seminoncol.2022.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is common both in healthy individuals and patients with hematological cancers. Recent studies have showed worse prognosis for patients with multiple myeloma (MM) and non-Hodgkin lymphoma undergoing stem cell transplant, that have concomitant presence of CHIP. Data regarding the clinical and biological role of CHIP in plasma cell dyscrasias (PCDs) is rapidly increasing. However, the prevalence and prognostic implication of CHIP in patients with MM outside of the transplant setting, and in those with other more indolent PCDs remains elusive. Here we explored the prevalence and clinical implications of CHIP detected through next-generation sequencing in 209 patients with PCDs including MM, light chain (AL) amyloidosis (ALA), monoclonal gammopathy of undetermined significance (MGUS), and smoldering multiple myeloma (SMM). To avoid attributing the mutations to the plasma cell clone, CHIP was defined as the presence of DNMT3A, TET2, or ASXL1 mutations in the peripheral blood or bone marrow (DTA-CH). The prevalence of DTA-CH was 19% in patients with PCDs, with no difference between each PCD. TET2 (23%) and DNMT3A (22%), were the most frequently mutated genes. DTA-CH correlated with older age in MM (P = .001) and MGUS/SMM (P = 0.0007), as well as with coronary artery disease or congestive heart failure in MM (P = .03). DTA-CH did not predict worse OS or PFS in either MM or ALA, nor it predict higher risk of progression to MM in patients with MGUS/SMM. Our results overall further elucidate the prevalence and mutational spectrum of CHIP in PCDs, providing more information regarding the clinical relevance of CHIP in this patient population.
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Affiliation(s)
- Stefano Testa
- Department of Medicine, Stanford University, Stanford, CA, USA.
| | - Jyoti Kumar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alex J Goodell
- Department of Medicine, Stanford University, Stanford, CA, USA; Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kevin M Alexander
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Surbhi Sidana
- Division of BMT and Cellular Therapy, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Sally Arai
- Division of BMT and Cellular Therapy, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ronald M Witteles
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Michaela Liedtke
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA
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12
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Devereaux KA, Steiner DF, Ho C, Gomez AJ, Gilks B, Longacre TA, Zehnder JL, Howitt BE, Suarez CJ. A Multiplex SNaPshot Assay is a Rapid and Cost-Effective Method for Detecting POLE Exonuclease Domain Mutations in Endometrial Carcinoma. Int J Gynecol Pathol 2022; 41:541-551. [PMID: 34907997 DOI: 10.1097/pgp.0000000000000841] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Determining the replicative DNA polymerase epsilon ( POLE) mutation status in endometrial carcinomas (ECs) has important clinical implications given that the majority of "ultramutated" tumors harboring pathogenic exonuclease domain mutations in POLE ( POLE mut) have a favorable prognosis, even among high-grade histotypes. Currently, there are no specific morphologic or immunophenotypic features that allow accurate detection of POLE mut tumors without molecular testing. Consequently, identifying POLE mut tumors has been challenging without employing costly and/or time-consuming DNA sequencing approaches. Here we developed a novel SNaPshot assay to facilitate routine and efficient POLE mutation testing in EC. The SNaPshot assay interrogates 15 nucleotide sites within exons 9, 11, 13, and 14 encoding the POLE exonuclease domain. The variant sites were selected based on recurrence, evidence of functional impact, association with high tumor mutation burden and/or detection in EC clinical outcome studies. Based on the pathogenic somatic variants reported in the literature, the assay is predicted to have a clinical sensitivity of 90% to 95% for ECs. Validation studies showed 100% specificity and sensitivity for the variants covered, with expected genotypic results for both the positive (n=11) and negative (n=20) patient controls on multiple repeat tests and dilution series. Analytic sensitivity was conservatively approximated at a 10% variant allele fraction (VAF), with documented detection as low as 5% VAF. As expected, the SNaPshot assay demonstrated greater sensitivity than Sanger sequencing for VAFs below 20%, an important characteristic for somatic mutation detection. Here we have developed and validated the first SNaPshot assay to detect hotspot POLE mutations. While next-generation sequencing and Sanger sequencing-based approaches have also been used to detect POLE mutations, a SNaPshot approach provides useful balance of analytical sensitivity, cost-effectiveness, and efficiency in a high-volume case load setting.
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13
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Rohatgi N, Zehnder JL, Smilowitz NR. Management of Antiplatelet Therapy in Patients with Coronary Stents Undergoing Noncardiac Surgery. Am J Med 2022; 135:e305-e307. [PMID: 35636479 DOI: 10.1016/j.amjmed.2022.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Nidhi Rohatgi
- Division of Hospital Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, Calif.
| | - James L Zehnder
- Division of Hematology, Department of Medicine and Clinical Pathology, Stanford University School of Medicine, Stanford, Calif
| | - Nathaniel R Smilowitz
- Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY
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14
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Miller JA, Sahoo MK, Yamamoto F, Huang C, Wang H, Zehnder JL, Le QT, Pinsky BA. Multiplex Epstein-Barr virus BALF2 genotyping detects high-risk variants in plasma for population screening of nasopharyngeal carcinoma. Mol Cancer 2022; 21:154. [PMID: 35902864 PMCID: PMC9330640 DOI: 10.1186/s12943-022-01625-6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/04/2022] [Indexed: 11/10/2022] Open
Abstract
Background Epstein-Barr Virus (EBV)-associated nasopharyngeal carcinoma (NPC) exhibits unusual geographic restriction despite ubiquitous lifelong infection. Screening programs can detect most NPC cases at an early stage, but existing EBV diagnostics are limited by false positives and low positive predictive value (PPV), leading to excess screening endoscopies, MRIs, and repeated testing. Recent EBV genome-wide association studies (GWAS) suggest that EBV BALF2 variants account for more than 80% of attributable NPC risk. We therefore hypothesized that high-risk BALF2 variants could be readily detected in plasma for once-lifetime screening triage. Methods We designed and validated a multiplex genotyping assay to detect EBV BALF2 polymorphisms in human plasma. Targeted next-generation sequencing was used to validate this assay, conduct association studies with clinical phenotype, and longitudinally genotype plasma to assess within-host haplotype stability. We examined the association between NPC and BALF2 haplotypes in a large non-endemic population and three prior EBV GWAS. Finally, we estimated NPC mortality reduction, resource utilization, and cost-effectiveness of BALF2 variant-informed screening using a previously-validated cohort model. Results Following analytical validation, the BALF2 genotyping assay had 99.3% concordance with sequencing in a cohort of 24 NPC cases and 155 non-NPC controls. BALF2 haplotype was highly associated with NPC in this non-endemic population (I613V: odds ratio [OR] 7.9; V317M: OR 178.8). No other candidate BALF2 polymorphisms were significantly associated with NPC or hematologic disorders. Longitudinal genotyping revealed 97.8% within-host haplotype concordance, indicative of lifelong latent infection. In a meta-analysis of 755 NPC cases and 981 non-NPC controls, BALF2 I613V and V317M were significantly associated with NPC in both endemic and non-endemic populations. Modeled variant-informed screening strategies achieved a 46% relative increase in PPV with 7% decrease in effective screening sensitivity, thereby averting nearly half of screening endoscopies/MRIs among endemic populations in east/southeast Asia. Conclusions EBV BALF2 haplotypes are temporally stable within hosts and can be readily detected in plasma via an inexpensive multiplex genotyping assay that offers near-perfect sequencing concordance. In endemic and non-endemic populations, I613V and V317M were highly associated with NPC and could be leveraged to develop variant-informed screening programs that mitigate false positives with small reductions in screening sensitivity. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-022-01625-6.
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Affiliation(s)
- Jacob A Miller
- Department of Radiation Oncology, Stanford University School of Medicine, 875 Blake Wilbur Drive, Palo Alto, CA, 94304, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, CA, 94304, USA
| | - Fumiko Yamamoto
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, CA, 94304, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, CA, 94304, USA
| | - Hannah Wang
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, CA, 94304, USA
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, CA, 94304, USA
| | - Quynh-Thu Le
- Department of Radiation Oncology, Stanford University School of Medicine, 875 Blake Wilbur Drive, Palo Alto, CA, 94304, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, CA, 94304, USA. .,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
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15
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Serrano GE, Walker JE, Tremblay C, Piras IS, Huentelman MJ, Belden CM, Goldfarb D, Shprecher D, Atri A, Adler CH, Shill HA, Driver-Dunckley E, Mehta SH, Caselli R, Woodruff BK, Haarer CF, Ruhlen T, Torres M, Nguyen S, Schmitt D, Rapscak SZ, Bime C, Peters JL, Alevritis E, Arce RA, Glass MJ, Vargas D, Sue LI, Intorcia AJ, Nelson CM, Oliver J, Russell A, Suszczewicz KE, Borja CI, Cline MP, Hemmingsen SJ, Qiji S, Hobgood HM, Mizgerd JP, Sahoo MK, Zhang H, Solis D, Montine TJ, Berry GJ, Reiman EM, Röltgen K, Boyd SD, Pinsky BA, Zehnder JL, Talbot P, Desforges M, DeTure M, Dickson DW, Beach TG. SARS-CoV-2 Brain Regional Detection, Histopathology, Gene Expression, and Immunomodulatory Changes in Decedents with COVID-19. J Neuropathol Exp Neurol 2022; 81:666-695. [PMID: 35818336 PMCID: PMC9278252 DOI: 10.1093/jnen/nlac056] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Brains of 42 COVID-19 decedents and 107 non-COVID-19 controls were studied. RT-PCR screening of 16 regions from 20 COVID-19 autopsies found SARS-CoV-2 E gene viral sequences in 7 regions (2.5% of 320 samples), concentrated in 4/20 subjects (20%). Additional screening of olfactory bulb (OB), amygdala (AMY) and entorhinal area for E, N1, N2, RNA-dependent RNA polymerase, and S gene sequences detected one or more of these in OB in 8/21 subjects (38%). It is uncertain whether these RNA sequences represent viable virus. Significant histopathology was limited to 2/42 cases (4.8%), one with a large acute cerebral infarct and one with hemorrhagic encephalitis. Case-control RNAseq in OB and AMY found more than 5000 and 700 differentially expressed genes, respectively, unrelated to RT-PCR results; these involved immune response, neuronal constituents, and olfactory/taste receptor genes. Olfactory marker protein-1 reduction indicated COVID-19-related loss of OB olfactory mucosa afferents. Iba-1-immunoreactive microglia had reduced area fractions in cerebellar cortex and AMY, and cytokine arrays showed generalized downregulation in AMY and upregulation in blood serum in COVID-19 cases. Although OB is a major brain portal for SARS-CoV-2, COVID-19 brain changes are more likely due to blood-borne immune mediators and trans-synaptic gene expression changes arising from OB deafferentation.
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Affiliation(s)
- Geidy E Serrano
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Jessica E Walker
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Cécilia Tremblay
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | | | - Danielle Goldfarb
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - David Shprecher
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Alireza Atri
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA.,Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Charles H Adler
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Holly A Shill
- Barrow Neurological Institute, Phoenix, Arizona, USA
| | | | - Shyamal H Mehta
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Richard Caselli
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Bryan K Woodruff
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | | | - Thomas Ruhlen
- Banner Boswell Medical Center, Sun City, Arizona, USA
| | - Maria Torres
- Banner Boswell Medical Center, Sun City, Arizona, USA
| | - Steve Nguyen
- Banner Boswell Medical Center, Sun City, Arizona, USA
| | - Dasan Schmitt
- Banner Boswell Medical Center, Sun City, Arizona, USA
| | | | | | | | | | - Richard A Arce
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Michael J Glass
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Daisy Vargas
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Lucia I Sue
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Courtney M Nelson
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Javon Oliver
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Aryck Russell
- Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | | | - Claryssa I Borja
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Madison P Cline
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Sanaria Qiji
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Holly M Hobgood
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Joseph P Mizgerd
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Haiyu Zhang
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Daniel Solis
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Gerald J Berry
- Department of Pathology, Stanford University, Stanford, California, USA.,From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Katharina Röltgen
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University, Stanford, California, USA.,Division of Infectious Disease & Geographic Medicine, Department of Medicine, Stanford University, Stanford, California, USA
| | - James L Zehnder
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Pierre Talbot
- Laboratory of Neuroimmunology, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
| | - Marc Desforges
- Laboratory of Virology, Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec, Canada.,Département de microbiologie, infectiologie et Immunologie, Université de Montréal, Montréal, Quebec, Canada
| | - Michael DeTure
- Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville, Florida, USA
| | - Dennis W Dickson
- Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville, Florida, USA
| | - Thomas G Beach
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
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16
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Fei F, Natkunam Y, Zehnder JL, Stehr H, Gratzinger D. Diagnostic Impact of Next-Generation Sequencing Panels for Lymphoproliferative Neoplasms on Small-Volume Biopsies. Am J Clin Pathol 2022; 158:345-361. [PMID: 35552630 DOI: 10.1093/ajcp/aqac045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 11/20/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES We investigated the feasibility and utility of next-generation sequencing (NGS)-based targeted somatic mutation panels and IG/TR gene rearrangement assays in the diagnosis of lymphoproliferative disorders (LPDs) in small-volume biopsies. MATERIALS We performed a retrospective, single-institution review of all NGS assays requested over a 3-year period by hematopathologists for diagnostic purposes on small-volume biopsies. RESULTS We identified 59 small-volume biopsies. The TR assay was most commonly requested (42 [71%]), followed by the somatic mutation panel (32 [54%]) and IG assay (26 [44%]). NGS studies were associated with a change in the diagnostic line in about half of cases (28 [47%]) and in a change in the likelihood of a diagnosis in a further 16 cases (27%); there was no diagnostic impact of NGS testing in 15 cases (25%). CONCLUSIONS Implementation of NGS panel somatic mutation or IG/TR gene rearrangement assays on small-volume biopsies contributes to the diagnosis of LPDs in the majority of select cases for diagnostic purposes. The molecular diagnosis is considered in the context of the clinical, histologic, and immunophenotypic findings and does not by itself lead to a definitive diagnosis in small-volume biopsies.
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Affiliation(s)
- Fei Fei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yasodha Natkunam
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dita Gratzinger
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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17
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Wirz OF, Röltgen K, Stevens BA, Pandey S, Sahoo MK, Tolentino L, Verghese M, Nguyen K, Hunter M, Snow TT, Singh AR, Blish CA, Cochran JR, Zehnder JL, Nadeau KC, Pinsky BA, Pham TD, Boyd SD. Use of Outpatient-Derived COVID-19 Convalescent Plasma in COVID-19 Patients Before Seroconversion. Front Immunol 2021; 12:739037. [PMID: 34594341 PMCID: PMC8477649 DOI: 10.3389/fimmu.2021.739037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/24/2021] [Indexed: 11/13/2022] Open
Abstract
Background Transfusion of COVID-19 convalescent plasma (CCP) containing high titers of anti-SARS-CoV-2 antibodies serves as therapy for COVID-19 patients. Transfusions early during disease course was found to be beneficial. Lessons from the SARS-CoV-2 pandemic could inform early responses to future pandemics and may continue to be relevant in lower resource settings. We sought to identify factors correlating to high antibody titers in convalescent plasma donors and understand the magnitude and pharmacokinetic time course of both transfused antibody titers and the endogenous antibody titers in transfused recipients. Methods Plasma samples were collected up to 174 days after convalescence from 93 CCP donors with mild disease, and from 16 COVID-19 patients before and after transfusion. Using ELISA, anti-SARS-CoV-2 Spike RBD, S1, and N-protein antibodies, as well as capacity of antibodies to block ACE2 from binding to RBD was measured in an in vitro assay. As an estimate for viral load, viral RNA and N-protein plasma levels were assessed in COVID-19 patients. Results Anti-SARS-CoV-2 antibody levels and RBD-ACE2 blocking capacity were highest within the first 60 days after symptom resolution and markedly decreased after 120 days. Highest antibody titers were found in CCP donors that experienced fever. Effect of transfused CCP was detectable in COVID-19 patients who received high-titer CCP and had not seroconverted at the time of transfusion. Decrease in viral RNA was seen in two of these patients. Conclusion Our results suggest that high titer CCP should be collected within 60 days after recovery from donors with past fever. The much lower titers conferred by transfused antibodies compared to endogenous production in the patient underscore the importance of providing CCP prior to endogenous seroconversion.
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Affiliation(s)
- Oliver F. Wirz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Katharina Röltgen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Bryan A. Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Suchitra Pandey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Blood Center, Palo Alto, CA, United States
| | - Malaya K. Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | | | - Michelle Verghese
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Khoa Nguyen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | | | - Theo Thomas Snow
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, United States
| | - Abhay Raj Singh
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, United States
| | - Catherine A. Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Jennifer R. Cochran
- Department of Bioengineering, Stanford University, Stanford, CA, United States
| | - James L. Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, United States
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, United States
| | - Benjamin A. Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, United States
| | - Tho D. Pham
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Blood Center, Palo Alto, CA, United States
| | - Scott D. Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, United States
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18
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Tung JK, Suarez CJ, Chiang T, Zehnder JL, Stehr H. Accurate Detection and Quantification of FLT3 Internal Tandem Duplications in Clinical Hybrid Capture Next-Generation Sequencing Data. J Mol Diagn 2021; 23:1404-1413. [PMID: 34363960 DOI: 10.1016/j.jmoldx.2021.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 07/09/2021] [Accepted: 07/16/2021] [Indexed: 01/13/2023] Open
Abstract
FLT3 internal tandem duplications (ITDs) are found in approximately one-third of patients with acute myeloid leukemia and have important prognostic and therapeutic implications that have supported their assessment in routine clinical practice. Conventional methods for assessing FLT3-ITD status and allele burden have been primarily limited to PCR fragment size analysis because of the inherent difficulty in detecting large ITD variants by next-generation sequencing (NGS). In this study, we assess the performance of publicly available bioinformatic tools for the detection and quantification of FLT3-ITDs in clinical hybridization-capture NGS data. We found that FLT3_ITD_ext had the highest overall accuracy for detecting FLT3-ITDs and was able to accurately quantify allele burden. Although all other tools evaluated were able to detect FLT3-ITDs reasonably well, allele burden was consistently underestimated. We were able to significantly improve quantification of FLT3-ITD allelic burden independent of the detection method by utilizing soft-clipped reads and/or ITD junctional sequences. In addition, we show that identifying mutant reads by previously identified junctional sequences further improves the sensitivity of detecting FLT3-ITDs in post-treatment samples. Our results demonstrate that FLT3-ITDs can be reliably detected in clinical NGS data using available bioinformatic tools. We further describe how accurate quantification of FLT3-ITD allele burden can be added on to existing clinical NGS pipelines for routine assessment of FLT3-ITD status in patients with acute myeloid leukemia.
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Affiliation(s)
- Jack K Tung
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Carlos J Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Tsoyu Chiang
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
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19
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Ho CC, Tung JK, Zehnder JL, Zhang BM. Validation of a Next-Generation Sequencing-Based T-Cell Receptor Gamma Gene Rearrangement Diagnostic Assay: Transitioning from Capillary Electrophoresis to Next-Generation Sequencing. J Mol Diagn 2021; 23:805-815. [PMID: 33892183 DOI: 10.1016/j.jmoldx.2021.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 03/15/2021] [Accepted: 03/25/2021] [Indexed: 01/23/2023] Open
Abstract
Assessment of T-cell receptor γ gene (TRG) rearrangements is an importants consideration in the diagnostic workup of lymphoproliferative diseases. Although fragment analysis by PCR and capillary electrophoresis (CE) is the current standard of such assessment in clinical molecular diagnostic laboratories, it does not provide sequence information and is only semi-quantitative. Next-generation sequencing (NGS)-based assays are an attractive alternative to the conventional fragment size-based methods, given that they generate results with specific clonotype sequence information and allow for more accurate quantitation. The present study evaluated various test parameters and performance characteristics of a commercially available NGS-based TRG gene-rearrangement assay by testing 101 clinical samples previously characterized by fragment analysis. The NGS TRG assay showed an overall accuracy of 83% and an analytical specificity of 100%. The concordance rates were 88% to 95% in the Vγ1-8, Vγ10, and Vγ11 gene families, but lower in the Vγ9 gene family. This difference was mostly attributed to the incomplete polyclonal symmetry resulting from the two-tube CE assay versus the one-tube design of the NGS assay. The NGS assay also demonstrated strengths in distinguishing clonotypes of the same fragment size. This clinical validation demonstrated robust performance of the NGS-based TRG assay and identified potential pitfalls associated with CE assay design that are important for understanding the observed discrepancies with the CE-based assay.
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Affiliation(s)
- Chandler C Ho
- Molecular Pathology Laboratory, Stanford Health Care, Stanford, California
| | - Jack K Tung
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Bing M Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
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20
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Johnsrud A, Craig J, Baird J, Spiegel J, Muffly L, Zehnder JL, Negrin RS, Johnston L, Arai S, Shizuru JA, Lowsky R, Meyer EH, Weng WK, Shiraz P, Rezvani AR, Latchford TM, Mackall CL, Miklos DB, Frank MJ, Sidana S. Bleeding and Thrombosis Are Associated with Endothelial Dysfunction in CAR-T Cell Therapy and Are Increased in Patients Experiencing Neurologic Toxicity. Transplant Cell Ther 2021. [DOI: 10.1016/s2666-6367(21)00257-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Serrano GE, Walker JE, Arce R, Glass MJ, Vargas D, Sue LI, Intorcia AJ, Nelson CM, Oliver J, Papa J, Russell A, Suszczewicz KE, Borja CI, Belden C, Goldfarb D, Shprecher D, Atri A, Adler CH, Shill HA, Driver-Dunckley E, Mehta SH, Readhead B, Huentelman MJ, Peters JL, Alevritis E, Bimi C, Mizgerd JP, Reiman EM, Montine TJ, Desforges M, Zehnder JL, Sahoo MK, Zhang H, Solis D, Pinsky BA, Deture M, Dickson DW, Beach TG. Mapping of SARS-CoV-2 Brain Invasion and Histopathology in COVID-19 Disease. medRxiv 2021:2021.02.15.21251511. [PMID: 33619496 PMCID: PMC7899461 DOI: 10.1101/2021.02.15.21251511] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The coronavirus SARS-CoV-2 (SCV2) causes acute respiratory distress, termed COVID-19 disease, with substantial morbidity and mortality. As SCV2 is related to previously-studied coronaviruses that have been shown to have the capability for brain invasion, it seems likely that SCV2 may be able to do so as well. To date, although there have been many clinical and autopsy-based reports that describe a broad range of SCV2-associated neurological conditions, it is unclear what fraction of these have been due to direct CNS invasion versus indirect effects caused by systemic reactions to critical illness. Still critically lacking is a comprehensive tissue-based survey of the CNS presence and specific neuropathology of SCV2 in humans. We conducted an extensive neuroanatomical survey of RT-PCR-detected SCV2 in 16 brain regions from 20 subjects who died of COVID-19 disease. Targeted areas were those with cranial nerve nuclei, including the olfactory bulb, medullary dorsal motor nucleus of the vagus nerve and the pontine trigeminal nerve nuclei, as well as areas possibly exposed to hematogenous entry, including the choroid plexus, leptomeninges, median eminence of the hypothalamus and area postrema of the medulla. Subjects ranged in age from 38 to 97 (mean 77) with 9 females and 11 males. Most subjects had typical age-related neuropathological findings. Two subjects had severe neuropathology, one with a large acute cerebral infarction and one with hemorrhagic encephalitis, that was unequivocally related to their COVID-19 disease while most of the 18 other subjects had non-specific histopathology including focal β-amyloid precursor protein white matter immunoreactivity and sparse perivascular mononuclear cell cuffing. Four subjects (20%) had SCV2 RNA in one or more brain regions including the olfactory bulb, amygdala, entorhinal area, temporal and frontal neocortex, dorsal medulla and leptomeninges. The subject with encephalitis was SCV2-positive in a histopathologically-affected area, the entorhinal cortex, while the subject with the large acute cerebral infarct was SCV2-negative in all brain regions. Like other human coronaviruses, SCV2 can inflict acute neuropathology in susceptible patients. Much remains to be understood, including what viral and host factors influence SCV2 brain invasion and whether it is cleared from the brain subsequent to the acute illness.
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Affiliation(s)
| | | | - Richard Arce
- Banner Sun Health Research Institute, Sun City, AZ
| | | | - Daisy Vargas
- Banner Sun Health Research Institute, Sun City, AZ
| | - Lucia I. Sue
- Banner Sun Health Research Institute, Sun City, AZ
| | | | | | - Javon Oliver
- Banner Sun Health Research Institute, Sun City, AZ
| | - Jaclyn Papa
- Banner Sun Health Research Institute, Sun City, AZ
| | | | | | | | | | | | | | - Alireza Atri
- Banner Sun Health Research Institute, Sun City, AZ
- Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Charles H. Adler
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, AZ
| | | | | | - Shyamal H. Mehta
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, AZ
| | - Benjamin Readhead
- Arizona State University-Banner Neurodegenerative Disease Research Center, Tempe, AZ
| | | | | | | | | | | | | | - Thomas J. Montine
- Stanford University School of Medicine, Department of Pathology, Stanford, CA
| | - Marc Desforges
- Centre Hospitalier Universitaire Sainte-Justine, Laboratory of Virology, Montreal, Canada
| | - James L. Zehnder
- Stanford University School of Medicine, Department of Pathology, Stanford, CA
| | - Malaya K. Sahoo
- Stanford University School of Medicine, Department of Pathology, Stanford, CA
| | - Haiyu Zhang
- Stanford University School of Medicine, Department of Pathology, Stanford, CA
| | - Daniel Solis
- Stanford University School of Medicine, Department of Pathology, Stanford, CA
| | - Benjamin A. Pinsky
- Stanford University Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford, CA
| | - Michael Deture
- Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville FL
| | - Dennis W. Dickson
- Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville FL
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22
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Baker SA, Jin J, Pfaffroth C, Vu T, Zehnder JL. DOAC-Stop in lupus anticoagulant testing: Direct oral anticoagulant interference removed in most samples. Res Pract Thromb Haemost 2021; 5:314-325. [PMID: 33733031 PMCID: PMC7938630 DOI: 10.1002/rth2.12472] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/14/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The use of direct oral anticoagulants (DOACs) is a convenient therapeutic option for patients at risk of thrombosis. DOACs interfere with clot-based testing for the identification of lupus anticoagulant antibodies (LACs) in patients with antiphospholipid syndrome (APS), a common cause of acquired thrombotic disease. OBJECTIVES To evaluate a commercially available reagent DOAC-Stop for the removal of DOAC interference encountered in LAC testing. PATIENTS/METHODS We collected a cohort of 73 test samples from patients on DOAC therapy identified at a large institutional coagulation laboratory from March to December 2019, along with samples from 40 LAC positive and negative control patients not on therapy. Samples were treated with DOAC-Stop and tested for anti-Xa activity and thrombin time for the removal of apixaban, rivaroxaban, argatroban, and dabigatran activity from patient samples. Treated and untreated samples were tested using the activated partial thromboplastin time, silica clotting time, and dilute Russell's viper venom time to evaluate the reliability and utility of DOAC-Stop. RESULTS DOAC-Stop markedly reduced DOAC interference from test samples (P < .05). DOAC-Stop had no effect on LAC testing in the absence of DOAC therapy, permitting the identification of all LAC positive and negative controls. DOAC-Stop removed false positives and false negatives resulting from DOAC interference and allows the identification of patients meeting criteria for the diagnosis of APS by LAC testing, as well as the detection of patients on rivaroxaban who are triple positive for APS. CONCLUSIONS DOAC-Stop is an effective adjunct for the clinical laboratory faced with DOAC interference in LAC testing.
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Affiliation(s)
| | - Jing Jin
- Department of Special Coagulation Clinical LaboratoryStanford Health CarePalo AltoCAUSA
| | - Christopher Pfaffroth
- Department of Special Coagulation Clinical LaboratoryStanford Health CarePalo AltoCAUSA
| | - Trang Vu
- Department of Special Coagulation Clinical LaboratoryStanford Health CarePalo AltoCAUSA
| | - James L. Zehnder
- Department of PathologyStanford University School of MedicineStanfordCAUSA
- Division of HematologyStanford University School of MedicineStanfordCAUSA
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23
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Hou Y, Shao L, Zhou H, Liu Y, Fisk DG, Spiteri E, Zehnder JL, Peng J, Zhang BM, Hou M. Identification of a pathogenic TUBB1 variant in a Chinese family with congenital macrothrombocytopenia through whole genome sequencing. Platelets 2021; 32:1108-1112. [PMID: 33400601 DOI: 10.1080/09537104.2020.1869714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Congenital macrothrombocytopenia is a genetically heterogeneous group of rare disorders. We herein report a large Chinese family presented with phenotypic variability involving thrombocytopenia and/or giant platelets. Whole genome sequencing (WGS) of the proband and one of his affected brothers identified a potentially pathogenic c.952 C > T heterozygous variant in the TUBB1 gene. This p.R318W β1-tubulin variant was also identified in three additional siblings and five members of the next generation. These findings were consistent with an autosomal dominant inheritance with incomplete penetrance. Moreover, impaired platelet agglutination in response to ristocetin was detected in the patient's brother. Half of the family members harboring the p.R318W mutation displayed significantly decreased external release of p-selectin by stimulated platelets. The p.R318W β1-tubulin mutation was identified for the first time in a Chinese family with congenital macrothrombocytopenia using WGS as an unbiased sequencing approach. Affected individuals within the family demonstrated impaired platelet aggregation and/or release functions.
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Affiliation(s)
- Yu Hou
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Linlin Shao
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hai Zhou
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yanfeng Liu
- Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Dianna G Fisk
- Clinical Genomics Program, Stanford Health Care, Palo Alto, United States
| | - Elizabeth Spiteri
- Clinical Genomics Program, Stanford Health Care, Palo Alto, United States.,Department of Pathology, Stanford University School of Medicine, Palo Alto, United States
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Palo Alto, United States
| | - Jun Peng
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Bing M Zhang
- Department of Pathology, Stanford University School of Medicine, Palo Alto, United States
| | - Ming Hou
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Leading Research Group of Scientific Innovation, Department of Science and Technology of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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24
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Krieger MS, Moreau JM, Zhang H, Chien M, Zehnder JL, Craig M. A Blueprint for Identifying Phenotypes and Drug Targets in Complex Disorders with Empirical Dynamics. Patterns (N Y) 2020; 1:100138. [PMID: 33336196 PMCID: PMC7733879 DOI: 10.1016/j.patter.2020.100138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/25/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023]
Abstract
A central challenge in medicine is translating from observational understanding to mechanistic understanding, where some observations are recognized as causes for the others. This can lead not only to new treatments and understanding, but also to recognition of novel phenotypes. Here, we apply a collection of mathematical techniques (empirical dynamics), which infer mechanistic networks in a model-free manner from longitudinal data, to hematopoiesis. Our study consists of three subjects with markers for cyclic thrombocytopenia, in which multiple cells and proteins undergo abnormal oscillations. One subject has atypical markers and may represent a rare phenotype. Our analyses support this contention, and also lend new evidence to a theory for the cause of this disorder. Simulations of an intervention yield encouraging results, even when applied to patient data outside our three subjects. These successes suggest that this blueprint has broader applicability in understanding and treating complex disorders.
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Affiliation(s)
- Madison S. Krieger
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Joshua M. Moreau
- Department of Dermatology, University of California, San Francisco, CA, USA
| | - Haiyu Zhang
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - May Chien
- Department of Medicine (Hematology), Stanford, CA, USA
| | - James L. Zehnder
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
- Department of Medicine (Hematology), Stanford, CA, USA
| | - Morgan Craig
- Département de Mathématiques et de Statistique, Université de Montréal, Montréal, QC, Canada
- CHU Sainte-Justine Research Centre, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1C5, Canada
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25
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Röltgen K, Powell AE, Wirz OF, Stevens BA, Hogan CA, Najeeb J, Hunter M, Wang H, Sahoo MK, Huang C, Yamamoto F, Manohar M, Manalac J, Otrelo-Cardoso AR, Pham TD, Rustagi A, Rogers AJ, Shah NH, Blish CA, Cochran JR, Jardetzky TS, Zehnder JL, Wang TT, Narasimhan B, Gombar S, Tibshirani R, Nadeau KC, Kim PS, Pinsky BA, Boyd SD. Defining the features and duration of antibody responses to SARS-CoV-2 infection associated with disease severity and outcome. Sci Immunol 2020; 5:eabe0240. [PMID: 33288645 PMCID: PMC7857392 DOI: 10.1126/sciimmunol.abe0240] [Citation(s) in RCA: 325] [Impact Index Per Article: 81.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/05/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022]
Abstract
SARS-CoV-2-specific antibodies, particularly those preventing viral spike receptor binding domain (RBD) interaction with host angiotensin-converting enzyme 2 (ACE2) receptor, can neutralize the virus. It is, however, unknown which features of the serological response may affect clinical outcomes of COVID-19 patients. We analyzed 983 longitudinal plasma samples from 79 hospitalized COVID-19 patients and 175 SARS-CoV-2-infected outpatients and asymptomatic individuals. Within this cohort, 25 patients died of their illness. Higher ratios of IgG antibodies targeting S1 or RBD domains of spike compared to nucleocapsid antigen were seen in outpatients who had mild illness versus severely ill patients. Plasma antibody increases correlated with decreases in viral RNAemia, but antibody responses in acute illness were insufficient to predict inpatient outcomes. Pseudovirus neutralization assays and a scalable ELISA measuring antibodies blocking RBD-ACE2 interaction were well correlated with patient IgG titers to RBD. Outpatient and asymptomatic individuals' SARS-CoV-2 antibodies, including IgG, progressively decreased during observation up to five months post-infection.
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Affiliation(s)
- Katharina Röltgen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Abigail E Powell
- Stanford ChEM-H and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver F Wirz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan A Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Javaria Najeeb
- Department of Structural Biology, Stanford University, Stanford, USA
| | | | - Hannah Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Fumiko Yamamoto
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Monali Manohar
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
| | - Justin Manalac
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tho D Pham
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Blood Center, Palo Alto, CA, USA
| | - Arjun Rustagi
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Angela J Rogers
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
| | - Nigam H Shah
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
| | - Catherine A Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Taia T Wang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Balasubramanian Narasimhan
- Department of Statistics, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Sciences, Stanford University, Stanford, CA, USA
| | - Saurabh Gombar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert Tibshirani
- Department of Statistics, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Sciences, Stanford University, Stanford, CA, USA
| | - Kari C Nadeau
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
| | - Peter S Kim
- Stanford ChEM-H and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
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26
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Rojansky R, Fernandez-Pol S, Wang E, Rieger KE, Novoa RA, Zehnder JL, Kunder CA, Kim YH, Khodadoust MS, Brown RA. Cutaneous T-cell lymphomas with pathogenic somatic mutations and absence of detectable clonal T-cell receptor gene rearrangement: two case reports. Diagn Pathol 2020; 15:122. [PMID: 32988392 PMCID: PMC7523289 DOI: 10.1186/s13000-020-01022-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022] Open
Abstract
Background Cutaneous T-cell lymphomas (CTCL) are a heterogeneous group of extranodal non-Hodgkin lymphomas for which diagnosis can be challenging given the potential for overlap with inflammatory dermatoses. Current diagnostic criteria for CTCL incorporate clinical and histopathologic findings as well as results of T-cell receptor (TCR) gene sequencing. Molecular interrogation of TCR genes, TRG and TRB, has proven to be a critical tool for confirming diagnoses of CTCL and for disease tracking after initiation of therapy or after stem cell transplant. Methods for confirming a diagnosis of lymphoma in the absence of TCR gene clonality are lacking. We present two patients with CTCL with pathogenic somatic mutations in the absence of TRG and TRB clonality. Case presentations Case 1: A 38-year-old male had a 19-year history of a diffuse skin rash with papulosquamous, granulomatous, and verrucous features and progressive ulcerated plaques and tumors demonstrating an atypical CD4+ T-cell infiltrate with expression of cytotoxic markers CD56, TIA-1, granzyme, and perforin on histopathology. No definitive evidence for T-cell clonality was detected by conventional PCR of 6 biopsies or by next-generation sequencing (NGS) of 14 biopsies. Somatic mutational profiling of a skin biopsy revealed pathogenic mutations in PIKC3D and TERT promoter hotspots, confirming the presence of a clonal process. Case 2: A 69-year-old male with a 13-year history of progressive, diffuse hypertrophic and eroded plaques showed an atypical CD4+ T-cell infiltrate with subset expression of TIA-1 and granzyme on histopathology. No TCR clonality was detected by TCR-NGS of 6 biopsies. Somatic mutational profiling of a skin biopsy detected a pathogenic mutation in TP53, confirming the presence of a clonal process. Conclusions These cases highlight how detection of pathogenic somatic mutations can confirm a diagnosis of lymphoma in a clinically and histopathologically suspicious cutaneous lymphoid proliferation without detectable TCR clonality.
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Affiliation(s)
- Rebecca Rojansky
- Department of Pathology, Stanford Medicine, Stanford, CA, 94305, USA
| | | | - Erica Wang
- Department of Dermatology, Stanford Medicine, Stanford, CA, 94305, USA
| | - Kerri E Rieger
- Department of Pathology, Stanford Medicine, Stanford, CA, 94305, USA.,Department of Dermatology, Stanford Medicine, Stanford, CA, 94305, USA
| | - Roberto A Novoa
- Department of Pathology, Stanford Medicine, Stanford, CA, 94305, USA.,Department of Dermatology, Stanford Medicine, Stanford, CA, 94305, USA
| | - James L Zehnder
- Department of Pathology, Stanford Medicine, Stanford, CA, 94305, USA.,Division of Hematology, Department of Medicine, Stanford Medicine, Stanford, CA, 94305, USA
| | | | - Youn H Kim
- Department of Dermatology, Stanford Medicine, Stanford, CA, 94305, USA.,Division of Oncology, Department of Medicine, Stanford Medicine, Stanford, CA, 94305, USA
| | - Michael S Khodadoust
- Department of Dermatology, Stanford Medicine, Stanford, CA, 94305, USA.,Division of Oncology, Department of Medicine, Stanford Medicine, Stanford, CA, 94305, USA
| | - Ryanne A Brown
- Department of Pathology, Stanford Medicine, Stanford, CA, 94305, USA. .,Department of Dermatology, Stanford Medicine, Stanford, CA, 94305, USA. .,Department of Pathology, Veterans Affairs Palo Alto Health Care System, 3375 Hillview Ave, Room 1821, Palo Alto, CA, 94304-1204, USA.
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27
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Röltgen K, Wirz OF, Stevens BA, Powell AE, Hogan CA, Najeeb J, Hunter M, Sahoo MK, Huang C, Yamamoto F, Manalac J, Otrelo-Cardoso AR, Pham TD, Rustagi A, Rogers AJ, Shah NH, Blish CA, Cochran JR, Nadeau KC, Jardetzky TS, Zehnder JL, Wang TT, Kim PS, Gombar S, Tibshirani R, Pinsky BA, Boyd SD. SARS-CoV-2 Antibody Responses Correlate with Resolution of RNAemia But Are Short-Lived in Patients with Mild Illness. medRxiv 2020:2020.08.15.20175794. [PMID: 32839786 PMCID: PMC7444305 DOI: 10.1101/2020.08.15.20175794] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
SARS-CoV-2-specific antibodies, particularly those preventing viral spike receptor binding domain (RBD) interaction with host angiotensin-converting enzyme 2 (ACE2) receptor, could offer protective immunity, and may affect clinical outcomes of COVID-19 patients. We analyzed 625 serial plasma samples from 40 hospitalized COVID-19 patients and 170 SARS-CoV-2-infected outpatients and asymptomatic individuals. Severely ill patients developed significantly higher SARS-CoV-2-specific antibody responses than outpatients and asymptomatic individuals. The development of plasma antibodies was correlated with decreases in viral RNAemia, consistent with potential humoral immune clearance of virus. Using a novel competition ELISA, we detected antibodies blocking RBD-ACE2 interactions in 68% of inpatients and 40% of outpatients tested. Cross-reactive antibodies recognizing SARS-CoV RBD were found almost exclusively in hospitalized patients. Outpatient and asymptomatic individuals' serological responses to SARS-CoV-2 decreased within 2 months, suggesting that humoral protection may be short-lived.
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Affiliation(s)
- Katharina Röltgen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver F. Wirz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan A. Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Abigail E. Powell
- Stanford ChEM-H and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A. Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Javaria Najeeb
- Department of Structural Biology, Stanford University, Stanford, USA
| | | | - Malaya K. Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Fumiko Yamamoto
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin Manalac
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tho D. Pham
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Blood Center, Palo Alto, CA, USA
| | - Arjun Rustagi
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Angela J. Rogers
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
| | - Nigam H. Shah
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
| | - Catherine A. Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Kari C. Nadeau
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
| | | | - James L. Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Taia T. Wang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Peter S. Kim
- Stanford ChEM-H and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Saurabh Gombar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert Tibshirani
- Department of Biomedical Data Sciences, Stanford University, Stanford, CA, USA
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Benjamin A. Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Scott D. Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
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Lawrence LEB, Saleem A, Sahoo MK, Tan SK, Pinsky BA, Natkunam Y, Kunder CA, Stehr H, Zehnder JL. Is Merkel Cell Carcinoma of Lymph Node Actually Metastatic Cutaneous Merkel Cell Carcinoma? Am J Clin Pathol 2020; 154:369-380. [PMID: 32445471 DOI: 10.1093/ajcp/aqaa051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVES The possibility of a so-called primary lymph node neuroendocrine carcinoma has been described in the literature. Here we evaluate cases fitting such a diagnosis and find that the cases demonstrate a convincing and pervasive pattern consistent with metastatic Merkel cell carcinoma. METHODS Six cases of primary lymph node Merkel cell carcinoma and one case of metastatic neuroendocrine carcinoma at a bony site, all with unknown primary, were sequenced using a combination of whole-exome and targeted panel methods. Sequencing results were analyzed for the presence of an ultraviolet (UV) mutational signature or off-target detection of Merkel cell polyomavirus (MCPyV). RESULTS Four of six primary lymph node cases were positive for a UV mutational signature, with the remaining two cases positive for off-target alignment of MCPyV. One case of neuroendocrine carcinoma occurring at a bony site was also positive for a UV mutational signature. CONCLUSIONS We find no evidence to corroborate the existence of so-called primary Merkel cell carcinoma of lymph node.
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Affiliation(s)
- Lauren E B Lawrence
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Atif Saleem
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Susanna K Tan
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA
| | - Yasodha Natkunam
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Christian A Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
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Abstract
OBJECTIVES Lupus anticoagulant (LAC) is typically associated with thrombosis but also rarely with hemorrhage. Some patients exhibit a prozone effect on LAC testing. Antiphosphatidylserine/prothrombin (aPS/PT) antibodies may provide a mechanism for both hemorrhage and prozone effect. Our goal was to evaluate whether antibody specificities, isotypes, and titers were associated with LAC prozone effect, factor II levels, hemorrhage, and thrombosis. METHODS Patients with prozone effect noted on LAC testing were entered into a database over 3 years. Factor II activity and aPS/PT antibody testing were performed when a sufficient residual sample was available. RESULTS All patients with LAC prozone effect and antibody testing were positive for at least 1 class of aPS/PT antibodies. In addition, aPS/PT IgG titers were significantly associated with thrombosis and significantly inversely associated with factor II levels. CONCLUSIONS In prozone effect patients, aPS/PT antibodies are associated with LAC prozone effect as well as thrombosis and decreased factor II levels.
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Affiliation(s)
- Colin H Murphy
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA
| | - Jing Jin
- Stanford Coagulation and Hemostasis Laboratory, Stanford Medical Center, Palo Alto, CA
| | - James L Zehnder
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA
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Chen JW, Kunder CA, Bui N, Zehnder JL, Costa HA, Stehr H. Increasing Clinical Trial Accrual via Automated Matching of Biomarker Criteria. Pac Symp Biocomput 2020; 25:31-42. [PMID: 31797584] [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] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Successful implementation of precision oncology requires both the deployment of nucleic acid sequencing panels to identify clinically actionable biomarkers, and the efficient screening of patient biomarker eligibility to on-going clinical trials and therapies. This process is typically performed manually by biocurators, geneticists, pathologists, and oncologists; however, this is a time-intensive, and inconsistent process amongst healthcare providers. We present the development of a feature matching algorithmic pipeline that identifies patients who meet eligibility criteria of precision medicine clinical trials via genetic biomarkers and apply it to patients undergoing treatment at the Stanford Cancer Center. This study demonstrates, through our patient eligibility screening algorithm that leverages clinical sequencing derived biomarkers with precision medicine clinical trials, the successful use of an automated algorithmic pipeline as a feasible, accurate and effective alternative to the traditional manual clinical trial curation.
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Affiliation(s)
- Jessica W Chen
- Departments of Biomedical Data Science and of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA,
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31
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Silberman R, F. Steiner D, Lo AA, Gomez A, Zehnder JL, Chu G, Suarez CJ. Complete and Prolonged Response to Immune Checkpoint Blockade in POLE-Mutated Colorectal Cancer. JCO Precis Oncol 2019; 3:1-5. [DOI: 10.1200/po.18.00214] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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Choi HG, Zehnder JL, Lee YK, Lim H, Kim M. Increased risk of lymphoid malignancy in patients with herpes zoster: a longitudinal follow-up study using a national cohort. BMC Cancer 2019; 19:1148. [PMID: 31775678 PMCID: PMC6882027 DOI: 10.1186/s12885-019-6349-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/08/2019] [Indexed: 12/23/2022] Open
Abstract
Background The association between herpes zoster and the risk of lymphoid neoplasms in Asian populations has not yet been established. We performed a longitudinal follow-up study using a nationwide cohort to assess the risk of lymphoid neoplasms arising after herpes zoster infection in the adult Korean population. Methods Data from participants ≥20 years of age who were registered in the Korean National Health Insurance Service-National Sample Cohort database between 2002 and 2013 were collected. We extracted the data of participants with herpes zoster (n = 59,495) as well as those of matched references at a ratio of 1:4 (n = 237,980) and investigated the subsequent occurrence of lymphoid neoplasms. A stratified Cox proportional hazards model was used to calculate unadjusted hazard ratios (HRs) as well as those adjusted for the Charlson comorbidity index score. Results The rate of lymphoid neoplasms was higher in the herpes zoster group (0.15% [90/59,495]) than in the reference group (0.08% [212/237,980], P < 0.001). The unadjusted and adjusted HRs of herpes zoster in patients with lymphoid neoplasms were 1.68 (95% confidence interval [CI] = 1.31–2.15) and 1.58 (95% CI = 1.23–2.02), respectively (P < 0.001 for both). On subgroup analyses according to age and sex, herpes zoster was associated with an increased risk of lymphoid neoplasms in all subgroups; the adjusted HRs were 1.53 (95% CI = 1.05–2.24) for patients < 60 years old, 1.58 (95% CI = 1.14–2.20) for patients ≥60 years old, 1.64 (95% CI = 1.16–2.31) for men, and 1.51 (95% CI = 1.06–2.16) for women (P < 0.05 for all). On subgroup analysis of lymphoid neoplasm subtypes, herpes zoster was associated with the risk of Hodgkin’s disease (adjusted HR: 3.23 [95% CI = 1.17–8.93]) and multiple myeloma/malignant plasma cell neoplasms (adjusted HR: 2.17 [95% CI = 1.33–3.54]) (P < 0.05 for both). Conclusion Herpes zoster is associated with lymphoid neoplasm development in the Korean population irrespective of age and sex. The risks of Hodgkin’s disease and plasma cell neoplasms are significantly elevated in patients with herpes zoster.
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Affiliation(s)
- Hyo Geun Choi
- Department of Otorhinolaryngology-Head & Neck Surgery, Hallym University College of Medicine, Anyang, Republic of Korea
| | - James L Zehnder
- Department of Pathology, Stanford University, Stanford, CA, USA.,Division of Hematology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Young Kyung Lee
- Department of Laboratory Medicine, Hallym University College of Medicine, Anyang, Republic of Korea
| | - Hyun Lim
- Department of Internal Medicine, Hallym University College of Medicine, Anyang, Republic of Korea
| | - Miyoung Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Anyang, Republic of Korea. .,Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, 22, Gwanpyeong-ro 170 beon-gil, Dongan-gu, Anyang-si, Gyeonggi-do, 14068, South Korea.
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Yang SR, Mooney KL, Libiran P, Jones CD, Joshi R, Lau HD, Stehr H, Berry GJ, Zehnder JL, Long SR, Kong CS, Kunder CA. Targeted deep sequencing of cell-free DNA in serous body cavity fluids with malignant, suspicious, and benign cytology. Cancer Cytopathol 2019; 128:43-56. [PMID: 31751001 DOI: 10.1002/cncy.22205] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 06/11/2019] [Revised: 08/15/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Liquid biopsy using cell-free DNA (cfDNA) presents new opportunities for solid tumor genotyping. While studies have demonstrated the utility of cfDNA from plasma, cfDNA from other body fluids remains underexplored. METHODS We evaluated the molecular features and clinicopathologic correlates of cfDNA from serous body cavity fluids by performing hybrid capture-based next-generation sequencing (NGS) on cfDNA isolated from residual effusion supernatants. Twenty-one serous effusions from pleural (n = 15), peritoneal (n = 5), and pericardial (n = 1) cavity were analyzed. RESULTS The supernatants provided a median cfDNA concentration of 10.3 ng/µL. Notably, all effusions were sequenced successfully to a median depth >1000×, revealing a broad range of genetic alterations including single nucleotide variants, small insertions and deletions, amplifications, and fusions. Specifically, pathogenic alterations were identified in all malignant fluids (13/13), all fluids suspicious for malignancy (2/2), and 1 benign fluid (1/6) from a patient with metastatic cancer. To validate our findings, we examined matching results from 11 patients who underwent additional testing using formalin-fixed, paraffin-embedded (FFPE) specimens. In 8 patients, the paired results between FFPE and supernatant testing were concordant, whereas in the remaining 3 patients, supernatant analysis identified additional variants likely associated with resistance to targeted therapies. Additional comparison between FFPE and supernatant testing showed no difference in DNA concentration (P = .5), depth of coverage (P = .6), or allele frequency of pathogenic mutations (P = .7). CONCLUSION cfDNA isolated from serous body cavity fluids represents a promising source of genomic input for targeted NGS.
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Affiliation(s)
- Soo-Ryum Yang
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Kelly L Mooney
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Paolo Libiran
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Carol D Jones
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Rohan Joshi
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Hubert D Lau
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Gerald J Berry
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Steven R Long
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Christina S Kong
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Christian A Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
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Lin CY, Saleem A, Stehr H, Zehnder JL, Pinsky BA, Kunder CA. Molecular profiling of clear cell adenocarcinoma of the urinary tract. Virchows Arch 2019; 475:727-734. [PMID: 31372739 DOI: 10.1007/s00428-019-02634-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/20/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022]
Abstract
Clear cell adenocarcinoma (CCA) of the urinary tract is a rare type of malignancy whose molecular profiles remain undefined. Here we reported an integrated clinicopathologic and molecular profiling analysis of four cases of clear cell adenocarcinoma arising in the urethra or the bladder. Utilizing a clinically validated 130-gene exon-sequencing assay, we identified recurrent pathogenic PIK3CA (p. E545K) and KRAS (p.G12D) variants in three of four (75%) of the cases. In addition, an APC variant (P.S2310X), a TP53 variant (p.R273C), and a MYC amplification event were identified. The only CCA case without either PIK3CA or KRAS variants has a distinct pathogenesis through BK virus, demonstrated by positive BK virus PCR and SV40 immunohistochemistry. The novel finding of recurrent variants in the PI3K/AKT/mTOR pathway provides not only insights into oncogenesis but also potential clinical therapeutic targets for patients with clear cell adenocarcinoma of the urinary tract.
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Affiliation(s)
- Chieh-Yu Lin
- Department of Pathology and Immunology, Washington University School of Medicine, Campus box 8118, 660 South Euclid Ave., St. Louis, MO, 63110, USA. .,Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Atif Saleem
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Christian A Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
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35
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Zhang H, Zhang BM, Guo X, Xu L, You X, West RB, Bussel JB, Zehnder JL. Blood transcriptome and clonal T-cell correlates of response and non-response to eltrombopag therapy in a cohort of patients with chronic immune thrombocytopenia. Haematologica 2019; 105:e129-e132. [PMID: 31296576 DOI: 10.3324/haematol.2019.226688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Haiyu Zhang
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Bing M Zhang
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Xiangqian Guo
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.,Department of Preventive Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Liwen Xu
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Xiaoqing You
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Robert B West
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - James B Bussel
- Platelet Disorders Center, Department of Pediatrics, Weill-Cornell Medicine, New York, NY, USA
| | - James L Zehnder
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
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36
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Hayward CPM, Moffat KA, Brunet J, Carlino SA, Plumhoff E, Meijer P, Zehnder JL. Update on diagnostic testing for platelet function disorders: What is practical and useful? Int J Lab Hematol 2019; 41 Suppl 1:26-32. [PMID: 31069975 DOI: 10.1111/ijlh.12995] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 12/21/2018] [Accepted: 02/07/2019] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Platelet function disorders (PFD) are an important group of bleeding disorders that require validated and practical laboratory strategies for diagnosis. METHODS This review summarizes the authors' experiences, current literature, and an international survey to evaluate the practices of diagnostic laboratories that offer tests for PFD. RESULTS Blood counts, blood film review, and aggregation tests are the most commonly performed investigations for PFD and help determine whether there is thrombocytopenia and/or defective platelet function due to a variety of causes. The performance characteristics of tests for PFD, and the level of evidence that these tests detect bleeding problems, are important issues to determine where tests are useful for diagnostic or correlative purposes, or research only uses. Platelet aggregation assays, and quantitative analysis of platelet dense granule numbers, are tests with good performance characteristics that detect abnormalities associated with increased bleeding in a significant proportion of individuals referred for PFD investigations. Lumiaggregometry estimates of platelet adenosine triphosphate release show greater variability which limits the diagnostic usefulness. Diagnostic laboratories report that fiscal and other constraints, including a lack of high-quality evidence, limit their ability to offer an expanded test menu for PFD. CONCLUSION PFD are clinically important bleeding disorders that remain challenging for diagnostic laboratories to investigate. While some PFD tests are well validated for diagnostic purposes, gaps in scientific evidence and resource limitations influence diagnostic laboratory decisions on which PFD tests to offer.
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Affiliation(s)
- Catherine P M Hayward
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.,Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Hamilton Regional Laboratory Medicine Program, Hamilton, Ontario, Canada
| | - Karen A Moffat
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Hamilton Regional Laboratory Medicine Program, Hamilton, Ontario, Canada
| | - Justin Brunet
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Stephen A Carlino
- Hamilton Regional Laboratory Medicine Program, Hamilton, Ontario, Canada
| | | | - Piet Meijer
- ECAT Foundation, Voorschoten, The Netherlands
| | - James L Zehnder
- Departments of Pathology and Medicine, Stanford University, Stanford, California
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Jin J, Baker SA, Hall ET, Gombar S, Bao A, Zehnder JL. Implementation of Whole-Blood Impedance Aggregometry for Heparin-Induced Thrombocytopenia Functional Assay and Case Discussion. Am J Clin Pathol 2019; 152:50-58. [PMID: 31165165 DOI: 10.1093/ajcp/aqz013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 11/14/2022] Open
Abstract
OBJECTIVES The diagnosis of heparin-induced thrombocytopenia (HIT) ideally requires a functional assay to confirm. 14C-serotonin release assay (SRA) as "gold standard" is technically challenging and unsuitable for routine use. We conducted a study to assess the performance of whole-blood impedance aggregometry (WBIA) as a simple and rapid HIT functional assay. METHODS Platelet factor 4 (PF4)/immunoglobulin G (IgG) antibody, WBIA, and SRA were tested on 70 patients suspected of having HIT. Patients with a 4Ts score of 4 or more, positive PF4/IgG, and positive SRA were considered HIT positive; others were designated HIT negative. RESULTS WBIA had 85.7% (6/7) sensitivity and 98.4% (61/62) specificity, which were not statistically different compared with SRA. Sixty-two of 70 patients had concordant results (five positive and 57 negative) by both WBIA and SRA. Eight discordant cases revealed the importance of recognizing donor effect, interferences, and the presence of heparin-independent or non-heparin-dependent antibodies in functional assays. CONCLUSIONS Implementation of WBIA could facilitate timely diagnosis and management of HIT.
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Affiliation(s)
- Jing Jin
- Department of Special Coagulation, Clinical Laboratory, Stanford Medical Center, Stanford, CA
| | | | - Evan T Hall
- Division of Hematology, School of Medicine, Stanford University, Stanford, CA
| | - Saurabh Gombar
- Department of Pathology, Stanford University, Stanford, CA
| | | | - James L Zehnder
- Department of Pathology, Stanford University, Stanford, CA
- Division of Hematology, School of Medicine, Stanford University, Stanford, CA
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38
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Li P, Shahmarvand N, Lynch D, Gotlib JR, Merker JD, Zehnder JL, George TI, Ohgami RS. Revisiting diagnostic criteria for myelodysplastic/myeloproliferative neoplasms with ring sideroblasts and thrombocytosis: Borderline cases without anemia exist. Int J Lab Hematol 2019; 41:345-352. [PMID: 30811101 DOI: 10.1111/ijlh.12981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 12/31/2018] [Accepted: 01/07/2019] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Myelodysplastic/myeloproliferative neoplasm with ring sideroblasts and thrombocytosis (MDS/MPN-RS-T) is a rare disease in the 2016 revised World Health Organization (WHO) classification. Diagnostic criteria include the following: persistent thrombocytosis (>450 × 109 /L) with clustering of atypical megakaryocytes, refractory anemia, dyserythropoiesis with ring sideroblasts, and the presence of the spliceosome factor 3b subunit (SF3B1) mutation. It is unclear if anemia should be a required criterion for this diagnosis as cases which show all other features of MDS/MPN-RS-T but without anemia exist. METHODS We searched for borderline cases of MDS/MPN-RS-T in which refractory anemia was absent at diagnosis in two major academic institutes. RESULTS Three cases without anemia were identified. These cases all showed other classic morphologic and clinical features of MDS/MPN-RS-T, including thrombocytosis, atypical megakaryocytes with clustering, and characteristic SF3B1 and JAK2 V617F mutations. CONCLUSION Given these findings, the requirement of refractory anemia as a diagnostic criterion for MDS/MPN-RS-T should be re-evaluated. Removal of refractory anemia as a diagnostic criterion would incorporate current borderline cases and extend the spectrum of this disorder.
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Affiliation(s)
- Peng Li
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida
| | - Nahid Shahmarvand
- Department of Pathology, Stanford University Medical Center, Stanford, California
| | - David Lynch
- Department of Pathology, Brooke Army Medical Center, San Antonio, Texas
| | - Jason R Gotlib
- Department of Pathology, Stanford University Medical Center, Stanford, California.,Department of Medicine, Stanford University Medical Center, Stanford, California
| | - Jason D Merker
- Department of Pathology, Stanford University Medical Center, Stanford, California.,University of North Carolina, Chapel Hill, North Carolina
| | - James L Zehnder
- Department of Pathology, Stanford University Medical Center, Stanford, California.,Department of Medicine, Stanford University Medical Center, Stanford, California
| | - Tracy I George
- University of Utah, Salt Lake City, Utah.,Department of Pathology, University of New Mexico, Albuquerque, New Mexico
| | - Robert S Ohgami
- Department of Pathology, Stanford University Medical Center, Stanford, California
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Troll CJ, Putnam NH, Hartley PD, Rice B, Blanchette M, Siddiqui S, Ganbat JO, Powers MP, Ramakrishnan R, Kunder CA, Bustamante CD, Zehnder JL, Green RE, Costa HA. Structural Variation Detection by Proximity Ligation from Formalin-Fixed, Paraffin-Embedded Tumor Tissue. J Mol Diagn 2018; 21:375-383. [PMID: 30605765 DOI: 10.1016/j.jmoldx.2018.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 10/23/2018] [Accepted: 11/17/2018] [Indexed: 12/11/2022] Open
Abstract
The clinical management and therapy of many solid tumor malignancies depends on detection of medically actionable or diagnostically relevant genetic variation. However, a principal challenge for genetic assays from tumors is the fragmented and chemically damaged state of DNA in formalin-fixed, paraffin-embedded (FFPE) samples. From highly fragmented DNA and RNA there is no current technology for generating long-range DNA sequence data as is required to detect genomic structural variation or long-range genotype phasing. We have developed a high-throughput chromosome conformation capture approach for FFPE samples that we call Fix-C, which is similar in concept to Hi-C. Fix-C enables structural variation detection from archival FFPE samples. This method was applied to 15 clinical adenocarcinoma- and sarcoma-positive control specimens spanning a broad range of tumor purities. In this panel, Fix-C analysis achieves a 90% concordance rate with fluorescence in situ hybridization assays, the current clinical gold standard. In addition, novel structural variation undetected by other methods could be identified, and long-range chromatin configuration information recovered from these FFPE samples harboring highly degraded DNA. This powerful approach will enable detailed resolution of global genome rearrangement events during cancer progression from FFPE material and will inform the development of targeted molecular diagnostic assays for patient care.
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Affiliation(s)
- Christopher J Troll
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Nicholas H Putnam
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Paul D Hartley
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Brandon Rice
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Marco Blanchette
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Sameed Siddiqui
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Javkhlan-Ochir Ganbat
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Martin P Powers
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Ramesh Ramakrishnan
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Christian A Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Carlos D Bustamante
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California; Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California.
| | - Helio A Costa
- Department of Pathology, Stanford University School of Medicine, Stanford, California; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California.
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Costa HA, Reyes R, Mills M, Zehnder JL, Sledge G, Curtis C, Ford JM, Suarez CJ. Tumor Molecular Profiling Aids in Determining Tissue of Origin and Therapy for Metastatic Adenocarcinoma in a Patient With Multiple Primary Malignancies. JCO Precis Oncol 2018; 2:1-4. [DOI: 10.1200/po.18.00177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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)
- Helio A. Costa
- All authors: Stanford University School of Medicine, Stanford, CA
| | - Rochelle Reyes
- All authors: Stanford University School of Medicine, Stanford, CA
| | - Meredith Mills
- All authors: Stanford University School of Medicine, Stanford, CA
| | - James L. Zehnder
- All authors: Stanford University School of Medicine, Stanford, CA
| | - George Sledge
- All authors: Stanford University School of Medicine, Stanford, CA
| | - Christina Curtis
- All authors: Stanford University School of Medicine, Stanford, CA
| | - James M. Ford
- All authors: Stanford University School of Medicine, Stanford, CA
| | - Carlos J. Suarez
- All authors: Stanford University School of Medicine, Stanford, CA
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41
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Eastburn DJ, Pellegrino M, Sciambi A, Treusch S, Xu L, Durruthy-Durruthy R, Gokhale K, Jacob J, Chen TX, Oldham W, Matthews J, Kantarjian H, Futreal A, Patel K, Jones KW, Zehnder JL, Takahashi K. Abstract 5348: Single-cell analysis of mutational heterogeneity in acute myeloid leukemia tumors with high-throughput droplet microfluidics. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5348] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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
To make possible the routine characterization of genetic diversity within cancer cell populations, we developed a novel two-step microfluidic droplet workflow that enables efficient and massively-parallel single-cell PCR-based genomic barcoding for single-cell DNA sequencing applications. We demonstrate that the two-step microfluidic approach is required for robust DNA amplification on thousands of individual cells per run with high coverage uniformity and low allelic dropout of targeted genomic loci. To apply our single-cell sequencing technology to human tumor samples, we developed a targeted panel to partially sequence 26 genes frequently mutated in acute myeloid leukemia (AML) including TP53, DNMT3A, FLT3, NPM1, NRAS, IDH1 and IDH2. Using this panel, we were able to sensitively identify SNV and indel-defined clones within AML samples and assess their distribution at the time of diagnosis, remission and relapse. We also used single cell SNVs to monitor host and donor cell populations during bone marrow transplantation (BMT), which allowed us to accurately evaluate engraftment and disease relapse. Collectively, our single-cell data indicates that clonal populations inferred from VAFs obtained from bulk sequencing data may not fully resolve the heterogeneity within tumors; moreover, the single-cell nature of our approach enabled the unambiguous identification of multiple co-occurring mutations within subclones that is not possible with bulk measurements. Collectively, our results show a greater degree of heterogeneity in AML tumor samples than is commonly appreciated with traditional sequencing paradigms and demonstrate the value of single-cell analysis for AML.
Citation Format: Dennis J. Eastburn, Maurizio Pellegrino, Adam Sciambi, Sebastian Treusch, Liwen Xu, Robert Durruthy-Durruthy, Kaustubh Gokhale, Jose Jacob, Tina X. Chen, William Oldham, Jairo Matthews, Hagop Kantarjian, Andrew Futreal, Keyur Patel, Keith W. Jones, James L. Zehnder, Koichi Takahashi. Single-cell analysis of mutational heterogeneity in acute myeloid leukemia tumors with high-throughput droplet microfluidics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5348.
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Affiliation(s)
| | | | | | | | - Liwen Xu
- 2Stanford School of Medicine, Stanford, CA
| | | | | | - Jose Jacob
- 1Mission Bio, Inc., South San Francisco, CA
| | | | | | - Jairo Matthews
- 3MD Anderson Cancer Center, University of Texas, Houston, TX
| | | | - Andrew Futreal
- 3MD Anderson Cancer Center, University of Texas, Houston, TX
| | - Keyur Patel
- 3MD Anderson Cancer Center, University of Texas, Houston, TX
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42
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Costa HA, Neal JW, Bustamante CD, Zehnder JL. Identification of a Novel Somatic Mutation Leading to Allele Dropout for EGFR L858R Genotyping in Non-Small Cell Lung Cancer. Mol Diagn Ther 2018; 21:431-436. [PMID: 28357677 DOI: 10.1007/s40291-017-0275-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVE While PCR-based genotyping methods abound in molecular testing for lung cancer therapy, these approaches may not provide the robust sensitivity to detect accurate genotypes in a variable cancer genomic background. METHODS Here, we describe a study of a clinical tumor specimen containing a novel somatic single nucleotide variant that caused allele drop-out in EGFR L858R genotyping, resulting in a false-negative interpretation and impacting patient clinical management. RESULTS We demonstrate that a subsequent unbiased next-generation sequencing approach correctly identified the driver mutation, and therefore may be more reliable for somatic variant detection. CONCLUSIONS These findings magnify the potential pitfalls of PCR amplification-based approaches and stress the importance of unbiased and sensitive molecular testing strategies for therapeutic marker detection as molecular testing becomes the standard for determining clinical management of cancer patients.
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Affiliation(s)
- Helio A Costa
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Joel W Neal
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Carlos D Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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43
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Nagy A, Bhaduri A, Shahmarvand N, Shahryari J, Zehnder JL, Warnke RA, Mughal T, Ali S, Ohgami RS. Next-generation sequencing of idiopathic multicentric and unicentric Castleman disease and follicular dendritic cell sarcomas. Blood Adv 2018; 2:481-491. [PMID: 29496669 PMCID: PMC5851414 DOI: 10.1182/bloodadvances.2017009654] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/30/2018] [Indexed: 02/06/2023] Open
Abstract
Castleman disease (CD) is a rare lymphoproliferative disorder subclassified as unicentric CD (UCD) or multicentric CD (MCD) based on clinical features and the distribution of enlarged lymph nodes with characteristic histopathology. MCD can be further subtyped based on human herpes virus 8 (HHV8) infection into HHV8-associated MCD, HHV8-/idiopathic MCD (iMCD), and polyneuropathy, organomegaly, endocrinopathy, monoclonal gammopathy, and skin change (POEMS)-associated MCD. In a subset of cases of UCD, an associated follicular dendritic cell sarcoma (FDCS) may be seen. Although numerous reports of the clinical and histologic features of UCD, MCD, and FDCS exist, an understanding of the genetic and epigenetic landscape of these rare diseases is lacking. Given this paucity of knowledge, we analyzed 15 cases of UCD and 3 cases of iMCD by targeted next-generation sequencing (NGS; 405 genes) and 3 cases of FDCS associated with UCD hyaline vascular variant (UCD-HVV) by whole-exome sequencing. Common amplifications of ETS1, PTPN6, and TGFBR2 were seen in 1 iMCD and 1 UCD case; the iMCD case also had a somatic DNMT3A L295Q mutation. This iMCD patient also showed clinicopathologic features consistent with a specific subtype known as Castleman-Kojima disease (thrombocytopenia, anasarca, fever, reticulin fibrosis, and organomegaly [TAFRO] clinical subtype). Additionally, 1 case of UCD-HVV showed amplification of the cluster of histone genes on chromosome 6p. FDCS associated with UCD-HVV showed mutations and copy number changes in known oncogenes, tumor suppressors, and chromatin structural-remodeling proteins.
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Affiliation(s)
- Alexandra Nagy
- Department of Pathology, Stanford University, Stanford, CA
| | - Aparna Bhaduri
- Department of Regeneration Medicine, University of California San Francisco, San Francisco, CA
| | | | | | | | - Roger A Warnke
- Department of Pathology, Stanford University, Stanford, CA
| | - Tariq Mughal
- Foundation Medicine Inc, Cambridge, MA; and
- Department of Medicine, Tufts University Medical Center, Boston, MA
| | - Siraj Ali
- Foundation Medicine Inc, Cambridge, MA; and
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44
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Yang SR, Lin CY, Stehr H, Long SR, Kong CS, Berry GJ, Zehnder JL, Kunder CA. Comprehensive Genomic Profiling of Malignant Effusions in Patients with Metastatic Lung Adenocarcinoma. J Mol Diagn 2017; 20:184-194. [PMID: 29269277 DOI: 10.1016/j.jmoldx.2017.10.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 10/17/2017] [Accepted: 10/25/2017] [Indexed: 12/20/2022] Open
Abstract
Cytology samples are increasingly used for comprehensive molecular testing. Although fine-needle aspirates are adequate substrates for high-throughput sequencing, the suitability of malignant body fluids remains largely unexplored. We investigated the adequacy and utility of performing targeted next-generation sequencing (NGS) on malignant effusions from patients with metastatic lung adenocarcinoma. Thirty-two effusion samples submitted for hybrid capture-based NGS using a clinically validated solid tumor genotyping panel were examined. All cases showed ≥5% tumor cellularity; however, 28 (88%) provided sufficient DNA for NGS (≥1 ng/μL). The sequencing reads showed satisfactory quality control statistics, and the variant allele frequencies were correlated with tumor cellularity. Furthermore, pathogenic or likely pathogenic genomic alterations were identified in 26 of 28 samples (93%), whereas clinically actionable alterations were present in 18 (64%). Notably, nine patients had additional molecular testing performed on preceding or subsequent biopsy specimens, and the results across multiple samples were compared. In two patients, the NGS-based fluid analysis identified clinically actionable alterations that were not detected by other hotspot testing. In four patients treated with tyrosine kinase inhibitors, malignant fluid sequencing confirmed driver alterations from prior testing and revealed new resistance mechanisms. Hence, given adequate DNA input and tumor cellularity, comprehensive genomic profiling of malignant effusions may be used to establish mutational status at diagnosis and inform treatment resistance during targeted therapy.
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Affiliation(s)
- Soo-Ryum Yang
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Chieh-Yu Lin
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Steven R Long
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Christina S Kong
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Gerald J Berry
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Christian A Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
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45
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Traynis I, Jones CD, Gibb CB, Acharya SS, Zehnder JL. First molecular characterization of a patient with combined factor V and factor VII deficiency. Thromb Haemost 2017; 95:1031-2. [PMID: 16732384 DOI: 10.1160/th06-03-0177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ilana Traynis
- Department of Pathology, L235, Stanford University School of Medicine, CA 94305, USA
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46
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Chung A, Hou Y, Ohgami RS, Von Gehr A, Fisk DG, Roskin KM, Li X, Gojenola L, Bangs CD, Arber DA, Fire AZ, Cherry AM, Zehnder JL, Gotlib J, Merker JD. A novel TRIP11-FLT3 fusion in a patient with a myeloid/lymphoid neoplasm with eosinophilia. Cancer Genet 2017; 216-217:10-15. [DOI: 10.1016/j.cancergen.2017.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/14/2017] [Accepted: 05/08/2017] [Indexed: 01/30/2023]
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Affiliation(s)
- Bing M Zhang
- Stanford University School of Medicine, Stanford, CA
| | | | - Chieh Y Lin
- Stanford University School of Medicine, Stanford, CA
| | - James Ford
- Stanford University School of Medicine, Stanford, CA
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48
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Zheng P, You X, Tamaresis J, Xu L, Hsu K, Than R, Iliopoulou BP, Pierini A, Schneidawind D, Zehnder JL, Blazar BR, Negrin RS, Meyer E. Repertoire of Murine T Cells in Target Tissues of MHC-Matched and -Mismatched Graft-Versus-Host Disease. Biol Blood Marrow Transplant 2017. [DOI: 10.1016/j.bbmt.2016.12.230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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49
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Xu L, You X, Zheng P, Zhang BM, Gupta PK, Lavori P, Meyer E, Zehnder JL. Methodologic Considerations in the Application of Next-Generation Sequencing of Human TRB Repertoires for Clinical Use. J Mol Diagn 2016; 19:72-83. [PMID: 27815002 DOI: 10.1016/j.jmoldx.2016.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/24/2016] [Accepted: 07/28/2016] [Indexed: 01/08/2023] Open
Abstract
Next-generation sequencing (NGS) of immune receptors has become a standard tool to assess minimal residual disease (MRD) in patients treated for lymphoid malignancy, and it is being used to study the T-cell repertoire in many clinical settings. To better understanding the potential clinical utility and limitations of this application outside of MRD, we developed a BIOMED-2 primer-based NGS method and characterized its performance in controls and patients with graft-versus-host disease (GVHD) after allogeneic hematopoietic transplant. For controls and patients with GVHD, replicate sequencing of the same T-cell receptor β (TRB) libraries was highly reproducible. Higher variability was observed in sequencing of different TRB libraries made from the same DNA stock. Variability was increased in patients with GVHD compared with controls; patients with GVHD also had lower diversity than controls. In the T-cell repertoire of a healthy person, approximately 99.6% of the CDR3 clones were in low abundance, with frequency <10-3. A single library could identify >93% of the clones with frequency ≥10-3 in the repertoire. Sequencing in duplicate increased the average detection rate to >97%. This work demonstrates that NGS reliably and robustly characterizes TRB populations in healthy individuals and patients with GVHD with frequency ≥10-3 and provides a methodologic framework for applying NGS immune repertoire methods to clinical testing applications beyond MRD.
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Affiliation(s)
- Liwen Xu
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - Xiaoqing You
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - PingPing Zheng
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - Bing M Zhang
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - Puja K Gupta
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - Philip Lavori
- Department of Biomedical Data Science, Stanford School of Medicine, Stanford University, Stanford, California
| | - Everett Meyer
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California.
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50
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Chapin J, Lee CS, Zhang H, Zehnder JL, Bussel JB. Gender and duration of disease differentiate responses to rituximab-dexamethasone therapy in adults with immune thrombocytopenia. Am J Hematol 2016; 91:907-11. [PMID: 27220625 DOI: 10.1002/ajh.24434] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 05/19/2016] [Accepted: 05/22/2016] [Indexed: 01/19/2023]
Abstract
Adults often develop chronic immune thrombocytopenia (ITP) for which treatment order is uncertain. Rituximab and three cycles of dexamethasone (4R + 3Dex) improve treatment responses and short-term disease control but long-term outcome is not known. In adults with ITP treated with 4R + 3D, we sought long-term outcome and associated prognostic variables. Forty-nine adults treated at Weill-Cornell received 4R + 3Dex. Their clinical characteristics were reviewed. Duration was median time to treatment failure; Kaplan-Meier estimates were developed. Vbeta Tcell receptor (VBTCR) repertoire was obtained after treatment in 36 patients. Patients were adults with ITP 18-64 years old, median age 37. The 27 females were twice as likely to have an ongoing response to 4R + 3Dex (44.1%) as males (19.6%; P = 0.009). For ITP duration <12 months, 52.7% of patients had continuing responses to 4R + 3Dex compared to 15.3% of patients with diagnosis >12 months (P = 0.02). Females with ITP duration of <12 months had continuing responses in 78.6%, compared to males with <12 months duration of ITP (21.2%). For patients with disease duration <12 months, 67% of females had continuing responses, compared to 31% of males (P = 0.004). Post-treatment polyclonal VBTCR was seen in 9/10 continuing responders (six female, three male) but only 13/26 relapsers/nonresponders (P = 0.068). Durable remissions after treatment with 4R + 3Dex were more frequent in female patients with <12 months of ITP duration and those with polyclonal VBTCR after treatment, emphasizing the roles of duration of disease, gender and T cells in chronic ITP. Differences in pathophysiology of ITP by gender and by duration of ITP require further study. Am. J. Hematol. 91:907-911, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- John Chapin
- Division of Hematology-Oncology, Department of Medicine; New York Presbyterian Hospital, Weill Cornell Medicine; New York New York
| | - Christina S. Lee
- Division of Hematology-Oncology, Department of Pediatrics; Weill Cornell Medicine; New York New York
| | - Haiyu Zhang
- Department of Pathology; Stanford University School of Medicine; Palo Alto California
| | - James L. Zehnder
- Department of Pathology; Stanford University School of Medicine; Palo Alto California
| | - James B. Bussel
- Division of Hematology-Oncology, Department of Medicine; New York Presbyterian Hospital, Weill Cornell Medicine; New York New York
- Division of Hematology-Oncology, Department of Pediatrics; Weill Cornell Medicine; New York New York
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